diff --git a/.config/config.json b/.config/config.json index 035648c7a3..8f00ec01e9 100644 --- a/.config/config.json +++ b/.config/config.json @@ -5,6 +5,7 @@ "tools": "tools", "dev": "dev", "test": "test", + "test-spi": "test", "prod": "prod" }, "version": "1.0.0", @@ -20,17 +21,20 @@ "staticUrls": { "dev": "dev-biohubbc.apps.silver.devops.gov.bc.ca", "test": "test-biohubbc.apps.silver.devops.gov.bc.ca", + "test-spi": "test-spi-biohubbc.apps.silver.devops.gov.bc.ca", "prod": "biohubbc.apps.silver.devops.gov.bc.ca", "prodVanityUrl": "sims.nrs.gov.bc.ca" }, "staticUrlsAPI": { "dev": "api-dev-biohubbc.apps.silver.devops.gov.bc.ca", "test": "api-test-biohubbc.apps.silver.devops.gov.bc.ca", + "test-spi": "api-test-spi-biohubbc.apps.silver.devops.gov.bc.ca", "prod": "api-biohubbc.apps.silver.devops.gov.bc.ca" }, "siteminderLogoutURL": { "dev": "https://logontest7.gov.bc.ca/clp-cgi/logoff.cgi", "test": "https://logontest7.gov.bc.ca/clp-cgi/logoff.cgi", + "test-spi": "https://logontest7.gov.bc.ca/clp-cgi/logoff.cgi", "prod": "https://logon7.gov.bc.ca/clp-cgi/logoff.cgi" }, "sso": { @@ -68,6 +72,23 @@ "cssApiEnvironment": "test" } }, + "test-spi": { + "host": "https://test.loginproxy.gov.bc.ca/auth", + "realm": "standard", + "clientId": "sims-4461", + "keycloakSecret": "keycloak", + "serviceClient": { + "serviceClientName": "sims-svc-4464", + "keycloakSecretServiceClientPasswordKey": "sims_svc_client_password" + }, + "cssApi": { + "cssApiTokenUrl": "https://loginproxy.gov.bc.ca/auth/realms/standard/protocol/openid-connect/token", + "cssApiClientId": "service-account-team-1190-4229", + "cssApiHost": "https://api.loginproxy.gov.bc.ca/api/v1", + "keycloakSecretCssApiSecretKey": "css_api_client_secret", + "cssApiEnvironment": "test" + } + }, "prod": { "host": "https://loginproxy.gov.bc.ca/auth", "realm": "standard", diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 8637ad769a..feed15693d 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -7,6 +7,7 @@ on: types: [opened, reopened, synchronize, ready_for_review] branches-ignore: - test + - test-spi - prod concurrency: diff --git a/.github/workflows/deployStatic.yml b/.github/workflows/deployStatic.yml index d7db1e5f35..c827de0242 100644 --- a/.github/workflows/deployStatic.yml +++ b/.github/workflows/deployStatic.yml @@ -8,6 +8,7 @@ on: branches: - dev - test + - test-spi - prod jobs: diff --git a/Makefile b/Makefile index 31f78ed505..8c18d71028 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ -include .env -# Apply the contents of the .env to the terminal, so that the docker-compose file can use them in its builds +# Apply the contents of the .env to the terminal, so that the compose file can use them in its builds export $(shell sed 's/=.*//' .env) ## ------------------------------------------------------------------------------ @@ -46,13 +46,13 @@ close: ## Closes all project containers @echo "===============================================" @echo "Make: close - closing Docker containers" @echo "===============================================" - @docker-compose -f docker-compose.yml down + @docker compose down clean: ## Closes and cleans (removes) all project containers @echo "===============================================" @echo "Make: clean - closing and cleaning Docker containers" @echo "===============================================" - @docker-compose -f docker-compose.yml down -v --rmi all --remove-orphans + @docker compose down -v --rmi all --remove-orphans prune: ## Deletes ALL docker artifacts (even those not associated to this project) @echo -n "Delete ALL docker artifacts? [y/n] " && read ans && [ $${ans:-n} = y ] @@ -77,13 +77,13 @@ build-postgres: ## Builds the postgres db containers @echo "===============================================" @echo "Make: build-postgres - building postgres db images" @echo "===============================================" - @docker-compose -f docker-compose.yml build db db_setup + @docker compose build db db_setup run-postgres: ## Runs the postgres db containers @echo "===============================================" @echo "Make: run-postgres - running postgres db images" @echo "===============================================" - @docker-compose -f docker-compose.yml up -d db db_setup + @docker compose up -d db db_setup ## ------------------------------------------------------------------------------ ## Build/Run Backend Commands @@ -94,13 +94,13 @@ build-backend: ## Builds all backend containers @echo "===============================================" @echo "Make: build-backend - building backend images" @echo "===============================================" - @docker-compose -f docker-compose.yml build db db_setup api + @docker compose build db db_setup api run-backend: ## Runs all backend containers @echo "===============================================" @echo "Make: run-backend - running backend images" @echo "===============================================" - @docker-compose -f docker-compose.yml up -d db db_setup api + @docker compose up -d db db_setup api ## ------------------------------------------------------------------------------ ## Build/Run Backend+Web Commands (backend + web frontend) @@ -111,13 +111,13 @@ build-web: ## Builds all backend+web containers @echo "===============================================" @echo "Make: build-web - building web images" @echo "===============================================" - @docker-compose -f docker-compose.yml build db db_setup api app + @docker compose build db db_setup api app run-web: ## Runs all backend+web containers @echo "===============================================" @echo "Make: run-web - running web images" @echo "===============================================" - @docker-compose -f docker-compose.yml up -d db db_setup api app + @docker compose up -d db db_setup api app ## ------------------------------------------------------------------------------ ## Commands to shell into the target container @@ -128,19 +128,19 @@ db-container: ## Executes into database container. @echo "Make: Shelling into database container" @echo "===============================================" @export PGPASSWORD=$(DB_ADMIN_PASS) - @docker-compose exec db psql -U $(DB_ADMIN) -d $(DB_DATABASE) + @docker compose exec db psql -U $(DB_ADMIN) -d $(DB_DATABASE) app-container: ## Executes into the app container. @echo "===============================================" @echo "Shelling into app container" @echo "===============================================" - @docker-compose exec app bash + @docker compose exec app bash api-container: ## Executes into the api container. @echo "===============================================" @echo "Shelling into api container" @echo "===============================================" - @docker-compose exec api bash + @docker compose exec api bash ## ------------------------------------------------------------------------------ ## Database migration commands @@ -150,37 +150,37 @@ build-db-setup: ## Build the db knex setup (migrations + seeding) image @echo "===============================================" @echo "Make: build-db-setup - building db knex setup image" @echo "===============================================" - @docker-compose -f docker-compose.yml build db_setup + @docker compose build db_setup run-db-setup: ## Run the database migrations and seeding @echo "===============================================" @echo "Make: run-db-setup - running database migrations and seeding" @echo "===============================================" - @docker-compose -f docker-compose.yml up db_setup + @docker compose up db_setup build-db-migrate: ## Build the db knex migrations image @echo "===============================================" @echo "Make: build-db-migrate - building db knex migrate image" @echo "===============================================" - @docker-compose -f docker-compose.yml build db_migrate + @docker compose build db_migrate run-db-migrate: ## Run the database migrations @echo "===============================================" @echo "Make: run-db-migrate - running database migrations" @echo "===============================================" - @docker-compose -f docker-compose.yml up db_migrate + @docker compose up db_migrate build-db-rollback: ## Build the db knex rollback image @echo "===============================================" @echo "Make: build-db-rollback - building db knex rollback image" @echo "===============================================" - @docker-compose -f docker-compose.yml build db_rollback + @docker compose build db_rollback run-db-rollback: ## Rollback the latest database migrations @echo "===============================================" @echo "Make: run-db-rollback - rolling back the latest database migrations" @echo "===============================================" - @docker-compose -f docker-compose.yml up db_rollback + @docker compose up db_rollback ## ------------------------------------------------------------------------------ ## clamav commands @@ -190,13 +190,13 @@ build-clamav: ## Build the clamav image @echo "===============================================" @echo "Make: build-clamav - building clamav image" @echo "===============================================" - @docker-compose -f docker-compose.yml build clamav + @docker compose build clamav run-clamav: ## Run clamav @echo "===============================================" @echo "Make: run-clamav - running clamav" @echo "===============================================" - @docker-compose -f docker-compose.yml up -d clamav + @docker compose up -d clamav ## ------------------------------------------------------------------------------ ## Run `npm` commands for all projects @@ -314,11 +314,11 @@ pipeline-install: ## Runs `npm install` for all projects args ?= --tail 2000 ## Default args if none are provided -log: ## Runs `docker-compose logs -f` for all containers +log: ## Runs `docker compose logs -f` for all containers @echo "===============================================" @echo "Running docker logs for the app container" @echo "===============================================" - @docker-compose logs -f $(args) + @docker compose logs -f $(args) log-app: ## Runs `docker logs -f` for the app container @echo "===============================================" diff --git a/README.md b/README.md index 020a947546..b23d85a04e 100644 --- a/README.md +++ b/README.md @@ -125,7 +125,7 @@ Below are all of the relevant files that need to be updated when modifying envir #### Local Development - `env.docker` -- `docker-compose.yml` +- `compose.yml` - `app/src/contexts/configContext.tsx` #### Deployed to OpenShift diff --git a/api/.docker/api/Dockerfile b/api/.docker/api/Dockerfile index 1501d7cfdc..a5052b22ce 100644 --- a/api/.docker/api/Dockerfile +++ b/api/.docker/api/Dockerfile @@ -1,5 +1,5 @@ # ######################################################################################################## -# This DockerFile is used for local development (via docker-compose) only. +# This DockerFile is used for local development (via compose.yml) only. # ######################################################################################################## FROM node:20 @@ -21,6 +21,9 @@ ENV PATH ${HOME}/node_modules/.bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/us # Copy the rest of the files COPY . ./ +# Update log directory file permissions, prevents permission errors for linux environments +RUN chmod -R a+rw data/logs/* + VOLUME ${HOME} # start api with live reload diff --git a/api/.gitignore b/api/.gitignore index 8461edfea1..a64b16b540 100644 --- a/api/.gitignore +++ b/api/.gitignore @@ -12,6 +12,9 @@ dist # Testing coverage +# persistent storage +data + # SonarQube .sonarqube diff --git a/api/.pipeline/config.js b/api/.pipeline/config.js index f52e3223a9..7d6556d3f1 100644 --- a/api/.pipeline/config.js +++ b/api/.pipeline/config.js @@ -52,7 +52,6 @@ const phases = { build: { namespace: 'af2668-tools', name: `${name}`, - dbName: `${dbName}`, phase: 'build', changeId: changeId, suffix: `-build-${changeId}`, @@ -91,7 +90,14 @@ const phases = { tz: config.timezone.api, sso: config.sso.dev, featureFlags: '', - logLevel: 'info', + logLevel: (isStaticDeployment && 'info') || 'debug', + logLevelFile: (isStaticDeployment && 'debug') || 'debug', + logFileDir: 'data/logs', + logFileName: 'sims-api-%DATE%.log', + logFileDatePattern: 'YYYY-MM-DD-HH', + logFileMaxSize: '50m', + logFileMaxFiles: (isStaticDeployment && '10') || '2', + volumeCapacity: (isStaticDeployment && '500Mi') || '100Mi', apiResponseValidationEnabled: true, databaseResponseValidationEnabled: true, nodeOptions: '--max_old_space_size=3000', // 75% of memoryLimit (bytes) @@ -126,8 +132,58 @@ const phases = { s3KeyPrefix: 'sims', tz: config.timezone.api, sso: config.sso.test, - logLevel: 'info', featureFlags: '', + logLevel: 'warn', + logLevelFile: 'debug', + logFileDir: 'data/logs', + logFileName: 'sims-api-%DATE%.log', + logFileDatePattern: 'YYYY-MM-DD-HH', + logFileMaxSize: '50m', + logFileMaxFiles: '10', + volumeCapacity: '500Mi', + apiResponseValidationEnabled: true, + databaseResponseValidationEnabled: true, + nodeOptions: '--max_old_space_size=3000', // 75% of memoryLimit (bytes) + cpuRequest: '50m', + cpuLimit: '1000m', + memoryRequest: '100Mi', + memoryLimit: '4Gi', + replicas: '2', + replicasMax: '2' + }, + 'test-spi': { + namespace: 'af2668-test', + name: `${name}-spi`, + dbName: `${dbName}-spi`, + phase: 'test-spi', + changeId: deployChangeId, + suffix: `-test-spi`, + instance: `${name}-spi-test-spi`, + version: `${version}`, + tag: `test-spi-${version}`, + host: staticUrlsAPI['test-spi'], + appHost: staticUrls['test-spi'], + backboneInternalApiHost: 'https://api-test-biohub-platform.apps.silver.devops.gov.bc.ca', + backbonePublicApiHost: 'https://api-test-biohub-platform.apps.silver.devops.gov.bc.ca', + backboneIntakePath: '/api/submission/intake', + backboneArtifactIntakePath: '/api/artifact/intake', + biohubTaxonPath: '/api/taxonomy/taxon', + biohubTaxonTsnPath: '/api/taxonomy/taxon/tsn', + bctwApiHost: 'https://moe-bctw-api-test.apps.silver.devops.gov.bc.ca', + critterbaseApiHost: 'https://moe-critterbase-api-test.apps.silver.devops.gov.bc.ca/api', + nodeEnv: 'production', + s3KeyPrefix: 'sims', + tz: config.timezone.api, + sso: config.sso['test-spi'], + featureFlags: '', + logLevel: 'warn', + logLevelFile: 'debug', + logFileDir: 'data/logs', + logFileName: 'sims-api-%DATE%.log', + logFileDatePattern: 'YYYY-MM-DD-HH', + logFileMaxSize: '50m', + logFileMaxFiles: '10', + volumeCapacity: '500Mi', apiResponseValidationEnabled: true, databaseResponseValidationEnabled: true, nodeOptions: '--max_old_space_size=3000', // 75% of memoryLimit (bytes) @@ -163,7 +219,14 @@ const phases = { tz: config.timezone.api, sso: config.sso.prod, featureFlags: 'API_FF_SUBMIT_BIOHUB', - logLevel: 'warn', + logLevel: 'silent', + logLevelFile: 'debug', + logFileDir: 'data/logs', + logFileName: 'sims-api-%DATE%.log', + logFileDatePattern: 'YYYY-MM-DD-HH', + logFileMaxSize: '50m', + logFileMaxFiles: '10', + volumeCapacity: '500Mi', apiResponseValidationEnabled: false, databaseResponseValidationEnabled: false, nodeOptions: '--max_old_space_size=6000', // 75% of memoryLimit (bytes) diff --git a/api/.pipeline/lib/api.deploy.js b/api/.pipeline/lib/api.deploy.js index 220710a02f..08a1266580 100644 --- a/api/.pipeline/lib/api.deploy.js +++ b/api/.pipeline/lib/api.deploy.js @@ -34,6 +34,8 @@ const apiDeploy = async (settings) => { // Node NODE_ENV: phases[phase].nodeEnv, NODE_OPTIONS: phases[phase].nodeOptions, + // Persistent Volume + VOLUME_CAPACITY: phases[phase].volumeCapacity, // BioHub Platform (aka: Backbone) BACKBONE_INTERNAL_API_HOST: phases[phase].backboneInternalApiHost, BACKBONE_INTAKE_PATH: phases[phase].backboneIntakePath, @@ -65,6 +67,13 @@ const apiDeploy = async (settings) => { KEYCLOAK_API_ENVIRONMENT: phases[phase].sso.cssApi.cssApiEnvironment, // Log Level LOG_LEVEL: phases[phase].logLevel, + LOG_LEVEL_FILE: phases[phase].logLevelFile, + LOG_FILE_DIR: phases[phase].logFileDir, + LOG_FILE_NAME: phases[phase].logFileName, + LOG_FILE_DATE_PATTERN: phases[phase].logFileDatePattern, + LOG_FILE_MAX_SIZE: phases[phase].logFileMaxSize, + LOG_FILE_MAX_FILES: phases[phase].logFileMaxFiles, + // Api Validation API_RESPONSE_VALIDATION_ENABLED: phases[phase].apiResponseValidationEnabled, DATABASE_RESPONSE_VALIDATION_ENABLED: phases[phase].databaseResponseValidationEnabled, // Feature Flags diff --git a/api/.pipeline/templates/api.dc.yaml b/api/.pipeline/templates/api.dc.yaml index dc2518910a..deda7421d7 100644 --- a/api/.pipeline/templates/api.dc.yaml +++ b/api/.pipeline/templates/api.dc.yaml @@ -32,6 +32,12 @@ parameters: - name: API_PORT_DEFAULT_NAME description: Api default port name value: '6100-tcp' + # Volume (for API logs and other persistent data) + - description: Volume space available for data, e.g. 512Mi, 2Gi. + displayName: Volume Capacity + name: VOLUME_CAPACITY + required: true + value: '500Mi' # Clamav - name: ENABLE_FILE_VIRUS_SCAN value: 'true' @@ -115,9 +121,29 @@ parameters: description: S3 key optional prefix required: false value: 'sims' - # Logging and Validation + # Logging - name: LOG_LEVEL - value: 'warn' + value: 'silent' + description: Log level for logs written to the console (console transport) + - name: LOG_LEVEL_FILE + value: 'debug' + description: Log level for logs written to log files (file transport) + - name: LOG_FILE_DIR + value: data/logs + description: Directory where log files are stored + - name: LOG_FILE_NAME + value: sims-api-%DATE%.log + description: Name of the log file + - name: LOG_FILE_DATE_PATTERN + value: YYYY-MM-DD-HH + description: Date pattern for log the files + - name: LOG_FILE_MAX_SIZE + value: 50m + description: Maximum size an individual log file can reach before a new file is created + - name: LOG_FILE_MAX_FILES + value: '10' + description: Either the maximum number of log files to keep (10) or the maximum number of days to keep log files (10d) + # Api Validation - name: API_RESPONSE_VALIDATION_ENABLED value: 'false' - name: DATABASE_RESPONSE_VALIDATION_ENABLED @@ -160,8 +186,8 @@ parameters: - name: REPLICAS_MAX value: '1' objects: - - apiVersion: image.openshift.io/v1 - kind: ImageStream + - kind: ImageStream + apiVersion: image.openshift.io/v1 metadata: annotations: description: Nodejs Runtime Image @@ -175,6 +201,17 @@ objects: status: dockerImageRepository: null + - kind: PersistentVolumeClaim + apiVersion: v1 + metadata: + name: ${NAME}${SUFFIX} + spec: + accessModes: + - ReadWriteMany + resources: + requests: + storage: '${VOLUME_CAPACITY}' + - kind: DeploymentConfig apiVersion: apps.openshift.io/v1 metadata: @@ -320,9 +357,22 @@ objects: secretKeyRef: key: object_store_bucket_name name: ${OBJECT_STORE_SECRETS} - # Logging and Validation + # Logging - name: LOG_LEVEL value: ${LOG_LEVEL} + - name: LOG_LEVEL_FILE + value: ${LOG_LEVEL_FILE} + - name: LOG_FILE_DIR + value: ${LOG_FILE_DIR} + - name: LOG_FILE_NAME + value: ${LOG_FILE_NAME} + - name: LOG_FILE_DATE_PATTERN + value: ${LOG_FILE_DATE_PATTERN} + - name: LOG_FILE_MAX_SIZE + value: ${LOG_FILE_MAX_SIZE} + - name: LOG_FILE_MAX_FILES + value: ${LOG_FILE_MAX_FILES} + # Api Validation - name: API_RESPONSE_VALIDATION_ENABLED value: ${API_RESPONSE_VALIDATION_ENABLED} - name: DATABASE_RESPONSE_VALIDATION_ENABLED @@ -380,16 +430,17 @@ objects: terminationMessagePath: /dev/termination-log terminationMessagePolicy: File volumeMounts: - - mountPath: /opt/app-root/app - name: ${NAME}${SUFFIX} + - name: ${NAME}${SUFFIX} + mountPath: /opt/app-root/src/data dnsPolicy: ClusterFirst restartPolicy: Always schedulerName: default-scheduler securityContext: {} terminationGracePeriodSeconds: 30 volumes: - - emptyDir: {} - name: ${NAME}${SUFFIX} + - name: ${NAME}${SUFFIX} + persistentVolumeClaim: + claimName: ${NAME}${SUFFIX} test: false triggers: - imageChangeParams: @@ -421,8 +472,8 @@ objects: name: ${NAME}${SUFFIX} type: Opaque - - apiVersion: v1 - kind: Service + - kind: Service + apiVersion: v1 metadata: annotations: null labels: {} diff --git a/api/README.md b/api/README.md index 2724f9c2de..da2287b939 100644 --- a/api/README.md +++ b/api/README.md @@ -84,12 +84,10 @@ A centralized logger has been created (see `api/utils/logger.ts`). ## Logger configuration -The loggers log level can be configured via an environment variable: `LOG_LEVEL` +The loggers log level can be configured via environment variables: `LOG_LEVEL` and `LOG_LEVEL_FILE` Set this variable to one of: `silent`, `error`, `warn`, `info`, `debug`, `silly` -Default value: `info` - ## Instantiating the logger in your class/file ``` diff --git a/api/package-lock.json b/api/package-lock.json index bd71e90473..6ac5daca69 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -15,7 +15,7 @@ "@turf/circle": "^6.5.0", "@turf/helpers": "^6.5.0", "@turf/meta": "^6.5.0", - "adm-zip": "^0.5.5", + "adm-zip": "0.5.12", "ajv": "^8.12.0", "axios": "^1.6.7", "clamscan": "^2.2.1", @@ -30,7 +30,7 @@ "form-data": "^4.0.0", "http-proxy-middleware": "^2.0.6", "jsonpath-plus": "^7.2.0", - "jsonwebtoken": "^8.5.1", + "jsonwebtoken": "^9.0.2", "jwks-rsa": "^3.1.0", "knex": "^2.4.2", "lodash": "^4.17.21", @@ -45,9 +45,9 @@ "utm": "^1.1.1", "uuid": "^8.3.2", "winston": "^3.3.3", + "winston-daily-rotate-file": "^5.0.0", "xlsx": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz", - "xml2js": "^0.4.23", - "zod": "^3.22.4" + "zod": "^3.23.8" }, "devDependencies": { "@istanbuljs/nyc-config-typescript": "^1.0.1", @@ -68,7 +68,6 @@ "@types/swagger-ui-express": "^4.1.6", "@types/utm": "^1.1.1", "@types/uuid": "^8.3.1", - "@types/xml2js": "^0.4.9", "@types/yamljs": "^0.2.31", "@typescript-eslint/eslint-plugin": "~7.6.0", "@typescript-eslint/parser": "~7.6.0", @@ -2805,15 +2804,6 @@ "integrity": "sha512-c/I8ZRb51j+pYGAu5CrFMRxqZ2ke4y2grEBO5AUjgSkSk+qT2Ea+OdWElz/OiMf5MNpn2b17kuVBwZLQJXzihw==", "dev": true }, - "node_modules/@types/xml2js": { - "version": "0.4.14", - "resolved": "https://registry.npmjs.org/@types/xml2js/-/xml2js-0.4.14.tgz", - "integrity": "sha512-4YnrRemBShWRO2QjvUin8ESA41rH+9nQGLUGZV/1IDhi3SL9OhdpNC/MrulTWuptXKwhx/aDxE7toV0f/ypIXQ==", - "dev": true, - "dependencies": { - "@types/node": "*" - } - }, "node_modules/@types/yamljs": { "version": "0.2.34", "resolved": "https://registry.npmjs.org/@types/yamljs/-/yamljs-0.2.34.tgz", @@ -4820,6 +4810,14 @@ "node": "^10.12.0 || >=12.0.0" } }, + "node_modules/file-stream-rotator": { + "version": "0.6.1", + "resolved": "https://registry.npmjs.org/file-stream-rotator/-/file-stream-rotator-0.6.1.tgz", + "integrity": "sha512-u+dBid4PvZw17PmDeRcNOtCP9CCK/9lRN2w+r1xIS7yOL9JFrIBKTvrYsxT4P0pGtThYTn++QS5ChHaUov3+zQ==", + "dependencies": { + "moment": "^2.29.1" + } + }, "node_modules/fill-range": { "version": "7.0.1", "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz", @@ -6112,9 +6110,9 @@ } }, "node_modules/jsonwebtoken": { - "version": "8.5.1", - "resolved": "https://registry.npmjs.org/jsonwebtoken/-/jsonwebtoken-8.5.1.tgz", - "integrity": "sha512-XjwVfRS6jTMsqYs0EsuJ4LGxXV14zQybNd4L2r0UvbVnSF9Af8x7p5MzbJ90Ioz/9TI41/hTCvznF/loiSzn8w==", + "version": "9.0.2", + "resolved": "https://registry.npmjs.org/jsonwebtoken/-/jsonwebtoken-9.0.2.tgz", + "integrity": "sha512-PRp66vJ865SSqOlgqS8hujT5U4AOgMfhrwYIuIhfKaoSCZcirrmASQr8CX7cUg+RMih+hgznrjp99o+W4pJLHQ==", "dependencies": { "jws": "^3.2.2", "lodash.includes": "^4.3.0", @@ -6125,19 +6123,11 @@ "lodash.isstring": "^4.0.1", "lodash.once": "^4.0.0", "ms": "^2.1.1", - "semver": "^5.6.0" + "semver": "^7.5.4" }, "engines": { - "node": ">=4", - "npm": ">=1.4.28" - } - }, - "node_modules/jsonwebtoken/node_modules/semver": { - "version": "5.7.2", - "resolved": "https://registry.npmjs.org/semver/-/semver-5.7.2.tgz", - "integrity": "sha512-cBznnQ9KjJqU67B52RMC65CMarK2600WFnbkcaiwWq3xy/5haFJlshgnpjovMVJ+Hff49d8GEn0b87C5pDQ10g==", - "bin": { - "semver": "bin/semver" + "node": ">=12", + "npm": ">=6" } }, "node_modules/just-extend": { @@ -6732,6 +6722,14 @@ "node": ">=10" } }, + "node_modules/moment": { + "version": "2.30.1", + "resolved": "https://registry.npmjs.org/moment/-/moment-2.30.1.tgz", + "integrity": "sha512-uEmtNhbDOrWPFS+hdjFCBfy9f2YoyzRpwcl+DqpC6taX21FzsTLQVbMV/W7PzNSX6x/bhC1zA3c2UQ5NzH6how==", + "engines": { + "node": "*" + } + }, "node_modules/mongodb-uri": { "version": "0.9.7", "resolved": "https://registry.npmjs.org/mongodb-uri/-/mongodb-uri-0.9.7.tgz", @@ -7299,6 +7297,14 @@ "node": ">=0.10.0" } }, + "node_modules/object-hash": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/object-hash/-/object-hash-3.0.0.tgz", + "integrity": "sha512-RSn9F68PjH9HqtltsSnqYC1XXoWe9Bju5+213R98cNGttag9q9yAOTzdbsqvIa7aNm5WffBZFpWYr2aWrklWAw==", + "engines": { + "node": ">= 6" + } + }, "node_modules/object-inspect": { "version": "1.13.1", "resolved": "https://registry.npmjs.org/object-inspect/-/object-inspect-1.13.1.tgz", @@ -8504,11 +8510,6 @@ "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz", "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==" }, - "node_modules/sax": { - "version": "1.2.1", - "resolved": "https://registry.npmjs.org/sax/-/sax-1.2.1.tgz", - "integrity": "sha512-8I2a3LovHTOpm7NV5yOyO8IHqgVsfK4+UuySrXU8YXkSRX7k6hCV9b3HrkKCr3nMpgj+0bmocaJJWpvp1oc7ZA==" - }, "node_modules/semver": { "version": "7.6.0", "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz", @@ -9719,6 +9720,23 @@ "node": ">= 12.0.0" } }, + "node_modules/winston-daily-rotate-file": { + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/winston-daily-rotate-file/-/winston-daily-rotate-file-5.0.0.tgz", + "integrity": "sha512-JDjiXXkM5qvwY06733vf09I2wnMXpZEhxEVOSPenZMii+g7pcDcTBt2MRugnoi8BwVSuCT2jfRXBUy+n1Zz/Yw==", + "dependencies": { + "file-stream-rotator": "^0.6.1", + "object-hash": "^3.0.0", + "triple-beam": "^1.4.1", + "winston-transport": "^4.7.0" + }, + "engines": { + "node": ">=8" + }, + "peerDependencies": { + "winston": "^3" + } + }, "node_modules/winston-transport": { "version": "4.7.0", "resolved": "https://registry.npmjs.org/winston-transport/-/winston-transport-4.7.0.tgz", @@ -9823,26 +9841,6 @@ "resolved": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz", "integrity": "sha512-8IfgFctB7fkvqkTGF2MnrDrC6vzE28Wcc1aSbdDQ+4/WFtzfS73YuapbuaPZwGqpR2e0EeDMIrFOJubQVLWFNA==" }, - "node_modules/xml2js": { - "version": "0.4.23", - "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.23.tgz", - "integrity": "sha512-ySPiMjM0+pLDftHgXY4By0uswI3SPKLDw/i3UXbnO8M/p28zqexCUoPmQFrYD+/1BzhGJSs2i1ERWKJAtiLrug==", - "dependencies": { - "sax": ">=0.6.0", - "xmlbuilder": "~11.0.0" - }, - "engines": { - "node": ">=4.0.0" - } - }, - "node_modules/xmlbuilder": { - "version": "11.0.1", - "resolved": "https://registry.npmjs.org/xmlbuilder/-/xmlbuilder-11.0.1.tgz", - "integrity": "sha512-fDlsI/kFEx7gLvbecc0/ohLG50fugQp8ryHzMTuW9vSa1GJ0XYWKnhsUx7oie3G98+r56aTQIUB4kht42R3JvA==", - "engines": { - "node": ">=4.0" - } - }, "node_modules/xtend": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", @@ -10021,9 +10019,9 @@ } }, "node_modules/zod": { - "version": "3.22.4", - "resolved": "https://registry.npmjs.org/zod/-/zod-3.22.4.tgz", - "integrity": "sha512-iC+8Io04lddc+mVqQ9AZ7OQ2MrUKGN+oIQyq1vemgt46jwCwLfhq7/pwnBnNXXXZb8VTVLKwp9EDkx+ryxIWmg==", + "version": "3.23.8", + "resolved": "https://registry.npmjs.org/zod/-/zod-3.23.8.tgz", + "integrity": "sha512-XBx9AXhXktjUqnepgTiE5flcKIYWi/rme0Eaj+5Y0lftuGBq+jyRu/md4WnuxqgP1ubdpNCsYEYPxrzVHD8d6g==", "funding": { "url": "https://github.com/sponsors/colinhacks" } diff --git a/api/package.json b/api/package.json index fba3cdd63d..fe2fd2dcb2 100644 --- a/api/package.json +++ b/api/package.json @@ -32,7 +32,7 @@ "@turf/circle": "^6.5.0", "@turf/helpers": "^6.5.0", "@turf/meta": "^6.5.0", - "adm-zip": "^0.5.5", + "adm-zip": "0.5.12", "ajv": "^8.12.0", "axios": "^1.6.7", "clamscan": "^2.2.1", @@ -47,7 +47,7 @@ "form-data": "^4.0.0", "http-proxy-middleware": "^2.0.6", "jsonpath-plus": "^7.2.0", - "jsonwebtoken": "^8.5.1", + "jsonwebtoken": "^9.0.2", "jwks-rsa": "^3.1.0", "knex": "^2.4.2", "lodash": "^4.17.21", @@ -62,9 +62,9 @@ "utm": "^1.1.1", "uuid": "^8.3.2", "winston": "^3.3.3", + "winston-daily-rotate-file": "^5.0.0", "xlsx": "https://cdn.sheetjs.com/xlsx-0.19.3/xlsx-0.19.3.tgz", - "xml2js": "^0.4.23", - "zod": "^3.22.4" + "zod": "^3.23.8" }, "devDependencies": { "@istanbuljs/nyc-config-typescript": "^1.0.1", @@ -85,7 +85,6 @@ "@types/swagger-ui-express": "^4.1.6", "@types/utm": "^1.1.1", "@types/uuid": "^8.3.1", - "@types/xml2js": "^0.4.9", "@types/yamljs": "^0.2.31", "@typescript-eslint/eslint-plugin": "~7.6.0", "@typescript-eslint/parser": "~7.6.0", diff --git a/api/src/app.ts b/api/src/app.ts index 0c22d7e5a7..00eb5b57b9 100644 --- a/api/src/app.ts +++ b/api/src/app.ts @@ -98,7 +98,7 @@ const openAPIFramework = initialize({ const multerFiles = req.files ?? []; req.files = multerFiles; - req.body.media = multerFiles; + req.body = { ...req.body, media: multerFiles }; return next(); }); diff --git a/api/src/constants/attachments.ts b/api/src/constants/attachments.ts index 061b01f49e..0dd2f7f738 100644 --- a/api/src/constants/attachments.ts +++ b/api/src/constants/attachments.ts @@ -1,5 +1,27 @@ +/** + * The type of project/survey attachment files. + * + * @export + * @enum {number} + */ export enum ATTACHMENT_TYPE { REPORT = 'Report', - KEYX = 'KeyX', OTHER = 'Other' } + +/** + * The type of survey telemetry credential attachment files. + * + * @export + * @enum {number} + */ +export enum TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE { + /** + * Lotek API key file type. + */ + KEYX = 'KeyX', + /** + * Vectronic API key file type. + */ + CFG = 'Cfg' +} diff --git a/api/src/models/bctw.ts b/api/src/models/bctw.ts new file mode 100644 index 0000000000..2c7931f4cf --- /dev/null +++ b/api/src/models/bctw.ts @@ -0,0 +1,99 @@ +import { z } from 'zod'; + +export const BctwDeployDevice = z.object({ + device_id: z.number(), + frequency: z.number().optional(), + frequency_unit: z.string().optional(), + device_make: z.string().optional(), + device_model: z.string().optional(), + attachment_start: z.string(), + attachment_end: z.string().nullable(), + critter_id: z.string(), + critterbase_start_capture_id: z.string().uuid(), + critterbase_end_capture_id: z.string().uuid().nullable(), + critterbase_end_mortality_id: z.string().uuid().nullable() +}); + +export type BctwDeployDevice = z.infer; + +export type BctwDevice = Omit & { + collar_id: string; +}; + +export const BctwDeploymentUpdate = z.object({ + deployment_id: z.string(), + attachment_start: z.string(), + attachment_end: z.string() +}); + +export type BctwDeploymentUpdate = z.infer; + +export const BctwUploadKeyxResponse = z.object({ + errors: z.array( + z.object({ + row: z.string(), + error: z.string(), + rownum: z.number() + }) + ), + results: z.array( + z.object({ + idcollar: z.number(), + comtype: z.string(), + idcom: z.string(), + collarkey: z.string(), + collartype: z.number(), + dtlast_fetch: z.string().nullable() + }) + ) +}); + +export type BctwUploadKeyxResponse = z.infer; + +export const BctwKeyXDetails = z.object({ + device_id: z.number(), + keyx: z + .object({ + idcom: z.string(), + comtype: z.string(), + idcollar: z.number(), + collarkey: z.string(), + collartype: z.number() + }) + .nullable() +}); + +export type BctwKeyXDetails = z.infer; + +export const IManualTelemetry = z.object({ + telemetry_manual_id: z.string().uuid(), + deployment_id: z.string().uuid(), + latitude: z.number(), + longitude: z.number(), + date: z.string() +}); + +export type IManualTelemetry = z.infer; + +export const BctwUser = z.object({ + keycloak_guid: z.string(), + username: z.string() +}); + +export interface ICodeResponse { + code_header_title: string; + code_header_name: string; + id: number; + code: string; + description: string; + long_description: string; +} + +export type BctwUser = z.infer; + +export interface ICreateManualTelemetry { + deployment_id: string; + latitude: number; + longitude: number; + acquisition_date: string; +} diff --git a/api/src/models/biohub-create.test.ts b/api/src/models/biohub-create.test.ts index 3a62f3734b..9f4ac679ee 100644 --- a/api/src/models/biohub-create.test.ts +++ b/api/src/models/biohub-create.test.ts @@ -191,8 +191,7 @@ describe('PostSurveySubmissionToBioHubObject', () => { const purpose_and_methodology: GetSurveyPurposeAndMethodologyData = { intended_outcome_ids: [], additional_details: 'A description of the purpose', - revision_count: 0, - vantage_code_ids: [] + revision_count: 0 }; const survey_geometry: FeatureCollection = { diff --git a/api/src/models/observation-analytics.ts b/api/src/models/observation-analytics.ts new file mode 100644 index 0000000000..faff4a53f8 --- /dev/null +++ b/api/src/models/observation-analytics.ts @@ -0,0 +1,76 @@ +import { z } from 'zod'; + +export const QualitativeMeasurementAnalyticsSchema = z.object({ + option: z.object({ + option_id: z.string(), + option_label: z.string() + }), + taxon_measurement_id: z.string(), + measurement_name: z.string() +}); + +export type QualitativeMeasurementAnalytics = z.infer; + +export const QuantitativeMeasurementAnalyticsSchema = z.object({ + value: z.number(), + taxon_measurement_id: z.string(), + measurement_name: z.string() +}); + +export type QuantitativeMeasurementAnalytics = z.infer; + +export const ObservationCountByGroupSchema = z.object({ + row_count: z.number(), + individual_count: z.number(), + individual_percentage: z.number() +}); + +export type ObservationCountByGroup = z.infer; + +export const ObservationCountByGroupWithNamedMeasurementsSchema = ObservationCountByGroupSchema.extend({ + qualitative_measurements: z.array(QualitativeMeasurementAnalyticsSchema), + quantitative_measurements: z.array(QuantitativeMeasurementAnalyticsSchema) +}); + +export type ObservationCountByGroupWithNamedMeasurements = z.infer< + typeof ObservationCountByGroupWithNamedMeasurementsSchema +>; + +export const ObservationCountByGroupWithMeasurementsSchema = z.object({ + quant_measurements: z.array( + z.object({ + value: z.number().nullable(), + critterbase_taxon_measurement_id: z.string() + }) + ), + qual_measurements: z.array( + z.object({ + option_id: z.string().nullable(), + critterbase_taxon_measurement_id: z.string() + }) + ) +}); + +export type ObservationCountByGroupWithMeasurements = z.infer; + +export const ObservationCountByGroupSQLResponse = z + .object({ + id: z.string(), + row_count: z.number(), + individual_count: z.number(), + individual_percentage: z.number(), + quant_measurements: z.record(z.string(), z.number().nullable()), + qual_measurements: z.record(z.string(), z.string().nullable()) + }) + // Allow additional properties + .catchall(z.any()); + +export type ObservationCountByGroupSQLResponse = z.infer; + +export const ObservationAnalyticsResponse = ObservationCountByGroupWithNamedMeasurementsSchema.merge( + ObservationCountByGroupSchema +) + // Allow additional properties + .catchall(z.any()); + +export type ObservationAnalyticsResponse = z.infer; diff --git a/api/src/models/project-view.ts b/api/src/models/project-view.ts index a6377fec11..b8aca002c0 100644 --- a/api/src/models/project-view.ts +++ b/api/src/models/project-view.ts @@ -34,7 +34,8 @@ export const FindProjectsResponse = z.object({ end_date: z.string().nullable(), regions: z.array(z.string()), focal_species: z.array(z.number()), - types: z.array(z.number()) + types: z.array(z.number()), + members: z.array(z.object({ system_user_id: z.number(), display_name: z.string() })) }); export type FindProjectsResponse = z.infer; diff --git a/api/src/models/standards-view.ts b/api/src/models/standards-view.ts new file mode 100644 index 0000000000..b611855b15 --- /dev/null +++ b/api/src/models/standards-view.ts @@ -0,0 +1,53 @@ +import { z } from 'zod'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition +} from '../services/critterbase-service'; + +const QualitativeMeasurementSchema = z.object({ + name: z.string(), + description: z.string().nullable(), + options: z.array( + z.object({ + name: z.string(), + description: z.string().nullable() + }) + ) +}); + +const QuantitativeMeasurementSchema = z.object({ + name: z.string(), + description: z.string().nullable(), + unit: z.string().nullable() +}); + +const MethodAttributesSchema = z.object({ + qualitative: z.array(QualitativeMeasurementSchema), + quantitative: z.array(QuantitativeMeasurementSchema) +}); + +export const EnvironmentStandardsSchema = z.object({ + qualitative: z.array(QualitativeMeasurementSchema), + quantitative: z.array(QuantitativeMeasurementSchema) +}); + +export type EnvironmentStandards = z.infer; + +export const MethodStandardSchema = z.object({ + method_lookup_id: z.number(), + name: z.string(), + description: z.string().nullable(), + attributes: MethodAttributesSchema +}); + +export type MethodStandard = z.infer; + +export interface ISpeciesStandards { + tsn: number; + scientificName: string; + measurements: { + quantitative: CBQuantitativeMeasurementTypeDefinition[]; + qualitative: CBQualitativeMeasurementTypeDefinition[]; + }; + markingBodyLocations: { id: string; key: string; value: string }[]; +} diff --git a/api/src/models/survey-create.test.ts b/api/src/models/survey-create.test.ts index fdd1ef06ba..c66980e1c9 100644 --- a/api/src/models/survey-create.test.ts +++ b/api/src/models/survey-create.test.ts @@ -192,18 +192,13 @@ describe('PostSpeciesData', () => { it('sets focal_species', () => { expect(data.focal_species).to.eql([]); }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([]); - }); }); describe('All values provided', () => { let data: PostSpeciesData; const obj = { - focal_species: [1, 2], - ancillary_species: [3] + focal_species: [1, 2] }; before(() => { @@ -213,10 +208,6 @@ describe('PostSpeciesData', () => { it('sets focal_species', () => { expect(data.focal_species).to.eql([1, 2]); }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([3]); - }); }); }); @@ -376,10 +367,6 @@ describe('PostPurposeAndMethodologyData', () => { it('sets additional_details', () => { expect(data.additional_details).to.equal(null); }); - - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql([]); - }); }); describe('All values provided with first nations id', () => { @@ -387,8 +374,7 @@ describe('PostPurposeAndMethodologyData', () => { const obj = { intended_outcome_ids: [1], - additional_details: 'additional_detail', - vantage_code_ids: [4, 5] + additional_details: 'additional_detail' }; before(() => { @@ -402,10 +388,6 @@ describe('PostPurposeAndMethodologyData', () => { it('sets additional_details', () => { expect(data.additional_details).to.eql(obj.additional_details); }); - - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql(obj.vantage_code_ids); - }); }); }); diff --git a/api/src/models/survey-create.ts b/api/src/models/survey-create.ts index 18e85a4f34..746fe7f5cf 100644 --- a/api/src/models/survey-create.ts +++ b/api/src/models/survey-create.ts @@ -1,6 +1,6 @@ import { SurveyStratum } from '../repositories/site-selection-strategy-repository'; import { PostSurveyBlock } from '../repositories/survey-block-repository'; -import { ITaxonomy } from '../services/platform-service'; +import { ITaxonomyWithEcologicalUnits } from '../services/platform-service'; import { PostSurveyLocationData } from './survey-update'; export class PostSurveyObject { @@ -89,12 +89,10 @@ export class PostSurveyDetailsData { } export class PostSpeciesData { - focal_species: ITaxonomy[]; - ancillary_species: ITaxonomy[]; + focal_species: ITaxonomyWithEcologicalUnits[]; constructor(obj?: any) { this.focal_species = (obj?.focal_species?.length && obj.focal_species) || []; - this.ancillary_species = (obj?.ancillary_species?.length && obj.ancillary_species) || []; } } @@ -126,12 +124,10 @@ export class PostProprietorData { export class PostPurposeAndMethodologyData { intended_outcome_ids: number[]; additional_details: string; - vantage_code_ids: number[]; constructor(obj?: any) { this.intended_outcome_ids = obj?.intended_outcome_ids || []; this.additional_details = obj?.additional_details || null; - this.vantage_code_ids = obj?.vantage_code_ids || []; } } diff --git a/api/src/models/survey-deployment.ts b/api/src/models/survey-deployment.ts new file mode 100644 index 0000000000..68d6d0841e --- /dev/null +++ b/api/src/models/survey-deployment.ts @@ -0,0 +1,18 @@ +import { z } from 'zod'; + +export const SurveyDeployment = z.object({ + deployment_id: z.number().int(), + critter_id: z.number(), + critterbase_critter_id: z.string().optional(), + bctw_deployment_id: z.string().uuid(), + critterbase_start_capture_id: z.string().uuid().nullable(), + critterbase_end_capture_id: z.string().uuid().nullable(), + critterbase_end_mortality_id: z.string().uuid().nullable() +}); + +export type SurveyDeployment = z.infer; + +export interface ICreateSurveyDeployment extends Omit {} + +export interface IUpdateSurveyDeployment + extends Omit {} diff --git a/api/src/models/survey-update.test.ts b/api/src/models/survey-update.test.ts index a4f6ef6408..d035d51fde 100644 --- a/api/src/models/survey-update.test.ts +++ b/api/src/models/survey-update.test.ts @@ -150,18 +150,13 @@ describe('PutSpeciesData', () => { it('sets focal_species', () => { expect(data.focal_species).to.eql([]); }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([]); - }); }); describe('All values provided', () => { let data: PutSurveySpeciesData; const obj = { - focal_species: [1, 2], - ancillary_species: [3] + focal_species: [1, 2] }; before(() => { @@ -171,10 +166,6 @@ describe('PutSpeciesData', () => { it('sets focal_species', () => { expect(data.focal_species).to.eql([1, 2]); }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([3]); - }); }); }); @@ -340,10 +331,6 @@ describe('PutPurposeAndMethodologyData', () => { expect(data.additional_details).to.equal(null); }); - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql([]); - }); - it('sets revision_count', () => { expect(data.revision_count).to.equal(null); }); @@ -355,7 +342,6 @@ describe('PutPurposeAndMethodologyData', () => { const obj = { intended_outcome_ids: [1], additional_details: 'additional_detail', - vantage_code_ids: [4, 5], revision_count: 0 }; @@ -371,10 +357,6 @@ describe('PutPurposeAndMethodologyData', () => { expect(data.additional_details).to.equal(obj.additional_details); }); - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql(obj.vantage_code_ids); - }); - it('sets revision_count', () => { expect(data.revision_count).to.equal(obj.revision_count); }); diff --git a/api/src/models/survey-update.ts b/api/src/models/survey-update.ts index b934badc18..5b87c118e7 100644 --- a/api/src/models/survey-update.ts +++ b/api/src/models/survey-update.ts @@ -1,7 +1,7 @@ import { Feature } from 'geojson'; import { SurveyStratum, SurveyStratumRecord } from '../repositories/site-selection-strategy-repository'; import { PostSurveyBlock } from '../repositories/survey-block-repository'; -import { ITaxonomy } from '../services/platform-service'; +import { ITaxonomyWithEcologicalUnits } from '../services/platform-service'; export class PutSurveyObject { survey_details: PutSurveyDetailsData; @@ -99,12 +99,10 @@ export class PutSurveyDetailsData { } export class PutSurveySpeciesData { - focal_species: ITaxonomy[]; - ancillary_species: ITaxonomy[]; + focal_species: ITaxonomyWithEcologicalUnits[]; constructor(obj?: any) { this.focal_species = (obj?.focal_species?.length && obj?.focal_species) || []; - this.ancillary_species = (obj?.ancillary_species?.length && obj?.ancillary_species) || []; } } @@ -136,13 +134,11 @@ export class PutSurveyProprietorData { export class PutSurveyPurposeAndMethodologyData { intended_outcome_ids: number[]; additional_details: string; - vantage_code_ids: number[]; revision_count: number; constructor(obj?: any) { this.intended_outcome_ids = (obj?.intended_outcome_ids?.length && obj?.intended_outcome_ids) || []; this.additional_details = obj?.additional_details || null; - this.vantage_code_ids = (obj?.vantage_code_ids?.length && obj.vantage_code_ids) || []; this.revision_count = obj?.revision_count ?? null; } } diff --git a/api/src/models/survey-view.test.ts b/api/src/models/survey-view.test.ts index 04245c0784..50f4f0751f 100644 --- a/api/src/models/survey-view.test.ts +++ b/api/src/models/survey-view.test.ts @@ -2,7 +2,6 @@ import { expect } from 'chai'; import { describe } from 'mocha'; import { IPermitModel } from '../repositories/permit-repository'; import { - GetAncillarySpeciesData, GetAttachmentsData, GetFocalSpeciesData, GetPermitData, @@ -101,40 +100,6 @@ describe('GetFocalSpeciesData', () => { }); }); -describe('GetAncillarySpeciesData', () => { - describe('No values provided', () => { - let data: GetAncillarySpeciesData; - - before(() => { - data = new GetAncillarySpeciesData(); - }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([]); - }); - }); - - describe('All values provided', () => { - let data: GetAncillarySpeciesData; - - const obj = [ - { tsn: 1, commonNames: ['species1'] }, - { tsn: 2, commonNames: ['species2'] } - ]; - - before(() => { - data = new GetAncillarySpeciesData(obj); - }); - - it('sets ancillary_species', () => { - expect(data.ancillary_species).to.eql([ - { tsn: 1, commonNames: ['species1'] }, - { tsn: 2, commonNames: ['species2'] } - ]); - }); - }); -}); - describe('GetPermitData', () => { describe('No values provided', () => { let data: GetPermitData; @@ -325,10 +290,6 @@ describe('GetSurveyPurposeAndMethodologyData', () => { it('sets additional_details', () => { expect(data.additional_details).to.equal(''); }); - - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql([]); - }); }); describe('All values provided with first nations id', () => { @@ -337,7 +298,6 @@ describe('GetSurveyPurposeAndMethodologyData', () => { const obj = { intended_outcome_ids: [1], additional_details: 'additional_detail', - vantage_ids: [4, 5], revision_count: 'count' }; @@ -353,10 +313,6 @@ describe('GetSurveyPurposeAndMethodologyData', () => { expect(data.additional_details).to.eql(obj.additional_details); }); - it('sets vantage_code_ids', () => { - expect(data.vantage_code_ids).to.eql(obj.vantage_ids); - }); - it('sets revision_count', function () { expect(data.revision_count).to.equal('count'); }); diff --git a/api/src/models/survey-view.ts b/api/src/models/survey-view.ts index 2c11556132..04148517e0 100644 --- a/api/src/models/survey-view.ts +++ b/api/src/models/survey-view.ts @@ -7,7 +7,7 @@ import { SurveyBlockRecord } from '../repositories/survey-block-repository'; import { SurveyLocationRecord } from '../repositories/survey-location-repository'; import { SurveyUser } from '../repositories/survey-participation-repository'; import { SystemUser } from '../repositories/user-repository'; -import { ITaxonomy } from '../services/platform-service'; +import { ITaxonomyWithEcologicalUnits } from '../services/platform-service'; export interface ISurveyAdvancedFilters { keyword?: string; @@ -35,7 +35,7 @@ export type FindSurveysResponse = z.infer; export type SurveyObject = { survey_details: GetSurveyData; - species: GetFocalSpeciesData & GetAncillarySpeciesData; + species: GetFocalSpeciesData; permit: GetPermitData; funding_sources: GetSurveyFundingSourceData[]; purpose_and_methodology: GetSurveyPurposeAndMethodologyData; @@ -101,7 +101,7 @@ export class GetSurveyFundingSourceData { } export class GetFocalSpeciesData { - focal_species: ITaxonomy[]; + focal_species: ITaxonomyWithEcologicalUnits[]; constructor(obj?: any[]) { this.focal_species = []; @@ -113,18 +113,6 @@ export class GetFocalSpeciesData { } } -export class GetAncillarySpeciesData { - ancillary_species: ITaxonomy[]; - - constructor(obj?: any[]) { - this.ancillary_species = []; - - obj?.length && - obj.forEach((item: any) => { - this.ancillary_species.push(item); - }); - } -} export class GetPermitData { permits: { permit_id: IPermitModel['permit_id']; @@ -146,12 +134,10 @@ export class GetSurveyPurposeAndMethodologyData { intended_outcome_ids: number[]; additional_details: string; revision_count: number; - vantage_code_ids: number[]; constructor(obj?: any) { this.intended_outcome_ids = (obj?.intended_outcome_ids?.length && obj?.intended_outcome_ids) || []; this.additional_details = obj?.additional_details || ''; - this.vantage_code_ids = (obj?.vantage_ids?.length && obj.vantage_ids) || []; this.revision_count = obj?.revision_count ?? 0; } } diff --git a/api/src/models/telemetry-view.ts b/api/src/models/telemetry-view.ts index 148579fdfa..f04c9dba5d 100644 --- a/api/src/models/telemetry-view.ts +++ b/api/src/models/telemetry-view.ts @@ -1,4 +1,4 @@ -export interface ITelemetryAdvancedFilters { +export interface IAllTelemetryAdvancedFilters { keyword?: string; itis_tsns?: number[]; itis_tsn?: number; diff --git a/api/src/openapi/schemas/critter.ts b/api/src/openapi/schemas/critter.ts index 2b5de50b79..404ad27dfd 100644 --- a/api/src/openapi/schemas/critter.ts +++ b/api/src/openapi/schemas/critter.ts @@ -1,13 +1,46 @@ import { OpenAPIV3 } from 'openapi-types'; +export const collectionUnitsSchema: OpenAPIV3.SchemaObject = { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + required: ['collection_category_id', 'collection_unit_id'], + properties: { + critter_collection_unit_id: { + type: 'string', + format: 'uuid' + }, + collection_category_id: { + type: 'string', + format: 'uuid' + }, + collection_unit_id: { + type: 'string', + format: 'uuid' + }, + unit_name: { + type: 'string' + }, + category_name: { + type: 'string' + } + } + } +}; + export const critterSchema: OpenAPIV3.SchemaObject = { type: 'object', additionalProperties: false, properties: { - critter_id: { + critterbase_critter_id: { type: 'string', format: 'uuid' }, + critter_id: { + type: 'integer', + minimum: 1 + }, animal_id: { type: 'string', nullable: true @@ -33,7 +66,24 @@ export const critterSchema: OpenAPIV3.SchemaObject = { critter_comment: { type: 'string', nullable: true - } + }, + mortality: { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + required: ['mortality_id', 'mortality_timestamp'], + properties: { + mortality_id: { + type: 'string' + }, + mortality_timestamp: { + type: 'string' + } + } + } + }, + collection_units: collectionUnitsSchema } }; diff --git a/api/src/openapi/schemas/deployment.ts b/api/src/openapi/schemas/deployment.ts new file mode 100644 index 0000000000..a742ebbc3f --- /dev/null +++ b/api/src/openapi/schemas/deployment.ts @@ -0,0 +1,256 @@ +import { OpenAPIV3 } from 'openapi-types'; +import { GeoJSONFeatureCollection } from './geoJson'; + +export const getDeploymentSchema: OpenAPIV3.SchemaObject = { + type: 'object', + // TODO: REMOVE unnecessary columns from BCTW response + additionalProperties: false, + required: [ + // BCTW properties + 'assignment_id', + 'collar_id', + 'critter_id', + 'device_id', + 'attachment_start_date', + 'attachment_start_time', + 'attachment_end_date', + 'attachment_end_time', + 'bctw_deployment_id', + 'device_make', + 'device_model', + 'frequency', + 'frequency_unit', + // SIMS properties + 'deployment_id', + 'critterbase_critter_id', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id' + ], + properties: { + // BCTW properties + assignment_id: { + type: 'string', + format: 'uuid' + }, + collar_id: { + type: 'string', + description: 'Id of the collar in BCTW' + }, + attachment_start_date: { + type: 'string', + description: 'start date of the deployment.' + }, + attachment_start_time: { + type: 'string', + description: 'start time of the deployment.' + }, + attachment_end_date: { + type: 'string', + description: 'End date of the deployment.', + nullable: true + }, + attachment_end_time: { + type: 'string', + description: 'End time of the deployment.', + nullable: true + }, + bctw_deployment_id: { + type: 'string', + format: 'uuid', + description: 'Id of the deployment in BCTW. May match multiple records in BCTW' + }, + device_id: { + type: 'integer', + description: 'Id of the device, as reported by users. Not unique.' + }, + device_make: { + type: 'number', + nullable: true + }, + device_model: { + type: 'string', + nullable: true + }, + frequency: { + type: 'number', + nullable: true + }, + frequency_unit: { + type: 'number', + nullable: true + }, + // SIMS properties + deployment_id: { + type: 'integer', + description: 'Id of the deployment in the Survey.' + }, + critter_id: { + type: 'integer', + minimum: 1, + description: 'Id of the critter in the Survey' + }, + critterbase_critter_id: { + type: 'string', + format: 'uuid', + description: 'Id of the critter in Critterbase.' + }, + critterbase_start_capture_id: { + type: 'string' + }, + critterbase_end_capture_id: { + type: 'string', + nullable: true + }, + critterbase_end_mortality_id: { + type: 'string', + nullable: true + } + } +}; + +const GeoJSONFeatureCollectionFeaturesItems = ( + GeoJSONFeatureCollection.properties?.features as OpenAPIV3.ArraySchemaObject +)?.items as OpenAPIV3.SchemaObject; + +export const GeoJSONTelemetryPointsAPISchema: OpenAPIV3.SchemaObject = { + ...GeoJSONFeatureCollection, + properties: { + ...GeoJSONFeatureCollection.properties, + features: { + type: 'array', + items: { + ...GeoJSONFeatureCollectionFeaturesItems, + properties: { + ...GeoJSONFeatureCollectionFeaturesItems?.properties, + properties: { + type: 'object', + additionalProperties: false, + required: ['collar_id', 'device_id', 'date_recorded', 'deployment_id', 'critter_id'], + properties: { + collar_id: { + type: 'string', + format: 'uuid' + }, + device_id: { + type: 'integer' + }, + elevation: { + type: 'number', + nullable: true + }, + frequency: { + type: 'number', + nullable: true + }, + critter_id: { + type: 'string', + format: 'uuid' + }, + date_recorded: { + type: 'string' + }, + deployment_id: { + type: 'string', + format: 'uuid' + }, + device_status: { + type: 'string', + nullable: true + }, + device_vendor: { + type: 'string', + nullable: true + }, + frequency_unit: { + type: 'number', + nullable: true + }, + wlh_id: { + type: 'string', + nullable: true + }, + animal_id: { + type: 'string', + nullable: true + }, + sex: { + type: 'string' + }, + taxon: { + type: 'string' + }, + collection_units: { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + properties: { + collection_unit_id: { + type: 'string', + format: 'uuid' + }, + unit_name: { + type: 'string' + }, + collection_category_id: { + type: 'string', + format: 'uuid' + }, + category_name: { + type: 'string' + } + } + } + }, + mortality_timestamp: { + type: 'string', + nullable: true + }, + _merged: { + type: 'boolean' + }, + map_colour: { + type: 'string' + } + } + } + } + } + } + } +}; + +export const GeoJSONTelemetryTracksAPISchema: OpenAPIV3.SchemaObject = { + ...GeoJSONFeatureCollection, + properties: { + ...GeoJSONFeatureCollection.properties, + features: { + type: 'array', + items: { + ...GeoJSONFeatureCollectionFeaturesItems, + properties: { + ...GeoJSONFeatureCollectionFeaturesItems?.properties, + properties: { + type: 'object', + additionalProperties: false, + required: ['critter_id', 'deployment_id'], + properties: { + critter_id: { + type: 'string', + format: 'uuid' + }, + deployment_id: { + type: 'string', + format: 'uuid' + }, + map_colour: { + type: 'string' + } + } + } + } + } + } + } +}; diff --git a/api/src/openapi/schemas/file.ts b/api/src/openapi/schemas/file.ts index e52ba63484..fba9ec9c5b 100644 --- a/api/src/openapi/schemas/file.ts +++ b/api/src/openapi/schemas/file.ts @@ -58,7 +58,17 @@ export const csvFileSchema: OpenAPIV3.SchemaObject = { mimetype: { description: 'CSV File type.', type: 'string', - enum: ['text/csv'] + // https://christianwood.net/posts/csv-file-upload-validation/ + enum: [ + 'text/csv', + 'text/x-csv', + 'application/vnd.ms-excel', + 'application/csv', + 'application/x-csv', + 'text/comma-seperated-values', + 'text/x-comma-seperated-values', + 'text/tab-seperated-values' + ] } } }; diff --git a/api/src/openapi/schemas/standards.ts b/api/src/openapi/schemas/standards.ts new file mode 100644 index 0000000000..6457fcdba7 --- /dev/null +++ b/api/src/openapi/schemas/standards.ts @@ -0,0 +1,137 @@ +import { OpenAPIV3 } from 'openapi-types'; + +export const EnvironmentStandardsSchema: OpenAPIV3.SchemaObject = { + type: 'object', + description: + 'Environment standards response object showing supported environmental variables and associated information', + additionalProperties: false, + properties: { + qualitative: { + type: 'array', + description: 'Array of qualitative environmental variables', + items: { + type: 'object', + properties: { + name: { + type: 'string', + description: 'Name of the environmental variable' + }, + description: { + type: 'string', + description: 'Description of the environmental variable', + nullable: true + }, + options: { + type: 'array', + description: 'Array of options for the qualitative variable', + items: { + type: 'object', + properties: { + name: { + type: 'string', + description: 'Description of the environmental variable option' + }, + description: { + type: 'string', + description: 'Description of the environmental variable option', + nullable: true + } + } + } + } + } + } + }, + quantitative: { + type: 'array', + description: 'Array of quantitative environmental variables', + items: { + type: 'object', + properties: { + name: { + type: 'string', + description: 'Name of the quantitative environmental variable' + }, + description: { + type: 'string', + description: 'Description of the quantitative environmental variable', + nullable: true + }, + unit: { + type: 'string', + description: 'Unit of measurement of the quantitative environmental variable', + nullable: true + } + } + } + } + } +}; + +export const MethodStandardSchema: OpenAPIV3.SchemaObject = { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + properties: { + method_lookup_id: { type: 'number' }, + name: { type: 'string' }, + description: { type: 'string', nullable: true }, + attributes: { + type: 'object', + additionalProperties: false, + properties: { + qualitative: { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + properties: { + name: { + type: 'string' + }, + description: { + type: 'string', + nullable: true + }, + options: { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + properties: { + name: { + type: 'string' + }, + description: { + type: 'string', + nullable: true + } + } + } + } + } + } + }, + quantitative: { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + properties: { + name: { + type: 'string' + }, + description: { + type: 'string', + nullable: true + }, + unit: { type: 'string', nullable: true } + } + } + } + } + } + } + } +}; diff --git a/api/src/openapi/schemas/survey.ts b/api/src/openapi/schemas/survey.ts index c7db5e593a..6e9a35a298 100644 --- a/api/src/openapi/schemas/survey.ts +++ b/api/src/openapi/schemas/survey.ts @@ -55,6 +55,30 @@ export const surveyDetailsSchema: OpenAPIV3.SchemaObject = { } }; +/** + * Schema for creating, updating and retrieving ecological units for focal species in a SIMS survey. + * Prefixed with critterbase_* to match database field names in SIMS. + * + */ +export const SurveyEcologicalUnitsSchema: OpenAPIV3.SchemaObject = { + type: 'array', + items: { + type: 'object', + additionalProperties: false, + required: ['critterbase_collection_category_id', 'critterbase_collection_unit_id'], + properties: { + critterbase_collection_category_id: { + type: 'string', + format: 'uuid' + }, + critterbase_collection_unit_id: { + type: 'string', + format: 'uuid' + } + } + } +}; + export const surveyFundingSourceSchema: OpenAPIV3.SchemaObject = { title: 'survey funding source response object', type: 'object', @@ -112,7 +136,7 @@ export const focalSpeciesSchema: OpenAPIV3.SchemaObject = { title: 'focal species response object', type: 'object', additionalProperties: false, - required: ['tsn', 'commonNames', 'scientificName'], + required: ['tsn', 'commonNames', 'scientificName', 'ecological_units'], properties: { tsn: { description: 'Taxonomy tsn', @@ -137,40 +161,8 @@ export const focalSpeciesSchema: OpenAPIV3.SchemaObject = { kingdom: { description: 'Taxonomy kingdom name', type: 'string' - } - } -}; - -export const ancillarySpeciesSchema: OpenAPIV3.SchemaObject = { - title: 'ancillary species response object', - type: 'object', - additionalProperties: false, - required: ['tsn', 'commonNames', 'scientificName'], - properties: { - tsn: { - description: 'Taxonomy tsn', - type: 'number' }, - commonNames: { - description: 'Taxonomy common names', - type: 'array', - items: { - type: 'string' - }, - nullable: true - }, - scientificName: { - description: 'Taxonomy scientific name', - type: 'string' - }, - rank: { - description: 'Taxonomy rank name', - type: 'string' - }, - kingdom: { - description: 'Taxonomy kingdom name', - type: 'string' - } + ecological_units: SurveyEcologicalUnitsSchema } }; @@ -178,13 +170,8 @@ export const surveySpeciesSchema: OpenAPIV3.SchemaObject = { description: 'Survey Species', type: 'object', additionalProperties: false, - required: ['focal_species', 'ancillary_species'], + required: ['focal_species'], properties: { - ancillary_species: { - nullable: true, - type: 'array', - items: ancillarySpeciesSchema - }, focal_species: { type: 'array', items: focalSpeciesSchema @@ -282,7 +269,7 @@ export const surveyPurposeAndMethodologySchema: OpenAPIV3.SchemaObject = { title: 'survey purpose and methodology response object', type: 'object', additionalProperties: false, - required: ['intended_outcome_ids', 'additional_details', 'vantage_code_ids'], + required: ['intended_outcome_ids', 'additional_details'], properties: { intended_outcome_ids: { description: 'Intended outcome ids', @@ -301,14 +288,6 @@ export const surveyPurposeAndMethodologySchema: OpenAPIV3.SchemaObject = { description: 'The integer of times the record has been revised.', type: 'integer', minimum: 0 - }, - vantage_code_ids: { - description: 'Vantage code ids', - type: 'array', - items: { - type: 'integer', - minimum: 1 - } } } }; diff --git a/api/src/openapi/schemas/telemetry.ts b/api/src/openapi/schemas/telemetry.ts new file mode 100644 index 0000000000..3de5f7081f --- /dev/null +++ b/api/src/openapi/schemas/telemetry.ts @@ -0,0 +1,57 @@ +import { OpenAPIV3 } from 'openapi-types'; + +export const AllTelemetrySchema: OpenAPIV3.SchemaObject = { + type: 'object', + additionalProperties: false, + required: [ + 'id', + 'deployment_id', + 'latitude', + 'longitude', + 'acquisition_date', + 'telemetry_type', + 'telemetry_id', + 'telemetry_manual_id' + ], + properties: { + id: { + type: 'string', + format: 'uuid', + description: + 'The unique identifier for the telemetry point. Will match whichever of telemetry_id or telemetry_manual_id is not null.' + }, + deployment_id: { + type: 'string', + format: 'uuid', + description: 'The unique identifier for the deployment that the telemetry point is associated with.' + }, + latitude: { + type: 'number', + description: 'The latitude of the telemetry point.' + }, + longitude: { + type: 'number', + description: 'The longitude of the telemetry point.' + }, + acquisition_date: { + type: 'string' + }, + telemetry_type: { + type: 'string', + description: "The type of telemetry point. Will either be 'MANUAL' or the name of the vendor." + }, + telemetry_id: { + type: 'string', + format: 'uuid', + nullable: true, + description: + "The unique identifier for the telemetry point. Will only be non-null if telemetry_type is not 'MANUAL'." + }, + telemetry_manual_id: { + type: 'string', + format: 'uuid', + nullable: true, + description: "The unique identifier for the telemetry point. Will only be non-null if telemetry_type is 'MANUAL'." + } + } +}; diff --git a/api/src/paths/administrative-activities.ts b/api/src/paths/administrative-activities.ts index 81d8d9b58d..31b7c2fbd1 100644 --- a/api/src/paths/administrative-activities.ts +++ b/api/src/paths/administrative-activities.ts @@ -108,6 +108,16 @@ GET.apiDoc = { create_date: { type: 'string', description: 'ISO 8601 date string' + }, + updated_by: { + type: 'string', + description: 'Display name of the user who last updated the record', + nullable: true + }, + update_date: { + type: 'string', + description: 'Date when the record was last updated', + nullable: true } } } diff --git a/api/src/paths/analytics/observations.ts b/api/src/paths/analytics/observations.ts new file mode 100644 index 0000000000..65cbc6265e --- /dev/null +++ b/api/src/paths/analytics/observations.ts @@ -0,0 +1,243 @@ +import { Operation } from 'express-openapi'; +import { RequestHandler } from 'http-proxy-middleware'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../constants/roles'; +import { getDBConnection } from '../../database/db'; +import { authorizeRequestHandler } from '../../request-handlers/security/authorization'; +import { AnalyticsService } from '../../services/analytics-service'; +import { getLogger } from '../../utils/logger'; + +const defaultLog = getLogger('paths/analytics/observations'); + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + }, + { + validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN], + discriminator: 'SystemRole' + } + ] + }; + }), + getObservationCountByGroup() +]; + +GET.apiDoc = { + description: 'get analytics about observations for one or more surveys', + tags: ['analytics'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'query', + name: 'surveyIds', + schema: { + type: 'array', + items: { + type: 'integer', + minimum: 1 + } + }, + required: true + }, + { + in: 'query', + name: 'groupByColumns', + schema: { + type: 'array', + items: { + type: 'string' + } + }, + description: 'An array of column names to group the observations data by' + }, + { + in: 'query', + name: 'groupByQuantitativeMeasurements', + schema: { + type: 'array', + items: { + type: 'string' + } + }, + description: 'An array of quantitative taxon_measurement_ids to group the observations data by' + }, + { + in: 'query', + name: 'groupByQualitativeMeasurements', + schema: { + type: 'array', + items: { + type: 'string' + } + }, + description: 'An array of qualitative taxon_measurement_ids to group the observations data by' + } + ], + responses: { + 200: { + description: 'Analytics calculated OK.', + content: { + 'application/json': { + schema: { + title: 'Observation analytics response object', + type: 'array', + items: { + type: 'object', + required: [ + 'id', + 'row_count', + 'individual_count', + 'individual_percentage', + 'quantitative_measurements', + 'qualitative_measurements' + ], + // Additional properties is intentionally true to allow for dynamic key-value measurement pairs + additionalProperties: true, + properties: { + id: { + type: 'string', + format: 'uuid', + description: 'Unique identifier for the group. Will not be consistent between requests.' + }, + row_count: { + type: 'number', + description: 'Number of rows in the group' + }, + individual_count: { + type: 'number', + description: 'Sum of subcount values across all rows in the group' + }, + individual_percentage: { + type: 'number', + description: + 'Sum of subcount values across the group divided by the sum of subcount values across all observations in the specified surveys' + }, + quantitative_measurements: { + type: 'array', + items: { + type: 'object', + description: 'Quantitative measurement groupings', + required: ['taxon_measurement_id', 'measurement_name', 'value'], + additionalProperties: false, + properties: { + taxon_measurement_id: { + type: 'string', + format: 'uuid' + }, + measurement_name: { + type: 'string' + }, + value: { + type: 'number', + nullable: true + } + } + } + }, + qualitative_measurements: { + type: 'array', + items: { + type: 'object', + description: 'Qualitative measurement groupings', + required: ['taxon_measurement_id', 'measurement_name', 'option'], + additionalProperties: false, + properties: { + taxon_measurement_id: { + type: 'string', + format: 'uuid' + }, + measurement_name: { + type: 'string' + }, + option: { + type: 'object', + required: ['option_id', 'option_label'], + additionalProperties: false, + properties: { + option_id: { + type: 'string', + format: 'uuid', + nullable: true + }, + option_label: { + type: 'string', + nullable: true + } + } + } + } + } + } + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function getObservationCountByGroup(): RequestHandler { + return async (req, res) => { + defaultLog.debug({ label: 'getObservationCountByGroup' }); + + const connection = getDBConnection(req.keycloak_token); + + try { + const { surveyIds, groupByColumns, groupByQuantitativeMeasurements, groupByQualitativeMeasurements } = req.query; + + await connection.open(); + + const analyticsService = new AnalyticsService(connection); + + const response = await analyticsService.getObservationCountByGroup( + (surveyIds as string[]).map(Number), + (groupByColumns as string[]) ?? [], + (groupByQuantitativeMeasurements as string[]) ?? [], + (groupByQualitativeMeasurements as string[]) ?? [] + ); + + await connection.commit(); + + return res.status(200).json(response); + } catch (error) { + defaultLog.error({ label: 'getObservationCountByGroup', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/codes.ts b/api/src/paths/codes.ts index 8f2c6e3644..a8df6080af 100644 --- a/api/src/paths/codes.ts +++ b/api/src/paths/codes.ts @@ -34,7 +34,6 @@ GET.apiDoc = { 'project_roles', 'administrative_activity_status_type', 'intended_outcomes', - 'vantage_codes', 'site_selection_strategies', 'survey_progress', 'method_response_metrics', @@ -252,21 +251,6 @@ GET.apiDoc = { } } }, - vantage_codes: { - type: 'array', - items: { - type: 'object', - additionalProperties: false, - properties: { - id: { - type: 'number' - }, - name: { - type: 'string' - } - } - } - }, survey_jobs: { type: 'array', items: { diff --git a/api/src/paths/gcnotify/send.ts b/api/src/paths/gcnotify/send.ts index 7bc157cc57..938cf5a44c 100644 --- a/api/src/paths/gcnotify/send.ts +++ b/api/src/paths/gcnotify/send.ts @@ -145,7 +145,7 @@ POST.apiDoc = { export function sendNotification(): RequestHandler { return async (req, res) => { const recipient = req.body?.recipient || null; - const message = { ...req.body?.message, footer: `To access the site, [${APP_HOST}](${APP_HOST})` } || null; + const message = { ...req.body?.message, footer: `To access the site, [${APP_HOST}](${APP_HOST})` }; try { const gcnotifyService = new GCNotifyService(); diff --git a/api/src/paths/logger.test.ts b/api/src/paths/logger.test.ts index 02731ce09d..2367c213a8 100644 --- a/api/src/paths/logger.test.ts +++ b/api/src/paths/logger.test.ts @@ -1,34 +1,19 @@ import { expect } from 'chai'; import { describe } from 'mocha'; -import { HTTPError } from '../errors/http-error'; import { getRequestHandlerMocks } from '../__mocks__/db'; import * as logger from './logger'; describe('logger', () => { describe('updateLoggerLevel', () => { - it('should throw a 400 error when `level` query param is missing', async () => { - const requestHandler = logger.updateLoggerLevel(); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - try { - await requestHandler(mockReq, mockRes, mockNext); - - expect.fail(); - } catch (error) { - expect((error as HTTPError).status).to.equal(400); - expect((error as HTTPError).message).to.equal('Missing required query param `level`'); - } - }); - it('should return 200 on success', async () => { const requestHandler = logger.updateLoggerLevel(); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - mockReq.query = { level: 'info' }; + mockReq.query = { + logLevel: 'info', + logLevelFile: 'debug' + }; await requestHandler(mockReq, mockRes, mockNext); diff --git a/api/src/paths/logger.ts b/api/src/paths/logger.ts index f370a9501a..39576522f3 100644 --- a/api/src/paths/logger.ts +++ b/api/src/paths/logger.ts @@ -1,9 +1,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { SYSTEM_ROLE } from '../constants/roles'; -import { HTTP400 } from '../errors/http-error'; import { authorizeRequestHandler } from '../request-handlers/security/authorization'; -import { setLogLevel, WinstonLogLevel, WinstonLogLevels } from '../utils/logger'; +import { setLogLevel, setLogLevelFile, WinstonLogLevel, WinstonLogLevels } from '../utils/logger'; export const GET: Operation = [ authorizeRequestHandler(() => { @@ -20,7 +19,7 @@ export const GET: Operation = [ ]; GET.apiDoc = { - description: "Update the log level for the API's default logger", + description: 'Update the logging level of the winston logger.', tags: ['misc'], security: [ { @@ -30,13 +29,23 @@ GET.apiDoc = { parameters: [ { in: 'query', - name: 'level', + name: 'logLevel', + description: 'Set the log level for the console transport (non-production environments only)', schema: { description: 'Log levels, from least logging to most logging', type: 'string', enum: [...WinstonLogLevels] - }, - required: true + } + }, + { + in: 'query', + name: 'logLevelFile', + description: 'Set the log level for the file transport', + schema: { + description: 'Log levels, from least logging to most logging', + type: 'string', + enum: [...WinstonLogLevels] + } } ], responses: { @@ -59,17 +68,19 @@ GET.apiDoc = { }; /** - * Get api version information. + * Update the logging level of the winston logger. * * @returns {RequestHandler} */ export function updateLoggerLevel(): RequestHandler { return (req, res) => { - if (!req.query?.level) { - throw new HTTP400('Missing required query param `level`'); + if (req.query.logLevel) { + setLogLevel(req.query.loglevel as WinstonLogLevel); } - setLogLevel(req.query.level as WinstonLogLevel); + if (req.query.logLevelFile) { + setLogLevelFile(req.query.logLevelFile as WinstonLogLevel); + } res.status(200).send(); }; diff --git a/api/src/paths/project/index.test.ts b/api/src/paths/project/index.test.ts index d36b2c6d0f..0a80991172 100644 --- a/api/src/paths/project/index.test.ts +++ b/api/src/paths/project/index.test.ts @@ -28,7 +28,8 @@ describe('findProjects', () => { end_date: '2021-12-31', regions: ['region1'], focal_species: [123, 456], - types: [1, 2, 3] + types: [1, 2, 3], + members: [{ system_user_id: 1, display_name: 'John Doe' }] } ]; @@ -87,7 +88,8 @@ describe('findProjects', () => { end_date: '2021-12-31', regions: ['region1'], focal_species: [123, 456], - types: [1, 2, 3] + types: [1, 2, 3], + members: [{ system_user_id: 1, display_name: 'John Doe' }] } ]; diff --git a/api/src/paths/project/index.ts b/api/src/paths/project/index.ts index 8d75b4294c..bf2b66367a 100644 --- a/api/src/paths/project/index.ts +++ b/api/src/paths/project/index.ts @@ -106,7 +106,16 @@ GET.apiDoc = { items: { type: 'object', additionalProperties: false, - required: ['project_id', 'name', 'start_date', 'end_date', 'focal_species', 'regions', 'types'], + required: [ + 'project_id', + 'name', + 'start_date', + 'end_date', + 'focal_species', + 'regions', + 'types', + 'members' + ], properties: { project_id: { type: 'integer', @@ -147,6 +156,19 @@ GET.apiDoc = { items: { type: 'integer' } + }, + members: { + type: 'array', + description: 'Members of the Project', + items: { + type: 'object', + additionalProperties: false, + required: ['system_user_id', 'display_name'], + properties: { + system_user_id: { type: 'number' }, + display_name: { type: 'string' } + } + } } } } diff --git a/api/src/paths/project/{projectId}/survey/create.ts b/api/src/paths/project/{projectId}/survey/create.ts index 9fd7b420be..23fb747756 100644 --- a/api/src/paths/project/{projectId}/survey/create.ts +++ b/api/src/paths/project/{projectId}/survey/create.ts @@ -12,7 +12,6 @@ import { surveyPermitSchema, surveyProprietorSchema, surveyPurposeAndMethodologySchema, - surveySiteSelectionSchema, surveySpeciesSchema } from '../../../../openapi/schemas/survey'; import { surveyParticipationAndSystemUserSchema } from '../../../../openapi/schemas/user'; @@ -104,7 +103,56 @@ POST.apiDoc = { type: 'array', items: surveyLocationSchema }, - site_selection: surveySiteSelectionSchema, + site_selection: { + title: 'survey site selection response object', + type: 'object', + additionalProperties: false, + required: ['strategies', 'stratums'], + properties: { + strategies: { + description: 'Strategies', + type: 'array', + items: { + type: 'string' + } + }, + stratums: { + description: 'Stratums', + type: 'array', + items: { + type: 'object', + additionalProperties: false, + required: ['name', 'description'], + properties: { + name: { + description: 'Name', + type: 'string' + }, + description: { + description: 'Description', + type: 'string', + nullable: true + }, + survey_id: { + description: 'Survey id', + type: 'integer', + nullable: true + }, + survey_stratum_id: { + description: 'Survey stratum id', + type: 'integer', + nullable: true, + minimum: 1 + }, + revision_count: { + description: 'Revision count', + type: 'integer' + } + } + } + } + } + }, participants: { type: 'array', items: { diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.test.ts deleted file mode 100644 index 95377ae9ef..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.test.ts +++ /dev/null @@ -1,148 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../../../../../database/db'; -import { HTTPError } from '../../../../../../../errors/http-error'; -import { AttachmentService } from '../../../../../../../services/attachment-service'; -import { BctwService } from '../../../../../../../services/bctw-service'; -import * as file_utils from '../../../../../../../utils/file-utils'; -import * as media_utils from '../../../../../../../utils/media/media-utils'; -import { getMockDBConnection } from '../../../../../../../__mocks__/db'; -import * as upload from './upload'; - -chai.use(sinonChai); - -describe('uploadMedia', () => { - afterEach(() => { - sinon.restore(); - }); - - const dbConnectionObj = getMockDBConnection(); - - const mockReq = { - keycloak_token: {}, - system_user: { user_guid: 'system_user_guid', user_identifier: 'system_user_identifier' }, - params: { - projectId: 1, - attachmentId: 2 - }, - files: [ - { - fieldname: 'media', - originalname: 'test.keyx', - encoding: '7bit', - mimetype: 'text/plain', - size: 340 - } - ], - body: {} - } as any; - - const mockBctwResponse = { totalKeyxFiles: 2, newRecords: 1, existingRecords: 1 }; - - it('should throw an error when file has malicious content', async () => { - sinon.stub(db, 'getDBConnection').returns({ - ...dbConnectionObj, - systemUserId: () => { - return 20; - } - }); - - sinon.stub(file_utils, 'scanFileForVirus').resolves(false); - - try { - const result = upload.uploadKeyxMedia(); - - await result(mockReq, null as unknown as any, null as unknown as any); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).status).to.equal(400); - expect((actualError as HTTPError).message).to.equal('Malicious content detected, upload cancelled'); - } - }); - - it('should throw an error when file type is invalid', async () => { - sinon.stub(db, 'getDBConnection').returns({ - ...dbConnectionObj, - systemUserId: () => { - return 20; - } - }); - - sinon.stub(file_utils, 'scanFileForVirus').resolves(true); - sinon.stub(media_utils, 'checkFileForKeyx').returns(false); - - try { - const result = upload.uploadKeyxMedia(); - - await result(mockReq, null as unknown as any, null as unknown as any); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).status).to.equal(400); - expect((actualError as HTTPError).message).to.equal( - 'The file must either be a keyx file or a zip containing only keyx files.' - ); - } - }); - - it('should throw an error if failure occurs', async () => { - sinon.stub(db, 'getDBConnection').returns({ - ...dbConnectionObj, - systemUserId: () => { - return 20; - } - }); - - sinon.stub(file_utils, 'scanFileForVirus').resolves(true); - - const expectedError = new Error('A test error'); - sinon.stub(BctwService.prototype, 'uploadKeyX').rejects(expectedError); - - try { - const result = upload.uploadKeyxMedia(); - - await result(mockReq, null as unknown as any, null as unknown as any); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal(expectedError.message); - } - }); - - it('should succeed with valid params', async () => { - sinon.stub(db, 'getDBConnection').returns({ - ...dbConnectionObj, - systemUserId: () => { - return 20; - } - }); - - sinon.stub(file_utils, 'scanFileForVirus').resolves(true); - const uploadKeyXStub = sinon.stub(BctwService.prototype, 'uploadKeyX').resolves(mockBctwResponse); - sinon.stub(file_utils, 'uploadFileToS3').resolves(); - - const expectedResponse = { attachmentId: 1, revision_count: 1, keyxResults: mockBctwResponse }; - - let actualResult: any = null; - const sampleRes = { - status: () => { - return { - json: (response: any) => { - actualResult = response; - } - }; - } - }; - - const upsertSurveyAttachmentStub = sinon - .stub(AttachmentService.prototype, 'upsertSurveyAttachment') - .resolves({ survey_attachment_id: 1, revision_count: 1, key: 'string' }); - - const result = upload.uploadKeyxMedia(); - - await result(mockReq, sampleRes as unknown as any, null as unknown as any); - expect(actualResult).to.eql(expectedResponse); - expect(uploadKeyXStub).to.be.calledOnce; - expect(upsertSurveyAttachmentStub).to.be.calledOnce; - }); -}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.ts deleted file mode 100644 index 6ec0a72418..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/keyx/upload.ts +++ /dev/null @@ -1,207 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { ATTACHMENT_TYPE } from '../../../../../../../constants/attachments'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; -import { getDBConnection } from '../../../../../../../database/db'; -import { HTTP400 } from '../../../../../../../errors/http-error'; -import { fileSchema } from '../../../../../../../openapi/schemas/file'; -import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; -import { AttachmentService } from '../../../../../../../services/attachment-service'; -import { BctwService, IBctwUser } from '../../../../../../../services/bctw-service'; -import { scanFileForVirus, uploadFileToS3 } from '../../../../../../../utils/file-utils'; -import { getLogger } from '../../../../../../../utils/logger'; -import { checkFileForKeyx } from '../../../../../../../utils/media/media-utils'; -import { getFileFromRequest } from '../../../../../../../utils/request'; - -const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/attachments/keyx/upload'); - -export const POST: Operation = [ - authorizeRequestHandler((req) => { - return { - or: [ - { - validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], - surveyId: Number(req.params.surveyId), - discriminator: 'ProjectPermission' - }, - { - validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - uploadKeyxMedia() -]; - -POST.apiDoc = { - tags: ['attachment'], - description: 'Upload a survey-specific keyx attachment.', - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'path', - name: 'surveyId', - schema: { - type: 'integer', - minimum: 1 - }, - required: true - }, - { - in: 'path', - name: 'projectId', - schema: { - type: 'integer', - minimum: 1 - }, - required: true - } - ], - requestBody: { - description: 'Keyx Attachment upload post request object.', - content: { - 'multipart/form-data': { - schema: { - type: 'object', - additionalProperties: false, - required: ['media'], - properties: { - media: { - description: 'Keyx import file.', - type: 'array', - minItems: 1, - maxItems: 1, - items: fileSchema - } - } - } - } - } - }, - - responses: { - 200: { - description: 'Keyx Attachment upload response.', - content: { - 'application/json': { - schema: { - type: 'object', - additionalProperties: false, - required: ['attachmentId', 'revision_count', 'keyxResults'], - properties: { - keyxResults: { - type: 'object', - additionalProperties: false, - required: ['totalKeyxFiles', 'newRecords', 'existingRecords'], - properties: { - totalKeyxFiles: { type: 'integer' }, - newRecords: { type: 'integer' }, - existingRecords: { type: 'integer' } - } - }, - attachmentId: { - type: 'integer' - }, - revision_count: { - type: 'integer' - } - } - } - } - } - }, - 401: { - $ref: '#/components/responses/400' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -/** - * Uploads any media in the request to S3, adding their keys to the request. - * Also adds the metadata to the survey_attachment DB table - * Does nothing if no media is present in the request. - * - * @returns {RequestHandler} - */ -export function uploadKeyxMedia(): RequestHandler { - return async (req, res) => { - const rawMediaFile = getFileFromRequest(req); - - defaultLog.debug({ - label: 'uploadKeyxMedia', - message: 'files', - files: { ...rawMediaFile, buffer: 'Too big to print' } - }); - - const connection = getDBConnection(req.keycloak_token); - - try { - await connection.open(); - - // Scan file for viruses using ClamAV - const virusScanResult = await scanFileForVirus(rawMediaFile); - - if (!virusScanResult) { - throw new HTTP400('Malicious content detected, upload cancelled'); - } - - // Send the file to BCTW Api - if (!checkFileForKeyx(rawMediaFile)) { - throw new HTTP400('The file must either be a keyx file or a zip containing only keyx files.'); - } - - const user: IBctwUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; - - const bctwService = new BctwService(user); - const bctwUploadResult = await bctwService.uploadKeyX(rawMediaFile); - - // Upsert attachment - const attachmentService = new AttachmentService(connection); - - const upsertResult = await attachmentService.upsertSurveyAttachment( - rawMediaFile, - Number(req.params.projectId), - Number(req.params.surveyId), - ATTACHMENT_TYPE.KEYX - ); - - const metadata = { - filename: rawMediaFile.originalname, - username: req.keycloak_token?.preferred_username ?? '', - email: req.keycloak_token?.email ?? '' - }; - - const result = await uploadFileToS3(rawMediaFile, upsertResult.key, metadata); - - defaultLog.debug({ label: 'uploadMedia', message: 'result', result }); - - await connection.commit(); - - return res.status(200).json({ - attachmentId: upsertResult.survey_attachment_id, - revision_count: upsertResult.revision_count, - keyxResults: bctwUploadResult - }); - } catch (error) { - defaultLog.error({ label: 'uploadMedia', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.test.ts new file mode 100644 index 0000000000..fe0d0f1a56 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.test.ts @@ -0,0 +1,318 @@ +import chai, { expect } from 'chai'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getSurveyTelemetryCredentialAttachments, postSurveyTelemetryCredentialAttachment } from '.'; +import * as db from '../../../../../../../database/db'; +import { HTTPError } from '../../../../../../../errors/http-error'; +import { SurveyTelemetryCredentialAttachment } from '../../../../../../../repositories/attachment-repository'; +import { AttachmentService } from '../../../../../../../services/attachment-service'; +import { BctwKeyxService } from '../../../../../../../services/bctw-service/bctw-keyx-service'; +import * as file_utils from '../../../../../../../utils/file-utils'; +import { KeycloakUserInformation } from '../../../../../../../utils/keycloak-utils'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; + +chai.use(sinonChai); + +describe('postSurveyTelemetryCredentialAttachment', () => { + afterEach(() => { + sinon.restore(); + }); + + it('should throw an error when file has malicious content', async () => { + const dbConnectionObj = getMockDBConnection(); + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + sinon.stub(file_utils, 'scanFileForVirus').resolves(false); // fail virus scan + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + mockReq.files = [ + { + fieldname: 'media', + originalname: 'test.keyx', + encoding: '7bit', + mimetype: 'text/plain', + size: 340 + } + ] as Express.Multer.File[]; + + const requestHandler = postSurveyTelemetryCredentialAttachment(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).status).to.equal(400); + expect((actualError as HTTPError).message).to.equal('Malicious content detected, upload cancelled'); + } + }); + + it('should throw an error when file type is invalid', async () => { + const dbConnectionObj = getMockDBConnection(); + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + sinon.stub(file_utils, 'scanFileForVirus').resolves(true); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + mockReq.files = [ + { + fieldname: 'media', + originalname: 'test.notValid', // not a supported file type + encoding: '7bit', + mimetype: 'text/plain', + size: 340 + } + ] as Express.Multer.File[]; + + const requestHandler = postSurveyTelemetryCredentialAttachment(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).status).to.equal(400); + expect((actualError as HTTPError).message).to.equal( + 'The file is neither a .keyx or .cfg file, nor is it an archive containing only files of these types.' + ); + } + }); + + it('succeeds and uploads a KeyX file to BCTW', async () => { + const dbConnectionObj = getMockDBConnection(); + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + sinon.stub(file_utils, 'scanFileForVirus').resolves(true); + + const upsertSurveyTelemetryCredentialAttachmentStub = sinon + .stub(AttachmentService.prototype, 'upsertSurveyTelemetryCredentialAttachment') + .resolves({ survey_telemetry_credential_attachment_id: 44, key: 'path/to/file/test.keyx' }); + + const uploadFileToS3Stub = sinon.stub(file_utils, 'uploadFileToS3').resolves(); + + const uploadKeyXStub = sinon.stub(BctwKeyxService.prototype, 'uploadKeyX').resolves(); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + mockReq.files = [ + { + fieldname: 'media', + originalname: 'test.keyx', + encoding: '7bit', + mimetype: 'text/plain', + size: 340 + } + ] as Express.Multer.File[]; + + const requestHandler = postSurveyTelemetryCredentialAttachment(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.jsonValue).to.eql({ survey_telemetry_credential_attachment_id: 44 }); + expect(upsertSurveyTelemetryCredentialAttachmentStub).to.be.calledOnce; + expect(uploadKeyXStub).to.be.calledOnce; + expect(uploadFileToS3Stub).to.be.calledOnce; + }); + + it('succeeds and does not upload a Cfg file to BCTW', async () => { + const dbConnectionObj = getMockDBConnection(); + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + sinon.stub(file_utils, 'scanFileForVirus').resolves(true); + + const upsertSurveyTelemetryCredentialAttachmentStub = sinon + .stub(AttachmentService.prototype, 'upsertSurveyTelemetryCredentialAttachment') + .resolves({ survey_telemetry_credential_attachment_id: 44, key: 'path/to/file/test.keyx' }); + + const uploadFileToS3Stub = sinon.stub(file_utils, 'uploadFileToS3').resolves(); + + const uploadKeyXStub = sinon.stub(BctwKeyxService.prototype, 'uploadKeyX').resolves(); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + mockReq.files = [ + { + fieldname: 'media', + originalname: 'test.cfg', + encoding: '7bit', + mimetype: 'text/plain', + size: 340 + } + ] as Express.Multer.File[]; + + const requestHandler = postSurveyTelemetryCredentialAttachment(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.jsonValue).to.eql({ survey_telemetry_credential_attachment_id: 44 }); + expect(upsertSurveyTelemetryCredentialAttachmentStub).to.be.calledOnce; + expect(uploadKeyXStub).not.to.be.called; // not called + expect(uploadFileToS3Stub).to.be.calledOnce; + }); + + it('should catch and re-throw an error', async () => { + const dbConnectionObj = getMockDBConnection(); + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + sinon.stub(file_utils, 'scanFileForVirus').resolves(true); + + const upsertSurveyTelemetryCredentialAttachmentStub = sinon + .stub(AttachmentService.prototype, 'upsertSurveyTelemetryCredentialAttachment') + .resolves({ survey_telemetry_credential_attachment_id: 44, key: 'path/to/file/test.keyx' }); + + const mockError = new Error('A test error'); + const uploadKeyXStub = sinon.stub(BctwKeyxService.prototype, 'uploadKeyX').rejects(mockError); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + mockReq.files = [ + { + fieldname: 'media', + originalname: 'test.keyx', + encoding: '7bit', + mimetype: 'text/plain', + size: 340 + } + ] as Express.Multer.File[]; + + const requestHandler = postSurveyTelemetryCredentialAttachment(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).message).to.equal(mockError.message); + + expect(upsertSurveyTelemetryCredentialAttachmentStub).to.have.been.calledOnce; + expect(uploadKeyXStub).to.have.been.calledOnce; + } + }); +}); + +describe('getSurveyTelemetryCredentialAttachments', () => { + afterEach(() => { + sinon.restore(); + }); + + it('returns an array of telemetry credential file records', async () => { + const mockDBConnection = getMockDBConnection({ + open: sinon.stub(), + commit: sinon.stub(), + release: sinon.stub() + }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockGetCredentialAttachmentsResponse: SurveyTelemetryCredentialAttachment[] = [ + { + survey_telemetry_credential_attachment_id: 1, + uuid: '123', + file_name: 'test.keyx', + file_type: 'keyx', + file_size: 340, + create_date: '2021-09-01T00:00:00Z', + update_date: null, + key: 'path/to/file/test.keyx', + title: null, + description: null + }, + { + survey_telemetry_credential_attachment_id: 2, + uuid: '456', + file_name: 'test.cfg', + file_type: 'cfg', + file_size: 340, + create_date: '2021-09-01T00:00:00Z', + update_date: null, + key: 'path/to/file/test.cfg', + title: null, + description: null + } + ]; + + const getSurveyTelemetryCredentialAttachmentsStub = sinon + .stub(AttachmentService.prototype, 'getSurveyTelemetryCredentialAttachments') + .resolves(mockGetCredentialAttachmentsResponse); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + + const requestHandler = getSurveyTelemetryCredentialAttachments(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.jsonValue).to.eql({ telemetryAttachments: mockGetCredentialAttachmentsResponse }); + expect(mockDBConnection.open).to.have.been.calledOnce; + expect(getSurveyTelemetryCredentialAttachmentsStub).to.have.been.calledOnceWith(2); + expect(mockDBConnection.commit).to.have.been.calledOnce; + expect(mockDBConnection.release).to.have.been.calledOnce; + }); + + it('catches and re-throws error', async () => { + const mockDBConnection = getMockDBConnection({ + open: sinon.stub(), + commit: sinon.stub(), + rollback: sinon.stub(), + release: sinon.stub() + }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockError = new Error('a test error'); + + const getSurveyTelemetryCredentialAttachmentsStub = sinon + .stub(AttachmentService.prototype, 'getSurveyTelemetryCredentialAttachments') + .rejects(mockError); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.keycloak_token = {} as KeycloakUserInformation; + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + + const requestHandler = getSurveyTelemetryCredentialAttachments(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).message).to.equal('a test error'); + + expect(mockDBConnection.open).to.have.been.calledOnce; + expect(getSurveyTelemetryCredentialAttachmentsStub).to.have.been.calledOnceWith(2); + expect(mockDBConnection.rollback).to.have.been.calledOnce; + expect(mockDBConnection.release).to.have.been.calledOnce; + } + }); +}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.ts new file mode 100644 index 0000000000..f798f3dfab --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/telemetry/index.ts @@ -0,0 +1,374 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE } from '../../../../../../../constants/attachments'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTP400 } from '../../../../../../../errors/http-error'; +import { fileSchema } from '../../../../../../../openapi/schemas/file'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { AttachmentService } from '../../../../../../../services/attachment-service'; +import { BctwKeyxService } from '../../../../../../../services/bctw-service/bctw-keyx-service'; +import { getBctwUser } from '../../../../../../../services/bctw-service/bctw-service'; +import { scanFileForVirus, uploadFileToS3 } from '../../../../../../../utils/file-utils'; +import { getLogger } from '../../../../../../../utils/logger'; +import { isValidTelementryCredentialFile } from '../../../../../../../utils/media/media-utils'; +import { getFileFromRequest } from '../../../../../../../utils/request'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/attachments/keyx/upload'); + +export const POST: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + postSurveyTelemetryCredentialAttachment() +]; + +POST.apiDoc = { + description: 'Upload a survey-specific telemetry device credential file.', + tags: ['attachment'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + requestBody: { + description: 'Telemetry device credential file upload post request object.', + content: { + 'multipart/form-data': { + schema: { + type: 'object', + additionalProperties: false, + required: ['media'], + properties: { + media: { + description: 'Telemetry device credential file.', + type: 'array', + minItems: 1, + maxItems: 1, + items: fileSchema + } + } + } + } + } + }, + responses: { + 201: { + description: 'Telemetry device credential file upload response.', + content: { + 'application/json': { + schema: { + type: 'object', + additionalProperties: false, + required: ['survey_telemetry_credential_attachment_id'], + properties: { + survey_telemetry_credential_attachment_id: { + type: 'integer', + minimum: 1 + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Handles the request to upload and import telemetry device credential files (ex: keyx files). + * + * @returns {RequestHandler} + */ +export function postSurveyTelemetryCredentialAttachment(): RequestHandler { + return async (req, res) => { + const connection = getDBConnection(req.keycloak_token); + + try { + const rawMediaFile = getFileFromRequest(req); + + defaultLog.debug({ + label: 'postSurveyTelemetryCredentialAttachment', + message: 'files', + files: { ...rawMediaFile, buffer: 'Too big to print' } + }); + + // Scan file for viruses using ClamAV + const virusScanResult = await scanFileForVirus(rawMediaFile); + + if (!virusScanResult) { + throw new HTTP400('Malicious content detected, upload cancelled'); + } + + const isTelemetryCredentialFile = isValidTelementryCredentialFile(rawMediaFile); + + if (isTelemetryCredentialFile.error) { + throw new HTTP400(isTelemetryCredentialFile.error); + } + + await connection.open(); + + // Insert telemetry credential file record in SIMS + const attachmentService = new AttachmentService(connection); + const upsertResult = await attachmentService.upsertSurveyTelemetryCredentialAttachment( + rawMediaFile, + Number(req.params.projectId), + Number(req.params.surveyId), + isTelemetryCredentialFile.type + ); + + // Upload telemetry credential file content to BCTW (for supported file types) + if (isTelemetryCredentialFile.type === TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX) { + const bctwKeyxService = new BctwKeyxService(getBctwUser(req)); + await bctwKeyxService.uploadKeyX(rawMediaFile); + } + + // Upload telemetry credential file to SIMS S3 Storage + const metadata = { + filename: rawMediaFile.originalname, + username: req.keycloak_token?.preferred_username ?? '', + email: req.keycloak_token?.email ?? '' + }; + await uploadFileToS3(rawMediaFile, upsertResult.key, metadata); + + await connection.commit(); + + return res.status(201).json({ + survey_telemetry_credential_attachment_id: upsertResult.survey_telemetry_credential_attachment_id + }); + } catch (error) { + defaultLog.error({ label: 'postSurveyTelemetryCredentialAttachment', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + getSurveyTelemetryCredentialAttachments() +]; + +GET.apiDoc = { + description: 'Fetches a list of telemetry attachments of a survey.', + tags: ['attachments'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + responses: { + 200: { + description: 'Survey get response file description array.', + content: { + 'application/json': { + schema: { + type: 'object', + additionalProperties: false, + required: ['telemetryAttachments'], + properties: { + telemetryAttachments: { + description: 'List of telemetry attachments.', + type: 'array', + items: { + description: 'Survey attachment data with supplementary data', + type: 'object', + additionalProperties: false, + required: [ + 'survey_telemetry_credential_attachment_id', + 'uuid', + 'file_name', + 'file_type', + 'file_size', + 'create_date', + 'update_date', + 'title', + 'description', + 'key' + ], + properties: { + survey_telemetry_credential_attachment_id: { + description: 'Attachment id', + type: 'integer', + minimum: 1 + }, + uuid: { + description: 'Attachment UUID', + type: 'string', + format: 'uuid' + }, + file_name: { + description: 'Attachment file name', + type: 'string' + }, + file_type: { + description: 'Attachment file type', + type: 'string' + }, + file_size: { + description: 'Attachment file size', + type: 'number' + }, + create_date: { + description: 'Attachment create date', + type: 'string' + }, + update_date: { + description: 'Attachment update date', + type: 'string', + nullable: true + }, + title: { + description: 'Attachment title', + type: 'string', + nullable: true + }, + description: { + description: 'Attachment description', + type: 'string', + nullable: true + }, + key: { + description: 'Attachment S3 key', + type: 'string' + } + } + } + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Fetches a list of telemetry device credential attachments for a survey. + * + * @export + * @return {*} {RequestHandler} + */ +export function getSurveyTelemetryCredentialAttachments(): RequestHandler { + return async (req, res) => { + defaultLog.debug({ label: 'getSurveyTelemetryCredentialAttachments', message: 'params', req_params: req.params }); + + const connection = getDBConnection(req.keycloak_token); + const surveyId = Number(req.params.surveyId); + + try { + await connection.open(); + + const attachmentService = new AttachmentService(connection); + + const telemetryAttachments = await attachmentService.getSurveyTelemetryCredentialAttachments(surveyId); + + await connection.commit(); + + return res.status(200).json({ telemetryAttachments }); + } catch (error) { + defaultLog.error({ label: 'getSurveyTelemetryCredentialAttachments', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/{attachmentId}/getSignedUrl.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/{attachmentId}/getSignedUrl.ts index d28ae2ab70..5bd8c215a6 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/{attachmentId}/getSignedUrl.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/attachments/{attachmentId}/getSignedUrl.ts @@ -1,6 +1,6 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; -import { ATTACHMENT_TYPE } from '../../../../../../../constants/attachments'; +import { ATTACHMENT_TYPE, TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE } from '../../../../../../../constants/attachments'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; import { getDBConnection } from '../../../../../../../database/db'; import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; @@ -74,7 +74,7 @@ GET.apiDoc = { name: 'attachmentType', schema: { type: 'string', - enum: ['Report', 'KeyX', 'Other'] + enum: ['Report', 'KeyX', 'Cfg', 'Other'] }, required: true } @@ -122,6 +122,7 @@ export function getSurveyAttachmentSignedURL(): RequestHandler { try { await connection.open(); + let s3Key; const attachmentService = new AttachmentService(connection); @@ -131,6 +132,14 @@ export function getSurveyAttachmentSignedURL(): RequestHandler { Number(req.params.surveyId), Number(req.params.attachmentId) ); + } else if ( + req.query.attachmentType === TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX || + req.query.attachmentType === TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG + ) { + s3Key = await attachmentService.getSurveyTelemetryCredentialAttachmentS3Key( + Number(req.params.surveyId), + Number(req.params.attachmentId) + ); } else { s3Key = await attachmentService.getSurveyAttachmentS3Key( Number(req.params.surveyId), diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/captures/import.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/captures/import.ts new file mode 100644 index 0000000000..c03e54f881 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/captures/import.ts @@ -0,0 +1,161 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTP400 } from '../../../../../../../errors/http-error'; +import { csvFileSchema } from '../../../../../../../openapi/schemas/file'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { ImportCapturesStrategy } from '../../../../../../../services/import-services/capture/import-captures-strategy'; +import { importCSV } from '../../../../../../../services/import-services/import-csv'; +import { scanFileForVirus } from '../../../../../../../utils/file-utils'; +import { getLogger } from '../../../../../../../utils/logger'; +import { parseMulterFile } from '../../../../../../../utils/media/media-utils'; +import { getFileFromRequest } from '../../../../../../../utils/request'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/captures/import'); + +export const POST: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + importCsv() +]; + +POST.apiDoc = { + description: 'Upload Critterbase CSV Captures file', + tags: ['observations'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + description: 'SIMS survey id', + name: 'projectId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + }, + { + in: 'path', + description: 'SIMS survey id', + name: 'surveyId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + } + ], + requestBody: { + description: 'Critterbase Captures CSV import file.', + content: { + 'multipart/form-data': { + schema: { + type: 'object', + additionalProperties: false, + required: ['media'], + properties: { + media: { + description: 'Critterbase Captures CSV import file.', + type: 'array', + minItems: 1, + maxItems: 1, + items: csvFileSchema + } + } + } + } + } + }, + responses: { + 201: { + description: 'Capture import success.', + content: { + 'application/json': { + schema: { + type: 'object', + additionalProperties: false, + properties: { + capturesCreated: { + description: 'Number of Critterbase captures created.', + type: 'integer' + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Imports a `Critterbase Capture CSV` which bulk adds captures to Critterbase. + * + * @return {*} {RequestHandler} + */ +export function importCsv(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + const rawFile = getFileFromRequest(req); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + // Check for viruses / malware + const virusScanResult = await scanFileForVirus(rawFile); + + if (!virusScanResult) { + throw new HTTP400('Malicious content detected, import cancelled.'); + } + + const importCsvCaptures = new ImportCapturesStrategy(connection, surveyId); + + // Pass CSV file and importer as dependencies + const capturesCreated = await importCSV(parseMulterFile(rawFile), importCsvCaptures); + + await connection.commit(); + + return res.status(201).json({ capturesCreated }); + } catch (error) { + defaultLog.error({ label: 'importCritterCsv', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.test.ts index 2c3dc79b62..e9fe818e6f 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.test.ts @@ -2,13 +2,11 @@ import { expect } from 'chai'; import sinon from 'sinon'; import * as db from '../../../../../../database/db'; import { HTTP400 } from '../../../../../../errors/http-error'; -import { ImportCrittersService } from '../../../../../../services/import-services/import-critters-service'; -import { parseMulterFile } from '../../../../../../utils/media/media-utils'; +import * as strategy from '../../../../../../services/import-services/import-csv'; +import * as fileUtils from '../../../../../../utils/file-utils'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../__mocks__/db'; import { importCsv } from './import'; -import * as fileUtils from '../../../../../../utils/file-utils'; - describe('importCsv', () => { afterEach(() => { sinon.restore(); @@ -16,8 +14,8 @@ describe('importCsv', () => { it('returns imported critters', async () => { const mockDBConnection = getMockDBConnection({ open: sinon.stub(), commit: sinon.stub(), release: sinon.stub() }); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockImportCsv = sinon.stub(ImportCrittersService.prototype, 'import').resolves([1, 2]); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const mockImportCSV = sinon.stub(strategy, 'importCSV').resolves([1, 2]); const mockFileScan = sinon.stub(fileUtils, 'scanFileForVirus').resolves(true); const mockFile = { originalname: 'test.csv', mimetype: 'test.csv', buffer: Buffer.alloc(1) } as Express.Multer.File; @@ -35,8 +33,10 @@ describe('importCsv', () => { expect(mockFileScan).to.have.been.calledOnceWithExactly(mockFile); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockImportCsv).to.have.been.calledOnceWithExactly(1, parseMulterFile(mockFile)); + expect(getDBConnectionStub).to.have.been.calledOnce; + + expect(mockImportCSV).to.have.been.calledOnce; + expect(mockRes.json).to.have.been.calledOnceWithExactly({ survey_critter_ids: [1, 2] }); expect(mockDBConnection.commit).to.have.been.calledOnce; @@ -50,8 +50,7 @@ describe('importCsv', () => { release: sinon.stub(), rollback: sinon.stub() }); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockImportCsv = sinon.stub(ImportCrittersService.prototype, 'import').resolves([1, 2]); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockFileScan = sinon.stub(fileUtils, 'scanFileForVirus').resolves(false); @@ -79,8 +78,7 @@ describe('importCsv', () => { expect(mockDBConnection.open).to.have.been.calledOnce; expect(mockFileScan).to.have.been.calledOnceWithExactly(mockFile); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockImportCsv).to.not.have.been.called; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockRes.json).to.not.have.been.called; expect(mockDBConnection.rollback).to.have.been.called; diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.ts index 7c87762d40..01a71c02aa 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/import.ts @@ -5,7 +5,8 @@ import { getDBConnection } from '../../../../../../database/db'; import { HTTP400 } from '../../../../../../errors/http-error'; import { csvFileSchema } from '../../../../../../openapi/schemas/file'; import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization'; -import { ImportCrittersService } from '../../../../../../services/import-services/import-critters-service'; +import { ImportCrittersStrategy } from '../../../../../../services/import-services/critter/import-critters-strategy'; +import { importCSV } from '../../../../../../services/import-services/import-csv'; import { scanFileForVirus } from '../../../../../../utils/file-utils'; import { getLogger } from '../../../../../../utils/logger'; import { parseMulterFile } from '../../../../../../utils/media/media-utils'; @@ -61,7 +62,7 @@ POST.apiDoc = { } ], requestBody: { - description: 'Survey critters submission file to import', + description: 'Survey critters csv file to import', content: { 'multipart/form-data': { schema: { @@ -129,7 +130,7 @@ POST.apiDoc = { export function importCsv(): RequestHandler { return async (req, res) => { const surveyId = Number(req.params.surveyId); - const rawMediaFile = getFileFromRequest(req); + const rawFile = getFileFromRequest(req); const connection = getDBConnection(req.keycloak_token); @@ -137,16 +138,16 @@ export function importCsv(): RequestHandler { await connection.open(); // Check for viruses / malware - const virusScanResult = await scanFileForVirus(rawMediaFile); + const virusScanResult = await scanFileForVirus(rawFile); if (!virusScanResult) { throw new HTTP400('Malicious content detected, import cancelled.'); } - const csvImporter = new ImportCrittersService(connection); + // Critter CSV import strategy - child of CSVImportStrategy + const importCsvCritters = new ImportCrittersStrategy(connection, surveyId); - // Pass the survey id and the csv (MediaFile) to the importer - const surveyCritterIds = await csvImporter.import(surveyId, parseMulterFile(rawMediaFile)); + const surveyCritterIds = await importCSV(parseMulterFile(rawFile), importCsvCritters); defaultLog.info({ label: 'importCritterCsv', message: 'result', survey_critter_ids: surveyCritterIds }); @@ -154,7 +155,7 @@ export function importCsv(): RequestHandler { return res.status(200).json({ survey_critter_ids: surveyCritterIds }); } catch (error) { - defaultLog.error({ label: 'uploadMedia', message: 'error', error }); + defaultLog.error({ label: 'importCritterCsv', message: 'error', error }); await connection.rollback(); throw error; } finally { diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.test.ts index 28036c38b0..f02cac77bc 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.test.ts @@ -13,8 +13,13 @@ describe('getCrittersFromSurvey', () => { it('returns critters from survey', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockSurveyCritter = { critter_id: 123, survey_id: 123, critterbase_critter_id: 'critterbase1' }; + const mockSurveyCritter = { + critter_id: 123, + survey_id: 123, + critterbase_critter_id: 'critterbase1' + }; const mockCBCritter = { critter_id: 'critterbase1', wlh_id: 'wlh1', @@ -25,7 +30,6 @@ describe('getCrittersFromSurvey', () => { critter_comment: 'comment1' }; - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockGetCrittersInSurvey = sinon .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') .resolves([mockSurveyCritter]); @@ -35,45 +39,142 @@ describe('getCrittersFromSurvey', () => { const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + const requestHandler = getCrittersFromSurvey(); await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockGetCrittersInSurvey).to.have.been.calledOnce; expect(mockGetMultipleCrittersByIds).to.be.calledOnceWith([mockSurveyCritter.critterbase_critter_id]); expect(mockRes.json).to.have.been.calledWith([ - { ...mockCBCritter, survey_critter_id: mockSurveyCritter.critter_id } + { + // SIMS properties + critter_id: mockSurveyCritter.critter_id, + critterbase_critter_id: mockSurveyCritter.critterbase_critter_id, + // Critterbase properties + wlh_id: mockCBCritter.wlh_id, + animal_id: mockCBCritter.animal_id, + sex: mockCBCritter.sex, + itis_tsn: mockCBCritter.itis_tsn, + itis_scientific_name: mockCBCritter.itis_scientific_name, + critter_comment: mockCBCritter.critter_comment + } ]); }); it('returns empty array if no critters in survey', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockGetCrittersInSurvey = sinon.stub(SurveyCritterService.prototype, 'getCrittersInSurvey').resolves([]); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + const requestHandler = getCrittersFromSurvey(); await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockGetCrittersInSurvey).to.have.been.calledOnce; + expect(mockRes.json).to.have.been.calledWith([]); + }); + + it('returns empty array if SIMS critter has no matching Critterbase critter record', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + + const mockSurveyCritter = { + critter_id: 123, + survey_id: 123, + critterbase_critter_id: 'critterbase1' + }; + const mockCBCritter = { + critter_id: 'critterbase_no_match', + wlh_id: 'wlh1', + animal_id: 'animal1', + sex: 'unknown', + itis_tsn: 12345, + itis_scientific_name: 'species1', + critter_comment: 'comment1' + }; + + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const mockGetCrittersInSurvey = sinon + .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') + .resolves([mockSurveyCritter]); + const mockGetMultipleCrittersByIds = sinon + .stub(CritterbaseService.prototype, 'getMultipleCrittersByIds') + .resolves([mockCBCritter] as unknown as ICritter[]); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + + const requestHandler = getCrittersFromSurvey(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockGetCrittersInSurvey).to.have.been.calledOnce; + expect(mockGetMultipleCrittersByIds).to.be.calledOnceWith([mockSurveyCritter.critterbase_critter_id]); + expect(mockRes.json).to.have.been.calledWith([]); + }); + + it('returns empty array if SIMS critter has no matching Critterbase critter record (Critterbase response empty)', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSurveyCritter = { + critter_id: 123, + survey_id: 123, + critterbase_critter_id: 'critterbase1' + }; + + const mockGetCrittersInSurvey = sinon + .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') + .resolves([mockSurveyCritter]); + const mockGetMultipleCrittersByIds = sinon + .stub(CritterbaseService.prototype, 'getMultipleCrittersByIds') + .resolves([]); // Empty response + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = getCrittersFromSurvey(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockGetCrittersInSurvey).to.have.been.calledOnce; + expect(mockGetMultipleCrittersByIds).to.be.calledOnceWith([mockSurveyCritter.critterbase_critter_id]); expect(mockRes.json).to.have.been.calledWith([]); }); it('catches and re-throws errors', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const mockGetCrittersInSurvey = sinon .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') .rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + const requestHandler = getCrittersFromSurvey(); try { @@ -81,8 +182,8 @@ describe('getCrittersFromSurvey', () => { expect.fail(); } catch (actualError) { expect(actualError).to.equal(mockError); - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; - expect(mockGetDBConnection.calledOnce).to.be.true; + expect(mockGetCrittersInSurvey).to.have.been.calledOnce; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.called; } }); @@ -95,67 +196,82 @@ describe('addCritterToSurvey', () => { it('does not create a new critter', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockSurveyCritter = { survey_critter_id: 123, critterbase_critter_id: 'critterbase1' }; + const mockSurveyCritter = { critter_id: 123, critterbase_critter_id: 'critterbase1' }; const mockCBCritter = { critter_id: 'critterbase1' }; - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockAddCritterToSurvey = sinon .stub(SurveyCritterService.prototype, 'addCritterToSurvey') - .resolves(mockSurveyCritter.survey_critter_id); + .resolves(mockSurveyCritter.critter_id); const mockCreateCritter = sinon.stub(CritterbaseService.prototype, 'createCritter').resolves(); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '1', + surveyId: '2' + }; mockReq.body = mockCBCritter; const requestHandler = addCritterToSurvey(); await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddCritterToSurvey.calledOnce).to.be.true; - expect(mockCreateCritter.notCalled).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockAddCritterToSurvey).to.have.been.calledOnce; + expect(mockCreateCritter).not.to.have.been.called; expect(mockRes.status).to.have.been.calledWith(201); expect(mockRes.json).to.have.been.calledWith(mockSurveyCritter); }); it('returns critters from survey', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockSurveyCritter = { survey_critter_id: 123, critterbase_critter_id: 'critterbase1' }; + const mockSurveyCritter = { critter_id: 123, critterbase_critter_id: 'critterbase1' }; const mockCBCritter = { critter_id: 'critterbase1' }; - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockAddCritterToSurvey = sinon .stub(SurveyCritterService.prototype, 'addCritterToSurvey') - .resolves(mockSurveyCritter.survey_critter_id); + .resolves(mockSurveyCritter.critter_id); const mockCreateCritter = sinon.stub(CritterbaseService.prototype, 'createCritter').resolves(mockCBCritter); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + const requestHandler = addCritterToSurvey(); await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddCritterToSurvey.calledOnce).to.be.true; - expect(mockCreateCritter.calledOnce).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockAddCritterToSurvey).to.have.been.calledOnce; + expect(mockCreateCritter).to.have.been.calledOnce; expect(mockRes.status).to.have.been.calledWith(201); expect(mockRes.json).to.have.been.calledWith(mockSurveyCritter); }); it('catches and re-throws errors', async () => { const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockCBCritter = { critter_id: 'critterbase1' }; const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockAddCritterToSurvey = sinon.stub(SurveyCritterService.prototype, 'addCritterToSurvey').rejects(mockError); const mockCreateCritter = sinon.stub(CritterbaseService.prototype, 'createCritter').resolves(mockCBCritter); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + mockReq.params = { + projectId: '1', + surveyId: '2' + }; + const requestHandler = addCritterToSurvey(); try { @@ -163,9 +279,9 @@ describe('addCritterToSurvey', () => { expect.fail(); } catch (actualError) { expect(actualError).to.equal(mockError); - expect(mockAddCritterToSurvey.calledOnce).to.be.true; - expect(mockCreateCritter.calledOnce).to.be.true; - expect(mockGetDBConnection.calledOnce).to.be.true; + expect(mockAddCritterToSurvey).to.have.been.calledOnce; + expect(mockCreateCritter).to.have.been.calledOnce; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.called; } }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.ts index 28260460a1..14ff420c2b 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.ts @@ -2,12 +2,14 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles'; import { getDBConnection } from '../../../../../../database/db'; +import { critterSchema } from '../../../../../../openapi/schemas/critter'; import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization'; import { CritterbaseService, ICritterbaseUser } from '../../../../../../services/critterbase-service'; import { SurveyCritterService } from '../../../../../../services/survey-critter-service'; import { getLogger } from '../../../../../../utils/logger'; const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters'); + export const POST: Operation = [ authorizeRequestHandler((req) => { return { @@ -61,18 +63,19 @@ GET.apiDoc = { parameters: [ { in: 'path', - name: 'surveyId', + name: 'projectId', schema: { type: 'integer' }, required: true }, { - in: 'query', - name: 'format', + in: 'path', + name: 'surveyId', schema: { - type: 'string' - } + type: 'integer' + }, + required: true } ], responses: { @@ -81,12 +84,9 @@ GET.apiDoc = { content: { 'application/json': { schema: { - title: 'Bulk creation response object', + title: 'Array of critters in survey.', type: 'array', - items: { - title: 'Default critter response', - type: 'object' - } + items: critterSchema } } } @@ -111,19 +111,29 @@ GET.apiDoc = { POST.apiDoc = { description: - 'Creates a new critter in critterbase, and if successful, adds the a link to the critter_id under this survey.', - tags: ['critterbase'], + 'Creates a new critter in CritterBase, and if successful, adds a corresponding SIMS critter record under this survey.', + tags: ['survey', 'critterbase'], security: [ { Bearer: [] } ], parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, { in: 'path', name: 'surveyId', schema: { - type: 'number' + type: 'integer', + minimum: 1 }, required: true } @@ -170,11 +180,11 @@ POST.apiDoc = { title: 'Response object for adding critter to survey', type: 'object', properties: { - survey_critter_id: { + critter_id: { type: 'number', description: 'SIMS internal ID of the critter within the survey' }, - critter_id: { + critterbase_critter_id: { type: 'string', description: 'Critterbase ID of the critter' } @@ -201,6 +211,12 @@ POST.apiDoc = { } }; +/** + * Get all critters under this survey that have a corresponding Critterbase critter record. + * + * @export + * @return {*} {RequestHandler} + */ export function getCrittersFromSurvey(): RequestHandler { return async (req, res) => { const surveyId = Number(req.params.surveyId); @@ -219,21 +235,40 @@ export function getCrittersFromSurvey(): RequestHandler { const critterIds = surveyCritters.map((critter) => String(critter.critterbase_critter_id)); - const result = await surveyService.critterbaseService.getMultipleCrittersByIds(critterIds); + const critterbaseCritters = await surveyService.critterbaseService.getMultipleCrittersByIds(critterIds); - const critterMap = new Map(); - for (const item of result) { - critterMap.set(item.critter_id, item); - } + const response = []; + // For all SIMS critters for (const surveyCritter of surveyCritters) { - if (critterMap.has(surveyCritter.critterbase_critter_id)) { - critterMap.get(surveyCritter.critterbase_critter_id).survey_critter_id = surveyCritter.critter_id; + // Find the corresponding Critterbase critter + const critterbaseCritter = critterbaseCritters.find( + (critter) => critter.critter_id === surveyCritter.critterbase_critter_id + ); + + if (!critterbaseCritter) { + // SIMS critter exists but Critterbase critter does not. As Critterbase is the source of truth for critter + // data, we should not return this critter, which SIMS cannot properly represent. + continue; } + + response.push({ + // SIMS properties + critter_id: surveyCritter.critter_id, + critterbase_critter_id: surveyCritter.critterbase_critter_id, + // Critterbase properties + wlh_id: critterbaseCritter.wlh_id, + animal_id: critterbaseCritter.animal_id, + sex: critterbaseCritter.sex, + itis_tsn: critterbaseCritter.itis_tsn, + itis_scientific_name: critterbaseCritter.itis_scientific_name, + critter_comment: critterbaseCritter.critter_comment + }); } - return res.status(200).json([...critterMap.values()]); + + return res.status(200).json(response); } catch (error) { - defaultLog.error({ label: 'createCritter', message: 'error', error }); + defaultLog.error({ label: 'getCrittersFromSurvey', message: 'error', error }); await connection.rollback(); throw error; } finally { @@ -267,10 +302,10 @@ export function addCritterToSurvey(): RequestHandler { } const surveyService = new SurveyCritterService(connection); - const response = await surveyService.addCritterToSurvey(surveyId, critterId); + const surveyCritterId = await surveyService.addCritterToSurvey(surveyId, critterId); await connection.commit(); - return res.status(201).json({ critterbase_critter_id: critterId, survey_critter_id: response }); + return res.status(201).json({ critterbase_critter_id: critterId, critter_id: surveyCritterId }); } catch (error) { defaultLog.error({ label: 'addCritterToSurvey', message: 'error', error }); await connection.rollback(); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/markings/import.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/markings/import.ts new file mode 100644 index 0000000000..4b5126bc5b --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/markings/import.ts @@ -0,0 +1,161 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTP400 } from '../../../../../../../errors/http-error'; +import { csvFileSchema } from '../../../../../../../openapi/schemas/file'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { importCSV } from '../../../../../../../services/import-services/import-csv'; +import { ImportMarkingsStrategy } from '../../../../../../../services/import-services/marking/import-markings-strategy'; +import { scanFileForVirus } from '../../../../../../../utils/file-utils'; +import { getLogger } from '../../../../../../../utils/logger'; +import { parseMulterFile } from '../../../../../../../utils/media/media-utils'; +import { getFileFromRequest } from '../../../../../../../utils/request'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/markings/import'); + +export const POST: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + importCsv() +]; + +POST.apiDoc = { + description: 'Upload Critterbase CSV Markings file', + tags: ['observations'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + description: 'SIMS survey id', + name: 'projectId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + }, + { + in: 'path', + description: 'SIMS survey id', + name: 'surveyId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + } + ], + requestBody: { + description: 'Critterbase Markings CSV import file.', + content: { + 'multipart/form-data': { + schema: { + type: 'object', + additionalProperties: false, + required: ['media'], + properties: { + media: { + description: 'Critterbase Markings CSV import file.', + type: 'array', + minItems: 1, + maxItems: 1, + items: csvFileSchema + } + } + } + } + } + }, + responses: { + 201: { + description: 'Marking import success.', + content: { + 'application/json': { + schema: { + type: 'object', + additionalProperties: false, + properties: { + markingsCreated: { + description: 'Number of Critterbase markings created.', + type: 'integer' + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Imports a `Critterbase Marking CSV` which bulk adds markings to Critterbase. + * + * @return {*} {RequestHandler} + */ +export function importCsv(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + const rawFile = getFileFromRequest(req); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + // Check for viruses / malware + const virusScanResult = await scanFileForVirus(rawFile); + + if (!virusScanResult) { + throw new HTTP400('Malicious content detected, import cancelled.'); + } + + const importCsvMarkingsStrategy = new ImportMarkingsStrategy(connection, surveyId); + + // Pass CSV file and importer as dependencies + const markingsCreated = await importCSV(parseMulterFile(rawFile), importCsvMarkingsStrategy); + + await connection.commit(); + + return res.status(201).json({ markingsCreated }); + } catch (error) { + defaultLog.error({ label: 'importMarkingsCSV', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/measurements/import.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/measurements/import.ts new file mode 100644 index 0000000000..9988b6bb00 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/measurements/import.ts @@ -0,0 +1,161 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTP400 } from '../../../../../../../errors/http-error'; +import { csvFileSchema } from '../../../../../../../openapi/schemas/file'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { importCSV } from '../../../../../../../services/import-services/import-csv'; +import { ImportMeasurementsStrategy } from '../../../../../../../services/import-services/measurement/import-measurements-strategy'; +import { scanFileForVirus } from '../../../../../../../utils/file-utils'; +import { getLogger } from '../../../../../../../utils/logger'; +import { parseMulterFile } from '../../../../../../../utils/media/media-utils'; +import { getFileFromRequest } from '../../../../../../../utils/request'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/measurements/import'); + +export const POST: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + importCsv() +]; + +POST.apiDoc = { + description: 'Upload Critterbase CSV Measurements file', + tags: ['observations'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + description: 'SIMS survey id', + name: 'projectId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + }, + { + in: 'path', + description: 'SIMS survey id', + name: 'surveyId', + required: true, + schema: { + type: 'integer', + minimum: 1 + } + } + ], + requestBody: { + description: 'Critterbase Measurements CSV import file.', + content: { + 'multipart/form-data': { + schema: { + type: 'object', + additionalProperties: false, + required: ['media'], + properties: { + media: { + description: 'Critterbase Measurements CSV import file.', + type: 'array', + minItems: 1, + maxItems: 1, + items: csvFileSchema + } + } + } + } + } + }, + responses: { + 201: { + description: 'Measurement import success.', + content: { + 'application/json': { + schema: { + type: 'object', + additionalProperties: false, + properties: { + measurementsCreated: { + description: 'Number of Critterbase measurements created.', + type: 'integer' + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Imports a `Critterbase Measurement CSV` which bulk adds measurements to Critterbase. + * + * @return {*} {RequestHandler} + */ +export function importCsv(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + const rawFile = getFileFromRequest(req); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + // Check for viruses / malware + const virusScanResult = await scanFileForVirus(rawFile); + + if (!virusScanResult) { + throw new HTTP400('Malicious content detected, import cancelled.'); + } + + const importCsvMeasurementsStrategy = new ImportMeasurementsStrategy(connection, surveyId); + + // Pass CSV file and importer as dependencies + const measurementsCreated = await importCSV(parseMulterFile(rawFile), importCsvMeasurementsStrategy); + + await connection.commit(); + + return res.status(201).json({ measurementsCreated }); + } catch (error) { + defaultLog.error({ label: 'importMeasurementsCSV', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.ts deleted file mode 100644 index d4236aa486..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.ts +++ /dev/null @@ -1,131 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles'; -import { getDBConnection } from '../../../../../../database/db'; -import { HTTPError, HTTPErrorType } from '../../../../../../errors/http-error'; -import { bulkUpdateResponse, critterBulkRequestObject } from '../../../../../../openapi/schemas/critter'; -import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization'; -import { CritterbaseService, ICritterbaseUser } from '../../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../../services/survey-critter-service'; -import { getLogger } from '../../../../../../utils/logger'; - -const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters/{critterId}'); - -export const PATCH: Operation = [ - authorizeRequestHandler((req) => { - return { - or: [ - { - validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], - surveyId: Number(req.params.surveyId), - discriminator: 'ProjectPermission' - }, - { - validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - updateSurveyCritter() -]; - -PATCH.apiDoc = { - description: 'Patches a critter in critterbase, also capable of deleting relevant rows if marked with _delete.', - tags: ['critterbase'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'path', - name: 'surveyId', - schema: { - type: 'number' - }, - required: true - } - ], - requestBody: { - description: 'Critterbase bulk patch request object', - content: { - 'application/json': { - schema: critterBulkRequestObject - } - } - }, - responses: { - 200: { - description: 'Responds with counts of objects created in critterbase.', - content: { - 'application/json': { - schema: bulkUpdateResponse - } - } - }, - 400: { - $ref: '#/components/responses/400' - }, - 401: { - $ref: '#/components/responses/401' - }, - 403: { - $ref: '#/components/responses/403' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -export function updateSurveyCritter(): RequestHandler { - return async (req, res) => { - const critterbaseCritterId = req.body.update.critter_id; - - const critterId = Number(req.params.critterId); - - const connection = getDBConnection(req.keycloak_token); - try { - const user: ICritterbaseUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; - - if (!critterbaseCritterId) { - throw new HTTPError(HTTPErrorType.BAD_REQUEST, 400, 'No external critter ID was found.'); - } - - await connection.open(); - - const surveyService = new SurveyCritterService(connection); - await surveyService.updateCritter(critterId, critterbaseCritterId); - - const critterbaseService = new CritterbaseService(user); - - let createResult, updateResult; - - if (req.body.update) { - updateResult = await critterbaseService.updateCritter(req.body.update); - } - - if (req.body.create) { - createResult = await critterbaseService.createCritter(req.body.create); - } - - await connection.commit(); - - return res.status(200).json({ ...createResult, ...updateResult }); - } catch (error) { - defaultLog.error({ label: 'updateSurveyCritter', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.test.ts index 564c94c488..924fc3abd5 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.test.ts @@ -1,100 +1,102 @@ -import Ajv from 'ajv'; import { expect } from 'chai'; import sinon from 'sinon'; +import { createDeployment } from '.'; import * as db from '../../../../../../../../database/db'; -import { BctwService } from '../../../../../../../../services/bctw-service'; -import { SurveyCritterService } from '../../../../../../../../services/survey-critter-service'; +import { + BctwDeploymentRecord, + BctwDeploymentService +} from '../../../../../../../../services/bctw-service/bctw-deployment-service'; +import { BctwService } from '../../../../../../../../services/bctw-service/bctw-service'; +import { CritterbaseService, ICapture } from '../../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../../services/deployment-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../../__mocks__/db'; -import { deployDevice, PATCH, POST, updateDeployment } from './index'; -describe('critter deployments', () => { +describe('createDeployment', () => { afterEach(() => { sinon.restore(); }); - const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); - - describe('openapi schema', () => { - const ajv = new Ajv(); - - it('is valid openapi v3 schema', () => { - expect(ajv.validateSchema(POST.apiDoc as unknown as object)).to.be.true; - expect(ajv.validateSchema(PATCH.apiDoc as unknown as object)).to.be.true; - }); - }); - - describe('upsertDeployment', () => { - it('updates an existing deployment', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').resolves(); - const mockBctwService = sinon.stub(BctwService.prototype, 'updateDeployment'); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = updateDeployment(); - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddDeployment.calledOnce).to.be.true; - expect(mockBctwService.calledOnce).to.be.true; - expect(mockRes.status).to.have.been.calledWith(200); - }); - - it('catches and re-throws errors', async () => { - const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').rejects(mockError); - const mockBctwService = sinon.stub(BctwService.prototype, 'updateDeployment').rejects(mockError); + it('creates a new deployment', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockCapture: ICapture = { + capture_id: '111', + critter_id: '222', + capture_method_id: null, + capture_location_id: '333', + release_location_id: null, + capture_date: '2021-01-01', + capture_time: '12:00:00', + release_date: null, + release_time: null, + capture_comment: null, + release_comment: null + }; + + const mockDeployment: BctwDeploymentRecord = { + assignment_id: '111', + collar_id: '222', + critter_id: '333', + created_at: '2021-01-01', + created_by_user_id: '444', + updated_at: '2021-01-01', + updated_by_user_id: '555', + valid_from: '2021-01-01', + valid_to: '2021-01-01', + attachment_start: '2021-01-01', + attachment_end: '2021-01-01', + deployment_id: '666', + device_id: 777 + }; + + const getCodeStub = sinon.stub(BctwService.prototype, 'getCode').resolves([ + { + code_header_title: 'device_make', + code_header_name: 'Device Make', + id: 1, + code: 'device_make_code', + description: '', + long_description: '' + } + ]); + const insertDeploymentStub = sinon.stub(DeploymentService.prototype, 'insertDeployment').resolves(); + const createDeploymentStub = sinon + .stub(BctwDeploymentService.prototype, 'createDeployment') + .resolves(mockDeployment); + const getCaptureByIdStub = sinon.stub(CritterbaseService.prototype, 'getCaptureById').resolves(mockCapture); - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = updateDeployment(); - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect(actualError).to.equal(mockError); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddDeployment.calledOnce).to.be.true; - expect(mockBctwService.notCalled).to.be.true; - } - }); - describe('deployDevice', () => { - it('deploys a new telemetry device', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').resolves(); - const mockBctwService = sinon.stub(BctwService.prototype, 'deployDevice'); + const requestHandler = createDeployment(); - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + await requestHandler(mockReq, mockRes, mockNext); - const requestHandler = deployDevice(); - await requestHandler(mockReq, mockRes, mockNext); + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(getCodeStub).to.have.been.calledTwice; + expect(insertDeploymentStub).to.have.been.calledOnce; + expect(createDeploymentStub).to.have.been.calledOnce; + expect(getCaptureByIdStub).to.have.been.calledOnce; + expect(mockRes.status).to.have.been.calledWith(201); + }); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddDeployment.calledOnce).to.be.true; - expect(mockBctwService.calledOnce).to.be.true; - expect(mockRes.status).to.have.been.calledWith(201); - }); + it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - it('catches and re-throws errors', async () => { - const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').rejects(mockError); - const mockBctwService = sinon.stub(BctwService.prototype, 'deployDevice').rejects(mockError); + const mockError = new Error('a test error'); + const insertDeploymentStub = sinon.stub(DeploymentService.prototype, 'insertDeployment').rejects(mockError); - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = deployDevice(); - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect(actualError).to.equal(mockError); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockAddDeployment.calledOnce).to.be.true; - expect(mockBctwService.notCalled).to.be.true; - } - }); - }); + const requestHandler = createDeployment(); + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(actualError).to.equal(mockError); + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(insertDeploymentStub).to.have.been.calledOnce; + } }); }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.ts index 41c06c9629..9b8b30af5f 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/index.ts @@ -1,14 +1,18 @@ +import dayjs from 'dayjs'; import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { v4 } from 'uuid'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../../constants/roles'; import { getDBConnection } from '../../../../../../../../database/db'; import { authorizeRequestHandler } from '../../../../../../../../request-handlers/security/authorization'; -import { BctwService } from '../../../../../../../../services/bctw-service'; -import { ICritterbaseUser } from '../../../../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../../../../services/survey-critter-service'; +import { BctwDeploymentService } from '../../../../../../../../services/bctw-service/bctw-deployment-service'; +import { BctwService, getBctwUser } from '../../../../../../../../services/bctw-service/bctw-service'; +import { CritterbaseService } from '../../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../../services/deployment-service'; import { getLogger } from '../../../../../../../../utils/logger'; + const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments'); + export const POST: Operation = [ authorizeRequestHandler((req) => { return { @@ -25,13 +29,13 @@ export const POST: Operation = [ ] }; }), - deployDevice() + createDeployment() ]; POST.apiDoc = { description: - 'Deploys a device, creating a record of the insertion in the SIMS deployment table. Will also upsert a collar in BCTW as well as insert a new deployment under the resultant collar_id.', - tags: ['critterbase'], + 'Creates a deployment in SIMS and BCTW. Upserts a collar in BCTW and inserts a new deployment of the resulting collar_id.', + tags: ['deployment', 'bctw', 'critterbase'], security: [ { Bearer: [] @@ -42,156 +46,87 @@ POST.apiDoc = { in: 'path', name: 'surveyId', schema: { - type: 'number' - }, - required: true + type: 'integer', + minimum: 1 + } }, { in: 'path', name: 'critterId', schema: { - type: 'number' + type: 'integer', + minimum: 1 } } ], requestBody: { - description: 'Specifies a critter, device, and timespan to complete deployment.', + description: 'Object with device information and associated captures to create a deployment', content: { 'application/json': { schema: { title: 'Deploy device request object', type: 'object', additionalProperties: false, + required: [ + 'device_id', + 'frequency', + 'frequency_unit', + 'device_make', + 'device_model', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id', + 'attachment_end_date', + 'attachment_end_time' + ], properties: { - critter_id: { - type: 'string', - format: 'uuid' - }, - attachment_start: { - type: 'string' - }, - attachment_end: { - type: 'string' - }, device_id: { - type: 'integer' + type: 'integer', + minimum: 1 }, frequency: { - type: 'number' + type: 'number', + nullable: true }, frequency_unit: { - type: 'string' + type: 'number', + nullable: true, + description: 'The ID of a BCTW frequency code.' }, device_make: { - type: 'string' + type: 'number', + description: 'The ID of a BCTW device make code.' }, device_model: { - type: 'string' - } - } - } - } - } - }, - responses: { - 201: { - description: 'Responds with count of rows created in SIMS DB Deployments.', - content: { - 'application/json': { - schema: { - title: 'Deployment response object', - type: 'object', - additionalProperties: false, - properties: { - message: { - type: 'string' - } - } - } - } - } - }, - 400: { - $ref: '#/components/responses/400' - }, - 401: { - $ref: '#/components/responses/401' - }, - 403: { - $ref: '#/components/responses/403' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -export const PATCH: Operation = [ - authorizeRequestHandler((req) => { - return { - or: [ - { - validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], - surveyId: Number(req.params.surveyId), - discriminator: 'ProjectPermission' - }, - { - validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - updateDeployment() -]; - -PATCH.apiDoc = { - description: - 'Allows you to update the deployment timespan for a device. Effectively ends a deployment if the attachment end is filled in, but should not delete anything.', - tags: ['critterbase'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'path', - name: 'surveyId', - schema: { - type: 'integer' - }, - required: true - }, - { - in: 'path', - name: 'critterId', - schema: { - type: 'integer' - } - } - ], - requestBody: { - description: 'Specifies a deployment id and the new timerange to update it with.', - content: { - 'application/json': { - schema: { - title: 'Deploy device request object', - type: 'object', - additionalProperties: false, - properties: { - deployment_id: { type: 'string', - format: 'uuid' + nullable: true + }, + critterbase_start_capture_id: { + type: 'string', + description: 'Critterbase capture record when the deployment started', + format: 'uuid', + nullable: true + }, + critterbase_end_capture_id: { + type: 'string', + description: 'Critterbase capture record when the deployment ended', + format: 'uuid', + nullable: true }, - attachment_start: { - type: 'string' + critterbase_end_mortality_id: { + type: 'string', + description: 'Critterbase mortality record when the deployment ended', + format: 'uuid', + nullable: true + }, + attachment_end_date: { + type: 'string', + description: 'End date of the deployment, without time.', + nullable: true }, - attachment_end: { + attachment_end_time: { type: 'string', + description: 'End time of the deployment.', nullable: true } } @@ -200,8 +135,8 @@ PATCH.apiDoc = { } }, responses: { - 200: { - description: 'Responds with count of rows created or updated in SIMS DB Deployments.', + 201: { + description: 'Responds with the created BCTW deployment uuid.', content: { 'application/json': { schema: { @@ -209,8 +144,10 @@ PATCH.apiDoc = { type: 'object', additionalProperties: false, properties: { - message: { - type: 'string' + deploymentId: { + type: 'string', + format: 'uuid', + description: 'The generated deployment Id, indicating that the deployment was succesfully created.' } } } @@ -235,68 +172,84 @@ PATCH.apiDoc = { } }; -export function deployDevice(): RequestHandler { +export function createDeployment(): RequestHandler { return async (req, res) => { - const critterId = Number(req.params.critterId); - const newDeploymentId = v4(); // New deployment ID - const newDeploymentDevice = { - ...req.body, - deploymentId: newDeploymentId - }; + const surveyCritterId = Number(req.params.critterId); + + // Create deployment Id for joining SIMS and BCTW deployment information + const newDeploymentId = v4(); + + const { + device_id, + frequency, + frequency_unit, + device_make, + device_model, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id, + attachment_end_date, + attachment_end_time + } = req.body; const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const user: ICritterbaseUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; - - const surveyCritterService = new SurveyCritterService(connection); - await surveyCritterService.upsertDeployment(critterId, newDeploymentId); + const user = getBctwUser(req); const bctwService = new BctwService(user); - await bctwService.deployDevice(newDeploymentDevice); + const bctwDeploymentService = new BctwDeploymentService(user); + const deploymentService = new DeploymentService(connection); + const critterbaseService = new CritterbaseService(user); - await connection.commit(); - return res.status(201).json({ message: 'Deployment created.' }); - } catch (error) { - defaultLog.error({ label: 'addDeployment', message: 'error', error }); - await connection.rollback(); + await deploymentService.insertDeployment({ + critter_id: surveyCritterId, + bctw_deployment_id: newDeploymentId, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id + }); - throw error; - } finally { - connection.release(); - } - }; -} + // Retrieve the capture to get the capture date for BCTW + const critterbaseCritter = await critterbaseService.getCaptureById(critterbase_start_capture_id); -export function updateDeployment(): RequestHandler { - return async (req, res) => { - const critterId = Number(req.params.critterId); + // Create attachment end date from provided end date (if not null) and end time (if not null). + const attachmentEnd = attachment_end_date + ? attachment_end_time + ? dayjs(`${attachment_end_date} ${attachment_end_time}`).toISOString() + : dayjs(`${attachment_end_date}`).toISOString() + : null; - const connection = getDBConnection(req.keycloak_token); - - try { - await connection.open(); + // Get BCTW code values + const [deviceMakeCodes, frequencyUnitCodes] = await Promise.all([ + bctwService.getCode('device_make'), + bctwService.getCode('frequency_unit') + ]); + // The BCTW API expects the device make and frequency unit as codes, not IDs. + const device_make_code = deviceMakeCodes.find((code) => code.id === device_make)?.code; + const frequency_unit_code = frequencyUnitCodes.find((code) => code.id === frequency_unit)?.code; - const user: ICritterbaseUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; + const deployment = await bctwDeploymentService.createDeployment({ + deployment_id: newDeploymentId, + device_id: device_id, + critter_id: critterbaseCritter.critter_id, + frequency: frequency, + frequency_unit: frequency_unit_code, + device_make: device_make_code, + device_model: device_model, + attachment_start: critterbaseCritter.capture_date, + attachment_end: attachmentEnd // TODO: ADD SEPARATE DATE AND TIME TO BCTW + }); - const surveyCritterService = new SurveyCritterService(connection); - const bctw = new BctwService(user); - - await surveyCritterService.upsertDeployment(critterId, req.body.deployment_id); - await bctw.updateDeployment(req.body); await connection.commit(); - return res.status(200).json({ message: 'Deployment updated.' }); + + return res.status(201).json({ deploymentId: deployment.deployment_id }); } catch (error) { - defaultLog.error({ label: 'updateDeployment', message: 'error', error }); + defaultLog.error({ label: 'createDeployment', message: 'error', error }); await connection.rollback(); + throw error; } finally { connection.release(); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.test.ts deleted file mode 100644 index 33aa5990ca..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.test.ts +++ /dev/null @@ -1,42 +0,0 @@ -import Ajv from 'ajv'; -import { expect } from 'chai'; -import sinon from 'sinon'; -import * as db from '../../../../../../../../database/db'; -import { BctwService } from '../../../../../../../../services/bctw-service'; -import { SurveyCritterService } from '../../../../../../../../services/survey-critter-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../../__mocks__/db'; -import { DELETE, deleteDeployment } from './{bctwDeploymentId}'; - -describe('critter deployments', () => { - afterEach(() => { - sinon.restore(); - }); - - const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); - - describe('openapi schema', () => { - const ajv = new Ajv(); - - it('is valid openapi v3 schema', () => { - expect(ajv.validateSchema(DELETE.apiDoc as unknown as object)).to.be.true; - }); - }); - - describe('deleteDeployment', () => { - it('deletes an existing deployment', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockRemoveDeployment = sinon.stub(SurveyCritterService.prototype, 'removeDeployment').resolves(); - const mockBctwService = sinon.stub(BctwService.prototype, 'deleteDeployment'); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = deleteDeployment(); - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockRemoveDeployment.calledOnce).to.be.true; - expect(mockBctwService.calledOnce).to.be.true; - expect(mockRes.status).to.have.been.calledWith(200); - }); - }); -}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.ts deleted file mode 100644 index 1538e5e5fd..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}.ts +++ /dev/null @@ -1,137 +0,0 @@ -import { AxiosError } from 'axios'; -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../../constants/roles'; -import { getDBConnection } from '../../../../../../../../database/db'; -import { authorizeRequestHandler } from '../../../../../../../../request-handlers/security/authorization'; -import { BctwService } from '../../../../../../../../services/bctw-service'; -import { ICritterbaseUser } from '../../../../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../../../../services/survey-critter-service'; -import { getLogger } from '../../../../../../../../utils/logger'; - -const defaultLog = getLogger( - 'paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}' -); -export const DELETE: Operation = [ - authorizeRequestHandler((req) => { - return { - or: [ - { - validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], - surveyId: Number(req.params.surveyId), - discriminator: 'ProjectPermission' - }, - { - validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - deleteDeployment() -]; - -DELETE.apiDoc = { - description: 'Deletes the deployment record in SIMS, and soft deletes the record in BCTW.', - tags: ['bctw'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'path', - name: 'surveyId', - schema: { - type: 'number' - }, - required: true - }, - { - in: 'path', - name: 'critterId', - schema: { - type: 'number' - }, - required: true - }, - { - in: 'path', - name: 'bctwDeploymentId', - schema: { - type: 'string', - format: 'uuid' - }, - required: true - } - ], - responses: { - 200: { - description: 'Removed deployment successfully.', - content: { - 'application/json': { - schema: { - title: 'Deployment response object', - type: 'object', - additionalProperties: false, - properties: { - message: { - type: 'string' - } - } - } - } - } - }, - 400: { - $ref: '#/components/responses/400' - }, - 401: { - $ref: '#/components/responses/401' - }, - 403: { - $ref: '#/components/responses/403' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -export function deleteDeployment(): RequestHandler { - return async (req, res) => { - const deploymentId = String(req.params.bctwDeploymentId); - const critterId = Number(req.params.critterId); - - const connection = getDBConnection(req.keycloak_token); - - try { - await connection.open(); - - const user: ICritterbaseUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; - - const surveyCritterService = new SurveyCritterService(connection); - await surveyCritterService.removeDeployment(critterId, deploymentId); - - const bctwService = new BctwService(user); - await bctwService.deleteDeployment(deploymentId); - - await connection.commit(); - return res.status(200).json({ message: 'Deployment deleted.' }); - } catch (error) { - defaultLog.error({ label: 'deleteDeployment', message: 'error', error }); - await connection.rollback(); - - return res.status(500).json((error as AxiosError).response); - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.test.ts new file mode 100644 index 0000000000..7ec000876d --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.test.ts @@ -0,0 +1,79 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { patchDeployment } from '.'; +import * as db from '../../../../../../../../../database/db'; +import { BctwDeploymentService } from '../../../../../../../../../services/bctw-service/bctw-deployment-service'; +import { CritterbaseService, ICapture } from '../../../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../../../services/deployment-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../../../__mocks__/db'; + +describe('patchDeployment', () => { + afterEach(() => { + sinon.restore(); + }); + + it('updates an existing deployment', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockCapture: ICapture = { + capture_id: '111', + critter_id: '222', + capture_method_id: null, + capture_location_id: '333', + release_location_id: null, + capture_date: '2021-01-01', + capture_time: '12:00:00', + release_date: null, + release_time: null, + capture_comment: null, + release_comment: null + }; + + const updateDeploymentStub = sinon.stub(DeploymentService.prototype, 'updateDeployment').resolves(); + const updateBctwDeploymentStub = sinon.stub(BctwDeploymentService.prototype, 'updateDeployment'); + const getCaptureByIdStub = sinon.stub(CritterbaseService.prototype, 'getCaptureById').resolves(mockCapture); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.body = { + deployment_id: '111', + bctw_deployment_id: '222', + critterbase_start_capture_id: '333', + critterbase_end_capture_id: '444', + critterbase_end_mortality_id: '555', + attachment_end_date: '2021-01-01', + attachment_end_time: '12:00:00' + }; + + const requestHandler = patchDeployment(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(updateDeploymentStub).to.have.been.calledOnce; + expect(updateBctwDeploymentStub).to.have.been.calledOnce; + expect(getCaptureByIdStub).to.have.been.calledOnce; + expect(mockRes.status).to.have.been.calledWith(200); + }); + + it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockError = new Error('a test error'); + const updateDeploymentStub = sinon.stub(DeploymentService.prototype, 'updateDeployment').rejects(mockError); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = patchDeployment(); + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(actualError).to.equal(mockError); + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(updateDeploymentStub).to.have.been.calledOnce; + } + }); +}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.ts new file mode 100644 index 0000000000..01afb217ee --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{deploymentId}/index.ts @@ -0,0 +1,244 @@ +import dayjs from 'dayjs'; +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../../../database/db'; +import { authorizeRequestHandler } from '../../../../../../../../../request-handlers/security/authorization'; +import { BctwDeploymentService } from '../../../../../../../../../services/bctw-service/bctw-deployment-service'; +import { CritterbaseService, ICritterbaseUser } from '../../../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../../../services/deployment-service'; +import { getLogger } from '../../../../../../../../../utils/logger'; + +const defaultLog = getLogger( + 'paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments/{bctwDeploymentId}' +); + +export const PATCH: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + patchDeployment() +]; + +PATCH.apiDoc = { + description: 'Updates information about the start and end of a deployment.', + tags: ['critterbase'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'critterId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'deploymentId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + requestBody: { + description: 'Specifies a deployment id and the new timerange to update it with.', + content: { + 'application/json': { + schema: { + title: 'Deploy device request object', + type: 'object', + additionalProperties: false, + required: [ + 'bctw_deployment_id', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id', + 'attachment_end_date', + 'attachment_end_time' + ], + properties: { + deployment_id: { + type: 'integer', + description: 'Id of the deployment in SIMS', + minimum: 1 + }, + bctw_deployment_id: { + type: 'string', + description: 'Id of the deployment in BCTW', + format: 'uuid' + }, + critterbase_start_capture_id: { + type: 'string', + description: 'Critterbase capture record for when the deployment start', + format: 'uuid', + nullable: true + }, + critterbase_end_capture_id: { + type: 'string', + description: 'Critterbase capture record for when the deployment ended', + format: 'uuid', + nullable: true + }, + critterbase_end_mortality_id: { + type: 'string', + description: 'Critterbase mortality record for when the deployment ended', + format: 'uuid', + nullable: true + }, + attachment_end_date: { + type: 'string', + description: 'End date of the deployment, without time.', + example: '2021-01-01', + pattern: '^[0-9]{4}-[0-9]{2}-[0-9]{2}$', + nullable: true + }, + attachment_end_time: { + type: 'string', + description: 'End time of the deployment.', + example: '12:00:00', + pattern: '^[0-9]{2}:[0-9]{2}:[0-9]{2}$', + nullable: true + } + } + } + } + } + }, + responses: { + 200: { + description: 'Responds with count of rows created or updated in SIMS DB Deployments.', + content: { + 'application/json': { + schema: { + title: 'Deployment response object', + type: 'object', + additionalProperties: false, + properties: { + message: { + type: 'string' + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function patchDeployment(): RequestHandler { + return async (req, res) => { + const critterId = Number(req.params.critterId); + const deploymentId = Number(req.params.deploymentId); + + const connection = getDBConnection(req.keycloak_token); + + const { + bctw_deployment_id, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id, + attachment_end_date, + attachment_end_time + } = req.body; + + try { + await connection.open(); + + const user: ICritterbaseUser = { + keycloak_guid: connection.systemUserGUID(), + username: connection.systemUserIdentifier() + }; + + const bctwDeploymentService = new BctwDeploymentService(user); + const deploymentService = new DeploymentService(connection); + const critterbaseService = new CritterbaseService(user); + + await deploymentService.updateDeployment({ + deployment_id: deploymentId, + critter_id: critterId, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id + }); + + const capture = await critterbaseService.getCaptureById(critterbase_start_capture_id); + + // Create attachment end date from provided end date (if not null) and end time (if not null). + const attachmentEnd = attachment_end_date + ? attachment_end_time + ? dayjs(`${attachment_end_date} ${attachment_end_time}`).toISOString() + : dayjs(`${attachment_end_date}`).toISOString() + : null; + + // Update the deployment in BCTW, which works by soft deleting and inserting a new deployment record + await bctwDeploymentService.updateDeployment({ + deployment_id: bctw_deployment_id, + attachment_start: capture.capture_date, + attachment_end: attachmentEnd // TODO: ADD SEPARATE DATE AND TIME TO BCTW + }); + + await connection.commit(); + + return res.status(200).send(); + } catch (error) { + defaultLog.error({ label: 'patchDeployment', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.test.ts similarity index 63% rename from api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.test.ts rename to api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.test.ts index ea88afd0d4..f25de6819c 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.test.ts @@ -1,31 +1,23 @@ -import Ajv from 'ajv'; import { expect } from 'chai'; import sinon from 'sinon'; -import * as db from '../../../../../../database/db'; -import { HTTPError } from '../../../../../../errors/http-error'; -import { CritterbaseService } from '../../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../../services/survey-critter-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../__mocks__/db'; -import { PATCH, updateSurveyCritter } from './{critterId}'; - -describe('critterId openapi schema', () => { - const ajv = new Ajv(); - - it('PATCH is valid openapi v3 schema', () => { - expect(ajv.validateSchema(PATCH.apiDoc as unknown as object)).to.be.true; - }); -}); +import { updateSurveyCritter } from '.'; +import * as db from '../../../../../../../database/db'; +import { HTTPError } from '../../../../../../../errors/http-error'; +import { CritterbaseService } from '../../../../../../../services/critterbase-service'; +import { SurveyCritterService } from '../../../../../../../services/survey-critter-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; describe('updateSurveyCritter', () => { afterEach(() => { sinon.restore(); }); - const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); - const mockCBCritter = { critter_id: 'critterbase1' }; - it('returns critters from survey', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockCBCritter = { critter_id: 'critterbase1' }; + const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').resolves(); const mockCritterbaseUpdateCritter = sinon .stub(CritterbaseService.prototype, 'updateCritter') @@ -33,31 +25,38 @@ describe('updateSurveyCritter', () => { const mockCritterbaseCreateCritter = sinon .stub(CritterbaseService.prototype, 'createCritter') .resolves(mockCBCritter); + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); mockReq.body = { create: {}, update: { critter_id: 'critterbase1' } }; + const requestHandler = updateSurveyCritter(); + await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockSurveyUpdateCritter.calledOnce).to.be.true; - expect(mockCritterbaseUpdateCritter.calledOnce).to.be.true; - expect(mockCritterbaseCreateCritter.calledOnce).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockSurveyUpdateCritter).to.have.been.calledOnce; + expect(mockCritterbaseUpdateCritter).to.have.been.calledOnce; + expect(mockCritterbaseCreateCritter).to.have.been.calledOnce; expect(mockRes.status).to.have.been.calledWith(200); expect(mockRes.json).to.have.been.calledWith(mockCBCritter); }); it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').rejects(mockError); + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); mockReq.body = { create: {}, update: { critter_id: 'critterbase1' } }; + const requestHandler = updateSurveyCritter(); try { @@ -65,20 +64,24 @@ describe('updateSurveyCritter', () => { expect.fail(); } catch (actualError) { expect(actualError).to.equal(mockError); - expect(mockSurveyUpdateCritter.calledOnce).to.be.true; - expect(mockGetDBConnection.calledOnce).to.be.true; + expect(mockSurveyUpdateCritter).to.have.been.calledOnce; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.called; } }); it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + const errMsg = 'No external critter ID was found.'; - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').resolves(); + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); mockReq.body = { update: {} }; + const requestHandler = updateSurveyCritter(); try { @@ -87,8 +90,8 @@ describe('updateSurveyCritter', () => { } catch (actualError) { expect((actualError as HTTPError).message).to.equal(errMsg); expect((actualError as HTTPError).status).to.equal(400); - expect(mockSurveyUpdateCritter.calledOnce).to.be.false; - expect(mockGetDBConnection.calledOnce).to.be.true; + expect(mockSurveyUpdateCritter).not.to.have.been.called; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.called; } }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.ts new file mode 100644 index 0000000000..3c22b02747 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/index.ts @@ -0,0 +1,252 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTPError, HTTPErrorType } from '../../../../../../../errors/http-error'; +import { bulkUpdateResponse, critterBulkRequestObject } from '../../../../../../../openapi/schemas/critter'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { getBctwUser } from '../../../../../../../services/bctw-service/bctw-service'; +import { CritterbaseService, ICritterbaseUser } from '../../../../../../../services/critterbase-service'; +import { SurveyCritterService } from '../../../../../../../services/survey-critter-service'; +import { getLogger } from '../../../../../../../utils/logger'; + +const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters/{critterId}'); + +export const PATCH: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + updateSurveyCritter() +]; + +PATCH.apiDoc = { + description: 'Patches a critter in critterbase, also capable of deleting relevant rows if marked with _delete.', + tags: ['critterbase'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'surveyId', + schema: { + type: 'number' + }, + required: true + } + ], + requestBody: { + description: 'Critterbase bulk patch request object', + content: { + 'application/json': { + schema: critterBulkRequestObject + } + } + }, + responses: { + 200: { + description: 'Responds with counts of objects created in critterbase.', + content: { + 'application/json': { + schema: bulkUpdateResponse + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function updateSurveyCritter(): RequestHandler { + return async (req, res) => { + const critterbaseCritterId = req.body.update.critter_id; + + const critterId = Number(req.params.critterId); + + const connection = getDBConnection(req.keycloak_token); + try { + await connection.open(); + const user = getBctwUser(req); + + if (!critterbaseCritterId) { + throw new HTTPError(HTTPErrorType.BAD_REQUEST, 400, 'No external critter ID was found.'); + } + + const surveyService = new SurveyCritterService(connection); + await surveyService.updateCritter(critterId, critterbaseCritterId); + + const critterbaseService = new CritterbaseService(user); + + let createResult, updateResult; + + if (req.body.update) { + updateResult = await critterbaseService.updateCritter(req.body.update); + } + + if (req.body.create) { + createResult = await critterbaseService.createCritter(req.body.create); + } + + await connection.commit(); + + return res.status(200).json({ ...createResult, ...updateResult }); + } catch (error) { + defaultLog.error({ label: 'updateSurveyCritter', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + getCrittersFromSurvey() +]; + +GET.apiDoc = { + description: 'Gets a specific critter by its integer Critter Id', + tags: ['critterbase'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer' + }, + required: true + }, + { + in: 'path', + name: 'critterId', + schema: { + type: 'integer' + }, + required: true + } + ], + responses: { + 200: { + description: 'Responds with a critter', + content: { + 'application/json': { + schema: { type: 'object' } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function getCrittersFromSurvey(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + const critterId = Number(req.params.critterId); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const user: ICritterbaseUser = { + keycloak_guid: connection.systemUserGUID(), + username: connection.systemUserIdentifier() + }; + + const surveyService = new SurveyCritterService(connection); + const critterbaseService = new CritterbaseService(user); + + const surveyCritter = await surveyService.getCritterById(surveyId, critterId); + + if (!surveyCritter) { + return res.status(404).json({ error: `Critter with id ${critterId} not found.` }); + } + + const critterbaseCritter = await critterbaseService.getCritter(surveyCritter.critterbase_critter_id); + + if (!critterbaseCritter || critterbaseCritter.length === 0) { + return res.status(404).json({ error: `Critter ${surveyCritter.critterbase_critter_id} not found.` }); + } + + const critterMapped = { + ...surveyCritter, + ...critterbaseCritter, + critterbase_critter_id: surveyCritter.critterbase_critter_id, + critter_id: surveyCritter.critter_id + }; + + return res.status(200).json(critterMapped); + } catch (error) { + defaultLog.error({ label: 'createCritter', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.test.ts index bc00790004..6c7b80beb6 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.test.ts @@ -1,66 +1,106 @@ -import Ajv from 'ajv'; import { expect } from 'chai'; import sinon from 'sinon'; import * as db from '../../../../../../../database/db'; -import { BctwService } from '../../../../../../../services/bctw-service'; -import { SurveyCritterService } from '../../../../../../../services/survey-critter-service'; +import { SurveyDeployment } from '../../../../../../../models/survey-deployment'; +import { BctwTelemetryService, IAllTelemetry } from '../../../../../../../services/bctw-service/bctw-telemetry-service'; +import { DeploymentService } from '../../../../../../../services/deployment-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; -import { GET, getCritterTelemetry } from './telemetry'; +import { getCritterTelemetry } from './telemetry'; -describe('critter telemetry', () => { +describe('getCritterTelemetry', () => { afterEach(() => { sinon.restore(); }); - const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + it('fetches telemetry object', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - describe('openapi schema', () => { - const ajv = new Ajv(); + const mockSurveyDeployment: SurveyDeployment = { + deployment_id: 1, + critter_id: 123, + critterbase_critter_id: 'critter-001', + bctw_deployment_id: '111', + critterbase_start_capture_id: '222', + critterbase_end_capture_id: '333', + critterbase_end_mortality_id: '444' + }; - it('is valid openapi v3 schema', () => { - expect(ajv.validateSchema(GET.apiDoc as unknown as object)).to.be.true; - }); + const mockTelemetry: IAllTelemetry[] = [ + { + id: '123e4567-e89b-12d3-a456-426614174111', + deployment_id: '123e4567-e89b-12d3-a456-426614174222', + latitude: 37.7749, + longitude: -122.4194, + acquisition_date: '2023-10-01T12:00:00Z', + telemetry_type: 'ATS', + telemetry_id: '123e4567-e89b-12d3-a456-426614174111', + telemetry_manual_id: null + }, + { + id: '123e4567-e89b-12d3-a456-426614174333', + deployment_id: '123e4567-e89b-12d3-a456-426614174444', + latitude: 37.775, + longitude: -122.4195, + acquisition_date: '2023-10-01T12:05:00Z', + telemetry_type: 'ATS', + telemetry_id: null, + telemetry_manual_id: '123e4567-e89b-12d3-a456-426614174333' + }, + { + id: '123e4567-e89b-12d3-a456-426614174555', + deployment_id: '123e4567-e89b-12d3-a456-426614174666', + latitude: 37.7751, + longitude: -122.4196, + acquisition_date: '2023-10-01T12:10:00Z', + telemetry_type: 'MANUAL', + telemetry_id: null, + telemetry_manual_id: '123e4567-e89b-12d3-a456-426614174555' + } + ]; + + const getDeploymentForCritterIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentForCritterId') + .resolves(mockSurveyDeployment); + + const getAllTelemetryByDeploymentIdsStub = sinon + .stub(BctwTelemetryService.prototype, 'getAllTelemetryByDeploymentIds') + .resolves(mockTelemetry); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params.critterId = '1'; + + const requestHandler = getCritterTelemetry(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.jsonValue).to.eql(mockTelemetry); + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(getDeploymentForCritterIdStub).to.have.been.calledOnce; + expect(getAllTelemetryByDeploymentIdsStub).to.have.been.calledOnce; }); - describe('getCritterTelemetry', () => { - it('fetches telemetry object', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockGetCrittersInSurvey = sinon - .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') - .resolves([{ critter_id: 1, survey_id: 1, critterbase_critter_id: 'asdf' }]); - const mockGetCritterPoints = sinon.stub(BctwService.prototype, 'getCritterTelemetryPoints').resolves(); - const mockGetCritterTracks = sinon.stub(BctwService.prototype, 'getCritterTelemetryTracks').resolves(); + it('catches and re-throws error', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = getCritterTelemetry(); + const mockError = new Error('a test error'); + const getDeploymentForCritterIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentForCritterId') + .rejects(mockError); - mockReq.params.critterId = '1'; + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - await requestHandler(mockReq, mockRes, mockNext); + const requestHandler = getCritterTelemetry(); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; - expect(mockGetCritterPoints.calledOnce).to.be.true; - expect(mockGetCritterTracks.calledOnce).to.be.true; - }); - - it('catches and re-throws error', async () => { - const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockGetCrittersInSurvey = sinon - .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') - .rejects(mockError); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = getCritterTelemetry(); - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect(actualError).to.eql(mockError); - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; - } - }); + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(actualError).to.eql(mockError); + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(getDeploymentForCritterIdStub).to.have.been.calledOnce; + } }); }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.ts index 20fcda05be..326264c6ef 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry.ts @@ -1,163 +1,15 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; -import { OpenAPIV3 } from 'openapi-types'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; import { getDBConnection } from '../../../../../../../database/db'; -import { HTTP400 } from '../../../../../../../errors/http-error'; -import { GeoJSONFeatureCollection } from '../../../../../../../openapi/schemas/geoJson'; +import { AllTelemetrySchema } from '../../../../../../../openapi/schemas/telemetry'; import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; -import { BctwService } from '../../../../../../../services/bctw-service'; +import { BctwTelemetryService } from '../../../../../../../services/bctw-service/bctw-telemetry-service'; import { ICritterbaseUser } from '../../../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../../../services/survey-critter-service'; +import { DeploymentService } from '../../../../../../../services/deployment-service'; import { getLogger } from '../../../../../../../utils/logger'; const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/telemetry'); -const GeoJSONFeatureCollectionFeaturesItems = ( - GeoJSONFeatureCollection.properties?.features as OpenAPIV3.ArraySchemaObject -)?.items as OpenAPIV3.SchemaObject; - -const GeoJSONTelemetryPointsAPISchema: OpenAPIV3.SchemaObject = { - ...GeoJSONFeatureCollection, - properties: { - ...GeoJSONFeatureCollection.properties, - features: { - type: 'array', - items: { - ...GeoJSONFeatureCollectionFeaturesItems, - properties: { - ...GeoJSONFeatureCollectionFeaturesItems?.properties, - properties: { - type: 'object', - additionalProperties: false, - required: ['collar_id', 'device_id', 'date_recorded', 'deployment_id', 'critter_id'], - properties: { - collar_id: { - type: 'string', - format: 'uuid' - }, - device_id: { - type: 'integer' - }, - elevation: { - type: 'number', - nullable: true - }, - frequency: { - type: 'number', - nullable: true - }, - critter_id: { - type: 'string', - format: 'uuid' - }, - date_recorded: { - type: 'string' - }, - deployment_id: { - type: 'string', - format: 'uuid' - }, - device_status: { - type: 'string', - nullable: true - }, - device_vendor: { - type: 'string', - nullable: true - }, - frequency_unit: { - type: 'string', - nullable: true - }, - wlh_id: { - type: 'string', - nullable: true - }, - animal_id: { - type: 'string', - nullable: true - }, - sex: { - type: 'string' - }, - taxon: { - type: 'string' - }, - collection_units: { - type: 'array', - items: { - type: 'object', - additionalProperties: false, - properties: { - collection_unit_id: { - type: 'string', - format: 'uuid' - }, - unit_name: { - type: 'string' - }, - collection_category_id: { - type: 'string', - format: 'uuid' - }, - category_name: { - type: 'string' - } - } - } - }, - mortality_timestamp: { - type: 'string', - nullable: true - }, - _merged: { - type: 'boolean' - }, - map_colour: { - type: 'string' - } - } - } - } - } - } - } -}; - -const GeoJSONTelemetryTracksAPISchema: OpenAPIV3.SchemaObject = { - ...GeoJSONFeatureCollection, - properties: { - ...GeoJSONFeatureCollection.properties, - features: { - type: 'array', - items: { - ...GeoJSONFeatureCollectionFeaturesItems, - properties: { - ...GeoJSONFeatureCollectionFeaturesItems?.properties, - properties: { - type: 'object', - additionalProperties: false, - required: ['critter_id', 'deployment_id'], - properties: { - critter_id: { - type: 'string', - format: 'uuid' - }, - deployment_id: { - type: 'string', - format: 'uuid' - }, - map_colour: { - type: 'string' - } - } - } - } - } - } - } -}; - export const GET: Operation = [ authorizeRequestHandler((req) => { return { @@ -225,14 +77,8 @@ GET.apiDoc = { content: { 'application/json': { schema: { - title: 'Telemetry response', - type: 'object', - additionalProperties: false, - required: ['tracks', 'points'], - properties: { - points: GeoJSONTelemetryPointsAPISchema, - tracks: GeoJSONTelemetryTracksAPISchema - } + type: 'array', + items: AllTelemetrySchema } } } @@ -261,7 +107,6 @@ export function getCritterTelemetry(): RequestHandler { const surveyId = Number(req.params.surveyId); const connection = getDBConnection(req.keycloak_token); - try { await connection.open(); @@ -270,28 +115,25 @@ export function getCritterTelemetry(): RequestHandler { username: connection.systemUserIdentifier() }; - const surveyCritterService = new SurveyCritterService(connection); - const surveyCritters = await surveyCritterService.getCrittersInSurvey(surveyId); + // TODO: Telemetry data should only ever be fetched by deployment Ids. To get telemetry for an animal, first find the + // relevant deployment Id, then fetch data for that deployment Id. + const deploymentService = new DeploymentService(connection); + const bctwTelemetryService = new BctwTelemetryService(user); - const critter = surveyCritters.find((surveyCritter) => surveyCritter.critter_id === critterId); - if (!critter) { - throw new HTTP400('Specified critter was not part of this survey.'); - } + const { bctw_deployment_id } = await deploymentService.getDeploymentForCritterId(surveyId, critterId); - const startDate = new Date(String(req.query.startDate)); - const endDate = new Date(String(req.query.endDate)); + // const startDate = new Date(String(req.query.startDate)); + // const endDate = new Date(String(req.query.endDate)); - const bctwService = new BctwService(user); - const points = await bctwService.getCritterTelemetryPoints(critter.critterbase_critter_id, startDate, endDate); - const tracks = await bctwService.getCritterTelemetryTracks(critter.critterbase_critter_id, startDate, endDate); + // TODO: Add start and end date filters received in the SIMS request to the BCTW request + const points = await bctwTelemetryService.getAllTelemetryByDeploymentIds([bctw_deployment_id]); await connection.commit(); - return res.status(200).json({ points, tracks }); + return res.status(200).json(points); } catch (error) { defaultLog.error({ label: 'telemetry', message: 'error', error }); await connection.rollback(); - throw error; } finally { connection.release(); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.test.ts deleted file mode 100644 index 9932141f89..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.test.ts +++ /dev/null @@ -1,74 +0,0 @@ -import { expect } from 'chai'; -import sinon from 'sinon'; -import * as db from '../../../../../database/db'; -import { BctwService, IDeploymentRecord } from '../../../../../services/bctw-service'; -import { SurveyCritterService } from '../../../../../services/survey-critter-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../__mocks__/db'; -import { getDeploymentsInSurvey } from './deployments'; - -describe('getDeploymentsInSurvey', () => { - afterEach(() => { - sinon.restore(); - }); - - const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); - const mockDeployments: IDeploymentRecord[] = [ - { - critter_id: 'critterbase1', - assignment_id: 'assignment1', - collar_id: 'collar1', - attachment_start: '2020-01-01', - attachment_end: '2020-01-02', - deployment_id: 'deployment1', - device_id: 123, - created_at: '2020-01-01', - created_by_user_id: 'user1', - updated_at: '2020-01-01', - updated_by_user_id: 'user1', - valid_from: '2020-01-01', - valid_to: '2020-01-02' - } - ]; - const mockCritters = [{ critter_id: 123, survey_id: 123, critterbase_critter_id: 'critterbase1' }]; - - it('gets deployments in survey', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockGetCrittersInSurvey = sinon - .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') - .resolves(mockCritters); - const getDeploymentsByCritterId = sinon - .stub(BctwService.prototype, 'getDeploymentsByCritterId') - .resolves(mockDeployments); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = getDeploymentsInSurvey(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; - expect(getDeploymentsByCritterId.calledOnce).to.be.true; - expect(mockRes.json.calledWith(mockDeployments)).to.be.true; - expect(mockRes.status.calledWith(200)).to.be.true; - }); - - it('catches and re-throws errors', async () => { - const mockError = new Error('a test error'); - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const mockGetCrittersInSurvey = sinon - .stub(SurveyCritterService.prototype, 'getCrittersInSurvey') - .rejects(mockError); - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - const requestHandler = getDeploymentsInSurvey(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect(actualError).to.equal(mockError); - expect(mockGetCrittersInSurvey.calledOnce).to.be.true; - expect(mockGetDBConnection.calledOnce).to.be.true; - expect(mockDBConnection.release).to.have.been.called; - } - }); -}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.ts deleted file mode 100644 index 2c5684841a..0000000000 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments.ts +++ /dev/null @@ -1,118 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../constants/roles'; -import { getDBConnection } from '../../../../../database/db'; -import { authorizeRequestHandler } from '../../../../../request-handlers/security/authorization'; -import { BctwService } from '../../../../../services/bctw-service'; -import { ICritterbaseUser } from '../../../../../services/critterbase-service'; -import { SurveyCritterService } from '../../../../../services/survey-critter-service'; -import { getLogger } from '../../../../../utils/logger'; - -const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/critters'); -export const GET: Operation = [ - authorizeRequestHandler((req) => { - return { - or: [ - { - validProjectPermissions: [ - PROJECT_PERMISSION.COORDINATOR, - PROJECT_PERMISSION.COLLABORATOR, - PROJECT_PERMISSION.OBSERVER - ], - surveyId: Number(req.params.surveyId), - discriminator: 'ProjectPermission' - }, - { - validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - getDeploymentsInSurvey() -]; - -GET.apiDoc = { - description: - 'Fetches a list of all the deployments under this survey. This is determined by the critters under this survey.', - tags: ['bctw'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'path', - name: 'surveyId', - schema: { - type: 'number' - }, - required: true - } - ], - responses: { - 200: { - description: 'Responds with all deployments under this survey, determined by critters under the survey.', - content: { - 'application/json': { - schema: { - title: 'Deployments', - type: 'array', - items: { - type: 'object' - } - } - } - } - }, - 400: { - $ref: '#/components/responses/400' - }, - 401: { - $ref: '#/components/responses/401' - }, - 403: { - $ref: '#/components/responses/403' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -export function getDeploymentsInSurvey(): RequestHandler { - return async (req, res) => { - const surveyId = Number(req.params.surveyId); - const connection = getDBConnection(req.keycloak_token); - - try { - await connection.open(); - - const user: ICritterbaseUser = { - keycloak_guid: connection.systemUserGUID(), - username: connection.systemUserIdentifier() - }; - - const surveyCritterService = new SurveyCritterService(connection); - const bctwService = new BctwService(user); - - const critter_ids = (await surveyCritterService.getCrittersInSurvey(surveyId)).map( - (critter) => critter.critterbase_critter_id - ); - - const results = critter_ids.length ? await bctwService.getDeploymentsByCritterId(critter_ids) : []; - return res.status(200).json(results); - } catch (error) { - defaultLog.error({ label: 'getDeploymentsInSurvey', message: 'error', error }); - await connection.rollback(); - - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.test.ts new file mode 100644 index 0000000000..0dfcbf2800 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.test.ts @@ -0,0 +1,355 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { getDeploymentsInSurvey } from '.'; +import * as db from '../../../../../../database/db'; +import { HTTPError } from '../../../../../../errors/http-error'; +import { SurveyDeployment } from '../../../../../../models/survey-deployment'; +import { + BctwDeploymentRecordWithDeviceMeta, + BctwDeploymentService +} from '../../../../../../services/bctw-service/bctw-deployment-service'; +import { DeploymentService } from '../../../../../../services/deployment-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../__mocks__/db'; + +describe('getDeploymentsInSurvey', () => { + afterEach(() => { + sinon.restore(); + }); + + it('gets deployments in survey', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSIMSDeployments = [ + { + deployment_id: 3, + critter_id: 2, + critterbase_critter_id: '333', + bctw_deployment_id: '444', + critterbase_start_capture_id: '555', + critterbase_end_capture_id: null, + critterbase_end_mortality_id: null + } + ]; + + const mockBCTWDeployments: BctwDeploymentRecordWithDeviceMeta[] = [ + { + critter_id: '333', + assignment_id: 'assignment1', + collar_id: 'collar1', + attachment_start: '2020-01-01T00:00:00', + attachment_end: '2020-01-02T12:12:12', + deployment_id: '444', + device_id: 123, + created_at: '2020-01-01', + created_by_user_id: 'user1', + updated_at: '2020-01-01', + updated_by_user_id: 'user1', + valid_from: '2020-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + } + ]; + + const getDeploymentsForSurveyIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentsForSurveyId') + .resolves(mockSIMSDeployments); + const getDeploymentsByIdsStub = sinon + .stub(BctwDeploymentService.prototype, 'getDeploymentsByIds') + .resolves(mockBCTWDeployments); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '55', + surveyId: '66' + }; + + const requestHandler = getDeploymentsInSurvey(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDeploymentsForSurveyIdStub).calledOnceWith(66); + expect(getDeploymentsByIdsStub).calledOnceWith(['444']); + expect(mockRes.json).to.have.been.calledOnceWith([ + { + // BCTW properties + assignment_id: mockBCTWDeployments[0].assignment_id, + collar_id: mockBCTWDeployments[0].collar_id, + attachment_start_date: '2020-01-01', + attachment_start_time: '00:00:00', + attachment_end_date: '2020-01-02', + attachment_end_time: '12:12:12', + bctw_deployment_id: mockBCTWDeployments[0].deployment_id, + device_id: mockBCTWDeployments[0].device_id, + device_make: mockBCTWDeployments[0].device_make, + device_model: mockBCTWDeployments[0].device_model, + frequency: mockBCTWDeployments[0].frequency, + frequency_unit: mockBCTWDeployments[0].frequency_unit, + // SIMS properties + deployment_id: mockSIMSDeployments[0].deployment_id, + critter_id: mockSIMSDeployments[0].critter_id, + critterbase_critter_id: mockSIMSDeployments[0].critterbase_critter_id, + critterbase_start_capture_id: mockSIMSDeployments[0].critterbase_start_capture_id, + critterbase_end_capture_id: mockSIMSDeployments[0].critterbase_end_capture_id, + critterbase_end_mortality_id: mockSIMSDeployments[0].critterbase_end_mortality_id + } + ]); + expect(mockRes.status).calledOnceWith(200); + expect(mockDBConnection.release).to.have.been.calledOnce; + }); + + it('returns early an empty array if no SIMS deployment records for survey', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSIMSDeployments: SurveyDeployment[] = []; // no SIMS deployment records + + const mockBCTWDeployments: BctwDeploymentRecordWithDeviceMeta[] = [ + { + critter_id: '333', + assignment_id: 'assignment1', + collar_id: 'collar1', + attachment_start: '2020-01-01', + attachment_end: '2020-01-02', + deployment_id: '444', + device_id: 123, + created_at: '2020-01-01', + created_by_user_id: 'user1', + updated_at: '2020-01-01', + updated_by_user_id: 'user1', + valid_from: '2020-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + } + ]; + + const getDeploymentsForSurveyIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentsForSurveyId') + .resolves(mockSIMSDeployments); + const getDeploymentsByIdsStub = sinon + .stub(BctwDeploymentService.prototype, 'getDeploymentsByIds') + .resolves(mockBCTWDeployments); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '55', + surveyId: '66' + }; + + const requestHandler = getDeploymentsInSurvey(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDeploymentsForSurveyIdStub).calledOnceWith(66); + expect(getDeploymentsByIdsStub).not.to.have.been.called; + expect(mockRes.json).calledOnceWith([]); + expect(mockRes.status).calledOnceWith(200); + expect(mockDBConnection.release).to.have.been.calledOnce; + }); + + it('throws a 409 error if more than 1 active deployment found in BCTW for a single SIMS deployment record', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSIMSDeployments = [ + { + deployment_id: 3, + critter_id: 2, + critterbase_critter_id: '333', + bctw_deployment_id: '444', + critterbase_start_capture_id: '555', + critterbase_end_capture_id: null, + critterbase_end_mortality_id: null + } + ]; + + const mockBCTWDeployments: BctwDeploymentRecordWithDeviceMeta[] = [ + { + critter_id: '333', + assignment_id: 'assignment1', + collar_id: 'collar1', + attachment_start: '2020-01-01', + attachment_end: '2020-01-02', + deployment_id: '444', + device_id: 123, + created_at: '2020-01-01', + created_by_user_id: 'user1', + updated_at: '2020-01-01', + updated_by_user_id: 'user1', + valid_from: '2020-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + }, + { + critter_id: '333', + assignment_id: 'assignment1', + collar_id: 'collar1', + attachment_start: '2020-01-01', + attachment_end: '2020-01-02', + deployment_id: '444', + device_id: 123, + created_at: '2020-01-01', + created_by_user_id: 'user1', + updated_at: '2020-01-01', + updated_by_user_id: 'user1', + valid_from: '2020-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + } + ]; + + const getDeploymentsForSurveyIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentsForSurveyId') + .resolves(mockSIMSDeployments); + const getDeploymentsByIdsStub = sinon + .stub(BctwDeploymentService.prototype, 'getDeploymentsByIds') + .resolves(mockBCTWDeployments); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '55', + surveyId: '66' + }; + + const requestHandler = getDeploymentsInSurvey(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).message).to.equal( + 'Multiple active deployments found for the same deployment ID' + ); + expect((actualError as HTTPError).status).to.equal(409); + expect(getDeploymentsForSurveyIdStub).calledOnceWith(66); + expect(getDeploymentsByIdsStub).calledOnceWith(['444']); + expect(mockDBConnection.release).to.have.been.calledOnce; + } + }); + + it('throws a 409 error if no active deployment found in BCTW for a single SIMS deployment record', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSIMSDeployments = [ + { + deployment_id: 3, + critter_id: 2, + critterbase_critter_id: '333', + bctw_deployment_id: '444', + critterbase_start_capture_id: '555', + critterbase_end_capture_id: null, + critterbase_end_mortality_id: null + } + ]; + + const mockBCTWDeployments: BctwDeploymentRecordWithDeviceMeta[] = [ + { + critter_id: '333', + assignment_id: 'assignment1', + collar_id: 'collar1', + attachment_start: '2020-01-01', + attachment_end: '2020-01-02', + deployment_id: '444_no_match', // different deployment ID + device_id: 123, + created_at: '2020-01-01', + created_by_user_id: 'user1', + updated_at: '2020-01-01', + updated_by_user_id: 'user1', + valid_from: '2020-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + } + ]; + + const getDeploymentsForSurveyIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentsForSurveyId') + .resolves(mockSIMSDeployments); + const getDeploymentsByIdsStub = sinon + .stub(BctwDeploymentService.prototype, 'getDeploymentsByIds') + .resolves(mockBCTWDeployments); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '55', + surveyId: '66' + }; + + const requestHandler = getDeploymentsInSurvey(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect((actualError as HTTPError).message).to.equal('No active deployments found for deployment ID'); + expect((actualError as HTTPError).status).to.equal(409); + expect(getDeploymentsForSurveyIdStub).calledOnceWith(66); + expect(getDeploymentsByIdsStub).calledOnceWith(['444']); + expect(mockDBConnection.release).to.have.been.calledOnce; + } + }); + + it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockSIMSDeployments = [ + { + deployment_id: 3, + critter_id: 2, + critterbase_critter_id: '333', + bctw_deployment_id: '444', + critterbase_start_capture_id: '555', + critterbase_end_capture_id: null, + critterbase_end_mortality_id: null + } + ]; + + const mockError = new Error('Test error'); + + const getDeploymentsForSurveyIdStub = sinon + .stub(DeploymentService.prototype, 'getDeploymentsForSurveyId') + .resolves(mockSIMSDeployments); + const getDeploymentsByIdsStub = sinon + .stub(BctwDeploymentService.prototype, 'getDeploymentsByIds') + .rejects(mockError); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '55', + surveyId: '66' + }; + + const requestHandler = getDeploymentsInSurvey(); + + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(actualError).to.equal(mockError); + expect(getDeploymentsForSurveyIdStub).calledOnceWith(66); + expect(getDeploymentsByIdsStub).calledOnceWith(['444']); + expect(mockDBConnection.release).to.have.been.calledOnce; + } + }); +}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.ts new file mode 100644 index 0000000000..0ec5eb68e1 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/index.ts @@ -0,0 +1,191 @@ +import dayjs from 'dayjs'; +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../database/db'; +import { HTTP409 } from '../../../../../../errors/http-error'; +import { getDeploymentSchema } from '../../../../../../openapi/schemas/deployment'; +import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization'; +import { BctwDeploymentService } from '../../../../../../services/bctw-service/bctw-deployment-service'; +import { ICritterbaseUser } from '../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../services/deployment-service'; +import { getLogger } from '../../../../../../utils/logger'; + +const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/deployments/index'); + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + getDeploymentsInSurvey() +]; + +GET.apiDoc = { + description: 'Returns information about all deployments under this survey.', + tags: ['deployment', 'bctw'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'surveyId', + schema: { + type: 'number' + }, + required: true + } + ], + responses: { + 200: { + description: 'Responds with information about all deployments under this survey.', + content: { + 'application/json': { + schema: { + title: 'Deployments', + type: 'array', + items: getDeploymentSchema + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 409: { + $ref: '#/components/responses/409' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function getDeploymentsInSurvey(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const user: ICritterbaseUser = { + keycloak_guid: connection.systemUserGUID(), + username: connection.systemUserIdentifier() + }; + + const deploymentService = new DeploymentService(connection); + const bctwDeploymentService = new BctwDeploymentService(user); + + // Fetch deployments from the deployment service for the given surveyId + const surveyDeployments = await deploymentService.getDeploymentsForSurveyId(surveyId); + + // Extract deployment IDs from survey deployments + const deploymentIds = surveyDeployments.map((deployment) => deployment.bctw_deployment_id); + + // Return early if there are no deployments + if (!deploymentIds.length) { + // TODO: 400 error instead? + return res.status(200).json([]); + } + + // Fetch additional deployment details from BCTW service + const bctwDeployments = await bctwDeploymentService.getDeploymentsByIds(deploymentIds); + + const surveyDeploymentsWithBctwData = []; + + // For each SIMS survey deployment record, find the matching BCTW deployment record. + // We expect exactly 1 matching record, otherwise we throw an error. + // More than 1 matching active record indicates an error in the BCTW data. + for (const surveyDeployment of surveyDeployments) { + const matchingBctwDeployments = bctwDeployments.filter( + (deployment) => deployment.deployment_id === surveyDeployment.bctw_deployment_id + ); + + if (matchingBctwDeployments.length > 1) { + throw new HTTP409('Multiple active deployments found for the same deployment ID', [ + 'This is an issue in the BC Telemetry Warehouse (BCTW) data. There should only be one active deployment record for a given deployment ID.', + `SIMS deployment ID: ${surveyDeployment.deployment_id}`, + `BCTW deployment ID: ${surveyDeployment.bctw_deployment_id}` + ]); + } + + if (matchingBctwDeployments.length === 0) { + throw new HTTP409('No active deployments found for deployment ID', [ + 'There should be no deployments recorded in SIMS that have no matching deployment record in BCTW.', + `SIMS Deployment ID: ${surveyDeployment.deployment_id}`, + `BCTW Deployment ID: ${surveyDeployment.bctw_deployment_id}` + ]); + } + + surveyDeploymentsWithBctwData.push({ + // BCTW properties + assignment_id: matchingBctwDeployments[0].assignment_id, + collar_id: matchingBctwDeployments[0].collar_id, + attachment_start_date: matchingBctwDeployments[0].attachment_start + ? dayjs(matchingBctwDeployments[0].attachment_start).format('YYYY-MM-DD') + : null, + attachment_start_time: matchingBctwDeployments[0].attachment_start + ? dayjs(matchingBctwDeployments[0].attachment_start).format('HH:mm:ss') + : null, + attachment_end_date: matchingBctwDeployments[0].attachment_end + ? dayjs(matchingBctwDeployments[0].attachment_end).format('YYYY-MM-DD') + : null, + attachment_end_time: matchingBctwDeployments[0].attachment_end + ? dayjs(matchingBctwDeployments[0].attachment_end).format('HH:mm:ss') + : null, + bctw_deployment_id: matchingBctwDeployments[0].deployment_id, + device_id: matchingBctwDeployments[0].device_id, + device_make: matchingBctwDeployments[0].device_make, + device_model: matchingBctwDeployments[0].device_model, + frequency: matchingBctwDeployments[0].frequency, + frequency_unit: matchingBctwDeployments[0].frequency_unit, + // SIMS properties + deployment_id: surveyDeployment.deployment_id, + critter_id: surveyDeployment.critter_id, + critterbase_critter_id: surveyDeployment.critterbase_critter_id, + critterbase_start_capture_id: surveyDeployment.critterbase_start_capture_id, + critterbase_end_capture_id: surveyDeployment.critterbase_end_capture_id, + critterbase_end_mortality_id: surveyDeployment.critterbase_end_mortality_id + }); + } + + return res.status(200).json(surveyDeploymentsWithBctwData); + } catch (error) { + defaultLog.error({ label: 'getDeploymentsInSurvey', message: 'error', error }); + await connection.rollback(); + + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.test.ts new file mode 100644 index 0000000000..e64d5af2b2 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.test.ts @@ -0,0 +1,182 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { deleteDeployment, getDeploymentById, updateDeployment } from '.'; +import * as db from '../../../../../../../database/db'; +import { BctwDeploymentService } from '../../../../../../../services/bctw-service/bctw-deployment-service'; +import { BctwDeviceService } from '../../../../../../../services/bctw-service/bctw-device-service'; +import { CritterbaseService, ICapture } from '../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../services/deployment-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; + +describe('getDeploymentById', () => { + afterEach(() => { + sinon.restore(); + }); + + it('Gets an existing deployment', async () => { + const mockDBConnection = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockRemoveDeployment = sinon.stub(DeploymentService.prototype, 'getDeploymentById').resolves({ + deployment_id: 3, + critter_id: 2, + critterbase_critter_id: '333', + bctw_deployment_id: '444', + critterbase_start_capture_id: '555', + critterbase_end_capture_id: null, + critterbase_end_mortality_id: null + }); + const mockBctwService = sinon.stub(BctwDeploymentService.prototype, 'getDeploymentsByIds').resolves([ + { + critter_id: '333', + assignment_id: '666', + collar_id: '777', + attachment_start: '2021-01-01', + attachment_end: '2021-01-02', + deployment_id: '444', + device_id: 888, + created_at: '2021-01-01', + created_by_user_id: '999', + updated_at: null, + updated_by_user_id: null, + valid_from: '2021-01-01', + valid_to: null, + device_make: 17, + device_model: 'model', + frequency: 1, + frequency_unit: 2 + } + ]); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '1', + surveyId: '2', + deploymentId: '3' + }; + + const requestHandler = getDeploymentById(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(mockRemoveDeployment).to.have.been.calledOnce; + expect(mockBctwService).to.have.been.calledOnce; + expect(mockRes.status).to.have.been.calledWith(200); + }); +}); + +describe('updateDeployment', () => { + afterEach(() => { + sinon.restore(); + }); + + it('updates an existing deployment', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockCapture: ICapture = { + capture_id: '111', + critter_id: '222', + capture_method_id: null, + capture_location_id: '333', + release_location_id: null, + capture_date: '2021-01-01', + capture_time: '12:00:00', + release_date: null, + release_time: null, + capture_comment: null, + release_comment: null + }; + + const mockBctwDeploymentResponse = [ + { + assignment_id: '666', + collar_id: '777', + critter_id: '333', + created_at: '2021-01-01', + created_by_user_id: '999', + updated_at: null, + updated_by_user_id: null, + valid_from: '2021-01-01', + valid_to: null, + attachment_start: '2021-01-01', + attachment_end: '2021-01-02', + deployment_id: '444' + } + ]; + + const updateDeploymentStub = sinon.stub(DeploymentService.prototype, 'updateDeployment').resolves(); + const getCaptureByIdStub = sinon.stub(CritterbaseService.prototype, 'getCaptureById').resolves(mockCapture); + const updateBctwDeploymentStub = sinon + .stub(BctwDeploymentService.prototype, 'updateDeployment') + .resolves(mockBctwDeploymentResponse); + const updateCollarStub = sinon.stub(BctwDeviceService.prototype, 'updateCollar').resolves(); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = updateDeployment(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(updateDeploymentStub).to.have.been.calledOnce; + expect(getCaptureByIdStub).to.have.been.calledOnce; + expect(updateBctwDeploymentStub).to.have.been.calledOnce; + expect(updateCollarStub).to.have.been.calledOnce; + expect(mockRes.status).to.have.been.calledWith(200); + }); + + it('catches and re-throws errors', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const mockError = new Error('a test error'); + const updateDeploymentStub = sinon.stub(DeploymentService.prototype, 'updateDeployment').rejects(mockError); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = updateDeployment(); + try { + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(actualError).to.equal(mockError); + expect(updateDeploymentStub).to.have.been.calledOnce; + } + }); +}); + +describe('deleteDeployment', () => { + afterEach(() => { + sinon.restore(); + }); + + it('deletes an existing deployment', async () => { + const mockDBConnection = getMockDBConnection({ release: sinon.stub() }); + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(mockDBConnection); + + const deleteDeploymentStub = sinon + .stub(DeploymentService.prototype, 'deleteDeployment') + .resolves({ bctw_deployment_id: '444' }); + const bctwDeleteDeploymentStub = sinon.stub(BctwDeploymentService.prototype, 'deleteDeployment'); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: '1', + surveyId: '2', + deploymentId: '3' + }; + + const requestHandler = deleteDeployment(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getDBConnectionStub).to.have.been.calledOnce; + expect(deleteDeploymentStub).to.have.been.calledOnce; + expect(bctwDeleteDeploymentStub).to.have.been.calledOnce; + expect(mockRes.status).to.have.been.calledWith(200); + }); +}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.ts new file mode 100644 index 0000000000..52de5e3260 --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index.ts @@ -0,0 +1,555 @@ +import { AxiosError } from 'axios'; +import dayjs from 'dayjs'; +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { HTTP409 } from '../../../../../../../errors/http-error'; +import { getDeploymentSchema } from '../../../../../../../openapi/schemas/deployment'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { BctwDeploymentService } from '../../../../../../../services/bctw-service/bctw-deployment-service'; +import { BctwDeviceService } from '../../../../../../../services/bctw-service/bctw-device-service'; +import { getBctwUser } from '../../../../../../../services/bctw-service/bctw-service'; +import { + CritterbaseService, + getCritterbaseUser, + ICritterbaseUser +} from '../../../../../../../services/critterbase-service'; +import { DeploymentService } from '../../../../../../../services/deployment-service'; +import { getLogger } from '../../../../../../../utils/logger'; + +const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/deployments/{deploymentId}/index'); + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + getDeploymentById() +]; + +GET.apiDoc = { + description: 'Returns information about a specific deployment.', + tags: ['deployment', 'bctw'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'deploymentId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'deploymentId', + description: 'SIMS deployment ID', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + responses: { + 200: { + description: 'Responds with information about a deployment under this survey.', + content: { + 'application/json': { + schema: { + oneOf: [getDeploymentSchema, { type: 'null' }] + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 409: { + $ref: '#/components/responses/409' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function getDeploymentById(): RequestHandler { + return async (req, res) => { + const deploymentId = Number(req.params.deploymentId); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const user: ICritterbaseUser = { + keycloak_guid: connection.systemUserGUID(), + username: connection.systemUserIdentifier() + }; + + const deploymentService = new DeploymentService(connection); + const bctwDeploymentService = new BctwDeploymentService(user); + + // Fetch deployments from the deployment service for the given surveyId + const surveyDeployment = await deploymentService.getDeploymentById(deploymentId); + + // Return early if there are no deployments + if (!surveyDeployment) { + // TODO: 400 error instead? + return res.status(200).send(); + } + + // Fetch additional deployment details from BCTW service + const bctwDeployments = await bctwDeploymentService.getDeploymentsByIds([surveyDeployment.bctw_deployment_id]); + + // For the SIMS survey deployment record, find the matching BCTW deployment record. + // We expect exactly 1 matching record, otherwise we throw an error. + // More than 1 matching active record indicates an error in the BCTW data. + const matchingBctwDeployments = bctwDeployments.filter( + (deployment) => deployment.deployment_id === surveyDeployment.bctw_deployment_id + ); + + if (matchingBctwDeployments.length > 1) { + throw new HTTP409('Multiple active deployments found for the same deployment ID', [ + 'This is an issue in the BC Telemetry Warehouse (BCTW) data. There should only be one active deployment record for a given deployment ID.', + `SIMS deployment ID: ${surveyDeployment.deployment_id}`, + `BCTW deployment ID: ${surveyDeployment.bctw_deployment_id}` + ]); + } + + if (matchingBctwDeployments.length === 0) { + throw new HTTP409('No active deployments found for deployment ID', [ + 'There should be no deployments recorded in SIMS that have no matching deployment record in BCTW.', + `SIMS Deployment ID: ${surveyDeployment.deployment_id}`, + `BCTW Deployment ID: ${surveyDeployment.bctw_deployment_id}` + ]); + } + + const surveyDeploymentWithBctwData = { + // BCTW properties + assignment_id: matchingBctwDeployments[0].assignment_id, + collar_id: matchingBctwDeployments[0].collar_id, + attachment_start_date: matchingBctwDeployments[0].attachment_start + ? dayjs(matchingBctwDeployments[0].attachment_start).format('YYYY-MM-DD') + : null, + attachment_start_time: matchingBctwDeployments[0].attachment_start + ? dayjs(matchingBctwDeployments[0].attachment_start).format('HH:mm:ss') + : null, + attachment_end_date: matchingBctwDeployments[0].attachment_end + ? dayjs(matchingBctwDeployments[0].attachment_end).format('YYYY-MM-DD') + : null, + attachment_end_time: matchingBctwDeployments[0].attachment_end + ? dayjs(matchingBctwDeployments[0].attachment_end).format('HH:mm:ss') + : null, + bctw_deployment_id: matchingBctwDeployments[0].deployment_id, + device_id: matchingBctwDeployments[0].device_id, + device_make: matchingBctwDeployments[0].device_make, + device_model: matchingBctwDeployments[0].device_model, + frequency: matchingBctwDeployments[0].frequency, + frequency_unit: matchingBctwDeployments[0].frequency_unit, + // SIMS properties + deployment_id: surveyDeployment.deployment_id, + critter_id: surveyDeployment.critter_id, + critterbase_critter_id: surveyDeployment.critterbase_critter_id, + critterbase_start_capture_id: surveyDeployment.critterbase_start_capture_id, + critterbase_end_capture_id: surveyDeployment.critterbase_end_capture_id, + critterbase_end_mortality_id: surveyDeployment.critterbase_end_mortality_id + }; + + return res.status(200).json(surveyDeploymentWithBctwData); + } catch (error) { + defaultLog.error({ label: 'getDeploymentById', message: 'error', error }); + await connection.rollback(); + + throw error; + } finally { + connection.release(); + } + }; +} + +export const PUT: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + updateDeployment() +]; + +PUT.apiDoc = { + description: 'Updates information about the start and end of a deployment.', + tags: ['deployment', 'bctw'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'deploymentId', + description: 'SIMS deployment ID', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + requestBody: { + description: 'Specifies a deployment id and the new timerange to update it with.', + content: { + 'application/json': { + schema: { + title: 'Deploy device request object', + type: 'object', + additionalProperties: false, + required: [ + 'critter_id', + 'device_id', + 'attachment_end_date', + 'attachment_end_time', + 'device_make', + 'device_model', + 'frequency', + 'frequency_unit', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id' + ], + properties: { + critter_id: { + type: 'integer', + minimum: 1 + }, + attachment_end_date: { + type: 'string', + description: 'End date of the deployment, without time.', + nullable: true + }, + attachment_end_time: { + type: 'string', + description: 'End time of the deployment.', + nullable: true + }, + device_id: { + type: 'integer', + minimum: 1 + }, + device_make: { + type: 'number', + nullable: true + }, + device_model: { + type: 'string', + nullable: true + }, + frequency: { + type: 'number' + }, + frequency_unit: { + type: 'number', + nullable: true + }, + critterbase_start_capture_id: { + type: 'string', + description: 'Critterbase capture record when the deployment started', + format: 'uuid', + nullable: true + }, + critterbase_end_capture_id: { + type: 'string', + description: 'Critterbase capture record when the deployment ended', + format: 'uuid', + nullable: true + }, + critterbase_end_mortality_id: { + type: 'string', + description: 'Critterbase mortality record when the deployment ended', + format: 'uuid', + nullable: true + } + } + } + } + } + }, + responses: { + 200: { + description: 'Deployment updated OK.' + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function updateDeployment(): RequestHandler { + return async (req, res) => { + const deploymentId = Number(req.params.deploymentId); + + const connection = getDBConnection(req.keycloak_token); + + const { + critter_id, + attachment_end_date, + attachment_end_time, + // device_id, // Do not allow the device_id to be updated + device_make, + device_model, + frequency, + frequency_unit, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id + } = req.body; + + try { + await connection.open(); + + // Update the deployment in SIMS + const deploymentService = new DeploymentService(connection); + const bctw_deployment_id = await deploymentService.updateDeployment({ + deployment_id: deploymentId, + critter_id: critter_id, + critterbase_start_capture_id, + critterbase_end_capture_id, + critterbase_end_mortality_id + }); + + // TODO: Decide whether to explicitly record attachment start date, or just reference the capture. Might remove this line. + const critterbaseService = new CritterbaseService(getCritterbaseUser(req)); + const capture = await critterbaseService.getCaptureById(critterbase_start_capture_id); + + // Create attachment end date from provided end date (if not null) and end time (if not null). + const attachmentEnd = attachment_end_date + ? attachment_end_time + ? dayjs(`${attachment_end_date} ${attachment_end_time}`).toISOString() + : dayjs(`${attachment_end_date}`).toISOString() + : null; + + // Update the deployment (collar_animal_assignment) in BCTW + const bctwDeploymentService = new BctwDeploymentService(getBctwUser(req)); + // Returns an array though we only expect one record + const bctwDeploymentRecords = await bctwDeploymentService.updateDeployment({ + deployment_id: bctw_deployment_id, + attachment_start: capture.capture_date, + attachment_end: attachmentEnd // TODO: ADD SEPARATE DATE AND TIME TO BCTW + }); + + // Update the collar details in BCTW + const bctwDeviceService = new BctwDeviceService(getBctwUser(req)); + await bctwDeviceService.updateCollar({ + collar_id: bctwDeploymentRecords[0].collar_id, + device_make: device_make, + device_model: device_model, + frequency: frequency, + frequency_unit: frequency_unit + }); + + await connection.commit(); + + return res.status(200).send(); + } catch (error) { + defaultLog.error({ label: 'updateDeployment', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} + +export const DELETE: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + deleteDeployment() +]; + +DELETE.apiDoc = { + description: 'Deletes the deployment record in SIMS, and soft deletes the record in BCTW.', + tags: ['deploymenty', 'bctw'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'deploymentId', + description: 'SIMS deployment ID', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + responses: { + 200: { + description: 'Delete deployment OK.' + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +export function deleteDeployment(): RequestHandler { + return async (req, res) => { + const deploymentId = Number(req.params.deploymentId); + const surveyId = Number(req.params.surveyId); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const user: ICritterbaseUser = { + keycloak_guid: connection.systemUserGUID(), + username: connection.systemUserIdentifier() + }; + + const deploymentService = new DeploymentService(connection); + const { bctw_deployment_id } = await deploymentService.deleteDeployment(surveyId, deploymentId); + + const bctwDeploymentService = new BctwDeploymentService(user); + await bctwDeploymentService.deleteDeployment(bctw_deployment_id); + + await connection.commit(); + return res.status(200).send(); + } catch (error) { + defaultLog.error({ label: 'deleteDeployment', message: 'error', error }); + await connection.rollback(); + + return res.status(500).json((error as AxiosError).response); + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/measurements/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/measurements/index.ts new file mode 100644 index 0000000000..c0e885ce6b --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/measurements/index.ts @@ -0,0 +1,134 @@ +import { Operation } from 'express-openapi'; +import { RequestHandler } from 'http-proxy-middleware'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { SubCountService } from '../../../../../../../services/subcount-service'; +import { getLogger } from '../../../../../../../utils/logger'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/observations/measurements'); + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], + discriminator: 'SystemRole' + } + ] + }; + }), + getSurveyObservationMeasurements() +]; + +GET.apiDoc = { + description: 'Get all measurement definitions for the survey.', + tags: ['observation'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + responses: { + 200: { + description: 'Observation measurements response', + content: { + 'application/json': { + schema: { + description: 'Qualitative and quantitative observation definitions for the survey', + type: 'object', + additionalProperties: false, + required: ['qualitative_measurements', 'quantitative_measurements'], + properties: { + qualitative_measurements: { + type: 'array', + items: {} + }, + quantitative_measurements: { + type: 'array', + items: {} + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Fetch definitions of all measured for a given survey. + * + * @export + * @return {*} {RequestHandler} + */ +export function getSurveyObservationMeasurements(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + + defaultLog.debug({ label: 'getSurveyObservationMeasurement', surveyId }); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const subcountService = new SubCountService(connection); + + const observationData = await subcountService.getMeasurementTypeDefinitionsForSurvey(surveyId); + + return res.status(200).json(observationData); + } catch (error) { + defaultLog.error({ label: 'getSurveyObservationMeasurements', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/process.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/process.test.ts index b4b7719988..a30a08ae38 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/process.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/process.test.ts @@ -48,7 +48,7 @@ describe('processFile', () => { }); it('should succeed with valid params', async () => { - const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns({ + const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns({ ...dbConnectionObj, systemUserId: () => { return 20; @@ -60,7 +60,7 @@ describe('processFile', () => { await requestHandler(mockReq, mockRes, mockNext); - expect(mockGetDBConnection.calledOnce).to.be.true; + expect(getDBConnectionStub).to.have.been.calledOnce; expect(mockRes.status).to.be.calledWith(200); expect(mockRes.json).not.to.have.been.called; }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.test.ts new file mode 100644 index 0000000000..4b2e0888af --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.test.ts @@ -0,0 +1,86 @@ +import chai, { expect } from 'chai'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getSurveyObservedSpecies } from '.'; +import * as db from '../../../../../../../database/db'; +import { HTTPError } from '../../../../../../../errors/http-error'; +import { ObservationService } from '../../../../../../../services/observation-service'; +import { PlatformService } from '../../../../../../../services/platform-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; + +chai.use(sinonChai); + +describe('getSurveyObservedSpecies', () => { + afterEach(() => { + sinon.restore(); + }); + + it('gets species observed in a survey', async () => { + const dbConnectionObj = getMockDBConnection(); + + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + const mockSurveyId = 2; + const mockProjectId = 1; + const mockTsns = [1, 2, 3]; + const mockSpecies = mockTsns.map((tsn) => ({ itis_tsn: tsn })); + const mockItisResponse = [ + { tsn: 1, commonNames: ['common name 1'], scientificName: 'scientific name 1' }, + { tsn: 2, commonNames: ['common name 2'], scientificName: 'scientific name 2' }, + { tsn: 3, commonNames: ['common name 3'], scientificName: 'scientific name 3' } + ]; + const mockFormattedItisResponse = mockItisResponse.map((species) => ({ ...species, tsn: Number(species.tsn) })); + + const getObservedSpeciesForSurveyStub = sinon + .stub(ObservationService.prototype, 'getObservedSpeciesForSurvey') + .resolves(mockSpecies); + + const getTaxonomyByTsnsStub = sinon.stub(PlatformService.prototype, 'getTaxonomyByTsns').resolves(mockItisResponse); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: String(mockProjectId), + surveyId: String(mockSurveyId) + }; + + const requestHandler = getSurveyObservedSpecies(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(getObservedSpeciesForSurveyStub).to.have.been.calledOnceWith(mockSurveyId); + expect(getTaxonomyByTsnsStub).to.have.been.calledOnceWith(mockTsns); + expect(mockRes.statusValue).to.equal(200); + expect(mockRes.jsonValue).to.eql(mockFormattedItisResponse); + }); + + it('catches and re-throws error', async () => { + const dbConnectionObj = getMockDBConnection({ release: sinon.stub() }); + + sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + + const mockSurveyId = 2; + const mockProjectId = 1; + + sinon.stub(ObservationService.prototype, 'getObservedSpeciesForSurvey').rejects(new Error('a test error')); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + mockReq.params = { + projectId: String(mockProjectId), + surveyId: String(mockSurveyId) + }; + + try { + const requestHandler = getSurveyObservedSpecies(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect.fail(); + } catch (actualError) { + expect(dbConnectionObj.release).to.have.been.called; + expect((actualError as HTTPError).message).to.equal('a test error'); + } + }); +}); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.ts new file mode 100644 index 0000000000..369be5171c --- /dev/null +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/observations/taxon/index.ts @@ -0,0 +1,140 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; +import { getDBConnection } from '../../../../../../../database/db'; +import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; +import { ObservationService } from '../../../../../../../services/observation-service'; +import { PlatformService } from '../../../../../../../services/platform-service'; +import { getLogger } from '../../../../../../../utils/logger'; + +const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/observation/taxon'); + +export const GET: Operation = [ + authorizeRequestHandler((req) => { + return { + or: [ + { + validProjectPermissions: [ + PROJECT_PERMISSION.COORDINATOR, + PROJECT_PERMISSION.COLLABORATOR, + PROJECT_PERMISSION.OBSERVER + ], + surveyId: Number(req.params.surveyId), + discriminator: 'ProjectPermission' + }, + { + validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR, SYSTEM_ROLE.SYSTEM_ADMIN], + discriminator: 'SystemRole' + } + ] + }; + }), + getSurveyObservedSpecies() +]; + +GET.apiDoc = { + description: 'Get observed species for a survey', + tags: ['observation'], + security: [ + { + Bearer: [] + } + ], + parameters: [ + { + in: 'path', + name: 'projectId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + }, + { + in: 'path', + name: 'surveyId', + schema: { + type: 'integer', + minimum: 1 + }, + required: true + } + ], + responses: { + 200: { + description: 'Survey observed species get response.', + content: { + 'application/json': { + schema: { + type: 'array', + description: 'Array of objects describing observed species in the survey', + items: { + type: 'object', + additionalProperties: false, + properties: { + tsn: { type: 'number', description: 'The TSN of the observed species' }, + commonNames: { + type: 'array', + items: { type: 'string' }, + description: 'Common names of the observed species' + }, + scientificName: { type: 'string', description: 'Scientific name of the observed species' } + } + } + } + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Fetch species that were observed in the survey + * + * @export + * @return {*} {RequestHandler} + */ +export function getSurveyObservedSpecies(): RequestHandler { + return async (req, res) => { + const surveyId = Number(req.params.surveyId); + defaultLog.debug({ label: 'getSurveyObservedSpecies', surveyId }); + + const connection = getDBConnection(req.keycloak_token); + + try { + await connection.open(); + + const observationService = new ObservationService(connection); + const platformService = new PlatformService(connection); + + const observedSpecies = await observationService.getObservedSpeciesForSurvey(surveyId); + + const species = await platformService.getTaxonomyByTsns(observedSpecies.flatMap((species) => species.itis_tsn)); + + const formattedResponse = species.map((taxon) => ({ ...taxon, tsn: taxon.tsn })); + + return res.status(200).json(formattedResponse); + } catch (error) { + defaultLog.error({ label: 'getSurveyObservedSpecies', message: 'error', error }); + await connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.test.ts index 2a42958220..d4212a07eb 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.test.ts @@ -2,12 +2,12 @@ import chai, { expect } from 'chai'; import { describe } from 'mocha'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; +import { createSurveySampleMethodRecord, getSurveySampleMethodRecords } from '.'; import * as db from '../../../../../../../../database/db'; import { HTTPError } from '../../../../../../../../errors/http-error'; +import { SampleLocationService } from '../../../../../../../../services/sample-location-service'; import { SampleMethodService } from '../../../../../../../../services/sample-method-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../../__mocks__/db'; -import * as create_survey_sample_method_record from './index'; -import * as get_survey_sample_method_record from './index'; chai.use(sinonChai); @@ -24,7 +24,7 @@ describe('getSurveySampleMethodRecords', () => { const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); try { - const requestHandler = get_survey_sample_method_record.getSurveySampleMethodRecords(); + const requestHandler = getSurveySampleMethodRecords(); await requestHandler(mockReq, mockRes, mockNext); expect.fail(); } catch (actualError) { @@ -47,7 +47,7 @@ describe('getSurveySampleMethodRecords', () => { sinon.stub(SampleMethodService.prototype, 'getSampleMethodsForSurveySampleSiteId').rejects(new Error('an error')); try { - const requestHandler = get_survey_sample_method_record.getSurveySampleMethodRecords(); + const requestHandler = getSurveySampleMethodRecords(); await requestHandler(mockReq, mockRes, mockNext); expect.fail(); @@ -83,7 +83,7 @@ describe('getSurveySampleMethodRecords', () => { sinon.stub(SampleMethodService.prototype, 'getSampleMethodsForSurveySampleSiteId').resolves([sampleMethod]); - const requestHandler = get_survey_sample_method_record.getSurveySampleMethodRecords(); + const requestHandler = getSurveySampleMethodRecords(); await requestHandler(mockReq, mockRes, mockNext); @@ -93,7 +93,7 @@ describe('getSurveySampleMethodRecords', () => { }); }); -describe('createSurveySampleSiteRecord', () => { +describe('createSurveySampleMethodRecord', () => { const dbConnectionObj = getMockDBConnection(); const sampleReq = { @@ -114,7 +114,7 @@ describe('createSurveySampleSiteRecord', () => { sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); try { - const result = create_survey_sample_method_record.createSurveySampleSiteRecord(); + const result = createSurveySampleMethodRecord(); await result( { ...sampleReq, params: { ...sampleReq.params, surveySampleSiteId: null } }, null as unknown as any, @@ -130,6 +130,23 @@ describe('createSurveySampleSiteRecord', () => { it('should work', async () => { sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); + const getSurveySampleSiteByIdStub = sinon + .stub(SampleLocationService.prototype, 'getSurveySampleSiteById') + .resolves({ + survey_sample_site_id: 1, + survey_id: 1, + name: 'name', + description: 'desc', + geometry: null, + geography: 'geography', + geojson: {}, + create_date: 'date', + create_user: 1, + update_date: 'date', + update_user: 1, + revision_count: 1 + }); + const insertSurveyParticipantStub = sinon.stub(SampleMethodService.prototype, 'insertSampleMethod').resolves(); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -155,11 +172,12 @@ describe('createSurveySampleSiteRecord', () => { sampleMethod: [sampleMethod] }; - const requestHandler = create_survey_sample_method_record.createSurveySampleSiteRecord(); + const requestHandler = createSurveySampleMethodRecord(); await requestHandler(mockReq, mockRes, mockNext); expect(mockRes.status).to.have.been.calledWith(201); + expect(getSurveySampleSiteByIdStub).to.have.been.calledOnce; expect(insertSurveyParticipantStub).to.have.been.calledOnce; }); }); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts index 2350e6d39c..fb6a28625b 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts @@ -216,7 +216,7 @@ export const POST: Operation = [ ] }; }), - createSurveySampleSiteRecord() + createSurveySampleMethodRecord() ]; POST.apiDoc = { @@ -302,7 +302,7 @@ POST.apiDoc = { } }; -export function createSurveySampleSiteRecord(): RequestHandler { +export function createSurveySampleMethodRecord(): RequestHandler { return async (req, res) => { if (!req.params.surveySampleSiteId) { throw new HTTP400('Missing required param `surveySampleSiteId`'); @@ -318,9 +318,10 @@ export function createSurveySampleSiteRecord(): RequestHandler { const connection = getDBConnection(req.keycloak_token); try { - const sampleSiteService = new SampleLocationService(connection); + const sampleLocationService = new SampleLocationService(connection); + + const sampleSite = await sampleLocationService.getSurveySampleSiteById(surveyId, surveySampleSiteId); - const sampleSite = sampleSiteService.getSurveySampleSiteById(surveyId, surveySampleSiteId); if (!sampleSite) { throw new HTTP400('The given sample site does not belong to the given survey'); } @@ -340,7 +341,7 @@ export function createSurveySampleSiteRecord(): RequestHandler { return res.status(201).send(); } catch (error) { - defaultLog.error({ label: 'insertProjectParticipants', message: 'error', error }); + defaultLog.error({ label: 'createSurveySampleMethodRecord', message: 'error', error }); await connection.rollback(); throw error; } finally { diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.test.ts index a7c91d6fa9..a01bd67b56 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.test.ts @@ -4,7 +4,7 @@ import sinon from 'sinon'; import sinonChai from 'sinon-chai'; import * as db from '../../../../../../database/db'; import { HTTPError } from '../../../../../../errors/http-error'; -import { ObservationService } from '../../../../../../services/observation-service'; +import { SampleMethodService } from '../../../../../../services/sample-method-service'; import { TechniqueService } from '../../../../../../services/technique-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../__mocks__/db'; import { deleteSurveyTechniqueRecords } from './delete'; @@ -20,8 +20,8 @@ describe('deleteSurveyTechniqueRecords', () => { const mockDBConnection = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(0); const deleteTechniqueStub = sinon @@ -45,8 +45,8 @@ describe('deleteSurveyTechniqueRecords', () => { await requestHandler(mockReq, mockRes, mockNext); expect.fail(); } catch (actualError) { - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnce; - expect(deleteTechniqueStub).to.have.been.calledOnce; + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnce; + expect(deleteTechniqueStub).to.have.been.calledThrice; expect(mockDBConnection.rollback).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.calledOnce; @@ -59,8 +59,8 @@ describe('deleteSurveyTechniqueRecords', () => { const mockDBConnection = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(10); // technique records are associated to 10 observation records const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -80,13 +80,13 @@ describe('deleteSurveyTechniqueRecords', () => { await requestHandler(mockReq, mockRes, mockNext); expect.fail(); } catch (actualError) { - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnce; + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnce; expect(mockDBConnection.rollback).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.calledOnce; expect((actualError as HTTPError).message).to.equal( - 'Cannot delete a technique that is associated with an observation' + 'Cannot delete a technique that is associated with a sampling site' ); expect((actualError as HTTPError).status).to.equal(409); } @@ -96,8 +96,8 @@ describe('deleteSurveyTechniqueRecords', () => { const mockDBConnection = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(0); const deleteTechniqueStub = sinon.stub(TechniqueService.prototype, 'deleteTechnique').resolves(); @@ -117,7 +117,7 @@ describe('deleteSurveyTechniqueRecords', () => { await requestHandler(mockReq, mockRes, mockNext); - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnce; + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnce; expect(deleteTechniqueStub).to.have.been.calledThrice; expect(mockDBConnection.commit).to.have.been.calledOnce; diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.ts index 9a21fdf7b0..f1c62cd0ef 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/delete.ts @@ -4,7 +4,7 @@ import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/rol import { getDBConnection } from '../../../../../../database/db'; import { HTTP409 } from '../../../../../../errors/http-error'; import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization'; -import { ObservationService } from '../../../../../../services/observation-service'; +import { SampleMethodService } from '../../../../../../services/sample-method-service'; import { TechniqueService } from '../../../../../../services/technique-service'; import { getLogger } from '../../../../../../utils/logger'; @@ -109,28 +109,25 @@ export function deleteSurveyTechniqueRecords(): RequestHandler { const surveyId = Number(req.params.surveyId); const methodTechniqueIds = req.body.methodTechniqueIds as number[]; - const connection = getDBConnection(req['keycloak_token']); + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const observationService = new ObservationService(connection); + const sampleMethodService = new SampleMethodService(connection); - const observationCount = await observationService.getObservationsCountByTechniqueIds( - surveyId, - methodTechniqueIds - ); + const samplingMethodsCount = await sampleMethodService.getSampleMethodsCountForTechniqueIds(methodTechniqueIds); - if (observationCount > 0) { - throw new HTTP409('Cannot delete a technique that is associated with an observation'); + if (samplingMethodsCount > 0) { + throw new HTTP409('Cannot delete a technique that is associated with a sampling site'); } const techniqueService = new TechniqueService(connection); - // TODO Update to handle all deletes in one request rather than one at a time - for (const methodTechniqueId of methodTechniqueIds) { - await techniqueService.deleteTechnique(surveyId, methodTechniqueId); - } + // TODO: Update to handle all deletes in one request rather than one at a time + await Promise.all( + methodTechniqueIds.map((methodTechniqueId) => techniqueService.deleteTechnique(surveyId, methodTechniqueId)) + ); await connection.commit(); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/index.ts index fd664d79c3..7f08d1ba13 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/index.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/index.ts @@ -2,7 +2,6 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles'; import { getDBConnection } from '../../../../../../database/db'; -import { HTTP400 } from '../../../../../../errors/http-error'; import { paginationRequestQueryParamSchema, paginationResponseSchema @@ -112,13 +111,12 @@ POST.apiDoc = { */ export function createTechniques(): RequestHandler { return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); + const surveyId = Number(req.params.surveyId); + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const surveyId = Number(req.params.surveyId); - const techniqueService = new TechniqueService(connection); await techniqueService.insertTechniquesForSurvey(surveyId, req.body.techniques); @@ -236,16 +234,12 @@ GET.apiDoc = { */ export function getTechniques(): RequestHandler { return async (req, res) => { - if (!req.params.surveyId) { - throw new HTTP400('Missing required param `surveyId`'); - } - - const connection = getDBConnection(req['keycloak_token']); + const surveyId = Number(req.params.surveyId); + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const surveyId = Number(req.params.surveyId); const paginationOptions = makePaginationOptionsFromRequest(req); const techniqueService = new TechniqueService(connection); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.test.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.test.ts index 6cd5ec809b..9a42471b43 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.test.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.test.ts @@ -6,7 +6,7 @@ import { deleteTechnique, updateTechnique } from '.'; import * as db from '../../../../../../../database/db'; import { HTTPError } from '../../../../../../../errors/http-error'; import { AttractantService } from '../../../../../../../services/attractants-service'; -import { ObservationService } from '../../../../../../../services/observation-service'; +import { SampleMethodService } from '../../../../../../../services/sample-method-service'; import { TechniqueAttributeService } from '../../../../../../../services/technique-attributes-service'; import { TechniqueService } from '../../../../../../../services/technique-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db'; @@ -30,8 +30,8 @@ describe('deleteTechnique', () => { techniqueId: '3' }; - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(0); const deleteTechniqueStub = sinon @@ -44,14 +44,14 @@ describe('deleteTechnique', () => { await requestHandler(mockReq, mockRes, mockNext); expect.fail(); } catch (actualError) { - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnceWith(2, [3]); + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnceWith([3]); expect(deleteTechniqueStub).to.have.been.calledOnceWith(2, 3); expect((actualError as HTTPError).message).to.equal('a test error'); } }); - it('throws an error if any technique records are associated to an observation record', async () => { + it('throws an error if any technique records are associated to a sampling site', async () => { const mockDBConnection = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); sinon.stub(db, 'getDBConnection').returns(mockDBConnection); @@ -63,8 +63,8 @@ describe('deleteTechnique', () => { techniqueId: '3' }; - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(10); // technique records are associated to 10 observation records const requestHandler = deleteTechnique(); @@ -73,13 +73,13 @@ describe('deleteTechnique', () => { await requestHandler(mockReq, mockRes, mockNext); expect.fail(); } catch (actualError) { - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnce; + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnce; expect(mockDBConnection.rollback).to.have.been.calledOnce; expect(mockDBConnection.release).to.have.been.calledOnce; expect((actualError as HTTPError).message).to.equal( - 'Cannot delete a technique that is associated with an observation' + 'Cannot delete a technique that is associated with a sampling site' ); expect((actualError as HTTPError).status).to.equal(409); } @@ -97,8 +97,8 @@ describe('deleteTechnique', () => { techniqueId: '3' }; - const getObservationsCountByTechniqueIdsStub = sinon - .stub(ObservationService.prototype, 'getObservationsCountByTechniqueIds') + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodService.prototype, 'getSampleMethodsCountForTechniqueIds') .resolves(0); const deleteTechniqueStub = sinon.stub(TechniqueService.prototype, 'deleteTechnique').resolves(); @@ -107,7 +107,7 @@ describe('deleteTechnique', () => { await requestHandler(mockReq, mockRes, mockNext); - expect(getObservationsCountByTechniqueIdsStub).to.have.been.calledOnceWith(2, [3]); + expect(getSampleMethodsCountForTechniqueIdsStub).to.have.been.calledOnceWith([3]); expect(deleteTechniqueStub).to.have.been.calledOnceWith(2, 3); expect(mockRes.statusValue).to.eql(200); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.ts index 11249e0e30..72454c0b40 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/technique/{techniqueId}/index.ts @@ -7,7 +7,7 @@ import { techniqueUpdateSchema, techniqueViewSchema } from '../../../../../../.. import { ITechniquePutData } from '../../../../../../../repositories/technique-repository'; import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; import { AttractantService } from '../../../../../../../services/attractants-service'; -import { ObservationService } from '../../../../../../../services/observation-service'; +import { SampleMethodService } from '../../../../../../../services/sample-method-service'; import { TechniqueAttributeService } from '../../../../../../../services/technique-attributes-service'; import { TechniqueService } from '../../../../../../../services/technique-service'; import { getLogger } from '../../../../../../../utils/logger'; @@ -103,22 +103,19 @@ DELETE.apiDoc = { */ export function deleteTechnique(): RequestHandler { return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); + const methodTechniqueId = Number(req.params.techniqueId); + const surveyId = Number(req.params.surveyId); + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const methodTechniqueId = Number(req.params.techniqueId); - const surveyId = Number(req.params.surveyId); + const sampleMethodService = new SampleMethodService(connection); - const observationService = new ObservationService(connection); + const samplingMethodsCount = await sampleMethodService.getSampleMethodsCountForTechniqueIds([methodTechniqueId]); - const observationCount = await observationService.getObservationsCountByTechniqueIds(surveyId, [ - methodTechniqueId - ]); - - if (observationCount > 0) { - throw new HTTP409('Cannot delete a technique that is associated with an observation'); + if (samplingMethodsCount > 0) { + throw new HTTP409('Cannot delete a technique that is associated with a sampling site'); } const techniqueService = new TechniqueService(connection); @@ -239,16 +236,14 @@ PUT.apiDoc = { */ export function updateTechnique(): RequestHandler { return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); + const surveyId = Number(req.params.surveyId); + const methodTechniqueId = Number(req.params.techniqueId); + const technique: ITechniquePutData = req.body.technique; + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const surveyId = Number(req.params.surveyId); - const methodTechniqueId = Number(req.params.techniqueId); - - const technique: ITechniquePutData = req.body.technique; - const { attributes, attractants, ...techniqueRow } = technique; // Update the technique record @@ -383,14 +378,13 @@ GET.apiDoc = { */ export function getTechniqueById(): RequestHandler { return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); + const surveyId = Number(req.params.surveyId); + const methodTechniqueId = Number(req.params.techniqueId); + const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const surveyId = Number(req.params.surveyId); - const methodTechniqueId = Number(req.params.techniqueId); - const techniqueService = new TechniqueService(connection); const sampleSite = await techniqueService.getTechniqueById(surveyId, methodTechniqueId); diff --git a/api/src/paths/project/{projectId}/survey/{surveyId}/view.ts b/api/src/paths/project/{projectId}/survey/{surveyId}/view.ts index 6c2cb398d7..e9c43481c7 100644 --- a/api/src/paths/project/{projectId}/survey/{surveyId}/view.ts +++ b/api/src/paths/project/{projectId}/survey/{surveyId}/view.ts @@ -20,8 +20,6 @@ import { authorizeRequestHandler } from '../../../../../request-handlers/securit import { SurveyService } from '../../../../../services/survey-service'; import { getLogger } from '../../../../../utils/logger'; -('../../../../../openapi/schemas/survey'); - const defaultLog = getLogger('paths/project/{projectId}/survey/{surveyId}/view'); export const GET: Operation = [ diff --git a/api/src/paths/standards/environment/index.test.ts b/api/src/paths/standards/environment/index.test.ts new file mode 100644 index 0000000000..2c7a3c0568 --- /dev/null +++ b/api/src/paths/standards/environment/index.test.ts @@ -0,0 +1,89 @@ +import chai, { expect } from 'chai'; +import { afterEach, describe, it } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import * as db from '../../../database/db'; +import { HTTPError } from '../../../errors/http-error'; +import { StandardsService } from '../../../services/standards-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; +import { getEnvironmentStandards } from './index'; // Adjust the import path based on your file structure + +chai.use(sinonChai); + +describe('standards/environment', () => { + describe('getEnvironmentStandards', () => { + afterEach(() => { + sinon.restore(); + }); + + it('should retrieve environment standards successfully', async () => { + const mockResponse = { + quantitative: [ + { name: 'Quantitative Standard 1', description: 'Description 1', unit: 'Unit' }, + { name: 'Quantitative Standard 2', description: 'Description 2', unit: 'Unit' } + ], + qualitative: [ + { + name: 'Qualitative Standard 1', + description: 'Description 1', + options: [ + { name: 'Option 1', description: 'Option 1 Description' }, + { name: 'Option 2', description: 'Option 2 Description' } + ] + }, + { + name: 'Qualitative Standard 2', + description: 'Description 2', + options: [ + { name: 'Option 3', description: 'Option 3 Description' }, + { name: 'Option 4', description: 'Option 4 Description' } + ] + } + ] + }; + + const mockDBConnection = getMockDBConnection(); + + sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection); + + sinon.stub(StandardsService.prototype, 'getEnvironmentStandards').resolves(mockResponse); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = getEnvironmentStandards(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.status).to.have.been.calledWith(200); + expect(mockRes.json).to.have.been.calledWith(mockResponse); + }); + + it('catches and re-throws error', async () => { + const mockDBConnection = getMockDBConnection({ + open: sinon.stub(), + commit: sinon.stub(), + rollback: sinon.stub(), + release: sinon.stub() + }); + + sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection); + + sinon + .stub(StandardsService.prototype, 'getEnvironmentStandards') + .rejects(new Error('Failed to retrieve environment standards')); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + try { + const requestHandler = getEnvironmentStandards(); + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(mockDBConnection.open).to.have.been.calledOnce; + expect(mockDBConnection.rollback).to.have.been.calledOnce; + expect(mockDBConnection.release).to.have.been.calledOnce; + expect((actualError as HTTPError).message).to.equal('Failed to retrieve environment standards'); + } + }); + }); +}); diff --git a/api/src/paths/standards/environment/index.ts b/api/src/paths/standards/environment/index.ts new file mode 100644 index 0000000000..42e2e24176 --- /dev/null +++ b/api/src/paths/standards/environment/index.ts @@ -0,0 +1,83 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { getAPIUserDBConnection } from '../../../database/db'; +import { EnvironmentStandardsSchema } from '../../../openapi/schemas/standards'; +import { StandardsService } from '../../../services/standards-service'; +import { getLogger } from '../../../utils/logger'; + +const defaultLog = getLogger('paths/projects'); + +export const GET: Operation = [getEnvironmentStandards()]; + +GET.apiDoc = { + description: 'Gets lookup values for environment variables', + tags: ['standards'], + parameters: [ + { + in: 'query', + name: 'keyword', + required: false, + schema: { + type: 'string', + nullable: true + } + } + ], + security: [], + responses: { + 200: { + description: 'Environment data standards response object.', + content: { + 'application/json': { + schema: EnvironmentStandardsSchema + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Get species data standards + * + * @returns {RequestHandler} + */ +export function getEnvironmentStandards(): RequestHandler { + return async (req, res) => { + const connection = getAPIUserDBConnection(); + + try { + await connection.open(); + + const standardsService = new StandardsService(connection); + + const keyword = (req.query.keyword as string) ?? ''; + + const response = await standardsService.getEnvironmentStandards(keyword); + + await connection.commit(); + + return res.status(200).json(response); + } catch (error) { + defaultLog.error({ label: 'getEnvironmentStandards', message: 'error', error }); + connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/standards/methods/index.test.ts b/api/src/paths/standards/methods/index.test.ts new file mode 100644 index 0000000000..3a5814a930 --- /dev/null +++ b/api/src/paths/standards/methods/index.test.ts @@ -0,0 +1,96 @@ +import chai, { expect } from 'chai'; +import { afterEach, describe, it } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getMethodStandards } from '.'; +import * as db from '../../../database/db'; +import { HTTPError } from '../../../errors/http-error'; +import { StandardsService } from '../../../services/standards-service'; +import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; + +chai.use(sinonChai); + +describe('standards/environment', () => { + describe('getMethodStandards', () => { + afterEach(() => { + sinon.restore(); + }); + + it('should retrieve environment standards successfully', async () => { + const mockResponse = [ + { + method_lookup_id: 1, + name: 'Name', + description: 'Description', + attributes: { + quantitative: [ + { name: 'Quantitative Standard 1', description: 'Description 1', unit: 'Unit' }, + { name: 'Quantitative Standard 2', description: 'Description 2', unit: 'Unit' } + ], + qualitative: [ + { + name: 'Qualitative Standard 1', + description: 'Description 1', + options: [ + { name: 'Option 1', description: 'Option 1 Description' }, + { name: 'Option 2', description: 'Option 2 Description' } + ] + }, + { + name: 'Qualitative Standard 2', + description: 'Description 2', + options: [ + { name: 'Option 3', description: 'Option 3 Description' }, + { name: 'Option 4', description: 'Option 4 Description' } + ] + } + ] + } + } + ]; + + const mockDBConnection = getMockDBConnection(); + + sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection); + + sinon.stub(StandardsService.prototype, 'getMethodStandards').resolves(mockResponse); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + const requestHandler = getMethodStandards(); + + await requestHandler(mockReq, mockRes, mockNext); + + expect(mockRes.status).to.have.been.calledWith(200); + expect(mockRes.json).to.have.been.calledWith(mockResponse); + }); + + it('catches and re-throws error', async () => { + const mockDBConnection = getMockDBConnection({ + open: sinon.stub(), + commit: sinon.stub(), + rollback: sinon.stub(), + release: sinon.stub() + }); + + sinon.stub(db, 'getAPIUserDBConnection').returns(mockDBConnection); + + sinon + .stub(StandardsService.prototype, 'getMethodStandards') + .rejects(new Error('Failed to retrieve environment standards')); + + const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); + + try { + const requestHandler = getMethodStandards(); + await requestHandler(mockReq, mockRes, mockNext); + expect.fail(); + } catch (actualError) { + expect(mockDBConnection.open).to.have.been.calledOnce; + expect(mockDBConnection.rollback).to.have.been.calledOnce; + expect(mockDBConnection.release).to.have.been.calledOnce; + expect((actualError as HTTPError).message).to.equal('Failed to retrieve environment standards'); + } + }); + }); +}); diff --git a/api/src/paths/standards/methods/index.ts b/api/src/paths/standards/methods/index.ts new file mode 100644 index 0000000000..f95e4d6bca --- /dev/null +++ b/api/src/paths/standards/methods/index.ts @@ -0,0 +1,83 @@ +import { RequestHandler } from 'express'; +import { Operation } from 'express-openapi'; +import { getAPIUserDBConnection } from '../../../database/db'; +import { MethodStandardSchema } from '../../../openapi/schemas/standards'; +import { StandardsService } from '../../../services/standards-service'; +import { getLogger } from '../../../utils/logger'; + +const defaultLog = getLogger('paths/standards/methods'); + +export const GET: Operation = [getMethodStandards()]; + +GET.apiDoc = { + description: 'Gets lookup values for method variables', + tags: ['standards'], + parameters: [ + { + in: 'query', + name: 'keyword', + required: false, + schema: { + type: 'string', + nullable: true + } + } + ], + security: [], + responses: { + 200: { + description: 'Method data standards response object.', + content: { + 'application/json': { + schema: MethodStandardSchema + } + } + }, + 400: { + $ref: '#/components/responses/400' + }, + 401: { + $ref: '#/components/responses/401' + }, + 403: { + $ref: '#/components/responses/403' + }, + 500: { + $ref: '#/components/responses/500' + }, + default: { + $ref: '#/components/responses/default' + } + } +}; + +/** + * Get species data standards + * + * @returns {RequestHandler} + */ +export function getMethodStandards(): RequestHandler { + return async (req, res) => { + const connection = getAPIUserDBConnection(); + + try { + await connection.open(); + + const standardsService = new StandardsService(connection); + + const keyword = (req.query.keyword as string) ?? ''; + + const response = await standardsService.getMethodStandards(keyword); + + await connection.commit(); + + return res.status(200).json(response); + } catch (error) { + defaultLog.error({ label: 'getMethodStandards', message: 'error', error }); + connection.rollback(); + throw error; + } finally { + connection.release(); + } + }; +} diff --git a/api/src/paths/standards/taxon/{tsn}/index.ts b/api/src/paths/standards/taxon/{tsn}/index.ts index a46bb597a1..483233ae06 100644 --- a/api/src/paths/standards/taxon/{tsn}/index.ts +++ b/api/src/paths/standards/taxon/{tsn}/index.ts @@ -1,26 +1,12 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; -import { SYSTEM_ROLE } from '../../../../constants/roles'; import { getDBConnection } from '../../../../database/db'; -import { authorizeRequestHandler } from '../../../../request-handlers/security/authorization'; import { StandardsService } from '../../../../services/standards-service'; import { getLogger } from '../../../../utils/logger'; const defaultLog = getLogger('paths/projects'); -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN, SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - getSpeciesStandards() -]; +export const GET: Operation = [getSpeciesStandards()]; GET.apiDoc = { description: 'Gets lookup values for a tsn to describe what information can be uploaded for a given species.', @@ -35,7 +21,7 @@ GET.apiDoc = { required: true } ], - security: [{ Bearer: [] }], + security: [], responses: { 200: { description: 'Species data standards response object.', @@ -199,7 +185,8 @@ GET.apiDoc = { */ export function getSpeciesStandards(): RequestHandler { return async (req, res) => { - // TODO: const connection = getAPIUserDBConnection(); + // API user DB connection does not work, possible because user does not exist in Critterbase? + // const connection = getAPIUserDBConnection(); const connection = getDBConnection(req.keycloak_token); try { @@ -216,6 +203,7 @@ export function getSpeciesStandards(): RequestHandler { return res.status(200).json(getSpeciesStandardsResponse); } catch (error) { defaultLog.error({ label: 'getSpeciesStandards', message: 'error', error }); + connection.rollback(); throw error; } finally { connection.release(); diff --git a/api/src/paths/telemetry/code.test.ts b/api/src/paths/telemetry/code.test.ts index 442a39d752..e510c3b65f 100644 --- a/api/src/paths/telemetry/code.test.ts +++ b/api/src/paths/telemetry/code.test.ts @@ -1,7 +1,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../repositories/user-repository'; -import { BctwService } from '../../services/bctw-service'; +import { BctwService } from '../../services/bctw-service/bctw-service'; import { getRequestHandlerMocks } from '../../__mocks__/db'; import { getCodeValues } from './code'; diff --git a/api/src/paths/telemetry/code.ts b/api/src/paths/telemetry/code.ts index 2386b3dc3c..a2537809a7 100644 --- a/api/src/paths/telemetry/code.ts +++ b/api/src/paths/telemetry/code.ts @@ -1,7 +1,7 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { authorizeRequestHandler } from '../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../services/bctw-service'; +import { BctwService, getBctwUser } from '../../services/bctw-service/bctw-service'; import { getLogger } from '../../utils/logger'; const defaultLog = getLogger('paths/telemetry/code'); @@ -73,10 +73,12 @@ export function getCodeValues(): RequestHandler { const user = getBctwUser(req); const bctwService = new BctwService(user); + const codeHeader = String(req.query.codeHeader); try { const result = await bctwService.getCode(codeHeader); + return res.status(200).json(result); } catch (error) { defaultLog.error({ label: 'getCodeValues', message: 'error', error }); diff --git a/api/src/paths/telemetry/deployments.test.ts b/api/src/paths/telemetry/deployments.test.ts index facb4c577c..471f6a2f23 100644 --- a/api/src/paths/telemetry/deployments.test.ts +++ b/api/src/paths/telemetry/deployments.test.ts @@ -1,12 +1,13 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../repositories/user-repository'; -import { BctwService, IAllTelemetry } from '../../services/bctw-service'; +import { BctwTelemetryService, IAllTelemetry } from '../../services/bctw-service/bctw-telemetry-service'; import { getRequestHandlerMocks } from '../../__mocks__/db'; import { getAllTelemetryByDeploymentIds } from './deployments'; const mockTelemetry: IAllTelemetry[] = [ { + id: '123-123-123', telemetry_id: null, telemetry_manual_id: '123-123-123', deployment_id: '345-345-345', @@ -16,6 +17,7 @@ const mockTelemetry: IAllTelemetry[] = [ telemetry_type: 'manual' }, { + id: '567-567-567', telemetry_id: '567-567-567', telemetry_manual_id: null, deployment_id: '345-345-345', @@ -32,7 +34,7 @@ describe('getAllTelemetryByDeploymentIds', () => { }); it('should retrieve both manual and vendor telemetry', async () => { const mockGetTelemetry = sinon - .stub(BctwService.prototype, 'getAllTelemetryByDeploymentIds') + .stub(BctwTelemetryService.prototype, 'getAllTelemetryByDeploymentIds') .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -49,7 +51,9 @@ describe('getAllTelemetryByDeploymentIds', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'getAllTelemetryByDeploymentIds').rejects(mockError); + const mockGetTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'getAllTelemetryByDeploymentIds') + .rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/deployments.ts b/api/src/paths/telemetry/deployments.ts index e4430dcdc3..035276ad86 100644 --- a/api/src/paths/telemetry/deployments.ts +++ b/api/src/paths/telemetry/deployments.ts @@ -1,12 +1,14 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; +import { AllTelemetrySchema } from '../../openapi/schemas/telemetry'; import { authorizeRequestHandler } from '../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../services/bctw-service'; +import { getBctwUser } from '../../services/bctw-service/bctw-service'; +import { BctwTelemetryService } from '../../services/bctw-service/bctw-telemetry-service'; import { getLogger } from '../../utils/logger'; -const defaultLog = getLogger('paths/telemetry/manual'); +const defaultLog = getLogger('paths/telemetry/deployments'); -export const POST: Operation = [ +export const GET: Operation = [ authorizeRequestHandler(() => { return { and: [ @@ -19,14 +21,25 @@ export const POST: Operation = [ getAllTelemetryByDeploymentIds() ]; -POST.apiDoc = { - description: 'Get list of manual and vendor telemetry by deployment ids', +GET.apiDoc = { + description: 'Get manual and vendor telemetry for a set of deployment Ids', tags: ['telemetry'], security: [ { Bearer: [] } ], + parameters: [ + { + in: 'query', + name: 'bctwDeploymentIds', + schema: { + type: 'array', + items: { type: 'string', format: 'uuid', minimum: 1 } + }, + required: true + } + ], responses: { 200: { description: 'Manual and Vendor telemetry response object', @@ -34,20 +47,7 @@ POST.apiDoc = { 'application/json': { schema: { type: 'array', - items: { - type: 'object', - additionalProperties: false, - properties: { - id: { type: 'string' }, - deployment_id: { type: 'string', format: 'uuid' }, - telemetry_manual_id: { type: 'string', nullable: true }, - telemetry_id: { type: 'number', nullable: true }, - latitude: { type: 'number' }, - longitude: { type: 'number' }, - acquisition_date: { type: 'string' }, - telemetry_type: { type: 'string' } - } - } + items: AllTelemetrySchema } } } @@ -67,34 +67,20 @@ POST.apiDoc = { default: { $ref: '#/components/responses/default' } - }, - - requestBody: { - description: 'Request body', - required: true, - content: { - 'application/json': { - schema: { - title: 'BCTW deployment ids', - type: 'array', - minItems: 1, - items: { - title: 'BCTW deployment ids', - type: 'string', - format: 'uuid' - } - } - } - } } }; export function getAllTelemetryByDeploymentIds(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + + const bctwTelemetryService = new BctwTelemetryService(user); + try { - const result = await bctwService.getAllTelemetryByDeploymentIds(req.body); + const bctwDeploymentIds = req.query.bctwDeploymentIds as string[]; + + const result = await bctwTelemetryService.getAllTelemetryByDeploymentIds(bctwDeploymentIds); + return res.status(200).json(result); } catch (error) { defaultLog.error({ label: 'getAllTelemetryByDeploymentIds', message: 'error', error }); diff --git a/api/src/paths/telemetry/device/index.test.ts b/api/src/paths/telemetry/device/index.test.ts index 9bfc486707..db121c53aa 100644 --- a/api/src/paths/telemetry/device/index.test.ts +++ b/api/src/paths/telemetry/device/index.test.ts @@ -3,7 +3,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { HTTPError } from '../../../errors/http-error'; import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService } from '../../../services/bctw-service'; +import { BctwDeviceService } from '../../../services/bctw-service/bctw-device-service'; import { getRequestHandlerMocks } from '../../../__mocks__/db'; import { POST, upsertDevice } from './index'; @@ -21,7 +21,7 @@ describe('upsertDevice', () => { }); it('upsert device details', async () => { - const mockUpsertDevice = sinon.stub(BctwService.prototype, 'updateDevice'); + const mockUpsertDevice = sinon.stub(BctwDeviceService.prototype, 'updateDevice'); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -37,7 +37,7 @@ describe('upsertDevice', () => { it('catches and re-throws errors', async () => { const mockError = new Error('a test error'); - const mockBctwService = sinon.stub(BctwService.prototype, 'updateDevice').rejects(mockError); + const mockBctwService = sinon.stub(BctwDeviceService.prototype, 'updateDevice').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -49,7 +49,7 @@ describe('upsertDevice', () => { expect.fail(); } catch (actualError) { expect((mockError as HTTPError).message).to.eql('a test error'); - expect(mockBctwService.calledOnce).to.be.true; + expect(mockBctwService).to.have.been.calledOnce; } }); }); diff --git a/api/src/paths/telemetry/device/index.ts b/api/src/paths/telemetry/device/index.ts index a166f4944b..4d26d80342 100644 --- a/api/src/paths/telemetry/device/index.ts +++ b/api/src/paths/telemetry/device/index.ts @@ -1,7 +1,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; +import { BctwDeviceService } from '../../../services/bctw-service/bctw-device-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; import { getLogger } from '../../../utils/logger'; const defaultLog = getLogger('paths/telemetry/device/{deviceId}'); @@ -94,9 +95,9 @@ export function upsertDevice(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + const bctwDeviceService = new BctwDeviceService(user); try { - const results = await bctwService.updateDevice(req.body); + const results = await bctwDeviceService.updateDevice(req.body); return res.status(200).json(results); } catch (error) { defaultLog.error({ label: 'upsertDevice', message: 'error', error }); diff --git a/api/src/paths/telemetry/device/{deviceId}.test.ts b/api/src/paths/telemetry/device/{deviceId}.test.ts deleted file mode 100644 index 6c90dff8f5..0000000000 --- a/api/src/paths/telemetry/device/{deviceId}.test.ts +++ /dev/null @@ -1,60 +0,0 @@ -import Ajv from 'ajv'; -import { expect } from 'chai'; -import sinon from 'sinon'; -import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService } from '../../../services/bctw-service'; -import { getRequestHandlerMocks } from '../../../__mocks__/db'; -import { GET, getDeviceDetails } from './{deviceId}'; - -describe('getDeviceDetails', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('openapi schema', () => { - const ajv = new Ajv(); - - it('is valid openapi v3 schema', () => { - expect(ajv.validateSchema(GET.apiDoc as unknown as object)).to.be.true; - }); - }); - - it('gets device details', async () => { - const mockGetDeviceDetails = sinon.stub(BctwService.prototype, 'getDeviceDetails').resolves([]); - const mockGetDeployments = sinon.stub(BctwService.prototype, 'getDeviceDeployments').resolves([]); - const mockGetKeyXDetails = sinon.stub(BctwService.prototype, 'getKeyXDetails').resolves([]); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.system_user = { user_identifier: 'user', user_guid: 'guid' } as SystemUser; - - const requestHandler = getDeviceDetails(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - expect(mockGetDeviceDetails).to.have.been.calledOnce; - expect(mockGetDeployments).to.have.been.calledOnce; - expect(mockGetKeyXDetails).to.have.been.calledOnce; - }); - - it('catches and re-throws errors', async () => { - const mockError = new Error('test error'); - const mockGetDeviceDetails = sinon.stub(BctwService.prototype, 'getDeviceDetails').rejects(mockError); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.system_user = { user_identifier: 'user', user_guid: 'guid' } as SystemUser; - - const requestHandler = getDeviceDetails(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (error) { - expect(error).to.equal(mockError); - expect(mockGetDeviceDetails).to.have.been.calledOnce; - expect(mockNext).not.to.have.been.called; - } - }); -}); diff --git a/api/src/paths/telemetry/device/{deviceId}.ts b/api/src/paths/telemetry/device/{deviceId}.ts deleted file mode 100644 index 7e1f4bfebe..0000000000 --- a/api/src/paths/telemetry/device/{deviceId}.ts +++ /dev/null @@ -1,83 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/telemetry/device/{deviceId}'); - -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - discriminator: 'SystemUser' - } - ] - }; - }), - getDeviceDetails() -]; - -GET.apiDoc = { - description: 'Get a list of metadata changes to a device from the exterior telemetry system.', - tags: ['telemetry'], - security: [ - { - Bearer: [] - } - ], - responses: { - 200: { - description: 'Device change history response', - content: { - 'application/json': { - schema: { - type: 'object' - } - } - } - }, - 400: { - $ref: '#/components/responses/400' - }, - 401: { - $ref: '#/components/responses/401' - }, - 403: { - $ref: '#/components/responses/403' - }, - 500: { - $ref: '#/components/responses/500' - }, - default: { - $ref: '#/components/responses/default' - } - } -}; - -export function getDeviceDetails(): RequestHandler { - return async (req, res) => { - const user = getBctwUser(req); - - const bctwService = new BctwService(user); - const deviceId = Number(req.params.deviceId); - const deviceMake = String(req.query.make); - - try { - const results = await bctwService.getDeviceDetails(deviceId, deviceMake); - const deployments = await bctwService.getDeviceDeployments(deviceId, deviceMake); - const keyXResult = await bctwService.getKeyXDetails([deviceId]); - const keyXStatus = keyXResult?.[0]?.keyx?.idcollar === deviceId; - const retObj = { - device: results?.[0], - keyXStatus: keyXStatus, - deployments: deployments - }; - return res.status(200).json(retObj); - } catch (error) { - defaultLog.error({ label: 'getDeviceDetails', message: 'error', error }); - throw error; - } - }; -} diff --git a/api/src/paths/telemetry/index.ts b/api/src/paths/telemetry/index.ts index be9e8ae91b..1f2f46cda5 100644 --- a/api/src/paths/telemetry/index.ts +++ b/api/src/paths/telemetry/index.ts @@ -2,7 +2,7 @@ import { Request, RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { SYSTEM_ROLE } from '../../constants/roles'; import { getDBConnection } from '../../database/db'; -import { ITelemetryAdvancedFilters } from '../../models/telemetry-view'; +import { IAllTelemetryAdvancedFilters } from '../../models/telemetry-view'; import { paginationRequestQueryParamSchema, paginationResponseSchema } from '../../openapi/schemas/pagination'; import { authorizeRequestHandler, userHasValidRole } from '../../request-handlers/security/authorization'; import { TelemetryService } from '../../services/telemetry-service'; @@ -99,7 +99,7 @@ GET.apiDoc = { additionalProperties: false, properties: { telemetry_id: { - type: 'number', + type: 'string', description: 'The BCTW telemetry record ID.' }, acquisition_date: { @@ -234,12 +234,12 @@ export function findTelemetry(): RequestHandler { /** * Parse the query parameters from the request into the expected format. * - * @param {Request} req - * @return {*} {ITelemetryAdvancedFilters} + * @param {Request} req + * @return {*} {IAllTelemetryAdvancedFilters} */ function parseQueryParams( - req: Request -): ITelemetryAdvancedFilters { + req: Request +): IAllTelemetryAdvancedFilters { return { keyword: req.query.keyword ?? undefined, itis_tsns: req.query.itis_tsns ?? undefined, diff --git a/api/src/paths/telemetry/manual/delete.test.ts b/api/src/paths/telemetry/manual/delete.test.ts index 0bd0c7837c..c0ce05f141 100644 --- a/api/src/paths/telemetry/manual/delete.test.ts +++ b/api/src/paths/telemetry/manual/delete.test.ts @@ -1,7 +1,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService, IManualTelemetry } from '../../../services/bctw-service'; +import { BctwTelemetryService, IManualTelemetry } from '../../../services/bctw-service/bctw-telemetry-service'; import { getRequestHandlerMocks } from '../../../__mocks__/db'; import { deleteManualTelemetry } from './delete'; @@ -19,7 +19,9 @@ describe('deleteManualTelemetry', () => { sinon.restore(); }); it('should retrieve all manual telemetry', async () => { - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'deleteManualTelemetry').resolves(mockTelemetry); + const mockGetTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'deleteManualTelemetry') + .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -35,7 +37,7 @@ describe('deleteManualTelemetry', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'deleteManualTelemetry').rejects(mockError); + const mockGetTelemetry = sinon.stub(BctwTelemetryService.prototype, 'deleteManualTelemetry').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/manual/delete.ts b/api/src/paths/telemetry/manual/delete.ts index b1f57b158e..90ed481f67 100644 --- a/api/src/paths/telemetry/manual/delete.ts +++ b/api/src/paths/telemetry/manual/delete.ts @@ -2,7 +2,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { manual_telemetry_responses } from '.'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; +import { BctwTelemetryService } from '../../../services/bctw-service/bctw-telemetry-service'; import { getLogger } from '../../../utils/logger'; const defaultLog = getLogger('paths/telemetry/manual/delete'); @@ -52,9 +53,9 @@ export function deleteManualTelemetry(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + const bctwTelemetryService = new BctwTelemetryService(user); try { - const result = await bctwService.deleteManualTelemetry(req.body); + const result = await bctwTelemetryService.deleteManualTelemetry(req.body); return res.status(200).json(result); } catch (error) { defaultLog.error({ label: 'deleteManualTelemetry', message: 'error', error }); diff --git a/api/src/paths/telemetry/manual/deployments.test.ts b/api/src/paths/telemetry/manual/deployments.test.ts index 1120703417..601da022d8 100644 --- a/api/src/paths/telemetry/manual/deployments.test.ts +++ b/api/src/paths/telemetry/manual/deployments.test.ts @@ -1,7 +1,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService, IManualTelemetry } from '../../../services/bctw-service'; +import { BctwTelemetryService, IManualTelemetry } from '../../../services/bctw-service/bctw-telemetry-service'; import { getRequestHandlerMocks } from '../../../__mocks__/db'; import { getManualTelemetryByDeploymentIds } from './deployments'; @@ -20,7 +20,7 @@ describe('getManualTelemetryByDeploymentIds', () => { }); it('should retrieve all manual telemetry', async () => { const mockGetTelemetry = sinon - .stub(BctwService.prototype, 'getManualTelemetryByDeploymentIds') + .stub(BctwTelemetryService.prototype, 'getManualTelemetryByDeploymentIds') .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -37,7 +37,9 @@ describe('getManualTelemetryByDeploymentIds', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'getManualTelemetryByDeploymentIds').rejects(mockError); + const mockGetTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'getManualTelemetryByDeploymentIds') + .rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/manual/deployments.ts b/api/src/paths/telemetry/manual/deployments.ts index 8b23fec263..83c497ba7b 100644 --- a/api/src/paths/telemetry/manual/deployments.ts +++ b/api/src/paths/telemetry/manual/deployments.ts @@ -2,7 +2,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { manual_telemetry_responses } from '.'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; +import { BctwTelemetryService } from '../../../services/bctw-service/bctw-telemetry-service'; import { getLogger } from '../../../utils/logger'; const defaultLog = getLogger('paths/telemetry/manual'); @@ -52,7 +53,9 @@ POST.apiDoc = { export function getManualTelemetryByDeploymentIds(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + + const bctwService = new BctwTelemetryService(user); + try { const result = await bctwService.getManualTelemetryByDeploymentIds(req.body); return res.status(200).json(result); diff --git a/api/src/paths/telemetry/manual/index.test.ts b/api/src/paths/telemetry/manual/index.test.ts index 47a5c92cd7..0ada27ba2b 100644 --- a/api/src/paths/telemetry/manual/index.test.ts +++ b/api/src/paths/telemetry/manual/index.test.ts @@ -3,7 +3,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { createManualTelemetry, GET, getManualTelemetry, PATCH, POST, updateManualTelemetry } from '.'; import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService, IManualTelemetry } from '../../../services/bctw-service'; +import { BctwTelemetryService, IManualTelemetry } from '../../../services/bctw-service/bctw-telemetry-service'; import { getRequestHandlerMocks } from '../../../__mocks__/db'; const mockTelemetry = [ @@ -28,7 +28,7 @@ describe('manual telemetry endpoints', () => { }); }); it('should retrieve all manual telemetry', async () => { - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'getManualTelemetry').resolves(mockTelemetry); + const mockGetTelemetry = sinon.stub(BctwTelemetryService.prototype, 'getManualTelemetry').resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -45,7 +45,7 @@ describe('manual telemetry endpoints', () => { it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'getManualTelemetry').rejects(mockError); + const mockGetTelemetry = sinon.stub(BctwTelemetryService.prototype, 'getManualTelemetry').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -70,7 +70,9 @@ describe('manual telemetry endpoints', () => { }); }); it('should bulk create manual telemetry', async () => { - const mockCreateTelemetry = sinon.stub(BctwService.prototype, 'createManualTelemetry').resolves(mockTelemetry); + const mockCreateTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'createManualTelemetry') + .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -86,7 +88,7 @@ describe('manual telemetry endpoints', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'createManualTelemetry').rejects(mockError); + const mockGetTelemetry = sinon.stub(BctwTelemetryService.prototype, 'createManualTelemetry').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -111,7 +113,9 @@ describe('manual telemetry endpoints', () => { }); }); it('should bulk update manual telemetry', async () => { - const mockCreateTelemetry = sinon.stub(BctwService.prototype, 'updateManualTelemetry').resolves(mockTelemetry); + const mockCreateTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'updateManualTelemetry') + .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -127,7 +131,7 @@ describe('manual telemetry endpoints', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'updateManualTelemetry').rejects(mockError); + const mockGetTelemetry = sinon.stub(BctwTelemetryService.prototype, 'updateManualTelemetry').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/manual/index.ts b/api/src/paths/telemetry/manual/index.ts index a2a051c4c6..9156ff8576 100644 --- a/api/src/paths/telemetry/manual/index.ts +++ b/api/src/paths/telemetry/manual/index.ts @@ -1,7 +1,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; +import { BctwTelemetryService } from '../../../services/bctw-service/bctw-telemetry-service'; import { getLogger } from '../../../utils/logger'; const defaultLog = getLogger('paths/telemetry/manual'); @@ -72,7 +73,8 @@ GET.apiDoc = { export function getManualTelemetry(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + + const bctwService = new BctwTelemetryService(user); try { const result = await bctwService.getManualTelemetry(); return res.status(200).json(result); @@ -144,7 +146,7 @@ POST.apiDoc = { export function createManualTelemetry(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + const bctwService = new BctwTelemetryService(user); try { const result = await bctwService.createManualTelemetry(req.body); return res.status(201).json(result); @@ -221,7 +223,7 @@ PATCH.apiDoc = { export function updateManualTelemetry(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + const bctwService = new BctwTelemetryService(user); try { const result = await bctwService.updateManualTelemetry(req.body); return res.status(201).json(result); diff --git a/api/src/paths/telemetry/manual/process.ts b/api/src/paths/telemetry/manual/process.ts index cad1db8208..fcf289e604 100644 --- a/api/src/paths/telemetry/manual/process.ts +++ b/api/src/paths/telemetry/manual/process.ts @@ -3,7 +3,7 @@ import { Operation } from 'express-openapi'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../constants/roles'; import { getDBConnection } from '../../../database/db'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { getBctwUser } from '../../../services/bctw-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; import { TelemetryService } from '../../../services/telemetry-service'; import { getLogger } from '../../../utils/logger'; diff --git a/api/src/paths/telemetry/vendor/deployments.test.ts b/api/src/paths/telemetry/vendor/deployments.test.ts index 709101c1f5..c1a0d360cd 100644 --- a/api/src/paths/telemetry/vendor/deployments.test.ts +++ b/api/src/paths/telemetry/vendor/deployments.test.ts @@ -1,7 +1,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../../repositories/user-repository'; -import { BctwService, IVendorTelemetry } from '../../../services/bctw-service'; +import { BctwTelemetryService, IVendorTelemetry } from '../../../services/bctw-service/bctw-telemetry-service'; import { getRequestHandlerMocks } from '../../../__mocks__/db'; import { getVendorTelemetryByDeploymentIds } from './deployments'; @@ -38,7 +38,7 @@ describe('getVendorTelemetryByDeploymentIds', () => { }); it('should retrieve all vendor telemetry by deployment ids', async () => { const mockGetTelemetry = sinon - .stub(BctwService.prototype, 'getVendorTelemetryByDeploymentIds') + .stub(BctwTelemetryService.prototype, 'getVendorTelemetryByDeploymentIds') .resolves(mockTelemetry); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -55,7 +55,9 @@ describe('getVendorTelemetryByDeploymentIds', () => { }); it('should catch error', async () => { const mockError = new Error('test error'); - const mockGetTelemetry = sinon.stub(BctwService.prototype, 'getVendorTelemetryByDeploymentIds').rejects(mockError); + const mockGetTelemetry = sinon + .stub(BctwTelemetryService.prototype, 'getVendorTelemetryByDeploymentIds') + .rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/vendor/deployments.ts b/api/src/paths/telemetry/vendor/deployments.ts index e0199ba094..de4f3e3e90 100644 --- a/api/src/paths/telemetry/vendor/deployments.ts +++ b/api/src/paths/telemetry/vendor/deployments.ts @@ -1,7 +1,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../../services/bctw-service'; +import { getBctwUser } from '../../../services/bctw-service/bctw-service'; +import { BctwTelemetryService } from '../../../services/bctw-service/bctw-telemetry-service'; import { getLogger } from '../../../utils/logger'; const defaultLog = getLogger('paths/telemetry/manual'); @@ -95,7 +96,8 @@ POST.apiDoc = { export function getVendorTelemetryByDeploymentIds(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + + const bctwService = new BctwTelemetryService(user); try { const result = await bctwService.getVendorTelemetryByDeploymentIds(req.body); return res.status(200).json(result); diff --git a/api/src/paths/telemetry/vendors.test.ts b/api/src/paths/telemetry/vendors.test.ts index ce9c5acc8e..329ea891fe 100644 --- a/api/src/paths/telemetry/vendors.test.ts +++ b/api/src/paths/telemetry/vendors.test.ts @@ -1,7 +1,7 @@ import { expect } from 'chai'; import sinon from 'sinon'; import { SystemUser } from '../../repositories/user-repository'; -import { BctwService } from '../../services/bctw-service'; +import { BctwDeviceService } from '../../services/bctw-service/bctw-device-service'; import { getRequestHandlerMocks } from '../../__mocks__/db'; import { getCollarVendors } from './vendors'; @@ -12,7 +12,7 @@ describe('getCollarVendors', () => { it('gets collar vendors', async () => { const mockVendors = ['vendor1', 'vendor2']; - const mockGetCollarVendors = sinon.stub(BctwService.prototype, 'getCollarVendors').resolves(mockVendors); + const mockGetCollarVendors = sinon.stub(BctwDeviceService.prototype, 'getCollarVendors').resolves(mockVendors); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); @@ -30,7 +30,7 @@ describe('getCollarVendors', () => { it('catches and re-throws error', async () => { const mockError = new Error('a test error'); - const mockGetCollarVendors = sinon.stub(BctwService.prototype, 'getCollarVendors').rejects(mockError); + const mockGetCollarVendors = sinon.stub(BctwDeviceService.prototype, 'getCollarVendors').rejects(mockError); const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); diff --git a/api/src/paths/telemetry/vendors.ts b/api/src/paths/telemetry/vendors.ts index b0901914ab..e9ea0e3561 100644 --- a/api/src/paths/telemetry/vendors.ts +++ b/api/src/paths/telemetry/vendors.ts @@ -1,7 +1,8 @@ import { RequestHandler } from 'express'; import { Operation } from 'express-openapi'; import { authorizeRequestHandler } from '../../request-handlers/security/authorization'; -import { BctwService, getBctwUser } from '../../services/bctw-service'; +import { BctwDeviceService } from '../../services/bctw-service/bctw-device-service'; +import { getBctwUser } from '../../services/bctw-service/bctw-service'; import { getLogger } from '../../utils/logger'; const defaultLog = getLogger('paths/telemetry/vendors'); @@ -63,9 +64,10 @@ export function getCollarVendors(): RequestHandler { return async (req, res) => { const user = getBctwUser(req); - const bctwService = new BctwService(user); + const bctwDeviceService = new BctwDeviceService(user); + try { - const result = await bctwService.getCollarVendors(); + const result = await bctwDeviceService.getCollarVendors(); return res.status(200).json(result); } catch (error) { defaultLog.error({ label: 'getCollarVendors', message: 'error', error }); diff --git a/api/src/paths/user/add.ts b/api/src/paths/user/add.ts index 13c7dfb144..add68d6994 100644 --- a/api/src/paths/user/add.ts +++ b/api/src/paths/user/add.ts @@ -148,10 +148,9 @@ export function addSystemRoleUser(): RequestHandler { const userService = new UserService(connection); - // If user already exists, do nothing and return early const user = await userService.getUserByIdentifier(userIdentifier, identitySource); - - if (user) { + if (user?.record_end_date === null) { + // User already exists and is active, do nothing and return early throw new HTTP409('Failed to add user. User with matching identifier already exists.'); } @@ -166,12 +165,16 @@ export function addSystemRoleUser(): RequestHandler { family_name ); - if (userObject) { - if (role_name) { - await userService.addUserSystemRoleByName(userObject.system_user_id, role_name); - } else { - await userService.addUserSystemRoles(userObject.system_user_id, [roleId]); - } + // Delete existin role + if (userObject.role_ids.length) { + await userService.deleteUserSystemRoles(userObject.system_user_id); + } + + // Add the new role + if (role_name) { + await userService.addUserSystemRoleByName(userObject.system_user_id, role_name); + } else { + await userService.addUserSystemRoles(userObject.system_user_id, [roleId]); } await connection.commit(); diff --git a/api/src/paths/user/self.test.ts b/api/src/paths/user/self.test.ts index 1a22331455..ee141b77d1 100644 --- a/api/src/paths/user/self.test.ts +++ b/api/src/paths/user/self.test.ts @@ -6,7 +6,7 @@ import * as db from '../../database/db'; import { HTTPError } from '../../errors/http-error'; import { UserService } from '../../services/user-service'; import { getMockDBConnection, getRequestHandlerMocks } from '../../__mocks__/db'; -import * as self from './self'; +import { getSelf } from './self'; chai.use(sinonChai); @@ -23,7 +23,7 @@ describe('getUser', () => { sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); try { - const requestHandler = self.getUser(); + const requestHandler = getSelf(); await requestHandler(mockReq, mockRes, mockNext); expect.fail(); @@ -57,7 +57,7 @@ describe('getUser', () => { agency: null }); - const requestHandler = self.getUser(); + const requestHandler = getSelf(); await requestHandler(mockReq, mockRes, mockNext); @@ -84,7 +84,7 @@ describe('getUser', () => { }); try { - const requestHandler = self.getUser(); + const requestHandler = getSelf(); await requestHandler(mockReq, mockRes, mockNext); expect.fail(); diff --git a/api/src/paths/user/self.ts b/api/src/paths/user/self.ts index 9a1333f893..58516a72a5 100644 --- a/api/src/paths/user/self.ts +++ b/api/src/paths/user/self.ts @@ -3,24 +3,12 @@ import { Operation } from 'express-openapi'; import { getDBConnection } from '../../database/db'; import { HTTP400 } from '../../errors/http-error'; import { systemUserSchema } from '../../openapi/schemas/user'; -import { authorizeRequestHandler } from '../../request-handlers/security/authorization'; import { UserService } from '../../services/user-service'; import { getLogger } from '../../utils/logger'; -const defaultLog = getLogger('paths/user/{userId}'); +const defaultLog = getLogger('paths/user/self'); -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - discriminator: 'SystemUser' - } - ] - }; - }), - getUser() -]; +export const GET: Operation = [getSelf()]; GET.apiDoc = { description: 'Get user details for the currently authenticated user.', @@ -64,29 +52,29 @@ GET.apiDoc = { * * @returns {RequestHandler} */ -export function getUser(): RequestHandler { +export function getSelf(): RequestHandler { return async (req, res) => { const connection = getDBConnection(req.keycloak_token); try { await connection.open(); - const userId = connection.systemUserId(); + const systemUserId = connection.systemUserId(); - if (!userId) { + if (!systemUserId) { throw new HTTP400('Failed to identify system user ID'); } const userService = new UserService(connection); // Fetch system user record - const userObject = await userService.getUserById(userId); + const userObject = await userService.getUserById(systemUserId); await connection.commit(); return res.status(200).json(userObject); } catch (error) { - defaultLog.error({ label: 'getUser', message: 'error', error }); + defaultLog.error({ label: 'getSelf', message: 'error', error }); await connection.rollback(); throw error; } finally { diff --git a/api/src/repositories/administrative-activity-repository.ts b/api/src/repositories/administrative-activity-repository.ts index 44f02a3a62..69a09b41b0 100644 --- a/api/src/repositories/administrative-activity-repository.ts +++ b/api/src/repositories/administrative-activity-repository.ts @@ -24,7 +24,9 @@ export const IAdministrativeActivity = z.object({ description: z.string().nullable(), data: shallowJsonSchema, notes: z.string().nullable(), - create_date: z.string() + create_date: z.string(), + updated_by: z.string().nullable(), + update_date: z.string().nullable() }); export type IAdministrativeActivity = z.infer; @@ -66,7 +68,9 @@ export class AdministrativeActivityRepository extends BaseRepository { aa.description, aa.data, aa.notes, - aa.create_date + aa.create_date, + su.display_name as updated_by, + aa.update_date FROM administrative_activity aa LEFT OUTER JOIN @@ -77,6 +81,10 @@ export class AdministrativeActivityRepository extends BaseRepository { administrative_activity_type aat ON aa.administrative_activity_type_id = aat.administrative_activity_type_id + LEFT OUTER JOIN + system_user su + ON + su.system_user_id = aa.update_user WHERE 1 = 1 `; @@ -115,7 +123,9 @@ export class AdministrativeActivityRepository extends BaseRepository { sqlStatement.append(SQL`)`); } - sqlStatement.append(`;`); + sqlStatement.append(` + ORDER BY create_date DESC; + `); const response = await this.connection.sql(sqlStatement, IAdministrativeActivity); return response.rows; diff --git a/api/src/repositories/analytics-repository.test.ts b/api/src/repositories/analytics-repository.test.ts new file mode 100644 index 0000000000..66f3decda4 --- /dev/null +++ b/api/src/repositories/analytics-repository.test.ts @@ -0,0 +1,76 @@ +import chai, { expect } from 'chai'; +import { QueryResult } from 'pg'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getMockDBConnection } from '../__mocks__/db'; +import { AnalyticsRepository } from './analytics-repository'; + +chai.use(sinonChai); + +describe('AnalyticsRepository', () => { + it('should construct', () => { + const mockDBConnection = getMockDBConnection(); + const analyticsRepository = new AnalyticsRepository(mockDBConnection); + + expect(analyticsRepository).to.be.instanceof(AnalyticsRepository); + }); + + describe('getObservationCountByGroup', () => { + it('Creates and executes sql query with empty params', async () => { + const mockRows = [ + { + row_count: 10, + individual_count: 5, + individual_percentage: 50, + quant_measurements: {}, + qual_measurements: { + critterbase_taxon_measurement_id: '1', + option_id: '2' + } + } + ]; + const mockQueryResponse = { rows: mockRows, rowCount: 1 } as unknown as QueryResult; + + const mockDBConnection = getMockDBConnection({ + knex: sinon.stub().resolves(mockQueryResponse) + }); + + const analyticsRepository = new AnalyticsRepository(mockDBConnection); + + const response = await analyticsRepository.getObservationCountByGroup([], [], [], []); + + expect(response).to.be.an('array'); + }); + + it('Creates and executes sql query with non-empty params', async () => { + const mockRows = [ + { + row_count: 10, + individual_count: 5, + individual_percentage: 50, + quant_measurements: {}, + qual_measurements: { + critterbase_taxon_measurement_id: '1', + option_id: '2' + } + } + ]; + const mockQueryResponse = { rows: mockRows, rowCount: 1 } as unknown as QueryResult; + + const mockDBConnection = getMockDBConnection({ + knex: sinon.stub().resolves(mockQueryResponse) + }); + + const analyticsRepository = new AnalyticsRepository(mockDBConnection); + + const response = await analyticsRepository.getObservationCountByGroup( + [1, 2, 3], + ['column1', 'column2'], + ['quant1', 'quant2'], + ['qual1', 'qual2'] + ); + + expect(response).to.be.an('array'); + }); + }); +}); diff --git a/api/src/repositories/analytics-repository.ts b/api/src/repositories/analytics-repository.ts new file mode 100644 index 0000000000..c9ebb232ba --- /dev/null +++ b/api/src/repositories/analytics-repository.ts @@ -0,0 +1,102 @@ +import { getKnex } from '../database/db'; +import { ObservationCountByGroupSQLResponse } from '../models/observation-analytics'; +import { BaseRepository } from './base-repository'; + +export class AnalyticsRepository extends BaseRepository { + /** + * Gets the observation count by group for given survey IDs + * + * @param {number[]} surveyIds - Array of survey IDs + * @param {string[]} groupByColumns - Columns to group by + * @param {string[]} groupByQuantitativeMeasurements - Quantitative measurements to group by + * @param {string[]} groupByQualitativeMeasurements - Qualitative measurements to group by + * @returns {Promise} - Observation count by group + * @memberof AnalyticsRepository + */ + async getObservationCountByGroup( + surveyIds: number[], + groupByColumns: string[], + groupByQuantitativeMeasurements: string[], + groupByQualitativeMeasurements: string[] + ): Promise { + const knex = getKnex(); + + const combinedColumns = [...groupByColumns, ...groupByQuantitativeMeasurements, ...groupByQualitativeMeasurements]; + + // Subquery to get the total count, used for calculating ratios + const totalCountSubquery = knex('observation_subcount as os') + .sum('os.subcount as total') + .leftJoin('survey_observation as so', 'so.survey_observation_id', 'os.survey_observation_id') + .whereIn('so.survey_id', surveyIds) + .first() + .toString(); + + // Create columns for quantitative measurements + const quantColumns = groupByQuantitativeMeasurements.map((id) => + knex.raw(`MAX(CASE WHEN quant.critterbase_taxon_measurement_id = ? THEN quant.value END) as ??`, [id, id]) + ); + + // Create columns for qualitative measurements + const qualColumns = groupByQualitativeMeasurements.map((id) => + knex.raw( + `STRING_AGG(DISTINCT CASE WHEN qual.critterbase_taxon_measurement_id = ? THEN qual.critterbase_measurement_qualitative_option_id::text END, ',') as ??`, + [id, id] + ) + ); + + const queryBuilder = knex + .with('temp_observations', (qb) => { + qb.select( + 'os.subcount', + 'os.observation_subcount_id', + 'so.survey_id', + ...groupByColumns.map((column) => knex.raw('??', [column])), + ...quantColumns, + ...qualColumns + ) + .from('observation_subcount as os') + .leftJoin('survey_observation as so', 'so.survey_observation_id', 'os.survey_observation_id') + .leftJoin( + 'observation_subcount_qualitative_measurement as qual', + 'qual.observation_subcount_id', + 'os.observation_subcount_id' + ) + .leftJoin( + 'observation_subcount_quantitative_measurement as quant', + 'quant.observation_subcount_id', + 'os.observation_subcount_id' + ) + .whereIn('so.survey_id', surveyIds) + .groupBy('os.subcount', 'os.observation_subcount_id', 'so.survey_id', ...groupByColumns); + }) + .select(knex.raw('public.gen_random_uuid() as id')) // Generate a unique ID for the row + .select(knex.raw('COUNT(subcount)::NUMERIC as row_count')) + .select(knex.raw('SUM(subcount)::NUMERIC as individual_count')) + .select(knex.raw(`ROUND(SUM(os.subcount)::NUMERIC / (${totalCountSubquery}) * 100, 2) as individual_percentage`)) + .select(groupByColumns.map((column) => knex.raw('??', [column]))) + // Measurement properties are objects of {'' : '', '' : ''} + .select( + knex.raw( + `jsonb_build_object(${groupByQuantitativeMeasurements + .map((column) => `'${column}', ??`) + .join(', ')}) as quant_measurements`, + groupByQuantitativeMeasurements + ) + ) + .select( + knex.raw( + `jsonb_build_object(${groupByQualitativeMeasurements + .map((column) => `'${column}', ??`) + .join(', ')}) as qual_measurements`, + groupByQualitativeMeasurements + ) + ) + .from('temp_observations as os') + .groupBy(combinedColumns) + .orderBy('individual_count', 'desc'); + + const response = await this.connection.knex(queryBuilder, ObservationCountByGroupSQLResponse); + + return response.rows; + } +} diff --git a/api/src/repositories/attachment-repository.ts b/api/src/repositories/attachment-repository.ts index 1baa9109de..6f797db3bd 100644 --- a/api/src/repositories/attachment-repository.ts +++ b/api/src/repositories/attachment-repository.ts @@ -1,6 +1,6 @@ import { QueryResult } from 'pg'; import SQL from 'sql-template-strings'; -import { ATTACHMENT_TYPE } from '../constants/attachments'; +import { z } from 'zod'; import { getKnex } from '../database/db'; import { ApiExecuteSQLError } from '../errors/api-error'; import { PostReportAttachmentMetadata, PutReportAttachmentMetadata } from '../models/project-survey-attachments'; @@ -70,6 +70,20 @@ export interface ISurveyReportAttachmentAuthor { revision_count: number; } +export const SurveyTelemetryCredentialAttachment = z.object({ + survey_telemetry_credential_attachment_id: z.number(), + uuid: z.string().uuid(), + file_name: z.string(), + file_type: z.string(), + file_size: z.number(), + create_date: z.string(), + update_date: z.string().nullable(), + title: z.string().nullable(), + description: z.string().nullable(), + key: z.string() +}); +export type SurveyTelemetryCredentialAttachment = z.infer; + const defaultLog = getLogger('repositories/attachment-repository'); /** @@ -461,9 +475,7 @@ export class AttachmentRepository extends BaseRepository { FROM survey_attachment WHERE - survey_id = ${surveyId} - AND - LOWER(file_type) != LOWER(${ATTACHMENT_TYPE.KEYX}); + survey_id = ${surveyId}; `; const response = await this.connection.sql(sqlStatement); @@ -644,6 +656,38 @@ export class AttachmentRepository extends BaseRepository { return response.rows; } + /** + * Get survey telemetry credential attachments. + * + * @param {number} surveyId The survey ID + * @return {Promise} Promise resolving all survey telemetry attachments + * @memberof AttachmentRepository + */ + async getSurveyTelemetryCredentialAttachments(surveyId: number): Promise { + defaultLog.debug({ label: 'getSurveyTelemetryCredentialAttachments' }); + + const sqlStatement = SQL` + SELECT + survey_telemetry_credential_attachment_id, + uuid, + file_name, + file_type, + file_size, + create_date, + update_date, + title, + description, + key + FROM + survey_telemetry_credential_attachment + WHERE + survey_id = ${surveyId}; + `; + + const response = await this.connection.sql(sqlStatement, SurveyTelemetryCredentialAttachment); + + return response.rows; + } /** * Insert new Project Attachment * @@ -1569,4 +1613,162 @@ export class AttachmentRepository extends BaseRepository { return response; } + + /** + * Update survey telemetry credential attachment record. + * + * @param {number} surveyId + * @param {string} fileName + * @param {string} fileType + * @return {*} {Promise<{ survey_telemetry_credential_attachment_id: number }>} + * @memberof AttachmentRepository + */ + async updateSurveyTelemetryCredentialAttachment( + surveyId: number, + fileName: string, + fileType: string + ): Promise<{ survey_telemetry_credential_attachment_id: number }> { + const sqlStatement = SQL` + UPDATE + survey_telemetry_credential_attachment + SET + file_name = ${fileName}, + file_type = ${fileType} + WHERE + file_name = ${fileName} + AND + survey_id = ${surveyId} + RETURNING + survey_telemetry_credential_attachment_id; + `; + + const response = await this.connection.sql( + sqlStatement, + z.object({ survey_telemetry_credential_attachment_id: z.number() }) + ); + + if (!response?.rows?.[0]) { + throw new ApiExecuteSQLError('Failed to update survey attachment data', [ + 'AttachmentRepository->updateSurveyTelemetryCredentialAttachment', + 'rows was null or undefined, expected rows != null' + ]); + } + + return response.rows[0]; + } + + /** + * Insert survey telemetry credential attachment record. + * + * @param {string} fileName + * @param {number} fileSize + * @param {string} fileType + * @param {number} surveyId + * @param {string} key + * @return {*} {Promise<{ survey_telemetry_credential_attachment_id: number }>} + * @memberof AttachmentRepository + */ + async insertSurveyTelemetryCredentialAttachment( + fileName: string, + fileSize: number, + fileType: string, + surveyId: number, + key: string + ): Promise<{ survey_telemetry_credential_attachment_id: number }> { + const sqlStatement = SQL` + INSERT INTO survey_telemetry_credential_attachment ( + survey_id, + file_name, + file_size, + file_type, + key + ) VALUES ( + ${surveyId}, + ${fileName}, + ${fileSize}, + ${fileType}, + ${key} + ) + RETURNING + survey_telemetry_credential_attachment_id; + `; + + const response = await this.connection.sql( + sqlStatement, + z.object({ survey_telemetry_credential_attachment_id: z.number() }) + ); + + if (!response?.rows?.[0]) { + throw new ApiExecuteSQLError('Failed to insert survey attachment data', [ + 'AttachmentRepository->insertSurveyTelemetryCredentialAttachment', + 'rows was null or undefined, expected rows != null' + ]); + } + + return response.rows[0]; + } + + /** + * Get Survey Telemetry Attachment By File Name + * + * @param {string} fileName + * @param {number} surveyId + * @return {*} {Promise} + * @memberof AttachmentRepository + */ + async getSurveyTelemetryCredentialAttachmentByFileName(fileName: string, surveyId: number): Promise { + const sqlStatement = SQL` + SELECT + survey_telemetry_credential_attachment_id, + uuid, + file_name, + title, + description, + update_date, + create_date, + file_size + from + survey_telemetry_credential_attachment + where + survey_id = ${surveyId} + and + file_name = ${fileName}; + `; + + const response = await this.connection.sql(sqlStatement); + + return response; + } + + /** + * Get survey telemetry credential attachment S3 key + * + * @param {number} surveyId + * @param {number} attachmentId + * @return {*} {Promise} + * @memberof AttachmentRepository + */ + async getSurveyTelemetryCredentialAttachmentS3Key(surveyId: number, attachmentId: number): Promise { + const sqlStatement = SQL` + SELECT + key + FROM + survey_telemetry_credential_attachment + WHERE + survey_telemetry_credential_attachment_id = ${attachmentId} + AND + survey_id = ${surveyId}; + `; + + const response = await this.connection.sql(sqlStatement); + + if (!response?.rows?.[0]) { + throw new ApiExecuteSQLError('Failed to get Survey Telemetry Credential Attachment S3 Key', [ + 'AttachmentRepository->getSurveyTelemetryCredentialAttachmentS3Key', + 'rows was null or undefined, expected rows != null' + ]); + } + + return response.rows[0].key; + } } diff --git a/api/src/repositories/code-repository.ts b/api/src/repositories/code-repository.ts index 27e5decc98..2ededfc12f 100644 --- a/api/src/repositories/code-repository.ts +++ b/api/src/repositories/code-repository.ts @@ -36,7 +36,6 @@ export const IAllCodeSets = z.object({ project_roles: CodeSet(), administrative_activity_status_type: CodeSet(), intended_outcomes: CodeSet(IntendedOutcomeCode.shape), - vantage_codes: CodeSet(), survey_jobs: CodeSet(), site_selection_strategies: CodeSet(), sample_methods: CodeSet(SampleMethodsCode.shape), @@ -172,26 +171,6 @@ export class CodeRepository extends BaseRepository { return response.rows; } - /** - * Fetch vantage codes. - * - * @return {*} - * @memberof CodeRepository - */ - async getVantageCodes() { - const sqlStatement = SQL` - SELECT - vantage_id as id, - name - FROM vantage - WHERE record_end_date is null; - `; - - const response = await this.connection.sql(sqlStatement, ICode); - - return response.rows; - } - /** * Fetch intended outcomes codes. * diff --git a/api/src/repositories/deployment-repository.ts b/api/src/repositories/deployment-repository.ts new file mode 100644 index 0000000000..af383837dd --- /dev/null +++ b/api/src/repositories/deployment-repository.ts @@ -0,0 +1,177 @@ +import { getKnex } from '../database/db'; +import { ICreateSurveyDeployment, IUpdateSurveyDeployment, SurveyDeployment } from '../models/survey-deployment'; +import { getLogger } from '../utils/logger'; +import { BaseRepository } from './base-repository'; + +const defaultLog = getLogger('repositories/deployment'); + +/** + * Repository layer for survey deployments + * + * @export + * @class DeploymentRepository + * @extends {BaseRepository} + */ +export class DeploymentRepository extends BaseRepository { + /** + * Returns deployments in a survey + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof DeploymentRepository + */ + async getDeploymentsForSurveyId(surveyId: number): Promise { + defaultLog.debug({ label: 'getDeploymentsForSurveyId', surveyId }); + + const queryBuilder = getKnex() + .select( + 'deployment_id', + 'd.critter_id as critter_id', + 'c.critterbase_critter_id', + 'bctw_deployment_id', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id' + ) + .from('deployment as d') + .leftJoin('critter as c', 'c.critter_id', 'd.critter_id') + .where('c.survey_id', surveyId); + + const response = await this.connection.knex(queryBuilder, SurveyDeployment); + + return response.rows; + } + + /** + * Returns a specific deployment + * + * @param {number} deploymentId + * @return {*} {Promise} + * @memberof DeploymentRepository + */ + async getDeploymentById(deploymentId: number): Promise { + defaultLog.debug({ label: 'getDeploymentById', deploymentId }); + + const queryBuilder = getKnex() + .select( + 'deployment_id', + 'd.critter_id as critter_id', + 'c.critterbase_critter_id', + 'bctw_deployment_id', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id' + ) + .from('deployment as d') + .leftJoin('critter as c', 'c.critter_id', 'd.critter_id') + .where('d.deployment_id', deploymentId); + + const response = await this.connection.knex(queryBuilder, SurveyDeployment); + + return response.rows[0]; + } + + /** + * Returns a specific deployment for a given critter Id + * + * @param {number} surveyId + * @param {number} critterId + * @return {*} {Promise} + * @memberof DeploymentRepository + */ + async getDeploymentForCritterId(surveyId: number, critterId: number): Promise { + defaultLog.debug({ label: 'getDeploymentById', critterId }); + + const queryBuilder = getKnex() + .select( + 'deployment_id', + 'd.critter_id as critter_id', + 'c.critterbase_critter_id', + 'bctw_deployment_id', + 'critterbase_start_capture_id', + 'critterbase_end_capture_id', + 'critterbase_end_mortality_id' + ) + .from('deployment as d') + .leftJoin('critter as c', 'c.critter_id', 'd.critter_id') + .where('d.critter_id', critterId) + .andWhere('c.survey_id', surveyId); + + const response = await this.connection.knex(queryBuilder, SurveyDeployment); + + return response.rows[0]; + } + + /** + * Insert a new deployment record. + * + * @param {ICreateSurveyDeployment} deployment + * @return {*} {Promise} + * @memberof DeploymentRepository + */ + async insertDeployment(deployment: ICreateSurveyDeployment): Promise { + defaultLog.debug({ label: 'insertDeployment', bctw_deployment_id: deployment.bctw_deployment_id }); + + const queryBuilder = getKnex().table('deployment').insert({ + critter_id: deployment.critter_id, + bctw_deployment_id: deployment.bctw_deployment_id, + critterbase_start_capture_id: deployment.critterbase_start_capture_id, + critterbase_end_capture_id: deployment.critterbase_end_capture_id, + critterbase_end_mortality_id: deployment.critterbase_end_mortality_id + }); + + await this.connection.knex(queryBuilder); + } + + /** + * Update an existing deployment record. + * + * @param {IUpdateSurveyDeployment} deployment + * @return {*} {Promise} + * @memberof DeploymentRepository + */ + async updateDeployment(deployment: IUpdateSurveyDeployment): Promise { + defaultLog.debug({ label: 'updateDeployment', deployment_id: deployment.deployment_id }); + + const queryBuilder = getKnex() + .table('deployment') + .where('deployment_id', deployment.deployment_id) + .update({ + critter_id: deployment.critter_id, + critterbase_start_capture_id: deployment.critterbase_start_capture_id, + critterbase_end_capture_id: deployment.critterbase_end_capture_id, + critterbase_end_mortality_id: deployment.critterbase_end_mortality_id + }) + .returning('bctw_deployment_id'); + + const response = await this.connection.knex(queryBuilder); + + return response.rows[0].bctw_deployment_id; + } + + /** + * Deletes a deployment row. + * + * @param {number} surveyId + * @param {number} deploymentId + * @return {*} + * @memberof DeploymentRepository + */ + async deleteDeployment(surveyId: number, deploymentId: number): Promise<{ bctw_deployment_id: string }> { + defaultLog.debug({ label: 'deleteDeployment', deploymentId }); + + const queryBuilder = getKnex() + .table('deployment') + .join('critter', 'deployment.critter_id', 'critter.critter_id') + .where({ + 'deployment.deployment_id': deploymentId, + 'critter.survey_id': surveyId + }) + .delete() + .returning('bctw_deployment_id'); + + const response = await this.connection.knex(queryBuilder); + + return response.rows[0]; + } +} diff --git a/api/src/repositories/observation-repository/observation-repository.test.ts b/api/src/repositories/observation-repository/observation-repository.test.ts index 4b3f953c5b..f4b3122b28 100644 --- a/api/src/repositories/observation-repository/observation-repository.test.ts +++ b/api/src/repositories/observation-repository/observation-repository.test.ts @@ -224,6 +224,22 @@ describe('ObservationRepository', () => { }); }); + describe('getObservedSpeciesForSurvey', () => { + it('gets observed species for a given survey', async () => { + const mockQueryResponse = { rows: [{ itis_tsn: 5 }], rowCount: 1 } as unknown as QueryResult; + + const mockDBConnection = getMockDBConnection({ + knex: sinon.stub().resolves(mockQueryResponse) + }); + + const repo = new ObservationRepository(mockDBConnection); + + const response = await repo.getObservedSpeciesForSurvey(1); + + expect(response).to.eql([{ itis_tsn: 5 }]); + }); + }); + describe('getObservationsCountBySampleSiteIds', () => { it('gets the observation count by sample site ids', async () => { const mockQueryResponse = { rows: [{ count: 50 }], rowCount: 1 } as unknown as QueryResult; diff --git a/api/src/repositories/observation-repository/observation-repository.ts b/api/src/repositories/observation-repository/observation-repository.ts index 80a0db0611..2402f68838 100644 --- a/api/src/repositories/observation-repository/observation-repository.ts +++ b/api/src/repositories/observation-repository/observation-repository.ts @@ -45,6 +45,12 @@ export const ObservationRecord = z.object({ export type ObservationRecord = z.infer; +export const ObservationSpecies = z.object({ + itis_tsn: z.number() +}); + +export type ObservationSpecies = z.infer; + const ObservationSamplingData = z.object({ survey_sample_site_name: z.string().nullable(), survey_sample_method_name: z.string().nullable(), @@ -416,6 +422,25 @@ export class ObservationRepository extends BaseRepository { return response.rows; } + /** + * Retrieves species observed in a given survey + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof ObservationRepository + */ + async getObservedSpeciesForSurvey(surveyId: number): Promise { + const knex = getKnex(); + const allRowsQuery = knex + .queryBuilder() + .distinct('itis_tsn') + .from('survey_observation') + .where('survey_id', surveyId); + + const response = await this.connection.knex(allRowsQuery, ObservationSpecies); + return response.rows; + } + /** * Retrieves the count of survey observations for the given survey * diff --git a/api/src/repositories/observation-repository/utils.test.ts b/api/src/repositories/observation-repository/utils.test.ts new file mode 100644 index 0000000000..8e09053fc6 --- /dev/null +++ b/api/src/repositories/observation-repository/utils.test.ts @@ -0,0 +1,193 @@ +import chai, { expect } from 'chai'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getKnex } from '../../database/db'; +import { getSurveyObservationsBaseQuery, makeFindObservationsQuery } from './utils'; + +chai.use(sinonChai); + +describe('Utils', () => { + afterEach(() => { + sinon.restore(); + }); + + describe('makeFindObservationsQuery', () => { + it('should return a knex query builder when no optional fields provided', async () => { + const isUserAdmin = false; + const systemUserId = null; + const filterFields = {}; + + const queryBuilder = makeFindObservationsQuery(isUserAdmin, systemUserId, filterFields); + + const normalize = (str: string) => { + // Remove all redundant whitespace and redeuce to one line, to make string comparison easier + return str.replace(/\s+/g, ' ').trim().replace('/\n/g', ' ').trim(); + }; + + expect(normalize(queryBuilder.toSQL().toNative().sql)).to.equal( + normalize(`with "w_survey_sample_site" as (select "survey_sample_site_id", "name" as "survey_sample_site_name" from "survey_sample_site" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null))), "w_survey_sample_method" as (select "survey_sample_method"."survey_sample_site_id", "survey_sample_method"."survey_sample_method_id", "method_technique"."name" as "survey_sample_method_name" from "survey_sample_method" inner join "method_technique" on "survey_sample_method"."method_technique_id" = "method_technique"."method_technique_id" inner join "w_survey_sample_site" on "survey_sample_method"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id"), "w_survey_sample_period" as (select "w_survey_sample_method"."survey_sample_site_id", "survey_sample_period"."survey_sample_method_id", "survey_sample_period"."survey_sample_period_id", (survey_sample_period.start_date::date + COALESCE(survey_sample_period.start_time, '00:00:00')::time)::timestamp as survey_sample_period_start_datetime from "survey_sample_period" inner join "w_survey_sample_method" on "survey_sample_period"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id"), "w_qualitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'critterbase_measurement_qualitative_option_id', critterbase_measurement_qualitative_option_id + )) as qualitative_measurements + from "observation_subcount_qualitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null)))) group by "observation_subcount_id"), "w_quantitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'value', value + )) as quantitative_measurements + from "observation_subcount_quantitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null)))) group by "observation_subcount_id"), "w_qualitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_qualitative_environment_id', observation_subcount_qualitative_environment_id, + 'environment_qualitative_id', environment_qualitative_id, + 'environment_qualitative_option_id', environment_qualitative_option_id + )) as qualitative_environments + from "observation_subcount_qualitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null)))) group by "observation_subcount_id"), "w_quantitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_quantitative_environment_id', observation_subcount_quantitative_environment_id, + 'environment_quantitative_id', environment_quantitative_id, + 'value', value + )) as quantitative_environments + from "observation_subcount_quantitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null)))) group by "observation_subcount_id"), "w_subcounts" as (select "survey_observation_id", + json_agg(json_build_object( + 'observation_subcount_id', observation_subcount.observation_subcount_id, + 'subcount', subcount, + 'qualitative_measurements', COALESCE(w_qualitative_measurements.qualitative_measurements, '[]'::json), + 'quantitative_measurements', COALESCE(w_quantitative_measurements.quantitative_measurements, '[]'::json), + 'qualitative_environments', COALESCE(w_qualitative_environments.qualitative_environments, '[]'::json), + 'quantitative_environments', COALESCE(w_quantitative_environments.quantitative_environments, '[]'::json) + )) as subcounts + from "observation_subcount" left join "w_qualitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_qualitative_measurements"."observation_subcount_id" left join "w_quantitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_quantitative_measurements"."observation_subcount_id" left join "w_qualitative_environments" on "observation_subcount"."observation_subcount_id" = "w_qualitative_environments"."observation_subcount_id" left join "w_quantitative_environments" on "observation_subcount"."observation_subcount_id" = "w_quantitative_environments"."observation_subcount_id" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null))) group by "survey_observation_id") select "survey_observation"."survey_observation_id", "survey_observation"."survey_id", "survey_observation"."itis_tsn", "survey_observation"."itis_scientific_name", "survey_observation"."survey_sample_site_id", "survey_observation"."survey_sample_method_id", "survey_observation"."survey_sample_period_id", "survey_observation"."latitude", "survey_observation"."longitude", "survey_observation"."count", "survey_observation"."observation_date", "survey_observation"."observation_time", "w_survey_sample_site"."survey_sample_site_name", "w_survey_sample_method"."survey_sample_method_name", "w_survey_sample_period"."survey_sample_period_start_datetime", COALESCE(w_subcounts.subcounts, '[]'::json) as subcounts from "survey_observation" left join "w_survey_sample_site" on "survey_observation"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id" left join "w_survey_sample_method" on "survey_observation"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id" left join "w_survey_sample_period" on "survey_observation"."survey_sample_period_id" = "w_survey_sample_period"."survey_sample_period_id" inner join "w_subcounts" on "w_subcounts"."survey_observation_id" = "survey_observation"."survey_observation_id" where "survey_observation"."survey_id" in (select "survey_id" from "survey" where "survey"."project_id" in (select "project"."project_id" from "project" left join "project_participation" on "project_participation"."project_id" = "project"."project_id" where "project_participation"."system_user_id" is null))`) + ); + expect(queryBuilder.toSQL().toNative().bindings).to.eql([]); + }); + + it('should return a knex query builder when all optional fields provided', async () => { + const isUserAdmin = true; + const systemUserId = 11; + const filterFields = { + keyword: 'caribou', + itis_tsns: [123456], + itis_tsn: 123456, + start_date: '2021-01-01', + end_date: '2024-01-01', + start_time: '00:00:00', + end_time: '23:59:59', + min_count: 0, + system_user_id: 22 + }; + + const queryBuilder = makeFindObservationsQuery(isUserAdmin, systemUserId, filterFields); + + const normalize = (str: string) => { + // Remove all redundant whitespace and redeuce to one line, to make string comparison easier + return str.replace(/\s+/g, ' ').trim().replace('/\n/g', ' ').trim(); + }; + + expect(normalize(queryBuilder.toSQL().toNative().sql)).to.equal( + normalize(`with "w_survey_sample_site" as (select "survey_sample_site_id", "name" as "survey_sample_site_name" from "survey_sample_site" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $1))), "w_survey_sample_method" as (select "survey_sample_method"."survey_sample_site_id", "survey_sample_method"."survey_sample_method_id", "method_technique"."name" as "survey_sample_method_name" from "survey_sample_method" inner join "method_technique" on "survey_sample_method"."method_technique_id" = "method_technique"."method_technique_id" inner join "w_survey_sample_site" on "survey_sample_method"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id"), "w_survey_sample_period" as (select "w_survey_sample_method"."survey_sample_site_id", "survey_sample_period"."survey_sample_method_id", "survey_sample_period"."survey_sample_period_id", (survey_sample_period.start_date::date + COALESCE(survey_sample_period.start_time, '00:00:00')::time)::timestamp as survey_sample_period_start_datetime from "survey_sample_period" inner join "w_survey_sample_method" on "survey_sample_period"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id"), "w_qualitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'critterbase_measurement_qualitative_option_id', critterbase_measurement_qualitative_option_id + )) as qualitative_measurements + from "observation_subcount_qualitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $2)))) group by "observation_subcount_id"), "w_quantitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'value', value + )) as quantitative_measurements + from "observation_subcount_quantitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $3)))) group by "observation_subcount_id"), "w_qualitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_qualitative_environment_id', observation_subcount_qualitative_environment_id, + 'environment_qualitative_id', environment_qualitative_id, + 'environment_qualitative_option_id', environment_qualitative_option_id + )) as qualitative_environments + from "observation_subcount_qualitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $4)))) group by "observation_subcount_id"), "w_quantitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_quantitative_environment_id', observation_subcount_quantitative_environment_id, + 'environment_quantitative_id', environment_quantitative_id, + 'value', value + )) as quantitative_environments + from "observation_subcount_quantitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $5)))) group by "observation_subcount_id"), "w_subcounts" as (select "survey_observation_id", + json_agg(json_build_object( + 'observation_subcount_id', observation_subcount.observation_subcount_id, + 'subcount', subcount, + 'qualitative_measurements', COALESCE(w_qualitative_measurements.qualitative_measurements, '[]'::json), + 'quantitative_measurements', COALESCE(w_quantitative_measurements.quantitative_measurements, '[]'::json), + 'qualitative_environments', COALESCE(w_qualitative_environments.qualitative_environments, '[]'::json), + 'quantitative_environments', COALESCE(w_quantitative_environments.quantitative_environments, '[]'::json) + )) as subcounts + from "observation_subcount" left join "w_qualitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_qualitative_measurements"."observation_subcount_id" left join "w_quantitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_quantitative_measurements"."observation_subcount_id" left join "w_qualitative_environments" on "observation_subcount"."observation_subcount_id" = "w_qualitative_environments"."observation_subcount_id" left join "w_quantitative_environments" on "observation_subcount"."observation_subcount_id" = "w_quantitative_environments"."observation_subcount_id" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $6))) group by "survey_observation_id") select "survey_observation"."survey_observation_id", "survey_observation"."survey_id", "survey_observation"."itis_tsn", "survey_observation"."itis_scientific_name", "survey_observation"."survey_sample_site_id", "survey_observation"."survey_sample_method_id", "survey_observation"."survey_sample_period_id", "survey_observation"."latitude", "survey_observation"."longitude", "survey_observation"."count", "survey_observation"."observation_date", "survey_observation"."observation_time", "w_survey_sample_site"."survey_sample_site_name", "w_survey_sample_method"."survey_sample_method_name", "w_survey_sample_period"."survey_sample_period_start_datetime", COALESCE(w_subcounts.subcounts, '[]'::json) as subcounts from "survey_observation" left join "w_survey_sample_site" on "survey_observation"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id" left join "w_survey_sample_method" on "survey_observation"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id" left join "w_survey_sample_period" on "survey_observation"."survey_sample_period_id" = "w_survey_sample_period"."survey_sample_period_id" inner join "w_subcounts" on "w_subcounts"."survey_observation_id" = "survey_observation"."survey_observation_id" where "survey_observation"."survey_id" in (select "survey_id" from "survey" where "p"."project_id" in (select "project_id" from "project_participation" where "system_user_id" = $7)) and "observation_date" >= $8 and "observation_date" <= $9 and ("itis_scientific_name" ilike $10) and "time" >= $11 and "time" <= $12 and "itis_tsn" in ($13)`) + ); + expect(queryBuilder.toSQL().toNative().bindings).to.eql([ + 22, + 22, + 22, + 22, + 22, + 22, + 22, + '2021-01-01', + '2024-01-01', + '%caribou%', + '00:00:00', + '23:59:59', + 123456 + ]); + }); + }); + + describe('getSurveyObservationsBaseQuery', () => { + it('should return a knex query builder', async () => { + const surveyId = 1; + + const knex = getKnex(); + const getSurveyIdsQuery = knex + .select('survey_id') + .from('survey') + .where('survey_id', surveyId); + + const queryBuilder = getSurveyObservationsBaseQuery(knex, getSurveyIdsQuery); + + const normalize = (str: string) => { + // Remove all whitespace and trim, to make string comparison easier + return str.replace(/\s+/g, ' ').trim(); + }; + + expect(normalize(queryBuilder.toSQL().toNative().sql)).to.equal( + normalize(`with "w_survey_sample_site" as (select "survey_sample_site_id", "name" as "survey_sample_site_name" from "survey_sample_site" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $1)), "w_survey_sample_method" as (select "survey_sample_method"."survey_sample_site_id", "survey_sample_method"."survey_sample_method_id", "method_technique"."name" as "survey_sample_method_name" from "survey_sample_method" inner join "method_technique" on "survey_sample_method"."method_technique_id" = "method_technique"."method_technique_id" inner join "w_survey_sample_site" on "survey_sample_method"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id"), "w_survey_sample_period" as (select "w_survey_sample_method"."survey_sample_site_id", "survey_sample_period"."survey_sample_method_id", "survey_sample_period"."survey_sample_period_id", (survey_sample_period.start_date::date + COALESCE(survey_sample_period.start_time, '00:00:00')::time)::timestamp as survey_sample_period_start_datetime from "survey_sample_period" inner join "w_survey_sample_method" on "survey_sample_period"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id"), "w_qualitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'critterbase_measurement_qualitative_option_id', critterbase_measurement_qualitative_option_id + )) as qualitative_measurements + from "observation_subcount_qualitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $2))) group by "observation_subcount_id"), "w_quantitative_measurements" as (select "observation_subcount_id", + json_agg(json_build_object( + 'critterbase_taxon_measurement_id', critterbase_taxon_measurement_id, + 'value', value + )) as quantitative_measurements + from "observation_subcount_quantitative_measurement" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $3))) group by "observation_subcount_id"), "w_qualitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_qualitative_environment_id', observation_subcount_qualitative_environment_id, + 'environment_qualitative_id', environment_qualitative_id, + 'environment_qualitative_option_id', environment_qualitative_option_id + )) as qualitative_environments + from "observation_subcount_qualitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $4))) group by "observation_subcount_id"), "w_quantitative_environments" as (select "observation_subcount_id", + json_agg(json_build_object( + 'observation_subcount_quantitative_environment_id', observation_subcount_quantitative_environment_id, + 'environment_quantitative_id', environment_quantitative_id, + 'value', value + )) as quantitative_environments + from "observation_subcount_quantitative_environment" where "observation_subcount_id" in (select "observation_subcount_id" from "observation_subcount" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $5))) group by "observation_subcount_id"), "w_subcounts" as (select "survey_observation_id", + json_agg(json_build_object( + 'observation_subcount_id', observation_subcount.observation_subcount_id, + 'subcount', subcount, + 'qualitative_measurements', COALESCE(w_qualitative_measurements.qualitative_measurements, '[]'::json), + 'quantitative_measurements', COALESCE(w_quantitative_measurements.quantitative_measurements, '[]'::json), + 'qualitative_environments', COALESCE(w_qualitative_environments.qualitative_environments, '[]'::json), + 'quantitative_environments', COALESCE(w_quantitative_environments.quantitative_environments, '[]'::json) + )) as subcounts + from "observation_subcount" left join "w_qualitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_qualitative_measurements"."observation_subcount_id" left join "w_quantitative_measurements" on "observation_subcount"."observation_subcount_id" = "w_quantitative_measurements"."observation_subcount_id" left join "w_qualitative_environments" on "observation_subcount"."observation_subcount_id" = "w_qualitative_environments"."observation_subcount_id" left join "w_quantitative_environments" on "observation_subcount"."observation_subcount_id" = "w_quantitative_environments"."observation_subcount_id" where "survey_observation_id" in (select "survey_observation_id" from "survey_observation" where "survey_id" in (select "survey_id" from "survey" where "survey_id" = $6)) group by "survey_observation_id") select "survey_observation"."survey_observation_id", "survey_observation"."survey_id", "survey_observation"."itis_tsn", "survey_observation"."itis_scientific_name", "survey_observation"."survey_sample_site_id", "survey_observation"."survey_sample_method_id", "survey_observation"."survey_sample_period_id", "survey_observation"."latitude", "survey_observation"."longitude", "survey_observation"."count", "survey_observation"."observation_date", "survey_observation"."observation_time", "w_survey_sample_site"."survey_sample_site_name", "w_survey_sample_method"."survey_sample_method_name", "w_survey_sample_period"."survey_sample_period_start_datetime", COALESCE(w_subcounts.subcounts, '[]'::json) as subcounts from "survey_observation" left join "w_survey_sample_site" on "survey_observation"."survey_sample_site_id" = "w_survey_sample_site"."survey_sample_site_id" left join "w_survey_sample_method" on "survey_observation"."survey_sample_method_id" = "w_survey_sample_method"."survey_sample_method_id" left join "w_survey_sample_period" on "survey_observation"."survey_sample_period_id" = "w_survey_sample_period"."survey_sample_period_id" inner join "w_subcounts" on "w_subcounts"."survey_observation_id" = "survey_observation"."survey_observation_id" where "survey_observation"."survey_id" in (select "survey_id" from "survey" where "survey_id" = $7)`) + ); + expect(queryBuilder.toSQL().toNative().bindings).to.eql([1, 1, 1, 1, 1, 1, 1]); + }); + }); +}); diff --git a/api/src/repositories/project-repository.ts b/api/src/repositories/project-repository.ts index ab587d3b43..5e1ae63074 100644 --- a/api/src/repositories/project-repository.ts +++ b/api/src/repositories/project-repository.ts @@ -48,8 +48,16 @@ export class ProjectRepository extends BaseRepository { knex.raw(`MIN(s.start_date) as start_date`), knex.raw('MAX(s.end_date) as end_date'), knex.raw(`COALESCE(array_remove(array_agg(DISTINCT rl.region_name), null), '{}') as regions`), - knex.raw('array_remove(array_agg(distinct sp.itis_tsn), null) as focal_species'), - knex.raw('array_remove(array_agg(distinct st.type_id), null) as types') + knex.raw('array_remove(array_agg(DISTINCT sp.itis_tsn), null) as focal_species'), + knex.raw('array_remove(array_agg(DISTINCT st.type_id), null) as types'), + knex.raw(` + array_agg( + DISTINCT jsonb_build_object( + 'system_user_id', su.system_user_id, + 'display_name', su.display_name + ) + ) as members + `) ]) .from('project as p') .leftJoin('survey as s', 's.project_id', 'p.project_id') @@ -58,7 +66,8 @@ export class ProjectRepository extends BaseRepository { .leftJoin('survey_region as sr', 'sr.survey_id', 's.survey_id') .leftJoin('region_lookup as rl', 'sr.region_id', 'rl.region_id') .leftJoin('project_participation as ppa', 'p.project_id', 'ppa.project_id') - .groupBy(['p.project_id', 'p.name', 'p.objectives']); + .leftJoin('system_user as su', 'ppa.system_user_id', 'su.system_user_id') + .groupBy(['p.project_id', 'p.name']); // Ensure that users can only see projects that they are participating in, unless they are an administrator. if (!isUserAdmin) { diff --git a/api/src/repositories/sample-method-repository.test.ts b/api/src/repositories/sample-method-repository.test.ts index d95ead8b13..59bade8618 100644 --- a/api/src/repositories/sample-method-repository.test.ts +++ b/api/src/repositories/sample-method-repository.test.ts @@ -44,6 +44,22 @@ describe('SampleMethodRepository', () => { }); }); + describe('getSampleMethodsCountForTechniqueId', () => { + it('should return a non-zero count', async () => { + const count = 2; + const mockRows: any[] = [{ count }]; + const mockResponse = { rows: mockRows, rowCount: 1 } as any as Promise>; + const dbConnectionObj = getMockDBConnection({ knex: sinon.stub().resolves(mockResponse) }); + + const techniqueIds = [1, 2]; + const repo = new SampleMethodRepository(dbConnectionObj); + const response = await repo.getSampleMethodsCountForTechniqueIds(techniqueIds); + + expect(dbConnectionObj.knex).to.have.been.calledOnce; + expect(response).to.eql(count); + }); + }); + describe('updateSampleMethod', () => { it('should update the record and return a single row', async () => { const mockRow = {}; diff --git a/api/src/repositories/sample-method-repository.ts b/api/src/repositories/sample-method-repository.ts index 608e0ed177..882044c70b 100644 --- a/api/src/repositories/sample-method-repository.ts +++ b/api/src/repositories/sample-method-repository.ts @@ -1,5 +1,6 @@ import SQL from 'sql-template-strings'; import { z } from 'zod'; +import { getKnex } from '../database/db'; import { ApiExecuteSQLError } from '../errors/api-error'; import { BaseRepository } from './base-repository'; import { InsertSamplePeriodRecord, UpdateSamplePeriodRecord } from './sample-period-repository'; @@ -97,6 +98,26 @@ export class SampleMethodRepository extends BaseRepository { return response.rows; } + /** + * Gets count of sample methods associated with one or more method technique Ids + * + * @param {number[]} techniqueIds + * @return {*} {Promise} + * @memberof SampleMethodRepository + */ + async getSampleMethodsCountForTechniqueIds(techniqueIds: number[]): Promise { + const knex = getKnex(); + const queryBuilder = knex + .queryBuilder() + .select(knex.raw('COUNT(*)::integer AS count')) + .from('survey_sample_method') + .whereIn('method_technique_id', techniqueIds); + + const response = await this.connection.knex(queryBuilder, z.object({ count: z.number() })); + + return response.rows[0].count; + } + /** * updates a survey Sample method. * diff --git a/api/src/repositories/standards-repository.test.ts b/api/src/repositories/standards-repository.test.ts new file mode 100644 index 0000000000..c37c5a0b91 --- /dev/null +++ b/api/src/repositories/standards-repository.test.ts @@ -0,0 +1,110 @@ +import chai, { expect } from 'chai'; +import { afterEach, describe, it } from 'mocha'; +import { QueryResult } from 'pg'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { getMockDBConnection } from '../__mocks__/db'; +import { StandardsRepository } from './standards-repository'; + +chai.use(sinonChai); + +describe('StandardsRepository', () => { + afterEach(() => { + sinon.restore(); + }); + + describe('getEnvironmentStandards', () => { + it('should successfully retrieve environment standards', async () => { + const mockData = { + quantitative: [ + { name: 'Quantitative Standard 1', description: 'Description 1' }, + { name: 'Quantitative Standard 2', description: 'Description 2' } + ], + qualitative: [ + { + name: 'Qualitative Standard 1', + description: 'Description 1', + options: [ + { name: 'Option 1', description: 'Option 1 Description' }, + { name: 'Option 2', description: 'Option 2 Description' } + ] + }, + { + name: 'Qualitative Standard 2', + description: 'Description 2', + options: [ + { name: 'Option 3', description: 'Option 3 Description' }, + { name: 'Option 4', description: 'Option 4 Description' } + ] + } + ] + }; + + const mockResponse = { + rows: [mockData], + rowCount: 1 + } as any as Promise>; + + const dbConnection = getMockDBConnection({ + sql: () => mockResponse + }); + + const repository = new StandardsRepository(dbConnection); + + const result = await repository.getEnvironmentStandards(); + + expect(result).to.deep.equal(mockData); + }); + }); + + describe('getMethodStandards', () => { + it('should successfully retrieve method standards', async () => { + const mockData = [ + { + method_lookup_id: 1, + name: 'Method 1', + description: ' Description 1', + attributes: { + quantitative: [ + { name: 'Method Standard 1', description: 'Description 1', unit: 'Unit 1' }, + { name: 'Method Standard 2', description: 'Description 2', unit: 'Unit 2' } + ], + qualitative: [ + { + name: 'Qualitative 1', + description: 'Description 1', + options: [ + { name: 'Option 1', description: 'Option 1 Description' }, + { name: 'Option 2', description: 'Option 2 Description' } + ] + }, + { + name: 'Qualitative 2', + description: 'Description 2', + options: [ + { name: 'Option 3', description: 'Option 3 Description' }, + { name: 'Option 4', description: 'Option 4 Description' } + ] + } + ] + } + } + ]; + + const mockResponse = { + rows: mockData, + rowCount: 1 + } as any as Promise>; + + const dbConnection = getMockDBConnection({ + sql: () => mockResponse + }); + + const repository = new StandardsRepository(dbConnection); + + const result = await repository.getMethodStandards(); + + expect(result).to.deep.equal(mockData); + }); + }); +}); diff --git a/api/src/repositories/standards-repository.ts b/api/src/repositories/standards-repository.ts new file mode 100644 index 0000000000..6e7893df94 --- /dev/null +++ b/api/src/repositories/standards-repository.ts @@ -0,0 +1,145 @@ +import SQL from 'sql-template-strings'; +import { + EnvironmentStandards, + EnvironmentStandardsSchema, + MethodStandard, + MethodStandardSchema +} from '../models/standards-view'; +import { BaseRepository } from './base-repository'; + +/** + * Standards repository + * + * @export + * @class standardsRepository + * @extends {BaseRepository} + */ +export class StandardsRepository extends BaseRepository { + /** + * Gets environment standards + * + * @param {string} keyword - search term for filtering the response based on environmental variable name + * @return {*} + * @memberof StandardsRepository + */ + async getEnvironmentStandards(keyword?: string): Promise { + const sql = SQL` + WITH + quan AS ( + SELECT + eq.name AS quant_name, + eq.description AS quant_description, + eq.unit + FROM + environment_quantitative eq + WHERE + eq.name ILIKE '%' || ${keyword ?? ''} || '%' + ), + qual AS ( + SELECT + eq.name AS qual_name, + eq.description AS qual_description, + json_agg(json_build_object('name', eqo.name, 'description', eqo.description)) as options + FROM + environment_qualitative_option eqo + LEFT JOIN + environment_qualitative eq ON eqo.environment_qualitative_id = eq.environment_qualitative_id + WHERE + eq.name ILIKE '%' || ${keyword ?? ''} || '%' + GROUP BY + eq.name, + eq.description + ) + SELECT + (SELECT json_agg(json_build_object('name', quant_name, 'description', quant_description, 'unit', unit)) FROM quan) as quantitative, + (SELECT json_agg(json_build_object('name', qual_name, 'description', qual_description, 'options', options)) FROM qual) as qualitative; + `; + + const response = await this.connection.sql(sql, EnvironmentStandardsSchema); + + return response.rows[0]; + } + + /** + * Gets method standards + * + * @param {string} keyword - search term for filtering the response based on method lookup name + * @return {*} + * @memberof StandardsRepository + */ + async getMethodStandards(keyword?: string): Promise { + const sql = SQL` + WITH + quan AS ( + SELECT + mlaq.method_lookup_id, + tq.name AS quant_name, + tq.description AS quant_description, + mlaq.unit + FROM + method_lookup_attribute_quantitative mlaq + LEFT JOIN + technique_attribute_quantitative tq ON mlaq.technique_attribute_quantitative_id = tq.technique_attribute_quantitative_id + ), + qual AS ( + SELECT + mlaq.method_lookup_id, + taq.name AS qual_name, + taq.description AS qual_description, + COALESCE(json_agg( + json_build_object( + 'name', mlaqo.name, + 'description', mlaqo.description + ) ORDER BY mlaqo.name + ), '[]'::json) AS options + FROM + method_lookup_attribute_qualitative_option mlaqo + LEFT JOIN + method_lookup_attribute_qualitative mlaq ON mlaqo.method_lookup_attribute_qualitative_id = mlaq.method_lookup_attribute_qualitative_id + LEFT JOIN + technique_attribute_qualitative taq ON mlaq.technique_attribute_qualitative_id = taq.technique_attribute_qualitative_id + GROUP BY + mlaq.method_lookup_id, + taq.name, + taq.description + ), + method_lookup AS ( + SELECT + ml.method_lookup_id, + ml.name, + ml.description, + json_build_object( + 'quantitative', ( + SELECT COALESCE(json_agg( + json_build_object( + 'name', quan.quant_name, + 'description', quan.quant_description, + 'unit', quan.unit + ) ORDER BY quan.quant_name + ), '[]'::json) FROM quan + WHERE quan.method_lookup_id = ml.method_lookup_id + ), + 'qualitative', ( + SELECT COALESCE(json_agg( + json_build_object( + 'name', qual.qual_name, + 'description', qual.qual_description, + 'options', qual.options + ) ORDER BY qual.qual_name + ), '[]'::json) FROM qual + WHERE qual.method_lookup_id = ml.method_lookup_id + ) + ) AS attributes + FROM + method_lookup ml + WHERE + ml.name ILIKE '%' || ${keyword ?? ''} || '%' + ) + SELECT * FROM method_lookup; + `; + + const response = await this.connection.sql(sql, MethodStandardSchema); + + return response.rows; + } +} diff --git a/api/src/repositories/survey-critter-repository.test.ts b/api/src/repositories/survey-critter-repository.test.ts index 9969e53269..b57eee437f 100644 --- a/api/src/repositories/survey-critter-repository.test.ts +++ b/api/src/repositories/survey-critter-repository.test.ts @@ -52,19 +52,6 @@ describe('SurveyRepository', () => { }); }); - describe('upsertDeployment', () => { - it('should update existing row', async () => { - const mockResponse = { rows: [{ submissionId: 1 }], rowCount: 1 } as any as Promise>; - const dbConnection = getMockDBConnection({ knex: () => mockResponse }); - - const repository = new SurveyCritterRepository(dbConnection); - - const response = await repository.upsertDeployment(1, 'deployment_id'); - - expect(response).to.be.undefined; - }); - }); - describe('updateCritter', () => { it('should update existing row', async () => { const mockResponse = { rows: [], rowCount: 0 } as any as Promise>; @@ -74,17 +61,4 @@ describe('SurveyRepository', () => { expect(response).to.be.undefined; }); }); - - describe('deleteDeployment', () => { - it('should delete existing row', async () => { - const mockResponse = { rows: [], rowCount: 0 } as any as Promise>; - const dbConnection = getMockDBConnection({ knex: () => mockResponse }); - - const repository = new SurveyCritterRepository(dbConnection); - - const response = await repository.removeDeployment(1, 'deployment_id'); - - expect(response).to.be.undefined; - }); - }); }); diff --git a/api/src/repositories/survey-critter-repository.ts b/api/src/repositories/survey-critter-repository.ts index 2da82b9cb8..602805178d 100644 --- a/api/src/repositories/survey-critter-repository.ts +++ b/api/src/repositories/survey-critter-repository.ts @@ -2,7 +2,7 @@ import { z } from 'zod'; import { getKnex } from '../database/db'; import { ApiExecuteSQLError } from '../errors/api-error'; import { IAnimalAdvancedFilters } from '../models/animal-view'; -import { ITelemetryAdvancedFilters } from '../models/telemetry-view'; +import { IAllTelemetryAdvancedFilters } from '../models/telemetry-view'; import { getLogger } from '../utils/logger'; import { ApiPaginationOptions } from '../zod-schema/pagination'; import { BaseRepository } from './base-repository'; @@ -42,6 +42,24 @@ export class SurveyCritterRepository extends BaseRepository { return response.rows; } + /** + * Get a specific critter by its integer Id + * + * @param {number} surveyId + * @param {number} critterId + * @return {*} {Promise} + * @memberof SurveyCritterRepository + */ + async getCritterById(surveyId: number, critterId: number): Promise { + defaultLog.debug({ label: 'getCritterById', critterId }); + + const queryBuilder = getKnex().table('critter').select().where({ survey_id: surveyId, critter_id: critterId }); + + const response = await this.connection.knex(queryBuilder); + + return response.rows[0]; + } + /** * Constructs a non-paginated query to retrieve critters that are available to the user based on the user's * permissions and filter criteria. @@ -83,7 +101,7 @@ export class SurveyCritterRepository extends BaseRepository { * * @param {boolean} isUserAdmin * @param {(number | null)} systemUserId The system user id of the user making the request - * @param {ITelemetryAdvancedFilters} [filterFields] + * @param {IAllTelemetryAdvancedFilters} [filterFields] * @param {ApiPaginationOptions} [pagination] * @return {*} {Promise} * @memberof SurveyCritterRepository @@ -91,7 +109,7 @@ export class SurveyCritterRepository extends BaseRepository { async findCritters( isUserAdmin: boolean, systemUserId: number | null, - filterFields?: ITelemetryAdvancedFilters, + filterFields?: IAllTelemetryAdvancedFilters, pagination?: ApiPaginationOptions ): Promise { const query = this._makeFindCrittersQuery(isUserAdmin, systemUserId, filterFields); @@ -115,14 +133,14 @@ export class SurveyCritterRepository extends BaseRepository { * * @param {boolean} isUserAdmin * @param {(number | null)} systemUserId The system user id of the user making the request - * @param {ITelemetryAdvancedFilters} [filterFields] + * @param {IAllTelemetryAdvancedFilters} [filterFields] * @return {*} {Promise} * @memberof SurveyCritterRepository */ async findCrittersCount( isUserAdmin: boolean, systemUserId: number | null, - filterFields?: ITelemetryAdvancedFilters + filterFields?: IAllTelemetryAdvancedFilters ): Promise { const findCrittersQuery = this._makeFindCrittersQuery(isUserAdmin, systemUserId, filterFields); @@ -202,44 +220,4 @@ export class SurveyCritterRepository extends BaseRepository { await this.connection.knex(queryBuilder); } - - /** - * Will insert a new critter - deployment uuid association, or update if it already exists. - * This update operation intentionally changes nothing. Only really being done to trigger update audit columns. - * - * @param {number} critterId - * @param {string} deplyomentId - * @return {*} {Promise} - * @memberof SurveyCritterRepository - */ - async upsertDeployment(critterId: number, deplyomentId: string): Promise { - defaultLog.debug({ label: 'addDeployment', deplyomentId }); - - const queryBuilder = getKnex() - .table('deployment') - .insert({ critter_id: critterId, bctw_deployment_id: deplyomentId }) - .onConflict(['critter_id', 'bctw_deployment_id']) - .merge(['critter_id', 'bctw_deployment_id']); - - await this.connection.knex(queryBuilder); - } - - /** - * Deletes a deployment row. - * - * @param {number} critterId - * @param {string} deploymentId - * @return {*} {Promise} - * @memberof SurveyCritterRepository - */ - async removeDeployment(critterId: number, deploymentId: string): Promise { - defaultLog.debug({ label: 'removeDeployment', deploymentId }); - - const queryBuilder = getKnex() - .table('deployment') - .where({ critter_id: critterId, bctw_deployment_id: deploymentId }) - .delete(); - - await this.connection.knex(queryBuilder); - } } diff --git a/api/src/repositories/survey-repository.test.ts b/api/src/repositories/survey-repository.test.ts index 134ec07c92..cfcffdb4e2 100644 --- a/api/src/repositories/survey-repository.test.ts +++ b/api/src/repositories/survey-repository.test.ts @@ -9,7 +9,12 @@ import { PostProprietorData, PostSurveyObject } from '../models/survey-create'; import { PutSurveyObject } from '../models/survey-update'; import { GetAttachmentsData, GetSurveyProprietorData, GetSurveyPurposeAndMethodologyData } from '../models/survey-view'; import { getMockDBConnection } from '../__mocks__/db'; -import { SurveyRecord, SurveyRepository, SurveyTypeRecord } from './survey-repository'; +import { + SurveyRecord, + SurveyRepository, + SurveyTaxonomyWithEcologicalUnits, + SurveyTypeRecord +} from './survey-repository'; chai.use(sinonChai); @@ -140,26 +145,46 @@ describe('SurveyRepository', () => { describe('getSpeciesData', () => { it('should return result', async () => { - const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; + const mockRows: SurveyTaxonomyWithEcologicalUnits[] = [ + { + itis_tsn: 123456, + ecological_units: [ + { + critterbase_collection_category_id: '123-456-789', + critterbase_collection_unit_id: '987-654-321' + } + ] + }, + { + itis_tsn: 654321, + ecological_units: [] + } + ]; + const mockResponse = { rows: mockRows, rowCount: 1 } as any as Promise>; const dbConnection = getMockDBConnection({ sql: () => mockResponse }); const repository = new SurveyRepository(dbConnection); - const response = await repository.getSpeciesData(1); + const surveyId = 1; - expect(response).to.eql([{ id: 1 }]); + const response = await repository.getSpeciesData(surveyId); + + expect(response).to.eql(mockRows); }); it('should return empty rows', async () => { - const mockResponse = { rows: [], rowCount: 1 } as any as Promise>; + const mockRows: SurveyTaxonomyWithEcologicalUnits[] = []; + const mockResponse = { rows: mockRows, rowCount: 1 } as any as Promise>; const dbConnection = getMockDBConnection({ sql: () => mockResponse }); const repository = new SurveyRepository(dbConnection); - const response = await repository.getSpeciesData(1); + const surveyId = 1; + + const response = await repository.getSpeciesData(surveyId); expect(response).to.not.be.null; - expect(response).to.eql([]); + expect(response).to.eql(mockRows); }); }); @@ -539,60 +564,6 @@ describe('SurveyRepository', () => { }); }); - describe('insertAncillarySpecies', () => { - it('should return result', async () => { - const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; - const dbConnection = getMockDBConnection({ sql: () => mockResponse }); - - const repository = new SurveyRepository(dbConnection); - - const response = await repository.insertAncillarySpecies(1, 1); - - expect(response).to.eql(1); - }); - - it('should throw an error', async () => { - const mockResponse = { rows: undefined, rowCount: 0 } as any as Promise>; - const dbConnection = getMockDBConnection({ sql: () => mockResponse }); - - const repository = new SurveyRepository(dbConnection); - - try { - await repository.insertAncillarySpecies(1, 1); - expect.fail(); - } catch (error) { - expect((error as Error).message).to.equal('Failed to insert ancillary species data'); - } - }); - }); - - describe('insertVantageCodes', () => { - it('should return result', async () => { - const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; - const dbConnection = getMockDBConnection({ sql: () => mockResponse }); - - const repository = new SurveyRepository(dbConnection); - - const response = await repository.insertVantageCodes(1, 1); - - expect(response).to.eql(1); - }); - - it('should throw an error', async () => { - const mockResponse = { rows: undefined, rowCount: 0 } as any as Promise>; - const dbConnection = getMockDBConnection({ sql: () => mockResponse }); - - const repository = new SurveyRepository(dbConnection); - - try { - await repository.insertVantageCodes(1, 1); - expect.fail(); - } catch (error) { - expect((error as Error).message).to.equal('Failed to insert vantage codes'); - } - }); - }); - describe('insertSurveyProprietor', () => { it('should return undefined if data is not proprietary', async () => { const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; @@ -759,19 +730,6 @@ describe('SurveyRepository', () => { }); }); - describe('deleteSurveyVantageCodes', () => { - it('should return result', async () => { - const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; - const dbConnection = getMockDBConnection({ sql: () => mockResponse }); - - const repository = new SurveyRepository(dbConnection); - - const response = await repository.deleteSurveyVantageCodes(1); - - expect(response).to.eql(undefined); - }); - }); - describe('updateSurveyDetailsData', () => { it('should return undefined and ue all inputs', async () => { const mockResponse = { rows: [{ id: 1 }], rowCount: 1 } as any as Promise>; diff --git a/api/src/repositories/survey-repository.ts b/api/src/repositories/survey-repository.ts index 42e30e7dd2..83c2193590 100644 --- a/api/src/repositories/survey-repository.ts +++ b/api/src/repositories/survey-repository.ts @@ -13,12 +13,12 @@ import { GetSurveyPurposeAndMethodologyData, ISurveyAdvancedFilters } from '../models/survey-view'; +import { IPostCollectionUnit } from '../services/critterbase-service'; import { ApiPaginationOptions } from '../zod-schema/pagination'; import { BaseRepository } from './base-repository'; export interface IGetSpeciesData { itis_tsn: number; - is_focal: boolean; } export interface IObservationSubmissionInsertDetails { @@ -118,6 +118,18 @@ export const SurveyBasicFields = z.object({ export type SurveyBasicFields = z.infer; +export const SurveyTaxonomyWithEcologicalUnits = z.object({ + itis_tsn: z.number(), + ecological_units: z.array( + z.object({ + critterbase_collection_unit_id: z.string().uuid(), + critterbase_collection_category_id: z.string().uuid() + }) + ) +}); + +export type SurveyTaxonomyWithEcologicalUnits = z.infer; + export class SurveyRepository extends BaseRepository { /** * Deletes a survey and any associations for a given survey @@ -358,21 +370,41 @@ export class SurveyRepository extends BaseRepository { * Get species data for a given survey ID * * @param {number} surveyId - * @returns {*} {Promise} + * @return {*} {Promise} * @memberof SurveyRepository */ - async getSpeciesData(surveyId: number): Promise { + async getSpeciesData(surveyId: number): Promise { const sqlStatement = SQL` + WITH w_ecological_units AS ( SELECT - itis_tsn, - is_focal + ssu.study_species_id, + json_agg( + json_build_object( + 'critterbase_collection_category_id', ssu.critterbase_collection_category_id, + 'critterbase_collection_unit_id', ssu.critterbase_collection_unit_id + ) + ) AS units FROM - study_species + study_species_unit ssu + LEFT JOIN + study_species ss ON ss.study_species_id = ssu.study_species_id WHERE - survey_id = ${surveyId}; + ss.survey_id = ${surveyId} + GROUP BY + ssu.study_species_id + ) + SELECT + ss.itis_tsn, + COALESCE(weu.units, '[]'::json) AS ecological_units + FROM + study_species ss + LEFT JOIN + w_ecological_units weu ON weu.study_species_id = ss.study_species_id + WHERE + ss.survey_id = ${surveyId}; `; - const response = await this.connection.sql(sqlStatement); + const response = await this.connection.sql(sqlStatement, SurveyTaxonomyWithEcologicalUnits); return response.rows; } @@ -387,15 +419,9 @@ export class SurveyRepository extends BaseRepository { const sqlStatement = SQL` SELECT s.additional_details, - array_remove(array_agg(DISTINCT io.intended_outcome_id), NULL) as intended_outcome_ids, - array_remove(array_agg(DISTINCT sv.vantage_id), NULL) as vantage_ids - + array_remove(array_agg(DISTINCT io.intended_outcome_id), NULL) as intended_outcome_ids FROM survey s - LEFT OUTER JOIN - survey_vantage sv - ON - sv.survey_id = s.survey_id LEFT OUTER JOIN survey_intended_outcome io ON @@ -759,7 +785,7 @@ export class SurveyRepository extends BaseRepository { if (!result?.id) { throw new ApiExecuteSQLError('Failed to insert focal species data', [ - 'SurveyRepository->insertSurveyData', + 'SurveyRepository->insertFocalSpecies', 'response was null or undefined, expected response != null' ]); } @@ -768,32 +794,32 @@ export class SurveyRepository extends BaseRepository { } /** - * Inserts a new Ancillary species record and returns the new ID + * Inserts focal ecological units for focal species * - * @param {number} ancillary_species_id - * @param {number} surveyId + * @param {IPostCollectionUnit} ecologicalUnitObject + * @param {number} studySpeciesId * @returns {*} Promise * @memberof SurveyRepository */ - async insertAncillarySpecies(ancillary_species_id: number, surveyId: number): Promise { + async insertFocalSpeciesUnits(ecologicalUnitObject: IPostCollectionUnit, studySpeciesId: number): Promise { const sqlStatement = SQL` - INSERT INTO study_species ( - itis_tsn, - is_focal, - survey_id + INSERT INTO study_species_unit ( + study_species_id, + critterbase_collection_category_id, + critterbase_collection_unit_id ) VALUES ( - ${ancillary_species_id}, - FALSE, - ${surveyId} - ) RETURNING study_species_id as id; + ${studySpeciesId}, + ${ecologicalUnitObject.critterbase_collection_category_id}, + ${ecologicalUnitObject.critterbase_collection_unit_id} + ) RETURNING study_species_id AS id; `; const response = await this.connection.sql(sqlStatement); const result = response.rows?.[0]; if (!result?.id) { - throw new ApiExecuteSQLError('Failed to insert ancillary species data', [ - 'SurveyRepository->insertSurveyData', + throw new ApiExecuteSQLError('Failed to insert focal species units data', [ + 'SurveyRepository->insertFocalSpeciesUnits', 'response was null or undefined, expected response != null' ]); } @@ -801,37 +827,6 @@ export class SurveyRepository extends BaseRepository { return result.id; } - /** - * Inserts a new vantage code record and returns the new ID - * - * @param {number} vantage_code_id - * @param {number} surveyId - * @returns {*} Promise - * @memberof SurveyRepository - */ - async insertVantageCodes(vantage_code_id: number, surveyId: number): Promise { - const sqlStatement = SQL` - INSERT INTO survey_vantage ( - vantage_id, - survey_id - ) VALUES ( - ${vantage_code_id}, - ${surveyId} - ) RETURNING survey_vantage_id as id; - `; - - const response = await this.connection.sql(sqlStatement); - const result = response.rows?.[0]; - - if (!result?.id) { - throw new ApiExecuteSQLError('Failed to insert vantage codes', [ - 'SurveyRepository->insertVantageCodes', - 'response was null or undefined, expected response != null' - ]); - } - return result.id; - } - /** * Insert many rows associating a survey id to various intended outcome ids. * @@ -869,7 +864,6 @@ export class SurveyRepository extends BaseRepository { /** * Inserts a new Survey Proprietor record and returns the new ID * - * @param {number} ancillary_species_id * @param {number} surveyId * @returns {*} Promise * @memberof SurveyRepository @@ -1076,36 +1070,36 @@ export class SurveyRepository extends BaseRepository { } /** - * Breaks permit survey link for a given survey ID + * Deletes ecological units data for focal species in a given survey ID * * @param {number} surveyId * @returns {*} Promise * @memberof SurveyRepository */ - async unassociatePermitFromSurvey(surveyId: number) { + async deleteSurveySpeciesUnitData(surveyId: number) { const sqlStatement = SQL` - UPDATE - permit - SET - survey_id = ${null} - WHERE - survey_id = ${surveyId}; + DELETE FROM study_species_unit ssu + USING study_species ss + WHERE ss.study_species_id = ssu.study_species_id + AND ss.survey_id = ${surveyId}; `; await this.connection.sql(sqlStatement); } /** - * Deletes Survey proprietor data for a given survey ID + * Breaks permit survey link for a given survey ID * * @param {number} surveyId * @returns {*} Promise * @memberof SurveyRepository */ - async deleteSurveyProprietorData(surveyId: number) { + async unassociatePermitFromSurvey(surveyId: number) { const sqlStatement = SQL` - DELETE - from survey_proprietor + UPDATE + permit + SET + survey_id = ${null} WHERE survey_id = ${surveyId}; `; @@ -1114,16 +1108,16 @@ export class SurveyRepository extends BaseRepository { } /** - * Deletes Survey vantage codes for a given survey ID + * Deletes Survey proprietor data for a given survey ID * * @param {number} surveyId * @returns {*} Promise * @memberof SurveyRepository */ - async deleteSurveyVantageCodes(surveyId: number) { + async deleteSurveyProprietorData(surveyId: number) { const sqlStatement = SQL` DELETE - from survey_vantage + from survey_proprietor WHERE survey_id = ${surveyId}; `; diff --git a/api/src/repositories/telemetry-repository.ts b/api/src/repositories/telemetry-repository.ts index 501ebae74e..4246e7ba9e 100644 --- a/api/src/repositories/telemetry-repository.ts +++ b/api/src/repositories/telemetry-repository.ts @@ -8,8 +8,17 @@ import { BaseRepository } from './base-repository'; const defaultLog = getLogger('repositories/telemetry-repository'); export const Deployment = z.object({ + /** + * SIMS deployment primary ID + */ deployment_id: z.number(), + /** + * SIMS critter primary ID + */ critter_id: z.number(), + /** + * BCTW deployment primary ID + */ bctw_deployment_id: z.string().uuid() }); @@ -113,4 +122,35 @@ export class TelemetryRepository extends BaseRepository { return response.rows; } + + /** + * Get deployments for the provided survey id. + * + * Note: SIMS does not store deployment information, beyond an ID. Deployment details must be fetched from the + * external BCTW API. + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof TelemetryRepository + */ + async getDeploymentsBySurveyId(surveyId: number): Promise { + const sqlStatement = SQL` + SELECT + deployment.deployment_id, + deployment.critter_id, + deployment.bctw_deployment_id + FROM + deployment + LEFT JOIN + critter + ON + critter.critter_id = deployment.critter_id + WHERE + critter.survey_id = ${surveyId}; + `; + + const response = await this.connection.sql(sqlStatement, Deployment); + + return response.rows; + } } diff --git a/api/src/services/administrative-activity-service.test.ts b/api/src/services/administrative-activity-service.test.ts index 0f570b87cf..74cc0e175f 100644 --- a/api/src/services/administrative-activity-service.test.ts +++ b/api/src/services/administrative-activity-service.test.ts @@ -42,7 +42,9 @@ describe('AdministrativeActivityService', () => { identitySource: 'BCEIDBASIC' }, notes: null, - create_date: '2023-05-02T02:04:10.751Z' + create_date: '2023-05-02T02:04:10.751Z', + update_date: '2023-05-02T02:04:10.751Z', + updated_by: 'Doe, John WLRS:EX' } ]); @@ -66,7 +68,9 @@ describe('AdministrativeActivityService', () => { identitySource: 'BCEIDBASIC' }, notes: null, - create_date: '2023-05-02T02:04:10.751Z' + create_date: '2023-05-02T02:04:10.751Z', + update_date: '2023-05-02T02:04:10.751Z', + updated_by: 'Doe, John WLRS:EX' } ]); }); diff --git a/api/src/services/analytics-service.test.ts b/api/src/services/analytics-service.test.ts new file mode 100644 index 0000000000..ccd67465f6 --- /dev/null +++ b/api/src/services/analytics-service.test.ts @@ -0,0 +1,518 @@ +import chai, { expect } from 'chai'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { + ObservationAnalyticsResponse, + ObservationCountByGroup, + ObservationCountByGroupSQLResponse, + ObservationCountByGroupWithMeasurements +} from '../models/observation-analytics'; +import { AnalyticsRepository } from '../repositories/analytics-repository'; +import { getMockDBConnection } from '../__mocks__/db'; +import { AnalyticsService } from './analytics-service'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition, + CritterbaseService +} from './critterbase-service'; + +chai.use(sinonChai); + +describe('AnalyticsService', () => { + afterEach(() => { + sinon.restore(); + }); + + describe('getObservationCountByGroup', () => { + it('returns an array of observation count analytics records', async () => { + const dbConnection = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnection); + + const mockGetObservationCountByGroupResponse: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 3, + individual_count: 62, + individual_percentage: 57.41, + survey_sample_site_id: 4, + survey_sample_period_id: 4, + quant_measurements: {}, + qual_measurements: { '337f67fa-296d-43a9-88b2-ffdc77891aee': '61d1532d-b06e-4300-8da6-d195cc98f34e' } + }, + { + id: '987-654-321', + row_count: 2, + individual_count: 46, + individual_percentage: 42.59, + survey_sample_site_id: 4, + survey_sample_period_id: 4, + quant_measurements: {}, + qual_measurements: { '337f67fa-296d-43a9-88b2-ffdc77891aee': 'dd9a1672-ac93-4598-b166-caad463ed6f2' } + } + ]; + + sinon + .stub(AnalyticsRepository.prototype, 'getObservationCountByGroup') + .resolves(mockGetObservationCountByGroupResponse); + + sinon.stub(CritterbaseService.prototype, 'getQualitativeMeasurementTypeDefinition').resolves([ + { + taxon_measurement_id: '337f67fa-296d-43a9-88b2-ffdc77891aee', + itis_tsn: 180692, + measurement_name: 'antler configuration', + measurement_desc: null, + options: [ + { + qualitative_option_id: '61d1532d-b06e-4300-8da6-d195cc98f34e', + option_label: 'less than 3 points', + option_value: 0, + option_desc: null + }, + { + qualitative_option_id: 'dd9a1672-ac93-4598-b166-caad463ed6f2', + option_label: 'more than 3 points', + option_value: 1, + option_desc: null + } + ] + } + ]); + + sinon.stub(CritterbaseService.prototype, 'getQuantitativeMeasurementTypeDefinition').resolves([]); + + const surveyIds = [4]; + const groupByColumns = ['survey_sample_site_id', 'survey_sample_period_id']; + const groupByQuantitativeMeasurements: string[] = []; + const groupByQualitativeMeasurements = ['337f67fa-296d-43a9-88b2-ffdc77891aee']; + + const response = await analyticsService.getObservationCountByGroup( + surveyIds, + groupByColumns, + groupByQuantitativeMeasurements, + groupByQualitativeMeasurements + ); + + const expectedResponse: ObservationAnalyticsResponse[] = [ + { + id: '123-456-789', + row_count: 3, + individual_count: 62, + individual_percentage: 57.41, + qualitative_measurements: [ + { + option: { option_id: '61d1532d-b06e-4300-8da6-d195cc98f34e', option_label: 'less than 3 points' }, + taxon_measurement_id: '337f67fa-296d-43a9-88b2-ffdc77891aee', + measurement_name: 'antler configuration' + } + ], + quantitative_measurements: [], + survey_sample_period_id: 4, + survey_sample_site_id: 4 + }, + { + id: '987-654-321', + row_count: 2, + individual_count: 46, + individual_percentage: 42.59, + qualitative_measurements: [ + { + option: { option_id: 'dd9a1672-ac93-4598-b166-caad463ed6f2', option_label: 'more than 3 points' }, + taxon_measurement_id: '337f67fa-296d-43a9-88b2-ffdc77891aee', + measurement_name: 'antler configuration' + } + ], + quantitative_measurements: [], + survey_sample_period_id: 4, + survey_sample_site_id: 4 + } + ]; + + expect(response).to.eql(expectedResponse); + }); + }); + + describe('_filterNonEmptyColumns', () => { + it('returns an array of non-empty columns', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const columns = ['a', '', 'b', 'c', '']; + + const result = analyticsService._filterNonEmptyColumns(columns); + + expect(result).to.eql(['a', 'b', 'c']); + }); + }); + + describe('_fetchQualitativeDefinitions', () => { + it('returns an array of qualitative measurement type definitions', async () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const mockQualitativeMeasurementTypeDefinitions: CBQualitativeMeasurementTypeDefinition[] = [ + { + itis_tsn: 123456, + taxon_measurement_id: '1', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + options: [ + { + qualitative_option_id: '3', + option_label: 'option_label', + option_value: 0, + option_desc: 'option_desc' + } + ] + } + ]; + + sinon + .stub(CritterbaseService.prototype, 'getQualitativeMeasurementTypeDefinition') + .resolves(mockQualitativeMeasurementTypeDefinitions); + + const counts: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 1, + individual_count: 1, + individual_percentage: 1, + life_stage: 'adult', + antler_length: 20, + quant_measurements: { + '1': 1 + }, + qual_measurements: { + '2': '2' + } + } + ]; + + const result = await analyticsService._fetchQualitativeDefinitions(counts); + + expect(result).to.eql(mockQualitativeMeasurementTypeDefinitions); + }); + }); + + describe('_fetchQuantitativeDefinitions', () => { + it('returns an array of quantitative measurement type definitions', async () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const mockQuantitativeMeasurementTypeDefinitions: CBQuantitativeMeasurementTypeDefinition[] = [ + { + itis_tsn: 123456, + taxon_measurement_id: '1', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + min_value: 1, + max_value: 2, + unit: 'millimeter' + } + ]; + + sinon + .stub(CritterbaseService.prototype, 'getQuantitativeMeasurementTypeDefinition') + .resolves(mockQuantitativeMeasurementTypeDefinitions); + + const counts: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 5, + individual_count: 10, + individual_percentage: 46, + life_stage: 'adult', + antler_length: 20, + quant_measurements: { + '1': 1 + }, + qual_measurements: { + '2': '2' + } + } + ]; + + const result = await analyticsService._fetchQuantitativeDefinitions(counts); + + expect(result).to.eql(mockQuantitativeMeasurementTypeDefinitions); + }); + }); + + describe('_getQualitativeMeasurementIds', () => { + it('returns an array of measurement IDs', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const counts: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 1, + individual_count: 1, + individual_percentage: 1, + life_stage: 'adult', + antler_length: 20, + quant_measurements: { + '1': 1, + '2': 2 + }, + qual_measurements: { + '3': '3', + '4': '4' + } + } + ]; + + const result = analyticsService._getQualitativeMeasurementIds(counts); + + expect(result).to.eql(['3', '4']); + }); + }); + + describe('_getQuantitativeMeasurementIds', () => { + it('returns an array of measurement IDs', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const counts: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 1, + individual_count: 1, + individual_percentage: 1, + life_stage: 'adult', + antler_length: 20, + quant_measurements: { + '1': 1, + '2': 2 + }, + qual_measurements: { + '3': '3', + '4': '4' + } + } + ]; + + const result = analyticsService._getQuantitativeMeasurementIds(counts); + + expect(result).to.eql(['1', '2']); + }); + }); + + describe('_processCounts', () => { + it('returns an array of observation analytics responses', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const counts: (ObservationCountByGroupWithMeasurements & ObservationCountByGroup)[] = [ + { + row_count: 1, + individual_count: 1, + individual_percentage: 1, + quant_measurements: [ + { + critterbase_taxon_measurement_id: '1', + value: 1 + } + ], + qual_measurements: [ + { + critterbase_taxon_measurement_id: '2', + option_id: '3' + } + ] + } + ]; + + const qualitativeDefinitions: CBQualitativeMeasurementTypeDefinition[] = []; + const quantitativeDefinitions: CBQuantitativeMeasurementTypeDefinition[] = []; + + const result = analyticsService._processCounts(counts, qualitativeDefinitions, quantitativeDefinitions); + + expect(result).to.be.an('array'); + expect(result.length).to.equal(1); + }); + }); + + describe('_mapQualitativeMeasurements', () => { + it('returns an array of qualitative measurement analytics', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const qualMeasurements = [ + { + critterbase_taxon_measurement_id: '11', + option_id: '1' + }, + { + critterbase_taxon_measurement_id: '22', + option_id: null + } + ]; + + const definitions: CBQualitativeMeasurementTypeDefinition[] = [ + { + itis_tsn: 123456, + taxon_measurement_id: '11', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + options: [ + { + qualitative_option_id: '1', + option_label: 'option_label', + option_value: 1, + option_desc: 'option_desc' + } + ] + }, + { + itis_tsn: 123456, + taxon_measurement_id: '22', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + options: [ + { + qualitative_option_id: '2', + option_label: 'option_label', + option_value: 2, + option_desc: 'option_desc' + } + ] + } + ]; + + const result = analyticsService._mapQualitativeMeasurements(qualMeasurements, definitions); + + expect(result).to.eql([ + { + taxon_measurement_id: '11', + measurement_name: 'measurement_name', + option: { + option_id: '1', + option_label: 'option_label' + } + }, + { + taxon_measurement_id: '22', + measurement_name: 'measurement_name', + option: { + option_id: null, + option_label: '' + } + } + ]); + }); + }); + + describe('_mapQuantitativeMeasurements', () => { + it('returns an array of quantitative measurement analytics', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const quantMeasurements = [ + { + critterbase_taxon_measurement_id: '11', + value: 1 + }, + { + critterbase_taxon_measurement_id: '22', + value: null + } + ]; + + const definitions: CBQuantitativeMeasurementTypeDefinition[] = [ + { + itis_tsn: 123456, + taxon_measurement_id: '11', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + min_value: 1, + max_value: 2, + unit: 'millimeter' + }, + { + itis_tsn: 123456, + taxon_measurement_id: '22', + measurement_name: 'measurement_name', + measurement_desc: 'measurement_desc', + min_value: 1, + max_value: 2, + unit: 'centimeter' + } + ]; + + const result = analyticsService._mapQuantitativeMeasurements(quantMeasurements, definitions); + + expect(result).to.eql([ + { + taxon_measurement_id: '11', + measurement_name: 'measurement_name', + value: 1 + }, + { + measurement_name: 'measurement_name', + taxon_measurement_id: '22', + value: null + } + ]); + }); + }); + + describe('_transformMeasurementObjectKeysToArrays', () => { + it('returns an array of transformed observation counts', () => { + const dbConnectionObj = getMockDBConnection(); + + const analyticsService = new AnalyticsService(dbConnectionObj); + + const counts: ObservationCountByGroupSQLResponse[] = [ + { + id: '123-456-789', + row_count: 1, + individual_count: 1, + individual_percentage: 1, + life_stage: 'adult', + antler_length: 20, + quant_measurements: { + '1': 1 + }, + qual_measurements: { + '2': '2' + } + } + ]; + + const result = analyticsService._transformMeasurementObjectKeysToArrays(counts); + + expect(result).to.eql([ + { + id: '123-456-789', + row_count: 1, + individual_count: 1, + individual_percentage: 1, + qual_measurements: [ + { + critterbase_taxon_measurement_id: '2', + option_id: '2' + } + ], + quant_measurements: [ + { + critterbase_taxon_measurement_id: '1', + value: 1 + } + ], + antler_length: 20, + life_stage: 'adult' + } + ]); + }); + }); +}); diff --git a/api/src/services/analytics-service.ts b/api/src/services/analytics-service.ts new file mode 100644 index 0000000000..06cf779344 --- /dev/null +++ b/api/src/services/analytics-service.ts @@ -0,0 +1,282 @@ +import { IDBConnection } from '../database/db'; +import { + ObservationAnalyticsResponse, + ObservationCountByGroup, + ObservationCountByGroupSQLResponse, + ObservationCountByGroupWithMeasurements, + QualitativeMeasurementAnalytics, + QuantitativeMeasurementAnalytics +} from '../models/observation-analytics'; +import { AnalyticsRepository } from '../repositories/analytics-repository'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition, + CritterbaseService +} from './critterbase-service'; +import { DBService } from './db-service'; + +/** + * Handles all business logic related to data analytics. + * + * @export + * @class AnalyticsService + * @extends {DBService} + */ +export class AnalyticsService extends DBService { + analyticsRepository: AnalyticsRepository; + + critterbaseService: CritterbaseService; + + constructor(connection: IDBConnection) { + super(connection); + this.analyticsRepository = new AnalyticsRepository(connection); + + this.critterbaseService = new CritterbaseService({ + keycloak_guid: this.connection.systemUserGUID(), + username: this.connection.systemUserIdentifier() + }); + } + + /** + * Gets observation counts by group for given survey IDs and groupings. + * + * @param {number[]} surveyIds Array of survey IDs + * @param {string[]} groupByColumns Columns to group by + * @param {string[]} groupByQuantitativeMeasurements Quantitative measurements to group by + * @param {string[]} groupByQualitativeMeasurements Qualitative measurements to group by + * @return {Promise} Array of ObservationCountByGroupWithNamedMeasurements + * @memberof AnalyticsService + */ + async getObservationCountByGroup( + surveyIds: number[], + groupByColumns: string[], + groupByQuantitativeMeasurements: string[], + groupByQualitativeMeasurements: string[] + ): Promise { + // Fetch observation counts from repository + const counts = await this.analyticsRepository.getObservationCountByGroup( + surveyIds, + this._filterNonEmptyColumns(groupByColumns), + this._filterNonEmptyColumns(groupByQuantitativeMeasurements), + this._filterNonEmptyColumns(groupByQualitativeMeasurements) + ); + + // Fetch measurement definitions in parallel + const [qualitativeDefinitions, quantitativeDefinitions] = await Promise.all([ + this._fetchQualitativeDefinitions(counts), + this._fetchQuantitativeDefinitions(counts) + ]); + + const transformedCounts = this._transformMeasurementObjectKeysToArrays(counts); + + return this._processCounts(transformedCounts, qualitativeDefinitions, quantitativeDefinitions); + } + + /** + * Filters out empty columns. + * + * @param {string[]} columns + * @return {*} {string[]} + * @memberof AnalyticsService + */ + _filterNonEmptyColumns(columns: string[]): string[] { + return columns.filter((column) => column.trim() !== ''); + } + + /** + * Fetches qualitative measurement definitions for given counts. + * + * @param {ObservationCountByGroupSQLResponse[]} counts + * @return {*} {Promise} + * @memberof AnalyticsService + */ + async _fetchQualitativeDefinitions( + counts: ObservationCountByGroupSQLResponse[] + ): Promise { + const qualTaxonMeasurementIds = this._getQualitativeMeasurementIds(counts); + + if (qualTaxonMeasurementIds.length === 0) { + return []; + } + + return this.critterbaseService.getQualitativeMeasurementTypeDefinition(qualTaxonMeasurementIds); + } + + /** + * Fetches quantitative measurement definitions for given counts. + * + * @param {ObservationCountByGroupSQLResponse[]} counts + * @return {*} {Promise} + * @memberof AnalyticsService + */ + async _fetchQuantitativeDefinitions( + counts: ObservationCountByGroupSQLResponse[] + ): Promise { + const quantTaxonMeasurementIds = this._getQuantitativeMeasurementIds(counts); + + if (quantTaxonMeasurementIds.length === 0) { + return []; + } + + return this.critterbaseService.getQuantitativeMeasurementTypeDefinition(quantTaxonMeasurementIds); + } + + /** + * Returns array of unique qualitative measurement IDs from given counts. + * + * @param {ObservationCountByGroupSQLResponse[]} counts + * @return {*} {string[]} + * @memberof AnalyticsService + */ + _getQualitativeMeasurementIds(counts: ObservationCountByGroupSQLResponse[]): string[] { + return Array.from(new Set(counts.flatMap((count) => Object.keys(count.qual_measurements)))); + } + + /** + * Returns array of unique quantitative measurement IDs from given counts. + * + * @param {ObservationCountByGroupSQLResponse[]} counts + * @return {*} {string[]} + * @memberof AnalyticsService + */ + _getQuantitativeMeasurementIds(counts: ObservationCountByGroupSQLResponse[]): string[] { + return Array.from(new Set(counts.flatMap((count) => Object.keys(count.quant_measurements)))); + } + + /** + * Parses the raw counts object, stripping out extra fields, and maps measurements to their definitions. + * + * @param {((ObservationCountByGroupWithMeasurements & ObservationCountByGroup)[])} counts + * @param {CBQualitativeMeasurementTypeDefinition[]} qualitativeDefinitions + * @param {CBQuantitativeMeasurementTypeDefinition[]} quantitativeDefinitions + * @return {*} {ObservationAnalyticsResponse[]} + * @memberof AnalyticsService + */ + _processCounts( + counts: (ObservationCountByGroupWithMeasurements & ObservationCountByGroup)[], + qualitativeDefinitions: CBQualitativeMeasurementTypeDefinition[], + quantitativeDefinitions: CBQuantitativeMeasurementTypeDefinition[] + ): ObservationAnalyticsResponse[] { + const newCounts: ObservationAnalyticsResponse[] = []; + + for (const count of counts) { + const { row_count, individual_count, individual_percentage, qual_measurements, quant_measurements, ...rest } = + count; + + newCounts.push({ + row_count, + individual_count, + individual_percentage, + ...rest, + qualitative_measurements: this._mapQualitativeMeasurements(qual_measurements, qualitativeDefinitions), + quantitative_measurements: this._mapQuantitativeMeasurements(quant_measurements, quantitativeDefinitions) + }); + } + + return newCounts; + } + + /** + * Maps qualitative measurements to their definitions. + * + * @param {({ option_id: string | null; critterbase_taxon_measurement_id: string }[])} qualMeasurements + * @param {CBQualitativeMeasurementTypeDefinition[]} definitions + * @return {*} {QualitativeMeasurementAnalytics[]} + * @memberof AnalyticsService + */ + _mapQualitativeMeasurements( + qualMeasurements: { option_id: string | null; critterbase_taxon_measurement_id: string }[], + definitions: CBQualitativeMeasurementTypeDefinition[] + ): QualitativeMeasurementAnalytics[] { + return qualMeasurements + .map((measurement) => { + const definition = definitions.find( + (def) => def.taxon_measurement_id === measurement.critterbase_taxon_measurement_id + ); + + if (!definition) { + return null; + } + + return { + taxon_measurement_id: measurement.critterbase_taxon_measurement_id, + measurement_name: definition.measurement_name ?? '', + option: { + option_id: measurement.option_id, + option_label: + definition.options.find((option) => option.qualitative_option_id === measurement.option_id) + ?.option_label ?? '' + } + }; + }) + .filter((item): item is QualitativeMeasurementAnalytics => item !== null); + } + + /** + * Maps quantitative measurements to their definitions. + * + * @param {({ value: number | null; critterbase_taxon_measurement_id: string }[])} quantMeasurements + * @param {CBQuantitativeMeasurementTypeDefinition[]} definitions + * @return {*} {QuantitativeMeasurementAnalytics[]} + * @memberof AnalyticsService + */ + _mapQuantitativeMeasurements( + quantMeasurements: { value: number | null; critterbase_taxon_measurement_id: string }[], + definitions: CBQuantitativeMeasurementTypeDefinition[] + ): QuantitativeMeasurementAnalytics[] { + return quantMeasurements + .map((measurement) => { + const definition = definitions.find( + (def) => def.taxon_measurement_id === measurement.critterbase_taxon_measurement_id + ); + + if (!definition) { + return null; + } + + return { + taxon_measurement_id: measurement.critterbase_taxon_measurement_id, + measurement_name: definition.measurement_name ?? '', + value: measurement.value + }; + }) + .filter((item): item is QuantitativeMeasurementAnalytics => item !== null); + } + + /** + * Transforms the keys of the measurement objects to arrays. + * + * @param {ObservationCountByGroupSQLResponse[]} counts + * @return {*} {((ObservationCountByGroupWithMeasurements & ObservationCountByGroup)[])} + * @memberof AnalyticsService + */ + _transformMeasurementObjectKeysToArrays( + counts: ObservationCountByGroupSQLResponse[] + ): (ObservationCountByGroupWithMeasurements & ObservationCountByGroup)[] { + return counts.map((count) => { + const { row_count, individual_count, individual_percentage, quant_measurements, qual_measurements, ...rest } = + count; + + // Transform quantitative measurements + const quantitative = Object.entries(quant_measurements).map(([measurementId, value]) => ({ + critterbase_taxon_measurement_id: measurementId, + value: value + })); + + // Transform qualitative measurements + const qualitative = Object.entries(qual_measurements).map(([measurementId, optionId]) => ({ + critterbase_taxon_measurement_id: measurementId, + option_id: optionId + })); + + return { + row_count, + individual_count, + individual_percentage, + ...rest, + qual_measurements: qualitative, + quant_measurements: quantitative + }; + }); + } +} diff --git a/api/src/services/attachment-service.test.ts b/api/src/services/attachment-service.test.ts index 7bcc38d4d6..3ad31469c4 100644 --- a/api/src/services/attachment-service.test.ts +++ b/api/src/services/attachment-service.test.ts @@ -221,7 +221,7 @@ describe('AttachmentService', () => { }); }); - it('should insert and return { id: number; revision_count: number; key: string }', async () => { + it('should insert and return { id: number; key: string }', async () => { const dbConnection = getMockDBConnection(); const service = new AttachmentService(dbConnection); @@ -921,7 +921,7 @@ describe('AttachmentService', () => { const service = new AttachmentService(dbConnection); const serviceStub1 = sinon - .stub(AttachmentService.prototype, 'getSurveyReportAttachmentByFileName') + .stub(AttachmentService.prototype, 'getSurveyAttachmentByFileName') .resolves({ rowCount: 1 } as unknown as QueryResult); const serviceStub2 = sinon @@ -949,7 +949,7 @@ describe('AttachmentService', () => { const service = new AttachmentService(dbConnection); const serviceStub1 = sinon - .stub(AttachmentService.prototype, 'getSurveyReportAttachmentByFileName') + .stub(AttachmentService.prototype, 'getSurveyAttachmentByFileName') .resolves({ rowCount: 0 } as unknown as QueryResult); const serviceStub2 = sinon diff --git a/api/src/services/attachment-service.ts b/api/src/services/attachment-service.ts index 7ad4ae160b..017ea1c44e 100644 --- a/api/src/services/attachment-service.ts +++ b/api/src/services/attachment-service.ts @@ -14,7 +14,8 @@ import { IProjectReportAttachmentAuthor, ISurveyAttachment, ISurveyReportAttachment, - ISurveyReportAttachmentAuthor + ISurveyReportAttachmentAuthor, + SurveyTelemetryCredentialAttachment } from '../repositories/attachment-repository'; import { deleteFileFromS3, generateS3FileKey } from '../utils/file-utils'; import { DBService } from './db-service'; @@ -261,6 +262,17 @@ export class AttachmentService extends DBService { return this.attachmentRepository.getSurveyReportAttachmentAuthors(reportAttachmentId); } + /** + * Gets all of the survey telemetry credential attachments for the given survey ID. + * + * @param {number} surveyId the ID of the survey + * @return {Promise} Promise resolving all survey telemetry attachments. + * @memberof AttachmentService + */ + async getSurveyTelemetryCredentialAttachments(surveyId: number): Promise { + return this.attachmentRepository.getSurveyTelemetryCredentialAttachments(surveyId); + } + /** *Insert Project Attachment * @@ -795,7 +807,7 @@ export class AttachmentService extends DBService { fileName: file.originalname }); - const getResponse = await this.getSurveyReportAttachmentByFileName(surveyId, file.originalname); + const getResponse = await this.getSurveyAttachmentByFileName(file.originalname, surveyId); let attachmentResult: { survey_attachment_id: number; revision_count: number }; @@ -892,4 +904,120 @@ export class AttachmentService extends DBService { // Delete the attachment from S3 await deleteFileFromS3(attachment.key); } + + /** + * Update survey telemetry credential attachment record. + * + * @param {number} surveyId + * @param {string} fileName + * @param {string} fileType + * @return {*} {Promise<{ survey_telemetry_credential_attachment_id: number }>} + * @memberof AttachmentService + */ + async updateSurveyTelemetryCredentialAttachment( + surveyId: number, + fileName: string, + fileType: string + ): Promise<{ survey_telemetry_credential_attachment_id: number }> { + return this.attachmentRepository.updateSurveyTelemetryCredentialAttachment(surveyId, fileName, fileType); + } + + /** + * Insert survey telemetry credential attachment record. + * + * @param {string} fileName + * @param {number} fileSize + * @param {string} fileType + * @param {number} surveyId + * @param {string} key + * @return {*} {Promise<{ survey_telemetry_credential_attachment_id: number }>} + * @memberof AttachmentService + */ + async insertSurveyTelemetryCredentialAttachment( + fileName: string, + fileSize: number, + fileType: string, + surveyId: number, + key: string + ): Promise<{ survey_telemetry_credential_attachment_id: number }> { + return this.attachmentRepository.insertSurveyTelemetryCredentialAttachment( + fileName, + fileSize, + fileType, + surveyId, + key + ); + } + + /** + * Get Survey Telemetry Attachment By File Name + * + * @param {string} fileName + * @param {number} surveyId + * @return {*} {Promise} + * @memberof AttachmentService + */ + async getSurveyTelemetryCredentialAttachmentByFileName(fileName: string, surveyId: number): Promise { + return this.attachmentRepository.getSurveyTelemetryCredentialAttachmentByFileName(fileName, surveyId); + } + + /** + * Upsert survey telemetry credential attachment record. + * + * @param {Express.Multer.File} file + * @param {number} projectId + * @param {number} surveyId + * @param {string} attachmentType + * @return {*} {Promise<{ survey_telemetry_credential_attachment_id: number; key: string }>} + * @memberof AttachmentService + */ + async upsertSurveyTelemetryCredentialAttachment( + file: Express.Multer.File, + projectId: number, + surveyId: number, + attachmentType: string + ): Promise<{ survey_telemetry_credential_attachment_id: number; key: string }> { + const key = generateS3FileKey({ + projectId: projectId, + surveyId: surveyId, + fileName: file.originalname, + folder: 'telemetry-credentials' + }); + + const getResponse = await this.getSurveyTelemetryCredentialAttachmentByFileName(file.originalname, surveyId); + + let attachmentResult: { survey_telemetry_credential_attachment_id: number }; + + if (getResponse && getResponse.rowCount) { + // Existing attachment with matching name found, update it + attachmentResult = await this.updateSurveyTelemetryCredentialAttachment( + surveyId, + file.originalname, + attachmentType + ); + } else { + // No matching attachment found, insert new attachment + attachmentResult = await this.insertSurveyTelemetryCredentialAttachment( + file.originalname, + file.size, + attachmentType, + surveyId, + key + ); + } + + return { ...attachmentResult, key }; + } + + /** + * Get Survey telemetry credential attachment S3 Key + * + * @param {number} surveyId + * @param {number} attachmentId + * @return {*} {Promise} + * @memberof AttachmentService + */ + async getSurveyTelemetryCredentialAttachmentS3Key(surveyId: number, attachmentId: number): Promise { + return this.attachmentRepository.getSurveyTelemetryCredentialAttachmentS3Key(surveyId, attachmentId); + } } diff --git a/api/src/services/bcgw-layer-service.test.ts b/api/src/services/bcgw-layer-service.test.ts index 461aa16efe..ea5835acd3 100644 --- a/api/src/services/bcgw-layer-service.test.ts +++ b/api/src/services/bcgw-layer-service.test.ts @@ -685,11 +685,11 @@ describe('BcgwLayerService', () => { const regions = await service.getIntersectingNrmRegionNamesFromFeatures([featureA, featureB], mockDbConnection); - expect(mockGetGeoJsonString.firstCall.calledWithExactly(featureA.geometry, Srid3005)).to.be.true; - expect(mockGetGeoJsonString.secondCall.calledWithExactly(featureB.geometry, Srid3005)).to.be.true; + expect(mockGetGeoJsonString.firstCall).to.have.been.calledWithExactly(featureA.geometry, Srid3005); + expect(mockGetGeoJsonString.secondCall).to.have.been.calledWithExactly(featureB.geometry, Srid3005); - expect(mockGetNrmRegionNames.firstCall.calledWithExactly('A')).to.be.true; - expect(mockGetNrmRegionNames.secondCall.calledWithExactly('B')).to.be.true; + expect(mockGetNrmRegionNames.firstCall).to.have.been.calledWithExactly('A'); + expect(mockGetNrmRegionNames.secondCall).to.have.been.calledWithExactly('B'); expect(regions).to.eqls(['Cariboo', 'South']); }); diff --git a/api/src/services/bctw-service.test.ts b/api/src/services/bctw-service.test.ts deleted file mode 100755 index e6b235c37f..0000000000 --- a/api/src/services/bctw-service.test.ts +++ /dev/null @@ -1,410 +0,0 @@ -import { AxiosResponse } from 'axios'; -import chai, { expect } from 'chai'; -import FormData from 'form-data'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { - BctwService, - DELETE_DEPLOYMENT_ENDPOINT, - DEPLOY_DEVICE_ENDPOINT, - GET_CODE_ENDPOINT, - GET_COLLAR_VENDORS_ENDPOINT, - GET_DEPLOYMENTS_BY_CRITTER_ENDPOINT, - GET_DEPLOYMENTS_BY_DEVICE_ENDPOINT, - GET_DEPLOYMENTS_ENDPOINT, - GET_DEVICE_DETAILS, - GET_KEYX_STATUS_ENDPOINT, - GET_TELEMETRY_POINTS_ENDPOINT, - GET_TELEMETRY_TRACKS_ENDPOINT, - HEALTH_ENDPOINT, - IDeployDevice, - IDeploymentUpdate, - MANUAL_AND_VENDOR_TELEMETRY, - MANUAL_TELEMETRY, - UPDATE_DEPLOYMENT_ENDPOINT, - UPSERT_DEVICE_ENDPOINT, - VENDOR_TELEMETRY -} from './bctw-service'; -import { KeycloakService } from './keycloak-service'; - -chai.use(sinonChai); - -describe('BctwService', () => { - afterEach(() => { - sinon.restore(); - }); - - const mockUser = { keycloak_guid: 'abc123', username: 'testuser' }; - - describe('getUserHeader', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return a JSON string', async () => { - const bctwService = new BctwService(mockUser); - const result = bctwService.getUserHeader(); - expect(result).to.be.a('string'); - expect(JSON.parse(result)).to.deep.equal(mockUser); - }); - }); - - describe('getToken', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return a string from the keycloak service', async () => { - const mockToken = 'abc123'; - const bctwService = new BctwService(mockUser); - const getKeycloakServiceTokenStub = sinon - .stub(KeycloakService.prototype, 'getKeycloakServiceToken') - .resolves(mockToken); - - const result = await bctwService.getToken(); - expect(result).to.equal(mockToken); - expect(getKeycloakServiceTokenStub).to.have.been.calledOnce; - }); - }); - - describe('_makeGetRequest', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should make an axios get request', async () => { - const bctwService = new BctwService(mockUser); - const endpoint = '/endpoint'; - const mockResponse = { data: 'data' } as AxiosResponse; - - const mockAxios = sinon.stub(bctwService.axiosInstance, 'get').resolves(mockResponse); - - const result = await bctwService._makeGetRequest(endpoint); - - expect(result).to.equal(mockResponse.data); - expect(mockAxios).to.have.been.calledOnceWith(`${endpoint}`); - }); - - it('should make an axios get request with params', async () => { - const bctwService = new BctwService(mockUser); - const endpoint = '/endpoint'; - const queryParams = { param: 'param' }; - const mockResponse = { data: 'data' } as AxiosResponse; - - const mockAxios = sinon.stub(bctwService.axiosInstance, 'get').resolves(mockResponse); - - const result = await bctwService._makeGetRequest(endpoint, queryParams); - - expect(result).to.equal(mockResponse.data); - expect(mockAxios).to.have.been.calledOnceWith(`${endpoint}?param=${queryParams['param']}`); - }); - }); - - describe('BctwService public methods', () => { - afterEach(() => { - sinon.restore(); - }); - - const bctwService = new BctwService(mockUser); - const mockDevice: IDeployDevice = { - device_id: 1, - frequency: 100, - device_make: 'Lotek', - device_model: 'model', - attachment_start: '2020-01-01', - attachment_end: '2020-01-02', - critter_id: 'abc123' - }; - const mockDeployment: IDeploymentUpdate = { - deployment_id: 'adcd', - attachment_start: '2020-01-01', - attachment_end: '2020-01-02' - }; - - describe('deployDevice', () => { - it('should send a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post'); - - await bctwService.deployDevice(mockDevice); - - expect(mockAxios).to.have.been.calledOnceWith(DEPLOY_DEVICE_ENDPOINT, mockDevice); - }); - }); - - describe('getDeployments', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getDeployments(); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_DEPLOYMENTS_ENDPOINT); - }); - }); - - describe('updateDeployment', () => { - it('should send a patch request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'patch'); - - await bctwService.updateDeployment(mockDeployment); - - expect(mockAxios).to.have.been.calledOnceWith(UPDATE_DEPLOYMENT_ENDPOINT, mockDeployment); - }); - }); - - describe('getCollarVendors', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getCollarVendors(); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_COLLAR_VENDORS_ENDPOINT); - }); - }); - - describe('getHealth', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getHealth(); - - expect(mockGetRequest).to.have.been.calledOnceWith(HEALTH_ENDPOINT); - }); - }); - - describe('getCode', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getCode('codeHeader'); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_CODE_ENDPOINT, { codeHeader: 'codeHeader' }); - }); - }); - - describe('getDeploymentsByCritterId', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getDeploymentsByCritterId(['abc123']); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_DEPLOYMENTS_BY_CRITTER_ENDPOINT, { - critter_ids: ['abc123'] - }); - }); - }); - - describe('getDeviceDetails', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getDeviceDetails(123, 'Lotek'); - - expect(mockGetRequest).to.have.been.calledOnceWith(`${GET_DEVICE_DETAILS}${123}`); - }); - }); - - describe('getDeviceDeployments', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getDeviceDeployments(123, 'Lotek'); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_DEPLOYMENTS_BY_DEVICE_ENDPOINT, { - device_id: '123', - make: 'Lotek' - }); - }); - }); - - describe('uploadKeyX', () => { - it('should send a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: { results: [], errors: [] } }); - const mockMulterFile = { buffer: 'buffer', originalname: 'originalname' } as unknown as Express.Multer.File; - sinon.stub(FormData.prototype, 'append'); - const mockGetFormDataHeaders = sinon - .stub(FormData.prototype, 'getHeaders') - .resolves({ 'content-type': 'multipart/form-data' }); - - const result = await bctwService.uploadKeyX(mockMulterFile); - - expect(mockGetFormDataHeaders).to.have.been.calledOnce; - expect(result).to.eql({ totalKeyxFiles: 0, newRecords: 0, existingRecords: 0 }); - expect(mockAxios).to.have.been.calledOnce; - }); - - it('should throw an error if the response body has errors', async () => { - sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: { results: [], errors: [{ error: 'error' }] } }); - const mockMulterFile = { buffer: 'buffer', originalname: 'originalname' } as unknown as Express.Multer.File; - sinon.stub(FormData.prototype, 'append'); - sinon.stub(FormData.prototype, 'getHeaders').resolves({ 'content-type': 'multipart/form-data' }); - - await bctwService - .uploadKeyX(mockMulterFile) - .catch((e) => expect(e.message).to.equal('API request failed with errors')); - }); - }); - - describe('getKeyXDetails', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - await bctwService.getKeyXDetails([123]); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_KEYX_STATUS_ENDPOINT, { device_ids: ['123'] }); - }); - }); - - describe('updateDevice', () => { - it('should send a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: { results: [], errors: [] } }); - - const body = { - device_id: 1, - collar_id: '' - }; - await bctwService.updateDevice(body); - - expect(mockAxios).to.have.been.calledOnceWith(UPSERT_DEVICE_ENDPOINT, body); - }); - it('should send a post request and get some errors back', async () => { - sinon - .stub(bctwService.axiosInstance, 'post') - .resolves({ data: { results: [], errors: [{ device_id: 'error' }] } }); - - const body = { - device_id: 1, - collar_id: '' - }; - await bctwService.updateDevice(body).catch((e) => expect(e.message).to.equal('[{"device_id":"error"}]')); - }); - }); - - describe('getCritterTelemetryPoints', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - const startDate = new Date(); - const endDate = new Date(); - - await bctwService.getCritterTelemetryPoints('asdf', startDate, endDate); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_TELEMETRY_POINTS_ENDPOINT, { - critter_id: 'asdf', - start: startDate.toISOString(), - end: endDate.toISOString() - }); - }); - }); - - describe('getCritterTelemetryTracks', () => { - it('should send a get request', async () => { - const mockGetRequest = sinon.stub(bctwService, '_makeGetRequest'); - - const startDate = new Date(); - const endDate = new Date(); - - await bctwService.getCritterTelemetryTracks('asdf', startDate, endDate); - - expect(mockGetRequest).to.have.been.calledOnceWith(GET_TELEMETRY_TRACKS_ENDPOINT, { - critter_id: 'asdf', - start: startDate.toISOString(), - end: endDate.toISOString() - }); - }); - }); - - describe('deleteDeployment', () => { - it('should sent a delete request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'delete').resolves(); - - await bctwService.deleteDeployment('asdf'); - - expect(mockAxios).to.have.been.calledOnceWith(`${DELETE_DEPLOYMENT_ENDPOINT}/asdf`); - }); - }); - - describe('getManualTelemetry', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'get').resolves({ data: true }); - - const ret = await bctwService.getManualTelemetry(); - - expect(mockAxios).to.have.been.calledOnceWith(MANUAL_TELEMETRY); - expect(ret).to.be.true; - }); - }); - - describe('deleteManualTelemetry', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: true }); - - const ids = ['a', 'b']; - const ret = await bctwService.deleteManualTelemetry(ids); - - expect(mockAxios).to.have.been.calledOnceWith(`${MANUAL_TELEMETRY}/delete`, ids); - expect(ret).to.be.true; - }); - }); - - describe('createManualTelemetry', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: true }); - - const payload: any = { key: 'value' }; - const ret = await bctwService.createManualTelemetry(payload); - - expect(mockAxios).to.have.been.calledOnceWith(MANUAL_TELEMETRY, payload); - expect(ret).to.be.true; - }); - }); - - describe('updateManualTelemetry', () => { - it('should sent a patch request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'patch').resolves({ data: true }); - - const payload: any = { key: 'value' }; - const ret = await bctwService.updateManualTelemetry(payload); - - expect(mockAxios).to.have.been.calledOnceWith(MANUAL_TELEMETRY, payload); - expect(ret).to.be.true; - }); - }); - - describe('getManualTelemetryByDeploymentIds', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: true }); - - const payload: any = { key: 'value' }; - const ret = await bctwService.getManualTelemetryByDeploymentIds(payload); - - expect(mockAxios).to.have.been.calledOnceWith(`${MANUAL_TELEMETRY}/deployments`, payload); - expect(ret).to.be.true; - }); - }); - - describe('getVendorTelemetryByDeploymentIds', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: true }); - - const payload: any = { key: 'value' }; - const ret = await bctwService.getVendorTelemetryByDeploymentIds(payload); - - expect(mockAxios).to.have.been.calledOnceWith(`${VENDOR_TELEMETRY}/deployments`, payload); - expect(ret).to.be.true; - }); - }); - - describe('getAllTelemetryByDeploymentIds', () => { - it('should sent a post request', async () => { - const mockAxios = sinon.stub(bctwService.axiosInstance, 'post').resolves({ data: true }); - - const payload: any = { key: 'value' }; - const ret = await bctwService.getAllTelemetryByDeploymentIds(payload); - - expect(mockAxios).to.have.been.calledOnceWith(`${MANUAL_AND_VENDOR_TELEMETRY}/deployments`, payload); - expect(ret).to.be.true; - }); - }); - }); -}); diff --git a/api/src/services/bctw-service.ts b/api/src/services/bctw-service.ts deleted file mode 100644 index 136aee209a..0000000000 --- a/api/src/services/bctw-service.ts +++ /dev/null @@ -1,584 +0,0 @@ -import axios, { AxiosError, AxiosInstance, AxiosResponse } from 'axios'; -import { Request } from 'express'; -import FormData from 'form-data'; -import { GeometryCollection } from 'geojson'; -import { URLSearchParams } from 'url'; -import { z } from 'zod'; -import { ApiError, ApiErrorType, ApiGeneralError } from '../errors/api-error'; -import { HTTP500 } from '../errors/http-error'; -import { getSystemUserFromRequest } from '../utils/request'; -import { KeycloakService } from './keycloak-service'; - -export const IDeployDevice = z.object({ - device_id: z.number(), - frequency: z.number().optional(), - frequency_unit: z.string().optional(), - device_make: z.string().optional(), - device_model: z.string().optional(), - attachment_start: z.string(), - attachment_end: z.string().nullable(), - critter_id: z.string() -}); - -export type IDeployDevice = z.infer; - -export type IDevice = Omit & { collar_id: string }; - -export const IDeploymentUpdate = z.object({ - deployment_id: z.string(), - attachment_start: z.string(), - attachment_end: z.string() -}); - -export type IDeploymentUpdate = z.infer; - -export const IDeploymentRecord = z.object({ - assignment_id: z.string(), - collar_id: z.string(), - critter_id: z.string(), - created_at: z.string(), - created_by_user_id: z.string(), - updated_at: z.string(), - updated_by_user_id: z.string(), - valid_from: z.string(), - valid_to: z.string(), - attachment_start: z.string(), - attachment_end: z.string(), - deployment_id: z.string(), - device_id: z.number() -}); - -export type IDeploymentRecord = z.infer; - -export const IUploadKeyxResponse = z.object({ - errors: z.array( - z.object({ - row: z.string(), - error: z.string(), - rownum: z.number() - }) - ), - results: z.array( - z.object({ - idcollar: z.number(), - comtype: z.string(), - idcom: z.string(), - collarkey: z.string(), - collartype: z.number(), - dtlast_fetch: z.string().nullable() - }) - ) -}); - -export type IUploadKeyxResponse = z.infer; - -export const IKeyXDetails = z.object({ - device_id: z.number(), - keyx: z - .object({ - idcom: z.string(), - comtype: z.string(), - idcollar: z.number(), - collarkey: z.string(), - collartype: z.number() - }) - .nullable() -}); - -export type IKeyXDetails = z.infer; - -export const IAllTelemetry = z - .object({ - deployment_id: z.string().uuid(), - latitude: z.number(), - longitude: z.number(), - acquisition_date: z.string(), - telemetry_type: z.string() - }) - .and( - // One of telemetry_id or telemetry_manual_id is expected to be non-null - z.union([ - z.object({ - telemetry_id: z.string().uuid(), - telemetry_manual_id: z.null() - }), - z.object({ - telemetry_id: z.null(), - telemetry_manual_id: z.string().uuid() - }) - ]) - ); - -export type IAllTelemetry = z.infer; - -export const IVendorTelemetry = z.object({ - telemetry_id: z.string(), - deployment_id: z.string().uuid(), - collar_transaction_id: z.string().uuid(), - critter_id: z.string().uuid(), - deviceid: z.number(), - latitude: z.number(), - longitude: z.number(), - elevation: z.number(), - vendor: z.string(), - acquisition_date: z.string() -}); - -export type IVendorTelemetry = z.infer; - -export const IManualTelemetry = z.object({ - telemetry_manual_id: z.string().uuid(), - deployment_id: z.string().uuid(), - latitude: z.number(), - longitude: z.number(), - acquisition_date: z.string() -}); - -export type IManualTelemetry = z.infer; - -export const IBctwUser = z.object({ - keycloak_guid: z.string(), - username: z.string() -}); - -interface ICodeResponse { - code_header_title: string; - code_header_name: string; - id: number; - code: string; - description: string; - long_description: string; -} - -export type IBctwUser = z.infer; - -export interface ICreateManualTelemetry { - deployment_id: string; - latitude: number; - longitude: number; - acquisition_date: string; -} - -export const BCTW_API_HOST = process.env.BCTW_API_HOST || ''; -export const DEPLOY_DEVICE_ENDPOINT = '/deploy-device'; -export const UPSERT_DEVICE_ENDPOINT = '/upsert-collar'; -export const GET_DEPLOYMENTS_ENDPOINT = '/get-deployments'; -export const GET_DEPLOYMENTS_BY_CRITTER_ENDPOINT = '/get-deployments-by-critter-id'; -export const GET_DEPLOYMENTS_BY_DEVICE_ENDPOINT = '/get-deployments-by-device-id'; -export const UPDATE_DEPLOYMENT_ENDPOINT = '/update-deployment'; -export const DELETE_DEPLOYMENT_ENDPOINT = '/delete-deployment'; -export const GET_COLLAR_VENDORS_ENDPOINT = '/get-collar-vendors'; -export const HEALTH_ENDPOINT = '/health'; -export const GET_CODE_ENDPOINT = '/get-code'; -export const GET_DEVICE_DETAILS = '/get-collar-history-by-device/'; -export const UPLOAD_KEYX_ENDPOINT = '/import-xml'; -export const GET_KEYX_STATUS_ENDPOINT = '/get-collars-keyx'; -export const GET_TELEMETRY_POINTS_ENDPOINT = '/get-critters'; -export const GET_TELEMETRY_TRACKS_ENDPOINT = '/get-critter-tracks'; -export const MANUAL_TELEMETRY = '/manual-telemetry'; -export const VENDOR_TELEMETRY = '/vendor-telemetry'; -export const DELETE_MANUAL_TELEMETRY = '/manual-telemetry/delete'; -export const MANUAL_AND_VENDOR_TELEMETRY = '/all-telemetry'; - -/** - * Safely attempt to retrieve system user fields for BCTW user dependency. - * - * @param {Request} req - * @throws {ApiGeneralError} - Missing required fields - * @returns {IBctwUser} - */ -export const getBctwUser = (req: Request): IBctwUser => { - const systemUser = getSystemUserFromRequest(req); - - if (!systemUser.user_guid || !systemUser.user_identifier) { - throw new ApiGeneralError('System user missing required fields', ['bctw-service->getBctwUser']); - } - - return { - keycloak_guid: systemUser.user_guid, - username: systemUser.user_identifier - }; -}; - -export class BctwService { - user: IBctwUser; - keycloak: KeycloakService; - axiosInstance: AxiosInstance; - - constructor(user: IBctwUser) { - this.user = user; - this.keycloak = new KeycloakService(); - this.axiosInstance = axios.create({ - headers: { - user: this.getUserHeader() - }, - baseURL: BCTW_API_HOST, - timeout: 10000 - }); - - this.axiosInstance.interceptors.response.use( - (response: AxiosResponse) => { - return response; - }, - (error: AxiosError) => { - if ( - error?.code === 'ECONNREFUSED' || - error?.code === 'ECONNRESET' || - error?.code === 'ETIMEOUT' || - error?.code === 'ECONNABORTED' - ) { - return Promise.reject( - new HTTP500('Connection to the BCTW API server was refused. Please try again later.', [error?.message]) - ); - } - const data: any = error.response?.data; - const errMsg = data?.error ?? data?.errors ?? data ?? 'Unknown error'; - - return Promise.reject( - new ApiError( - ApiErrorType.UNKNOWN, - `API request failed with status code ${error?.response?.status}, ${errMsg}`, - Array.isArray(errMsg) ? errMsg : [errMsg] - ) - ); - } - ); - - // Async request interceptor - this.axiosInstance.interceptors.request.use( - async (config) => { - const token = await this.getToken(); - config.headers['Authorization'] = `Bearer ${token}`; - - return config; - }, - (error) => { - return Promise.reject(error); - } - ); - } - - /** - * Return user information as a JSON string. - * - * @return {*} {string} - * @memberof BctwService - */ - getUserHeader(): string { - return JSON.stringify(this.user); - } - - /** - * Retrieve an authentication token using Keycloak service. - * - * @return {*} {Promise} - * @memberof BctwService - */ - async getToken(): Promise { - const token = await this.keycloak.getKeycloakServiceToken(); - return token; - } - - /** - * Send an authorized get request to the BCTW API. - * - * @param {string} endpoint - * @param {Record} [queryParams] - An object containing query parameters as key-value pairs - * @return {*} - * @memberof BctwService - */ - async _makeGetRequest(endpoint: string, queryParams?: Record) { - let url = endpoint; - if (queryParams) { - const params = new URLSearchParams(queryParams); - url += `?${params.toString()}`; - } - - const response = await this.axiosInstance.get(url); - return response.data; - } - - /** - * Create a new deployment for a telemetry device on a critter. - * - * @param {IDeployDevice} device - * @return {*} {Promise} - * @memberof BctwService - */ - async deployDevice(device: IDeployDevice): Promise { - return this.axiosInstance.post(DEPLOY_DEVICE_ENDPOINT, device); - } - - /** - * Update device hardware details in BCTW. - * - * @param {IDevice} device - * @returns {*} {IDevice} - * @memberof BctwService - */ - async updateDevice(device: IDevice): Promise { - const { data } = await this.axiosInstance.post(UPSERT_DEVICE_ENDPOINT, device); - if (data.errors.length) { - throw Error(JSON.stringify(data.errors)); - } - return data; - } - - /** - * Get device hardware details by device id and device make. - * - * @param {number} deviceId - * @param {deviceMake} deviceMake - * @returns {*} {Promise} - * @memberof BctwService - */ - async getDeviceDetails(deviceId: number, deviceMake: string): Promise { - return this._makeGetRequest(`${GET_DEVICE_DETAILS}${deviceId}`, { make: deviceMake }); - } - - /** - * Get deployments by device id and device make, may return results for multiple critters. - * - * @param {number} deviceId - * @param {string} deviceMake - * @returns {*} {Promise} - * @memberof BctwService - */ - async getDeviceDeployments(deviceId: number, deviceMake: string): Promise { - return this._makeGetRequest(GET_DEPLOYMENTS_BY_DEVICE_ENDPOINT, { - device_id: String(deviceId), - make: deviceMake - }); - } - - /** - * Get all existing deployments. - * - * @return {*} {Promise} - * @memberof BctwService - */ - async getDeployments(): Promise { - return this._makeGetRequest(GET_DEPLOYMENTS_ENDPOINT); - } - - /** - * Get all existing deployments for a list of critter IDs. - * - * @param {string[]} critter_ids - * @return {*} {Promise} - * @memberof BctwService - */ - async getDeploymentsByCritterId(critter_ids: string[]): Promise { - const query = { critter_ids: critter_ids }; - return this._makeGetRequest(GET_DEPLOYMENTS_BY_CRITTER_ENDPOINT, query); - } - - /** - * Update the start and end dates of an existing deployment. - * - * @param {IDeploymentUpdate} deployment - * @return {*} {Promise} - * @memberof BctwService - */ - async updateDeployment(deployment: IDeploymentUpdate): Promise { - return this.axiosInstance.patch(UPDATE_DEPLOYMENT_ENDPOINT, deployment); - } - - /** - * Soft deletes the deployment in BCTW. - * - * @param {string} deployment_id uuid - * @returns {*} {Promise} - * @memberof BctwService - */ - async deleteDeployment(deployment_id: string): Promise { - return this.axiosInstance.delete(`${DELETE_DEPLOYMENT_ENDPOINT}/${deployment_id}`); - } - - /** - * Get a list of all supported collar vendors. - * - * @return {*} {Promise} - * @memberof BctwService - */ - async getCollarVendors(): Promise { - return this._makeGetRequest(GET_COLLAR_VENDORS_ENDPOINT); - } - - /** - * Get the health of the platform. - * - * @return {*} {Promise} - * @memberof BctwService - */ - async getHealth(): Promise { - return this._makeGetRequest(HEALTH_ENDPOINT); - } - - /** - * Upload a single or multiple zipped keyX files to the BCTW API. - * - * @param {Express.Multer.File} keyX - * @return {*} {Promise} - * @memberof BctwService - */ - async uploadKeyX(keyX: Express.Multer.File) { - const formData = new FormData(); - formData.append('xml', keyX.buffer, keyX.originalname); - const config = { - headers: { - ...formData.getHeaders() - } - }; - const response = await this.axiosInstance.post(UPLOAD_KEYX_ENDPOINT, formData, config); - const data: IUploadKeyxResponse = response.data; - if (data.errors.length) { - const actualErrors: string[] = []; - for (const error of data.errors) { - // Ignore errors that indicate that a keyX already exists - if (!error.error.endsWith('already exists')) { - actualErrors.push(error.error); - } - } - if (actualErrors.length) { - throw new ApiError(ApiErrorType.UNKNOWN, 'API request failed with errors', actualErrors); - } - } - return { - totalKeyxFiles: data.results.length + data.errors.length, - newRecords: data.results.length, - existingRecords: data.errors.length - }; - } - - async getKeyXDetails(deviceIds: number[]): Promise { - return this._makeGetRequest(GET_KEYX_STATUS_ENDPOINT, { device_ids: deviceIds.map((id) => String(id)) }); - } - - /** - * Get a list of all BCTW codes with a given header name. - * - * @param {string} codeHeaderName - * @return {*} {Promise} - * @memberof BctwService - */ - async getCode(codeHeaderName: string): Promise { - return this._makeGetRequest(GET_CODE_ENDPOINT, { codeHeader: codeHeaderName }); - } - - /** - * Get all telemetry points for an animal. - * The geometry will be points, and the properties will include the critter id and deployment id. - * @param critterId uuid - * @param startDate - * @param endDate - * @return {*} {Promise} - * @memberof BctwService - */ - async getCritterTelemetryPoints(critterId: string, startDate: Date, endDate: Date): Promise { - return this._makeGetRequest(GET_TELEMETRY_POINTS_ENDPOINT, { - critter_id: critterId, - start: startDate.toISOString(), - end: endDate.toISOString() - }); - } - - /** - * Get all telemetry tracks for an animal. - * The geometry will be lines, and the properties will include the critter id and deployment id. - * The lines are actually just generated on the fly by the the db using the same points as getCritterTelemetryPoints. - * - * @param critterId uuid - * @param startDate - * @param endDate - * @return {*} {Promise} - * @memberof BctwService - */ - async getCritterTelemetryTracks(critterId: string, startDate: Date, endDate: Date): Promise { - return this._makeGetRequest(GET_TELEMETRY_TRACKS_ENDPOINT, { - critter_id: critterId, - start: startDate.toISOString(), - end: endDate.toISOString() - }); - } - - /** - * Get all manual telemetry records - * This set of telemetry is mostly useful for testing purposes. - * - * @returns {*} IManualTelemetry[] - **/ - async getManualTelemetry(): Promise { - return this._makeGetRequest(MANUAL_TELEMETRY); - } - - /** - * retrieves manual telemetry from list of deployment ids - * - * @async - * @param {string[]} deployment_ids - bctw deployments - * @returns {*} IManualTelemetry[] - */ - async getManualTelemetryByDeploymentIds(deployment_ids: string[]): Promise { - const res = await this.axiosInstance.post(`${MANUAL_TELEMETRY}/deployments`, deployment_ids); - return res.data; - } - - /** - * retrieves manual telemetry from list of deployment ids - * - * @async - * @param {string[]} deployment_ids - bctw deployments - * @returns {*} IManualTelemetry[] - */ - async getVendorTelemetryByDeploymentIds(deployment_ids: string[]): Promise { - const res = await this.axiosInstance.post(`${VENDOR_TELEMETRY}/deployments`, deployment_ids); - return res.data; - } - - /** - * retrieves manual and vendor telemetry from list of deployment ids - * - * @async - * @param {string[]} deployment_ids - bctw deployments - * @returns {*} IManualTelemetry[] - */ - async getAllTelemetryByDeploymentIds(deployment_ids: string[]): Promise { - const res = await this.axiosInstance.post(`${MANUAL_AND_VENDOR_TELEMETRY}/deployments`, deployment_ids); - return res.data; - } - - /** - * Delete manual telemetry records by telemetry_manual_id - * Note: This is a post request that accepts an array of ids - * @param {uuid[]} telemetry_manaual_ids - * - * @returns {*} IManualTelemetry[] - **/ - async deleteManualTelemetry(telemetry_manual_ids: string[]): Promise { - const res = await this.axiosInstance.post(DELETE_MANUAL_TELEMETRY, telemetry_manual_ids); - return res.data; - } - - /** - * Bulk create manual telemetry records - * @param {ICreateManualTelemetry[]} payload - * - * @returns {*} IManualTelemetry[] - **/ - async createManualTelemetry(payload: ICreateManualTelemetry[]): Promise { - const res = await this.axiosInstance.post(MANUAL_TELEMETRY, payload); - return res.data; - } - - /** - * Bulk update manual telemetry records - * @param {IManualTelemetry} payload - * - * @returns {*} IManualTelemetry[] - **/ - async updateManualTelemetry(payload: IManualTelemetry[]): Promise { - const res = await this.axiosInstance.patch(MANUAL_TELEMETRY, payload); - return res.data; - } -} diff --git a/api/src/services/bctw-service/bctw-deployment-service.ts b/api/src/services/bctw-service/bctw-deployment-service.ts new file mode 100644 index 0000000000..1d4a9da582 --- /dev/null +++ b/api/src/services/bctw-service/bctw-deployment-service.ts @@ -0,0 +1,129 @@ +import { z } from 'zod'; +import { BctwService } from './bctw-service'; + +export const BctwDeploymentRecordWithDeviceMeta = z.object({ + assignment_id: z.string().uuid(), + collar_id: z.string().uuid(), + critter_id: z.string().uuid(), + created_at: z.string(), + created_by_user_id: z.string().nullable(), + updated_at: z.string().nullable(), + updated_by_user_id: z.string().nullable(), + valid_from: z.string(), + valid_to: z.string().nullable(), + attachment_start: z.string(), + attachment_end: z.string().nullable(), + deployment_id: z.string(), + device_id: z.number().nullable(), + device_make: z.number().nullable(), + device_model: z.string().nullable(), + frequency: z.number().nullable(), + frequency_unit: z.number().nullable() +}); +export type BctwDeploymentRecordWithDeviceMeta = z.infer; + +export const BctwDeploymentRecord = z.object({ + assignment_id: z.string(), + collar_id: z.string(), + critter_id: z.string(), + created_at: z.string(), + created_by_user_id: z.string(), + updated_at: z.string().nullable(), + updated_by_user_id: z.string().nullable(), + valid_from: z.string(), + valid_to: z.string().nullable(), + attachment_start: z.string(), + attachment_end: z.string().nullable(), + deployment_id: z.string(), + device_id: z.number() +}); +export type BctwDeploymentRecord = z.infer; + +export const BctwDeploymentUpdate = z.object({ + deployment_id: z.string(), + attachment_start: z.string(), + attachment_end: z.string().nullable() +}); +export type BctwDeploymentUpdate = z.infer; + +export const BctwDeployDevice = z.object({ + deployment_id: z.string().uuid(), + device_id: z.number(), + frequency: z.number().optional(), + frequency_unit: z.string().optional(), + device_make: z.string().optional(), + device_model: z.string().optional(), + attachment_start: z.string(), + attachment_end: z.string().nullable(), + critter_id: z.string() +}); +export type BctwDeployDevice = z.infer; + +export class BctwDeploymentService extends BctwService { + /** + * Create a new deployment for a telemetry device on a critter. + * + * @param {BctwDeployDevice} device + * @return {*} {Promise} + * @memberof BctwDeploymentService + */ + async createDeployment(device: BctwDeployDevice): Promise { + const { data } = await this.axiosInstance.post('/deploy-device', device); + + return data; + } + + /** + * Get deployment records for a list of deployment IDs. + * + * @param {string[]} deploymentIds + * @return {*} {Promise} + * @memberof BctwDeploymentService + */ + async getDeploymentsByIds(deploymentIds: string[]): Promise { + const { data } = await this.axiosInstance.post('/get-deployments', deploymentIds); + + return data; + } + + /** + * Get all existing deployments for a list of critter IDs. + * + * @param {string[]} critter_ids + * @return {*} {Promise} + * @memberof BctwDeploymentService + */ + async getDeploymentsByCritterId(critter_ids: string[]): Promise { + const { data } = await this.axiosInstance.get('/get-deployments-by-critter-id', { + params: { critter_ids: critter_ids } + }); + + return data; + } + + /** + * Update the start and end dates of an existing deployment. + * + * @param {BctwDeploymentUpdate} deployment + * @return {*} {Promise} + * @memberof BctwDeploymentService + */ + async updateDeployment(deployment: BctwDeploymentUpdate): Promise[]> { + const { data } = await this.axiosInstance.patch('/update-deployment', deployment); + + return data; + } + + /** + * Soft deletes the deployment in BCTW. + * + * @param {string} deployment_id uuid + * @returns {*} {Promise} + * @memberof BctwDeploymentService + */ + async deleteDeployment(deployment_id: string): Promise { + const { data } = await this.axiosInstance.delete(`/delete-deployment/${deployment_id}`); + + return data; + } +} diff --git a/api/src/services/bctw-service/bctw-device-service.ts b/api/src/services/bctw-service/bctw-device-service.ts new file mode 100644 index 0000000000..e53e38088a --- /dev/null +++ b/api/src/services/bctw-service/bctw-device-service.ts @@ -0,0 +1,85 @@ +import { BctwDeployDevice } from './bctw-deployment-service'; +import { BctwService } from './bctw-service'; + +export type BctwDevice = Omit & { + collar_id: string; +}; + +export type BctwUpdateCollarRequest = { + /** + * The primary ID (uuid) of the collar record to update. + */ + collar_id: string; + device_make?: number | null; + device_model?: string | null; + frequency?: number | null; + frequency_unit?: number | null; +}; + +export class BctwDeviceService extends BctwService { + /** + * Get a list of all supported collar vendors. + * + * TODO: unused? + * + * @return {*} {Promise} + * @memberof BctwDeviceService + */ + async getCollarVendors(): Promise { + const { data } = await this.axiosInstance.get('/get-collar-vendors'); + + return data; + } + + /** + * Get device hardware details by device id and device make. + * + * TODO: unused? + * + * @param {number} deviceId + * @param {deviceMake} deviceMake + * @returns {*} {Promise} + * @memberof BctwService + */ + async getDeviceDetails(deviceId: number, deviceMake: string): Promise { + const { data } = await this.axiosInstance.get(`/get-collar-history-by-device/${deviceId}`, { + params: { make: deviceMake } + }); + + return data; + } + + /** + * Update device hardware details in BCTW. + * + * @param {BctwDevice} device + * @returns {*} {BctwDevice} + * @memberof BctwService + */ + async updateDevice(device: BctwDevice): Promise { + const { data } = await this.axiosInstance.post('/upsert-collar', device); + + if (data?.errors?.length) { + throw Error(JSON.stringify(data.errors)); + } + + return data; + } + + /** + * Update collar details in BCTW. + * + * @param {BctwUpdateCollarRequest} collar - The collar details to update. + * @return {*} {Promise} + * @memberof BctwDeviceService + */ + async updateCollar(collar: BctwUpdateCollarRequest): Promise { + const { data } = await this.axiosInstance.patch('/update-collar', collar); + + if (data?.errors?.length) { + throw Error(JSON.stringify(data.errors)); + } + + return data; + } +} diff --git a/api/src/services/bctw-service/bctw-keyx-service.test.ts b/api/src/services/bctw-service/bctw-keyx-service.test.ts new file mode 100644 index 0000000000..52ad7a64e1 --- /dev/null +++ b/api/src/services/bctw-service/bctw-keyx-service.test.ts @@ -0,0 +1,83 @@ +import chai, { expect } from 'chai'; +import FormData from 'form-data'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { BctwKeyxService } from '../bctw-service/bctw-keyx-service'; + +chai.use(sinonChai); + +describe('BctwKeyxService', () => { + afterEach(() => { + sinon.restore(); + }); + + describe('uploadKeyX', () => { + it('should send a post request', async () => { + const mockUser = { keycloak_guid: 'abc123', username: 'testuser' }; + + const bctwKeyxService = new BctwKeyxService(mockUser); + + const mockAxios = sinon + .stub(bctwKeyxService.axiosInstance, 'post') + .resolves({ data: { results: [], errors: [] } }); + + const mockMulterFile = { buffer: 'buffer', originalname: 'originalname.keyx' } as unknown as Express.Multer.File; + + sinon.stub(FormData.prototype, 'append'); + + const mockGetFormDataHeaders = sinon + .stub(FormData.prototype, 'getHeaders') + .resolves({ 'content-type': 'multipart/form-data' }); + + const result = await bctwKeyxService.uploadKeyX(mockMulterFile); + + expect(mockGetFormDataHeaders).to.have.been.calledOnce; + expect(result).to.eql({ totalKeyxFiles: 0, newRecords: 0, existingRecords: 0 }); + expect(mockAxios).to.have.been.calledOnce; + }); + + it('should throw an error if the file is not a valid keyx file', async () => { + const mockUser = { keycloak_guid: 'abc123', username: 'testuser' }; + + const bctwKeyxService = new BctwKeyxService(mockUser); + + sinon.stub(bctwKeyxService.axiosInstance, 'post').rejects(); + + const mockMulterFile = { + buffer: 'buffer', + originalname: 'originalname.notValid' // invalid file extension + } as unknown as Express.Multer.File; + + sinon.stub(FormData.prototype, 'append'); + + sinon.stub(FormData.prototype, 'getHeaders').resolves({ 'content-type': 'multipart/form-data' }); + + await bctwKeyxService + .uploadKeyX(mockMulterFile) + .catch((e) => + expect(e.message).to.equal('File is neither a .keyx file, nor an archive containing only .keyx files') + ); + }); + + it('should throw an error if the response body has errors', async () => { + const mockUser = { keycloak_guid: 'abc123', username: 'testuser' }; + + const bctwKeyxService = new BctwKeyxService(mockUser); + + sinon + .stub(bctwKeyxService.axiosInstance, 'post') + .resolves({ data: { results: [], errors: [{ error: 'error' }] } }); + + const mockMulterFile = { buffer: 'buffer', originalname: 'originalname.keyx' } as unknown as Express.Multer.File; + + sinon.stub(FormData.prototype, 'append'); + + sinon.stub(FormData.prototype, 'getHeaders').resolves({ 'content-type': 'multipart/form-data' }); + + await bctwKeyxService + .uploadKeyX(mockMulterFile) + .catch((e) => expect(e.message).to.equal('API request failed with errors')); + }); + }); +}); diff --git a/api/src/services/bctw-service/bctw-keyx-service.ts b/api/src/services/bctw-service/bctw-keyx-service.ts new file mode 100644 index 0000000000..5ced5e4c17 --- /dev/null +++ b/api/src/services/bctw-service/bctw-keyx-service.ts @@ -0,0 +1,102 @@ +import FormData from 'form-data'; +import { z } from 'zod'; +import { ApiError, ApiErrorType } from '../../errors/api-error'; +import { checkFileForKeyx } from '../../utils/media/media-utils'; +import { BctwService } from './bctw-service'; + +export const BctwUploadKeyxResponse = z.object({ + errors: z.array( + z.object({ + row: z.string(), + error: z.string(), + rownum: z.number() + }) + ), + results: z.array( + z.object({ + idcollar: z.number(), + comtype: z.string(), + idcom: z.string(), + collarkey: z.string(), + collartype: z.number(), + dtlast_fetch: z.string().nullable() + }) + ) +}); +export type BctwUploadKeyxResponse = z.infer; + +export const BctwKeyXDetails = z.object({ + device_id: z.number(), + keyx: z + .object({ + idcom: z.string(), + comtype: z.string(), + idcollar: z.number(), + collarkey: z.string(), + collartype: z.number() + }) + .nullable() +}); +export type BctwKeyXDetails = z.infer; + +export class BctwKeyxService extends BctwService { + /** + * Upload a single or multiple zipped keyX files to the BCTW API. + * + * @param {Express.Multer.File} keyX + * @return {*} {Promise} + * @memberof BctwKeyxService + */ + async uploadKeyX(keyX: Express.Multer.File) { + const isValidKeyX = checkFileForKeyx(keyX); + + if (isValidKeyX.error) { + throw new ApiError(ApiErrorType.GENERAL, isValidKeyX.error); + } + + const formData = new FormData(); + + formData.append('xml', keyX.buffer, keyX.originalname); + + const config = { + headers: { + ...formData.getHeaders() + } + }; + + const response = await this.axiosInstance.post('/import-xml', formData, config); + + const data: BctwUploadKeyxResponse = response.data; + + if (data.errors.length) { + const actualErrors: string[] = []; + + for (const error of data.errors) { + // Ignore errors that indicate that a keyX already exists + if (!error.error.endsWith('already exists')) { + actualErrors.push(error.error); + } + } + + if (actualErrors.length) { + throw new ApiError(ApiErrorType.UNKNOWN, 'API request failed with errors', actualErrors); + } + } + + return { + totalKeyxFiles: data.results.length + data.errors.length, + newRecords: data.results.length, + existingRecords: data.errors.length + }; + } + + async getKeyXDetails(deviceIds: number[]): Promise { + const { data } = await this.axiosInstance.get('/get-collars-keyx', { + params: { + device_ids: deviceIds.map((id) => String(id)) + } + }); + + return data; + } +} diff --git a/api/src/services/bctw-service/bctw-service.ts b/api/src/services/bctw-service/bctw-service.ts new file mode 100644 index 0000000000..eb28484b91 --- /dev/null +++ b/api/src/services/bctw-service/bctw-service.ts @@ -0,0 +1,124 @@ +import axios, { AxiosError, AxiosInstance, AxiosResponse } from 'axios'; +import { Request } from 'express'; +import { z } from 'zod'; +import { ApiError, ApiErrorType } from '../../errors/api-error'; +import { HTTP500 } from '../../errors/http-error'; +import { ICodeResponse } from '../../models/bctw'; +import { KeycloakService } from '../keycloak-service'; + +export const BctwUser = z.object({ + keycloak_guid: z.string(), + username: z.string() +}); +export type BctwUser = z.infer; + +export const getBctwUser = (req: Request): BctwUser => ({ + keycloak_guid: req.system_user?.user_guid ?? '', + username: req.system_user?.user_identifier ?? '' +}); + +export class BctwService { + user: BctwUser; + keycloak: KeycloakService; + axiosInstance: AxiosInstance; + + constructor(user: BctwUser) { + this.user = user; + this.keycloak = new KeycloakService(); + this.axiosInstance = axios.create({ + headers: { + user: this.getUserHeader() + }, + baseURL: process.env.BCTW_API_HOST || '', + timeout: 10000 + }); + + this.axiosInstance.interceptors.response.use( + (response: AxiosResponse) => { + return response; + }, + (error: AxiosError) => { + if ( + error?.code === 'ECONNREFUSED' || + error?.code === 'ECONNRESET' || + error?.code === 'ETIMEOUT' || + error?.code === 'ECONNABORTED' + ) { + return Promise.reject( + new HTTP500('Connection to the BCTW API server was refused. Please try again later.', [error?.message]) + ); + } + const data: any = error.response?.data; + const errMsg = data?.error ?? data?.errors ?? data ?? 'Unknown error'; + const issues = data?.issues ?? []; + + return Promise.reject( + new ApiError( + ApiErrorType.UNKNOWN, + `API request failed with status code ${error?.response?.status}: ${errMsg}`, + [].concat(errMsg).concat(issues) + ) + ); + } + ); + + // Async request interceptor + this.axiosInstance.interceptors.request.use( + async (config) => { + const token = await this.getToken(); + config.headers['Authorization'] = `Bearer ${token}`; + + return config; + }, + (error) => { + return Promise.reject(error); + } + ); + } + + /** + * Return user information as a JSON string. + * + * @return {*} {string} + * @memberof BctwService + */ + getUserHeader(): string { + return JSON.stringify(this.user); + } + + /** + * Retrieve an authentication token using Keycloak service. + * + * @return {*} {Promise} + * @memberof BctwService + */ + async getToken(): Promise { + const token = await this.keycloak.getKeycloakServiceToken(); + return token; + } + + /** + * Get the health of the platform. + * + * @return {*} {Promise} + * @memberof BctwService + */ + async getHealth(): Promise { + const { data } = await this.axiosInstance.get('/health'); + + return data; + } + + /** + * Get a list of all BCTW codes with a given header name. + * + * @param {string} codeHeaderName + * @return {*} {Promise} + * @memberof BctwService + */ + async getCode(codeHeaderName: string): Promise { + const { data } = await this.axiosInstance.get('/get-code', { params: { codeHeader: codeHeaderName } }); + + return data; + } +} diff --git a/api/src/services/bctw-service/bctw-telemetry-service.ts b/api/src/services/bctw-service/bctw-telemetry-service.ts new file mode 100644 index 0000000000..c8d1d2deba --- /dev/null +++ b/api/src/services/bctw-service/bctw-telemetry-service.ts @@ -0,0 +1,139 @@ +import { z } from 'zod'; +import { BctwService } from './bctw-service'; + +export const IAllTelemetry = z + .object({ + id: z.string().uuid(), + deployment_id: z.string().uuid(), + latitude: z.number(), + longitude: z.number(), + acquisition_date: z.string(), + telemetry_type: z.string() + }) + .and( + // One of telemetry_id or telemetry_manual_id is expected to be non-null + z.union([ + z.object({ + telemetry_id: z.string().uuid(), + telemetry_manual_id: z.null() + }), + z.object({ + telemetry_id: z.null(), + telemetry_manual_id: z.string().uuid() + }) + ]) + ); +export type IAllTelemetry = z.infer; + +export const IVendorTelemetry = z.object({ + telemetry_id: z.string(), + deployment_id: z.string().uuid(), + collar_transaction_id: z.string().uuid(), + critter_id: z.string().uuid(), + deviceid: z.number(), + latitude: z.number(), + longitude: z.number(), + elevation: z.number(), + vendor: z.string(), + acquisition_date: z.string() +}); +export type IVendorTelemetry = z.infer; + +export const IManualTelemetry = z.object({ + telemetry_manual_id: z.string().uuid(), + deployment_id: z.string().uuid(), + latitude: z.number(), + longitude: z.number(), + acquisition_date: z.string() +}); +export type IManualTelemetry = z.infer; + +export interface ICreateManualTelemetry { + deployment_id: string; + latitude: number; + longitude: number; + acquisition_date: string; +} + +export class BctwTelemetryService extends BctwService { + /** + * Get all manual telemetry records + * This set of telemetry is mostly useful for testing purposes. + * + * @returns {*} IManualTelemetry[] + **/ + async getManualTelemetry(): Promise { + const res = await this.axiosInstance.get('/manual-telemetry'); + return res.data; + } + + /** + * retrieves manual telemetry from list of deployment ids + * + * @async + * @param {string[]} deployment_ids - bctw deployments + * @returns {*} IManualTelemetry[] + */ + async getManualTelemetryByDeploymentIds(deployment_ids: string[]): Promise { + const res = await this.axiosInstance.post('/manual-telemetry/deployments', deployment_ids); + return res.data; + } + + /** + * retrieves manual telemetry from list of deployment ids + * + * @async + * @param {string[]} deployment_ids - bctw deployments + * @returns {*} IVendorTelemetry[] + */ + async getVendorTelemetryByDeploymentIds(deployment_ids: string[]): Promise { + const res = await this.axiosInstance.post('/vendor-telemetry/deployments', deployment_ids); + return res.data; + } + + /** + * retrieves manual and vendor telemetry from list of deployment ids + * + * @async + * @param {string[]} deploymentIds - bctw deployments + * @returns {*} IAllTelemetry[] + */ + async getAllTelemetryByDeploymentIds(deploymentIds: string[]): Promise { + const res = await this.axiosInstance.post('/all-telemetry/deployments', deploymentIds); + return res.data; + } + + /** + * Delete manual telemetry records by telemetry_manual_id + * Note: This is a post request that accepts an array of ids + * @param {string[]} telemetry_manual_ids + * + * @returns {*} IManualTelemetry[] + **/ + async deleteManualTelemetry(telemetry_manual_ids: string[]): Promise { + const res = await this.axiosInstance.post('/manual-telemetry/delete', telemetry_manual_ids); + return res.data; + } + + /** + * Bulk create manual telemetry records + * @param {ICreateManualTelemetry[]} payload + * + * @returns {*} IManualTelemetry[] + **/ + async createManualTelemetry(payload: ICreateManualTelemetry[]): Promise { + const res = await this.axiosInstance.post('/manual-telemetry', payload); + return res.data; + } + + /** + * Bulk update manual telemetry records + * @param {IManualTelemetry} payload + * + * @returns {*} IManualTelemetry[] + **/ + async updateManualTelemetry(payload: IManualTelemetry[]): Promise { + const res = await this.axiosInstance.patch('/manual-telemetry', payload); + return res.data; + } +} diff --git a/api/src/services/code-service.test.ts b/api/src/services/code-service.test.ts index 85a2e7a494..c65a6960cf 100644 --- a/api/src/services/code-service.test.ts +++ b/api/src/services/code-service.test.ts @@ -40,7 +40,6 @@ describe('CodeService', () => { 'project_roles', 'administrative_activity_status_type', 'intended_outcomes', - 'vantage_codes', 'site_selection_strategies', 'survey_jobs', 'sample_methods', diff --git a/api/src/services/code-service.ts b/api/src/services/code-service.ts index 2121227753..20de968419 100644 --- a/api/src/services/code-service.ts +++ b/api/src/services/code-service.ts @@ -38,7 +38,6 @@ export class CodeService extends DBService { project_roles, administrative_activity_status_type, intended_outcomes, - vantage_codes, survey_jobs, site_selection_strategies, sample_methods, @@ -59,7 +58,6 @@ export class CodeService extends DBService { await this.codeRepository.getProjectRoles(), await this.codeRepository.getAdministrativeActivityStatusType(), await this.codeRepository.getIntendedOutcomes(), - await this.codeRepository.getVantageCodes(), await this.codeRepository.getSurveyJobs(), await this.codeRepository.getSiteSelectionStrategies(), await this.codeRepository.getSampleMethods(), @@ -82,7 +80,6 @@ export class CodeService extends DBService { project_roles, administrative_activity_status_type, intended_outcomes, - vantage_codes, survey_jobs, site_selection_strategies, sample_methods, diff --git a/api/src/services/critterbase-service.test.ts b/api/src/services/critterbase-service.test.ts index e2ab4bc68b..6409fe9e46 100644 --- a/api/src/services/critterbase-service.test.ts +++ b/api/src/services/critterbase-service.test.ts @@ -1,9 +1,7 @@ -import { AxiosResponse } from 'axios'; import chai, { expect } from 'chai'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; import { CritterbaseService, ICreateCritter } from './critterbase-service'; -import { KeycloakService } from './keycloak-service'; chai.use(sinonChai); @@ -14,63 +12,6 @@ describe('CritterbaseService', () => { const mockUser = { keycloak_guid: 'abc123', username: 'testuser' }; - describe('getUserHeader', () => { - const cb = new CritterbaseService(mockUser); - const result = cb.getUserHeader(); - expect(result).to.be.a('string'); - }); - - describe('getToken', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return a string from the keycloak service', async () => { - const mockToken = 'abc123'; - const cb = new CritterbaseService(mockUser); - const getKeycloakServiceTokenStub = sinon - .stub(KeycloakService.prototype, 'getKeycloakServiceToken') - .resolves(mockToken); - - const result = await cb.getToken(); - expect(result).to.equal(mockToken); - expect(getKeycloakServiceTokenStub).to.have.been.calledOnce; - }); - }); - - describe('makeGetRequest', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should make an axios get request', async () => { - const cb = new CritterbaseService(mockUser); - const endpoint = '/endpoint'; - const mockResponse = { data: 'data' } as AxiosResponse; - - const mockAxios = sinon.stub(cb.axiosInstance, 'get').resolves(mockResponse); - - const result = await cb._makeGetRequest(endpoint, []); - - expect(result).to.equal(mockResponse.data); - expect(mockAxios).to.have.been.calledOnceWith(`${endpoint}?`); - }); - - it('should make an axios get request with params', async () => { - const cb = new CritterbaseService(mockUser); - const endpoint = '/endpoint'; - const queryParams = [{ key: 'param', value: 'param' }]; - const mockResponse = { data: 'data' } as AxiosResponse; - - const mockAxios = sinon.stub(cb.axiosInstance, 'get').resolves(mockResponse); - - const result = await cb._makeGetRequest(endpoint, queryParams); - - expect(result).to.equal(mockResponse.data); - expect(mockAxios).to.have.been.calledOnceWith(`${endpoint}?param=param`); - }); - }); - describe('Critterbase service public methods', () => { afterEach(() => { sinon.restore(); @@ -78,68 +19,58 @@ describe('CritterbaseService', () => { const cb = new CritterbaseService(mockUser); - describe('getLookupValues', () => { - it('should retrieve matching lookup values', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); - const mockParams = [{ key: 'format', value: 'asSelect ' }]; - await cb.getLookupValues('colours', mockParams); - expect(mockGetRequest).to.have.been.calledOnceWith('/lookups/colours', mockParams); - }); - }); - describe('getTaxonMeasurements', () => { it('should retrieve taxon measurements', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getTaxonMeasurements('123456'); - expect(mockGetRequest).to.have.been.calledOnceWith('/xref/taxon-measurements', [ - { key: 'tsn', value: '123456' } - ]); + expect(axiosStub).to.have.been.calledOnceWith('/xref/taxon-measurements', { params: { tsn: '123456' } }); }); }); describe('getTaxonBodyLocations', () => { it('should retrieve taxon body locations', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getTaxonBodyLocations('asdf'); - expect(mockGetRequest).to.have.been.calledOnceWith('/xref/taxon-marking-body-locations', [ - { key: 'tsn', value: 'asdf' }, - { key: 'format', value: 'asSelect' } - ]); + expect(axiosStub).to.have.been.calledOnceWith('/xref/taxon-marking-body-locations', { + params: { + tsn: 'asdf', + format: 'asSelect' + } + }); }); }); describe('getQualitativeOptions', () => { it('should retrieve qualitative options', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getQualitativeOptions('asdf'); - expect(mockGetRequest).to.have.been.calledOnceWith('/xref/taxon-qualitative-measurement-options', [ - { key: 'taxon_measurement_id', value: 'asdf' }, - { key: 'format', value: 'asSelect' } - ]); + expect(axiosStub).to.have.been.calledOnceWith('/xref/taxon-qualitative-measurement-options', { + params: { taxon_measurement_id: 'asdf', format: 'asSelect' } + }); }); }); describe('getFamilies', () => { it('should retrieve families', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getFamilies(); - expect(mockGetRequest).to.have.been.calledOnceWith('/family', []); + expect(axiosStub).to.have.been.calledOnceWith('/family'); }); }); describe('getFamilyById', () => { it('should retrieve a family', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getFamilyById('asdf'); - expect(mockGetRequest).to.have.been.calledOnceWith('/family/' + 'asdf', []); + expect(axiosStub).to.have.been.calledOnceWith('/family/' + 'asdf'); }); }); describe('getCritter', () => { it('should fetch a critter', async () => { - const mockGetRequest = sinon.stub(cb, '_makeGetRequest'); + const axiosStub = sinon.stub(cb.axiosInstance, 'get').resolves({ data: [] }); await cb.getCritter('asdf'); - expect(mockGetRequest).to.have.been.calledOnceWith('/critters/' + 'asdf', [{ key: 'format', value: 'detail' }]); + expect(axiosStub).to.have.been.calledOnceWith('/critters/' + 'asdf', { params: { format: 'detailed' } }); }); }); diff --git a/api/src/services/critterbase-service.ts b/api/src/services/critterbase-service.ts index 4f736139f0..9ca6e1274b 100644 --- a/api/src/services/critterbase-service.ts +++ b/api/src/services/critterbase-service.ts @@ -1,15 +1,23 @@ import axios, { AxiosError, AxiosInstance, AxiosResponse } from 'axios'; -import { URLSearchParams } from 'url'; +import { Request } from 'express'; +import qs from 'qs'; import { z } from 'zod'; import { ApiError, ApiErrorType } from '../errors/api-error'; import { getLogger } from '../utils/logger'; import { KeycloakService } from './keycloak-service'; +// TODO: TechDebt: Audit the existing types / return types in this file. + export interface ICritterbaseUser { username: string; keycloak_guid: string; } +export const getCritterbaseUser = (req: Request): ICritterbaseUser => ({ + keycloak_guid: req.system_user?.user_guid ?? '', + username: req.system_user?.user_identifier ?? '' +}); + export interface QueryParam { key: string; value: string; @@ -25,6 +33,11 @@ export interface ICritter { critter_comment: string | null; } +export interface ICritterDetailed extends ICritter { + captures: ICaptureDetailed[]; + mortality: IMortality; +} + export interface ICreateCritter { critter_id?: string; wlh_id?: string | null; @@ -39,13 +52,51 @@ export interface ICapture { critter_id: string; capture_method_id?: string | null; capture_location_id: string; - release_location_id: string; + release_location_id?: string | null; + capture_date: string; + capture_time?: string | null; + release_date?: string | null; + release_time?: string | null; + capture_comment?: string | null; + release_comment?: string | null; +} + +export interface ICaptureDetailed { + capture_id: string; + critter_id: string; + capture_method_id?: string | null; + capture_location_id?: string | null; + release_location_id?: string | null; + capture_date: string; + capture_time?: string | null; + release_date?: string | null; + release_time?: string | null; + capture_comment?: string | null; + release_comment?: string | null; + markings: IMarking[]; + quantitative_measurements: IQualMeasurement[]; + qualitative_measurements: IQuantMeasurement[]; + capture_location: { + latitude: number; + longitude: number; + }; + release_location: { + latitude: number; + longitude: number; + }; +} + +export interface ICreateCapture { + critter_id: string; + capture_method_id?: string; + capture_location: ILocation; + release_location?: ILocation; capture_date: string; capture_time?: string | null; release_date?: string | null; release_time?: string | null; - capture_comment: string; - release_comment: string; + capture_comment?: string | null; + release_comment?: string | null; } export interface IMortality { @@ -60,6 +111,10 @@ export interface IMortality { ultimate_cause_of_death_confidence: string; ultimate_predated_by_itis_tsn: string; mortality_comment: string; + mortality_location: { + latitude: number; + longitude: number; + }; } export interface ILocation { @@ -88,6 +143,34 @@ export interface IMarking { removed_timestamp: string; } +/** + * This is the more flexible interface for bulk importing Markings. + * + * Note: Critterbase bulk-create endpoint will attempt to patch + * english values to UUID's. + * ie: primary_colour: "red" -> primary_colour_id: + * + */ +export interface IBulkCreateMarking { + marking_id?: string; + critter_id: string; + capture_id?: string | null; + mortality_id?: string | null; + body_location: string; // Critterbase will patch to UUID + marking_type?: string | null; // Critterbase will patch to UUID + marking_material_id?: string | null; + primary_colour?: string | null; // Critterbase will patch to UUID + secondary_colour?: string | null; // Critterbase will patch to UUID + text_colour_id?: string | null; + identifier?: string | null; + frequency?: number | null; + frequency_unit?: string | null; + order?: number | null; + comment?: string | null; + attached_timestamp?: string | null; + removed_timestamp?: string | null; +} + export interface IQualMeasurement { measurement_qualitative_id?: string; critter_id: string; @@ -95,8 +178,8 @@ export interface IQualMeasurement { capture_id?: string; mortality_id?: string; qualitative_option_id: string; - measurement_comment: string; - measured_timestamp: string; + measurement_comment?: string; + measured_timestamp?: string; } export interface IQuantMeasurement { @@ -127,7 +210,7 @@ export interface IBulkCreate { collections?: ICollection[]; mortalities?: IMortality[]; locations?: ILocation[]; - markings?: IMarking[]; + markings?: IMarking[] | IBulkCreateMarking[]; quantitative_measurements?: IQuantMeasurement[]; qualitative_measurements?: IQualMeasurement[]; families?: IFamilyPayload[]; @@ -166,6 +249,21 @@ export interface ICollectionCategory { itis_tsn: number; } +/** + * Prefixed with critterbase_* to match SIMS database field names + */ +export interface IPostCollectionUnit { + critterbase_collection_unit_id: string; + critterbase_collection_category_id: string; +} + +// Lookup value `asSelect` format +export interface IAsSelectLookup { + id: string; + key: string; + value: string; +} + /** * A Critterbase quantitative measurement. */ @@ -258,56 +356,36 @@ export const CBMeasurementType = z.union([ export type CBMeasurementType = z.infer; -const lookups = '/lookups'; -const xref = '/xref'; -const lookupsEnum = lookups + '/enum'; -const lookupsTaxons = lookups + '/taxons'; -export const CbRoutes = { - // lookups - ['region-envs']: `${lookups}/region-envs`, - ['region_nrs']: `${lookups}/region-nrs`, - wmus: `${lookups}/wmus`, - cods: `${lookups}/cods`, - ['marking-materials']: `${lookups}/marking-materials`, - ['marking-types']: `${lookups}/marking-types`, - ['collection-categories']: `${lookups}/collection-unit-categories`, - taxons: lookupsTaxons, - species: `${lookupsTaxons}/species`, - colours: `${lookups}/colours`, - - // lookups/enum - sex: `${lookupsEnum}/sex`, - ['critter-status']: `${lookupsEnum}/critter-status`, - ['cause-of-death-confidence']: `${lookupsEnum}/cod-confidence`, - ['coordinate-uncertainty-unit']: `${lookupsEnum}/coordinate-uncertainty-unit`, - ['frequency-units']: `${lookupsEnum}/frequency-units`, - ['measurement-units']: `${lookupsEnum}/measurement-units`, - - // xref - ['collection-units']: `${xref}/collection-units`, - - // taxon xrefs - ['taxon-measurements']: `${xref}/taxon-measurements`, - ['taxon_qualitative_measurements']: `${xref}/taxon-qualitative-measurements`, - ['taxon-qualitative-measurement-options']: `${xref}/taxon-qualitative-measurement-options`, - ['taxon-quantitative-measurements']: `${xref}/taxon-quantitative-measurements`, - ['taxon-collection-categories']: `${xref}/taxon-collection-categories`, - ['taxon-marking-body-locations']: `${xref}/taxon-marking-body-locations` -} as const; - -export type CbRouteKey = keyof typeof CbRoutes; - export const CRITTERBASE_API_HOST = process.env.CB_API_HOST || ``; -const CRITTER_ENDPOINT = '/critters'; -const BULK_ENDPOINT = '/bulk'; -const SIGNUP_ENDPOINT = '/signup'; -const FAMILY_ENDPOINT = '/family'; const defaultLog = getLogger('CritterbaseServiceLogger'); +// Response formats +enum CritterbaseFormatEnum { + DETAILED = 'detailed', + AS_SELECT = 'asSelect' +} + +/** + * @export + * @class CritterbaseService + * + */ export class CritterbaseService { + /** + * User details for Critterbase auditing + * + */ user: ICritterbaseUser; + /** + * KeycloakService for retrieving token + * + */ keycloak: KeycloakService; + /** + * Critterbase specific axios instance + * + */ axiosInstance: AxiosInstance; constructor(user: ICritterbaseUser) { @@ -315,29 +393,43 @@ export class CritterbaseService { this.keycloak = new KeycloakService(); this.axiosInstance = axios.create({ - headers: { - user: this.getUserHeader() - }, + paramsSerializer: (params) => qs.stringify(params), baseURL: CRITTERBASE_API_HOST }); + /** + * Response interceptor + * + * Formats Critterbase errors into SIMS format + */ this.axiosInstance.interceptors.response.use( (response: AxiosResponse) => { return response; }, (error: AxiosError) => { - defaultLog.error({ label: 'CritterbaseService', message: error.message, error }); + defaultLog.error({ label: 'CritterbaseService', message: error.message, error: error.response?.data }); + return Promise.reject( - new ApiError(ApiErrorType.GENERAL, `API request failed with status code ${error?.response?.status}`) + new ApiError( + ApiErrorType.GENERAL, + `Critterbase API request failed with status code ${error?.response?.status}`, + [error.response?.data as object] + ) ); } ); - // Async request interceptor + /** + * Async request interceptor + * + * Injects the bearer authentication token and user details into headers + */ this.axiosInstance.interceptors.request.use( async (config) => { - const token = await this.getToken(); + const token = await this.keycloak.getKeycloakServiceToken(); + config.headers['Authorization'] = `Bearer ${token}`; + config.headers.user = JSON.stringify(this.user); return config; }, @@ -347,92 +439,208 @@ export class CritterbaseService { ); } - async getToken(): Promise { - const token = await this.keycloak.getKeycloakServiceToken(); - return token; - } - /** - * Return user information as a JSON string. + * Fetches Critterbase colour lookup values. * - * @return {*} {string} - * @memberof BctwService + * @async + * @returns {Promise} AsSelect format */ - getUserHeader(): string { - return JSON.stringify(this.user); - } - - async _makeGetRequest(endpoint: string, params: QueryParam[]) { - const appendParams = new URLSearchParams(); - for (const p of params) { - appendParams.append(p.key, p.value); - } - const url = `${endpoint}?${appendParams.toString()}`; + async getColours(): Promise { + const response = await this.axiosInstance.get('/lookups/colours', { + params: { format: CritterbaseFormatEnum.AS_SELECT } + }); - const response = await this.axiosInstance.get(url); return response.data; } - async getLookupValues(route: CbRouteKey, params: QueryParam[]) { - return this._makeGetRequest(CbRoutes[route], params); + /** + * Fetches Critterbase marking type lookup values. + * + * @async + * @returns {Promise} AsSelect format + */ + async getMarkingTypes(): Promise { + const response = await this.axiosInstance.get('/lookups/marking-types', { + params: { format: CritterbaseFormatEnum.AS_SELECT } + }); + + return response.data; } + /** + * Fetches qualitative and quantitative measurements for the specified taxon. + * + * @param {string} tsn - The taxon serial number (TSN). + * @returns {Promise<{ qualitative: CBQualitativeMeasurementTypeDefinition[], quantitative: CBQuantitativeMeasurementTypeDefinition[] }>} - The response data containing qualitative and quantitative measurements. + */ async getTaxonMeasurements(tsn: string): Promise<{ qualitative: CBQualitativeMeasurementTypeDefinition[]; quantitative: CBQuantitativeMeasurementTypeDefinition[]; }> { - const response = await this._makeGetRequest(CbRoutes['taxon-measurements'], [{ key: 'tsn', value: tsn }]); - return response; + const response = await this.axiosInstance.get('/xref/taxon-measurements', { params: { tsn } }); + + return response.data; } - async getTaxonBodyLocations(tsn: string) { - return this._makeGetRequest(CbRoutes['taxon-marking-body-locations'], [ - { key: 'tsn', value: tsn }, - { key: 'format', value: 'asSelect' } - ]); + /** + * Fetches body location information for the specified taxon. + * + * @param {string} tsn - The taxon serial number (TSN). + * @returns {Promise} - The response data containing body location information. + */ + async getTaxonBodyLocations(tsn: string): Promise { + const response = await this.axiosInstance.get('/xref/taxon-marking-body-locations', { + params: { tsn, format: CritterbaseFormatEnum.AS_SELECT } + }); + + return response.data; } - async getQualitativeOptions(taxon_measurement_id: string, format = 'asSelect') { - return this._makeGetRequest(CbRoutes['taxon-qualitative-measurement-options'], [ - { key: 'taxon_measurement_id', value: taxon_measurement_id }, - { key: 'format', value: format } - ]); + /** + * Fetches qualitative options for the specified taxon measurement. + * + * @param {string} taxon_measurement_id - The taxon measurement ID. + * @param {string} [format='asSelect'] - The format of the response data. + * @returns {Promise} - The response data containing qualitative options. + */ + async getQualitativeOptions(taxon_measurement_id: string, format = CritterbaseFormatEnum.AS_SELECT): Promise { + const response = await this.axiosInstance.get('/xref/taxon-qualitative-measurement-options', { + params: { taxon_measurement_id, format } + }); + + return response.data; } - async getFamilies() { - return this._makeGetRequest(FAMILY_ENDPOINT, []); + /** + * Fetches a list of all families. + * + * @returns {Promise} - The response data containing a list of families. + */ + async getFamilies(): Promise { + const response = await this.axiosInstance.get('/family'); + + return response.data; } - async getFamilyById(family_id: string) { - return this._makeGetRequest(`${FAMILY_ENDPOINT}/${family_id}`, []); + /** + * Fetches information about a family by its ID. + * + * @param {string} family_id - The ID of the family. + * @returns {Promise} - The response data containing family information. + */ + async getFamilyById(family_id: string): Promise { + const response = await this.axiosInstance.get(`/family/${family_id}`); + + return response.data; } - async getCritter(critter_id: string) { - return this._makeGetRequest(`${CRITTER_ENDPOINT}/${critter_id}`, [{ key: 'format', value: 'detail' }]); + /** + * Fetches information about a critter by its ID. + * + * @param {string} critter_id - The ID of the critter. + * @returns {Promise} - The response data containing critter information. + */ + async getCritter(critter_id: string): Promise { + const response = await this.axiosInstance.get(`/critters/${critter_id}`, { + params: { format: CritterbaseFormatEnum.DETAILED } + }); + + return response.data; } - async createCritter(data: ICreateCritter) { - const response = await this.axiosInstance.post(`${CRITTER_ENDPOINT}/create`, data); + async getCaptureById(capture_id: string): Promise { + const response = await this.axiosInstance.get(`/captures/${capture_id}`, { + params: { format: CritterbaseFormatEnum.DETAILED } + }); + return response.data; } - async updateCritter(data: IBulkCreate) { - const response = await this.axiosInstance.patch(BULK_ENDPOINT, data); + /** + * Creates a new critter with the provided data. + * + * @param {ICreateCritter} data - The data of the critter to be created. + * @returns {Promise} - The response data from the create operation. + */ + async createCritter(data: ICreateCritter): Promise { + const response = await this.axiosInstance.post(`/critters/create`, data); + return response.data; } + /** + * Updates critters in bulk with the provided data. + * + * @param {IBulkCreate} data - The data for the bulk update. + * @returns {Promise} - The response data from the update operation. + */ + async updateCritter(data: IBulkCreate): Promise { + const response = await this.axiosInstance.patch('/bulk', data); + + return response.data; + } + + /** + * Creates critters in bulk with the provided data. + * + * @param {IBulkCreate} data + * @return {*} {Promise} + * @memberof CritterbaseService + */ async bulkCreate(data: IBulkCreate): Promise { - const response = await this.axiosInstance.post(BULK_ENDPOINT, data); + const response = await this.axiosInstance.post('/bulk', data); + return response.data; } + /** + * Fetches multiple critters by their IDs. + * + * @param {string[]} critter_ids - The IDs of the critters. + * @returns {Promise} - The response data containing multiple critters. + */ async getMultipleCrittersByIds(critter_ids: string[]): Promise { - const response = await this.axiosInstance.post(CRITTER_ENDPOINT, { critter_ids }); + const response = await this.axiosInstance.post('/critters', { critter_ids }); + return response.data; } - async signUp() { - const response = await this.axiosInstance.post(SIGNUP_ENDPOINT); + /** + * Fetches detailed information about multiple critters by their IDs. + * + * @param {string[]} critter_ids - The IDs of the critters. + * @returns {Promise} - The response data containing detailed information about multiple critters. + */ + async getMultipleCrittersByIdsDetailed(critter_ids: string[]): Promise { + const response = await this.axiosInstance.post( + `/critters`, + { critter_ids }, + { params: { format: CritterbaseFormatEnum.DETAILED } } + ); + + return response.data; + } + + /** + * Fetches detailed information about multiple critters by their IDs. + * + * @param {string[]} critter_ids - The IDs of the critters. + * @returns {Promise} - The response data containing detailed information about multiple critters. + */ + async getMultipleCrittersGeometryByIds(critter_ids: string[]): Promise { + const response = await this.axiosInstance.post(`/critters/spatial`, { critter_ids }); + + return response.data; + } + + /** + * Signs up a user. + * + * @returns {Promise} - The response data from the sign-up operation. + */ + async signUp(): Promise { + const response = await this.axiosInstance.post('/signup'); + return response.data; } @@ -446,11 +654,11 @@ export class CritterbaseService { async getQualitativeMeasurementTypeDefinition( taxon_measurement_ids: string[] ): Promise { - const { data } = await this.axiosInstance.post(`/xref/taxon-qualitative-measurements`, { + const response = await this.axiosInstance.post(`/xref/taxon-qualitative-measurements`, { taxon_measurement_ids: taxon_measurement_ids }); - return data; + return response.data; } /** @@ -463,11 +671,11 @@ export class CritterbaseService { async getQuantitativeMeasurementTypeDefinition( taxon_measurement_ids: string[] ): Promise { - const { data } = await this.axiosInstance.post(`/xref/taxon-quantitative-measurements`, { + const response = await this.axiosInstance.post(`/xref/taxon-quantitative-measurements`, { taxon_measurement_ids: taxon_measurement_ids }); - return data; + return response.data; } /** @@ -478,7 +686,7 @@ export class CritterbaseService { * @returns {Promise} Collection categories */ async findTaxonCollectionCategories(tsn: string): Promise { - const response = await this.axiosInstance.get(`/xref/taxon-collection-categories?tsn=${tsn}`); + const response = await this.axiosInstance.get(`/xref/taxon-collection-categories`, { params: { tsn } }); return response.data; } @@ -491,7 +699,7 @@ export class CritterbaseService { * @returns {Promise} Collection units */ async findTaxonCollectionUnits(tsn: string): Promise { - const response = await this.axiosInstance.get(`/xref/taxon-collection-units?tsn=${tsn}`); + const response = await this.axiosInstance.get(`/xref/taxon-collection-units`, { params: { tsn } }); return response.data; } diff --git a/api/src/services/deployment-service.ts b/api/src/services/deployment-service.ts new file mode 100644 index 0000000000..c0cc0faf23 --- /dev/null +++ b/api/src/services/deployment-service.ts @@ -0,0 +1,89 @@ +import { IDBConnection } from '../database/db'; +import { ICreateSurveyDeployment, IUpdateSurveyDeployment, SurveyDeployment } from '../models/survey-deployment'; +import { DeploymentRepository } from '../repositories/deployment-repository'; +import { DBService } from './db-service'; + +/** + * Service layer for survey critters. + * + * @export + * @class DeploymentService + * @extends {DBService} + */ +export class DeploymentService extends DBService { + deploymentRepository: DeploymentRepository; + + constructor(connection: IDBConnection) { + super(connection); + + this.deploymentRepository = new DeploymentRepository(connection); + } + + /** + * Get deployments for a Survey + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof DeploymentService + */ + async getDeploymentsForSurveyId(surveyId: number): Promise { + return this.deploymentRepository.getDeploymentsForSurveyId(surveyId); + } + + /** + * Get a specific deployment by its integer ID + * + * @param {number} deploymentId + * @return {*} {Promise} + * @memberof DeploymentService + */ + async getDeploymentById(deploymentId: number): Promise { + return this.deploymentRepository.getDeploymentById(deploymentId); + } + + /** + * Get a specific deployment by its integer ID + * + * @param {number} surveyId + * @param {number} critterId + * @return {*} {Promise} + * @memberof DeploymentService + */ + async getDeploymentForCritterId(surveyId: number, critterId: number): Promise { + return this.deploymentRepository.getDeploymentForCritterId(surveyId, critterId); + } + + /** + * Create a new deployment + * + * @param {ICreateSurveyDeployment} deployment + * @return {*} {Promise} + * @memberof DeploymentService + */ + async insertDeployment(deployment: ICreateSurveyDeployment): Promise { + return this.deploymentRepository.insertDeployment(deployment); + } + + /** + * Update a deployment in SIMS + * + * @param {IUpdateSurveyDeployment} deployment + * @return {*} {Promise} + * @memberof DeploymentService + */ + async updateDeployment(deployment: IUpdateSurveyDeployment): Promise { + return this.deploymentRepository.updateDeployment(deployment); + } + + /** + * Deletes the deployment in SIMS. + * + * @param {number} surveyId + * @param {number} deploymentId + * @return {*} {Promise<{ bctw_deployment_id: string }>} + * @memberof DeploymentService + */ + async deleteDeployment(surveyId: number, deploymentId: number): Promise<{ bctw_deployment_id: string }> { + return this.deploymentRepository.deleteDeployment(surveyId, deploymentId); + } +} diff --git a/api/src/services/import-services/capture/import-captures-strategy.interface.ts b/api/src/services/import-services/capture/import-captures-strategy.interface.ts new file mode 100644 index 0000000000..b5dd346dec --- /dev/null +++ b/api/src/services/import-services/capture/import-captures-strategy.interface.ts @@ -0,0 +1,39 @@ +import { z } from 'zod'; + +/** + * Zod Csv Capture schema + * + */ +export const CsvCaptureSchema = z + .object({ + capture_id: z.string({ required_error: 'Capture exists using same date and time' }).uuid(), + critter_id: z.string({ required_error: 'Unable to map alias to Critter ID.' }).uuid(), + capture_location_id: z.string().uuid(), + capture_date: z.string().date(), + capture_time: z.string().time().optional(), + capture_latitude: z.number(), + capture_longitude: z.number(), + release_location_id: z.string().uuid().optional(), + release_date: z.string().date().optional(), + release_time: z.string().time().optional(), + release_latitude: z.number().optional(), + release_longitude: z.number().optional(), + capture_comment: z.string().optional(), + release_comment: z.string().optional() + }) + .refine((schema) => { + const hasReleaseLatLng = schema.release_latitude && schema.release_longitude; + return hasReleaseLatLng || !hasReleaseLatLng; + }, 'Both release latitude and longitude are required if one is provided.'); + +/** + * A validated CSV Capture object + * + */ +export type CsvCapture = z.infer; + +/** + * Partial CSV Capture object with defined `critter_id` + * + */ +export type PartialCsvCapture = Partial & { critter_id: string }; diff --git a/api/src/services/import-services/capture/import-captures-strategy.test.ts b/api/src/services/import-services/capture/import-captures-strategy.test.ts new file mode 100644 index 0000000000..b7df1d6eff --- /dev/null +++ b/api/src/services/import-services/capture/import-captures-strategy.test.ts @@ -0,0 +1,213 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { MediaFile } from '../../../utils/media/media-file'; +import * as worksheetUtils from '../../../utils/xlsx-utils/worksheet-utils'; +import { getMockDBConnection } from '../../../__mocks__/db'; +import { IBulkCreateResponse, ICritterDetailed } from '../../critterbase-service'; +import { importCSV } from '../import-csv'; +import { ImportCapturesStrategy } from './import-captures-strategy'; + +describe('import-captures-service', () => { + describe('importCSV capture worksheet', () => { + it('should validate successfully', async () => { + const worksheet = { + A1: { t: 's', v: 'CAPTURE_DATE' }, + B1: { t: 's', v: 'NICKNAME' }, + C1: { t: 's', v: 'CAPTURE_TIME' }, + D1: { t: 's', v: 'CAPTURE_LATITUDE' }, + E1: { t: 's', v: 'CAPTURE_LONGITUDE' }, + F1: { t: 's', v: 'RELEASE_DATE' }, + G1: { t: 's', v: 'RELEASE_TIME' }, + H1: { t: 's', v: 'RELEASE_LATITUDE' }, + I1: { t: 's', v: 'RELEASE_LONGITUDE' }, + J1: { t: 's', v: 'RELEASE_COMMENT' }, + K1: { t: 's', v: 'CAPTURE_COMMENT' }, + A2: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + B2: { t: 's', v: 'Carl' }, + C2: { t: 's', v: '10:10:10' }, + D2: { t: 'n', w: '90', v: 90 }, + E2: { t: 'n', w: '100', v: 100 }, + F2: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + G2: { t: 's', v: '9:09' }, + H2: { t: 'n', w: '90', v: 90 }, + I2: { t: 'n', w: '90', v: 90 }, + J2: { t: 's', v: 'release' }, + K2: { t: 's', v: 'capture' }, + A3: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + B3: { t: 's', v: 'Carlita' }, + D3: { t: 'n', w: '90', v: 90 }, + E3: { t: 'n', w: '100', v: 100 }, + '!ref': 'A1:K3' + }; + + const mockDBConnection = getMockDBConnection(); + + const importCapturesStrategy = new ImportCapturesStrategy(mockDBConnection, 1); + + const getDefaultWorksheetStub = sinon.stub(worksheetUtils, 'getDefaultWorksheet'); + const aliasMapStub = sinon.stub(importCapturesStrategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const critterbaseInsertStub = sinon.stub( + importCapturesStrategy.surveyCritterService.critterbaseService, + 'bulkCreate' + ); + + getDefaultWorksheetStub.returns(worksheet); + aliasMapStub.resolves( + new Map([ + [ + 'carl', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [{ capture_id: '', capture_date: '', capture_time: '' }] + } as ICritterDetailed + ], + [ + 'carlita', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [{ capture_id: '', capture_date: '', capture_time: '' }] + } as ICritterDetailed + ] + ]) + ); + critterbaseInsertStub.resolves({ created: { captures: 2 } } as IBulkCreateResponse); + + const data = await importCSV(new MediaFile('test', 'test', 'test' as unknown as Buffer), importCapturesStrategy); + + expect(data).to.deep.equal(2); + }); + }); + describe('validateRows', () => { + it('should format and validate the rows successfully', async () => { + const mockConnection = getMockDBConnection(); + const importCaptures = new ImportCapturesStrategy(mockConnection, 1); + const aliasMapStub = sinon.stub(importCaptures.surveyCritterService, 'getSurveyCritterAliasMap'); + + aliasMapStub.resolves( + new Map([ + [ + 'carl', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [{ capture_id: '', capture_date: '', capture_time: '' }] + } as ICritterDetailed + ] + ]) + ); + + const validate = await importCaptures.validateRows([ + { + ALIAS: 'Carl', + CAPTURE_DATE: '2024-01-01', + CAPTURE_TIME: '10:10:10', + CAPTURE_LATITUDE: 90, + CAPTURE_LONGITUDE: 90, + RELEASE_DATE: '2024-01-01', + RELEASE_TIME: '11:11:11', + RELEASE_LATITUDE: 80, + RELEASE_LONGITUDE: 80, + CAPTURE_COMMENT: 'capture', + RELEASE_COMMENT: 'release' + } + ]); + + if (validate.success) { + expect(validate.data[0]).to.contain({ + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + capture_date: '2024-01-01', + capture_time: '10:10:10', + capture_latitude: 90, + capture_longitude: 90, + release_date: '2024-01-01', + release_time: '11:11:11', + release_latitude: 80, + release_longitude: 80, + capture_comment: 'capture', + release_comment: 'release' + }); + expect(validate.data[0].capture_location_id).to.exist; + expect(validate.data[0].release_location_id).to.exist; + } else { + expect.fail(); + } + }); + + it('should format and validate the rows with optional values successfully', async () => { + const mockConnection = getMockDBConnection(); + const importCaptures = new ImportCapturesStrategy(mockConnection, 1); + const aliasMapStub = sinon.stub(importCaptures.surveyCritterService, 'getSurveyCritterAliasMap'); + + aliasMapStub.resolves( + new Map([ + [ + 'carl', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [{ capture_id: '', capture_date: '', capture_time: '' }] + } as ICritterDetailed + ] + ]) + ); + + const validate = await importCaptures.validateRows([ + { + ALIAS: 'Carl', + CAPTURE_DATE: '2024-01-01', + CAPTURE_LATITUDE: 90, + CAPTURE_LONGITUDE: 90 + } + ]); + + if (validate.success) { + expect(validate.data[0]).to.contain({ + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + capture_date: '2024-01-01', + capture_latitude: 90, + capture_longitude: 90, + capture_time: undefined, + release_date: undefined, + release_time: undefined, + release_latitude: undefined, + release_longitude: undefined, + capture_comment: undefined, + release_comment: undefined + }); + expect(validate.data[0].capture_location_id).to.exist; + } else { + expect.fail(); + } + }); + + it('should return error if invalid', async () => { + const mockConnection = getMockDBConnection(); + const importCaptures = new ImportCapturesStrategy(mockConnection, 1); + const aliasMapStub = sinon.stub(importCaptures.surveyCritterService, 'getSurveyCritterAliasMap'); + + aliasMapStub.resolves( + new Map([ + [ + 'carl', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [{ capture_id: '', capture_date: '', capture_time: '' }] + } as ICritterDetailed + ] + ]) + ); + + const validate = await importCaptures.validateRows([ + { + ALIAS: 'Carl', + CAPTURE_DATE: '2024-01-01', + CAPTURE_LATITUDE: 90 + } + ]); + + if (validate.success) { + expect.fail(); + } else { + expect(validate.error.issues.length).to.be.eql(1); + } + }); + }); +}); diff --git a/api/src/services/import-services/capture/import-captures-strategy.ts b/api/src/services/import-services/capture/import-captures-strategy.ts new file mode 100644 index 0000000000..f69ab1469e --- /dev/null +++ b/api/src/services/import-services/capture/import-captures-strategy.ts @@ -0,0 +1,157 @@ +import { v4 as uuid } from 'uuid'; +import { z } from 'zod'; +import { IDBConnection } from '../../../database/db'; +import { CSV_COLUMN_ALIASES } from '../../../utils/xlsx-utils/column-aliases'; +import { generateColumnCellGetterFromColumnValidator } from '../../../utils/xlsx-utils/column-validator-utils'; +import { IXLSXCSVValidator } from '../../../utils/xlsx-utils/worksheet-utils'; +import { ICapture, ILocation } from '../../critterbase-service'; +import { DBService } from '../../db-service'; +import { SurveyCritterService } from '../../survey-critter-service'; +import { CSVImportStrategy, Row } from '../import-csv.interface'; +import { findCapturesFromDateTime, formatTimeString } from '../utils/datetime'; +import { CsvCapture, CsvCaptureSchema } from './import-captures-strategy.interface'; + +/** + * + * @class ImportCapturesStrategy + * @extends DBService + * @see CSVImportStrategy + * + */ +export class ImportCapturesStrategy extends DBService implements CSVImportStrategy { + surveyCritterService: SurveyCritterService; + surveyId: number; + + /** + * An XLSX validation config for the standard columns of a Critterbase Capture CSV. + * + * Note: `satisfies` allows `keyof` to correctly infer keyof type, while also + * enforcing uppercase object keys. + */ + columnValidator = { + ALIAS: { type: 'string', aliases: CSV_COLUMN_ALIASES.ALIAS }, + CAPTURE_DATE: { type: 'date' }, + CAPTURE_TIME: { type: 'string', optional: true }, + CAPTURE_LATITUDE: { type: 'number' }, + CAPTURE_LONGITUDE: { type: 'number' }, + RELEASE_DATE: { type: 'date', optional: true }, + RELEASE_TIME: { type: 'string', optional: true }, + RELEASE_LATITUDE: { type: 'number', optional: true }, + RELEASE_LONGITUDE: { type: 'number', optional: true }, + CAPTURE_COMMENT: { type: 'string', optional: true }, + RELEASE_COMMENT: { type: 'string', optional: true } + } satisfies IXLSXCSVValidator; + + /** + * Construct an instance of ImportCapturesStrategy. + * + * @param {IDBConnection} connection - DB connection + * @param {string} surveyId + */ + constructor(connection: IDBConnection, surveyId: number) { + super(connection); + + this.surveyId = surveyId; + + this.surveyCritterService = new SurveyCritterService(connection); + } + + /** + * Validate the CSV rows against zod schema. + * + * @param {Row[]} rows - CSV rows + * @returns {*} + */ + async validateRows(rows: Row[]) { + // Generate type-safe cell getter from column validator + const getColumnCell = generateColumnCellGetterFromColumnValidator(this.columnValidator); + const critterAliasMap = await this.surveyCritterService.getSurveyCritterAliasMap(this.surveyId); + + const rowsToValidate = []; + + for (const row of rows) { + let critterId, captureId; + + const alias = getColumnCell(row, 'ALIAS'); + + const releaseLatitude = getColumnCell(row, 'RELEASE_LATITUDE'); + const releaseLongitude = getColumnCell(row, 'RELEASE_LONGITUDE'); + const captureDate = getColumnCell(row, 'CAPTURE_DATE'); + const captureTime = getColumnCell(row, 'CAPTURE_TIME'); + const releaseTime = getColumnCell(row, 'RELEASE_TIME'); + + const releaseLocationId = releaseLatitude.cell && releaseLongitude.cell ? uuid() : undefined; + const formattedCaptureTime = formatTimeString(captureTime.cell); + const formattedReleaseTime = formatTimeString(releaseTime.cell); + + // If the alias is included attempt to retrieve the critterId from row + // Checks if date time fields are unique for the critter's captures + if (alias.cell) { + const critter = critterAliasMap.get(alias.cell.toLowerCase()); + if (critter) { + const captures = findCapturesFromDateTime(critter.captures, captureDate.cell, captureTime.cell); + critterId = critter.critter_id; + // Only set the captureId if a capture does not exist with matching date time + captureId = captures.length > 0 ? undefined : uuid(); + } + } + + rowsToValidate.push({ + capture_id: captureId, // this will be undefined if capture exists with same date / time + critter_id: critterId, + capture_location_id: uuid(), + capture_date: captureDate.cell, + capture_time: formattedCaptureTime, + capture_latitude: getColumnCell(row, 'CAPTURE_LATITUDE').cell, + capture_longitude: getColumnCell(row, 'CAPTURE_LONGITUDE').cell, + release_location_id: releaseLocationId, + release_date: getColumnCell(row, 'RELEASE_DATE').cell, + release_time: formattedReleaseTime, + release_latitude: getColumnCell(row, 'RELEASE_LATITUDE').cell, + release_longitude: getColumnCell(row, 'RELEASE_LONGITUDE').cell, + capture_comment: getColumnCell(row, 'CAPTURE_COMMENT').cell, + release_comment: getColumnCell(row, 'RELEASE_COMMENT').cell + }); + } + + return z.array(CsvCaptureSchema).safeParseAsync(rowsToValidate); + } + + /** + * Insert captures into Critterbase. + * + * @async + * @param {CsvCapture[]} captures - List of CSV captures to create + * @returns {Promise} Number of created captures + */ + async insert(captures: CsvCapture[]): Promise { + const critterbasePayload: { captures: ICapture[]; locations: ILocation[] } = { captures: [], locations: [] }; + + for (const row of captures) { + const { capture_latitude, capture_longitude, release_latitude, release_longitude, ...capture } = row; + + // Push the critter captures into payload + critterbasePayload.captures.push(capture); + + // Push the capture location + critterbasePayload.locations.push({ + location_id: row.capture_location_id, + latitude: capture_latitude, + longitude: capture_longitude + }); + + // Push the capture release location if included + if (row.release_location_id && release_latitude && release_longitude) { + critterbasePayload.locations?.push({ + location_id: row.release_location_id, + latitude: release_latitude, + longitude: release_longitude + }); + } + } + + const response = await this.surveyCritterService.critterbaseService.bulkCreate(critterbasePayload); + + return response.created.captures; + } +} diff --git a/api/src/services/import-services/critter/import-critters-strategy.interface.ts b/api/src/services/import-services/critter/import-critters-strategy.interface.ts new file mode 100644 index 0000000000..7d50161433 --- /dev/null +++ b/api/src/services/import-services/critter/import-critters-strategy.interface.ts @@ -0,0 +1,20 @@ +/** + * A validated CSV Critter object + * + */ +export type CsvCritter = { + critter_id: string; + sex: string; + itis_tsn: number; + animal_id: string; + wlh_id?: string; + critter_comment?: string; +} & { + [collectionUnitColumn: string]: unknown; +}; + +/** + * Invalidated CSV Critter object + * + */ +export type PartialCsvCritter = Partial & { critter_id: string }; diff --git a/api/src/services/import-services/critter/import-critters-strategy.test.ts b/api/src/services/import-services/critter/import-critters-strategy.test.ts new file mode 100644 index 0000000000..9872119aa4 --- /dev/null +++ b/api/src/services/import-services/critter/import-critters-strategy.test.ts @@ -0,0 +1,596 @@ +import chai, { expect } from 'chai'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { WorkSheet } from 'xlsx'; +import { getMockDBConnection } from '../../../__mocks__/db'; +import { IBulkCreateResponse } from '../../critterbase-service'; +import { ImportCrittersStrategy } from './import-critters-strategy'; +import { CsvCritter } from './import-critters-strategy.interface'; + +chai.use(sinonChai); + +const mockConnection = getMockDBConnection(); + +describe('ImportCrittersStrategy', () => { + describe('_getRowsToValidate', () => { + it('it should correctly format rows', () => { + const rows = [ + { + SEX: 'Male', + ITIS_TSN: 1, + WLH_ID: '10-1000', + ALIAS: 'Carl', + COMMENT: 'Test', + COLLECTION: 'Unit', + BAD_COLLECTION: 'Bad' + } + ]; + const service = new ImportCrittersStrategy(mockConnection, 1); + + const parsedRow = service._getRowsToValidate(rows, ['COLLECTION'])[0]; + + expect(parsedRow.sex).to.be.eq('Male'); + expect(parsedRow.itis_tsn).to.be.eq(1); + expect(parsedRow.wlh_id).to.be.eq('10-1000'); + expect(parsedRow.animal_id).to.be.eq('Carl'); + expect(parsedRow.critter_comment).to.be.eq('Test'); + expect(parsedRow.COLLECTION).to.be.eq('Unit'); + expect(parsedRow.TEST).to.be.undefined; + expect(parsedRow.BAD_COLLECTION).to.be.undefined; + }); + }); + + describe('_getCritterFromRow', () => { + it('should get all critter properties', () => { + const row: any = { + critter_id: 'id', + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment', + extra_property: 'test' + }; + const service = new ImportCrittersStrategy(mockConnection, 1); + + const critter = service._getCritterFromRow(row); + + expect(critter).to.be.eql({ + critter_id: 'id', + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment' + }); + }); + }); + + describe('_getCollectionUnitsFromRow', () => { + it('should get all collection unit properties', () => { + const row: any = { + critter_id: 'id', + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment', + COLLECTION: 'ID1', + HERD: 'ID2' + }; + const service = new ImportCrittersStrategy(mockConnection, 1); + + const collectionUnits = service._getCollectionUnitsFromRow(row); + + expect(collectionUnits).to.be.deep.equal([ + { collection_unit_id: 'ID1', critter_id: 'id' }, + { collection_unit_id: 'ID2', critter_id: 'id' } + ]); + }); + }); + + describe('_getValidTsns', () => { + afterEach(() => { + sinon.restore(); + }); + + it('should return unique list of tsns', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const getTaxonomyStub = sinon.stub(service.platformService, 'getTaxonomyByTsns').resolves([ + { tsn: 1, scientificName: 'a' }, + { tsn: 2, scientificName: 'b' } + ]); + + const tsns = await service._getValidTsns([ + { critter_id: 'a', itis_tsn: 1 }, + { critter_id: 'b', itis_tsn: 2 } + ]); + + expect(getTaxonomyStub).to.have.been.calledWith(['1', '2']); + expect(tsns).to.deep.equal(['1', '2']); + }); + }); + + describe('_getCollectionUnitMap', () => { + afterEach(() => { + sinon.restore(); + }); + + const collectionUnitsA = [ + { + collection_unit_id: '1', + collection_category_id: '2', + category_name: 'COLLECTION', + unit_name: 'UNIT_A', + description: 'description' + }, + { + collection_unit_id: '2', + collection_category_id: '3', + category_name: 'COLLECTION', + unit_name: 'UNIT_B', + description: 'description' + } + ]; + + const collectionUnitsB = [ + { + collection_unit_id: '1', + collection_category_id: '2', + category_name: 'HERD', + unit_name: 'UNIT_A', + description: 'description' + }, + { + collection_unit_id: '2', + collection_category_id: '3', + category_name: 'HERD', + unit_name: 'UNIT_B', + description: 'description' + } + ]; + + it('should return collection unit mapping', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); + const mockWorksheet = {} as unknown as WorkSheet; + + const findCollectionUnitsStub = sinon.stub(service.critterbaseService, 'findTaxonCollectionUnits'); + + getColumnsStub.returns(['COLLECTION', 'HERD']); + findCollectionUnitsStub.onCall(0).resolves(collectionUnitsA); + findCollectionUnitsStub.onCall(1).resolves(collectionUnitsB); + + const mapping = await service._getCollectionUnitMap(mockWorksheet, ['1', '2']); + expect(getColumnsStub).to.have.been.calledWith(mockWorksheet); + expect(findCollectionUnitsStub).to.have.been.calledTwice; + + expect(mapping).to.be.instanceof(Map); + expect(mapping.get('COLLECTION')).to.be.deep.equal({ collectionUnits: collectionUnitsA, tsn: 1 }); + expect(mapping.get('HERD')).to.be.deep.equal({ collectionUnits: collectionUnitsB, tsn: 2 }); + }); + + it('should return empty map when no collection unit columns', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); + const mockWorksheet = {} as unknown as WorkSheet; + + const findCollectionUnitsStub = sinon.stub(service.critterbaseService, 'findTaxonCollectionUnits'); + getColumnsStub.returns([]); + + const mapping = await service._getCollectionUnitMap(mockWorksheet, ['1', '2']); + expect(getColumnsStub).to.have.been.calledWith(mockWorksheet); + expect(findCollectionUnitsStub).to.have.not.been.called; + + expect(mapping).to.be.instanceof(Map); + }); + }); + + describe('insert', () => { + afterEach(() => { + sinon.restore(); + }); + + const critters: CsvCritter[] = [ + { + critter_id: '1', + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment', + COLLECTION: 'Collection Unit' + }, + { + critter_id: '2', + sex: 'Female', + itis_tsn: 2, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment', + HERD: 'Herd Unit' + } + ]; + + it('should correctly parse collection units and critters and insert into sims / critterbase', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const critterbaseBulkCreateStub = sinon.stub(service.critterbaseService, 'bulkCreate'); + const simsAddSurveyCrittersStub = sinon.stub(service.surveyCritterService, 'addCrittersToSurvey'); + + critterbaseBulkCreateStub.resolves({ created: { critters: 2, collections: 1 } } as IBulkCreateResponse); + simsAddSurveyCrittersStub.resolves([1]); + + const ids = await service.insert(critters); + + expect(critterbaseBulkCreateStub).to.have.been.calledWithExactly({ + critters: [ + { + critter_id: '1', + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment' + }, + { + critter_id: '2', + sex: 'Female', + itis_tsn: 2, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'comment' + } + ], + collections: [ + { collection_unit_id: 'Collection Unit', critter_id: '1' }, + { collection_unit_id: 'Herd Unit', critter_id: '2' } + ] + }); + + expect(ids).to.be.deep.equal([1]); + }); + + it('should throw error if response from critterbase is less than provided critters', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const critterbaseBulkCreateStub = sinon.stub(service.critterbaseService, 'bulkCreate'); + const simsAddSurveyCrittersStub = sinon.stub(service.surveyCritterService, 'addCrittersToSurvey'); + + critterbaseBulkCreateStub.resolves({ created: { critters: 1, collections: 1 } } as IBulkCreateResponse); + simsAddSurveyCrittersStub.resolves([1]); + + try { + await service.insert(critters); + expect.fail(); + } catch (err: any) { + expect(err.message).to.be.equal('Unable to fully import critters from CSV'); + } + + expect(simsAddSurveyCrittersStub).to.not.have.been.called; + }); + }); + + describe('validateRows', () => { + afterEach(() => { + sinon.restore(); + }); + + const collectionUnitsA = [ + { + collection_unit_id: '1', + collection_category_id: '2', + category_name: 'COLLECTION', + unit_name: 'UNIT_A', + description: 'description' + }, + { + collection_unit_id: '2', + collection_category_id: '3', + category_name: 'COLLECTION', + unit_name: 'UNIT_B', + description: 'description' + } + ]; + + const collectionUnitsB = [ + { + collection_unit_id: '1', + collection_category_id: '2', + category_name: 'HERD', + unit_name: 'UNIT_A', + description: 'description' + }, + { + collection_unit_id: '2', + collection_category_id: '3', + category_name: 'HERD', + unit_name: 'UNIT_B', + description: 'description' + } + ]; + + it('should return successful', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); + + getColumnsStub.returns(['COLLECTION', 'HERD']); + surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); + getValidTsnsStub.resolves(['1', '2']); + collectionMapStub.resolves( + new Map([ + ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], + ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] + ]) + ); + + const rows = [ + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl', + WLH_ID: '10-1000', + DESCRIPTION: 'A', + COLLECTION: 'UNIT_A' + }, + { + ITIS_TSN: 2, + SEX: 'Female', + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'B', + HERD: 'UNIT_B' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + // Unable to spoof UUID so using contain + expect(validation.data[0]).to.contain({ + sex: 'Male', + itis_tsn: 1, + animal_id: 'Carl', + wlh_id: '10-1000', + critter_comment: 'A', + COLLECTION: '1' + }); + + expect(validation.data[1]).to.contain({ + sex: 'Female', + itis_tsn: 2, + animal_id: 'Carl2', + wlh_id: '10-1000', + critter_comment: 'B', + HERD: '2' + }); + } else { + expect.fail(); + } + }); + + it('should return error when sex undefined', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + + surveyAliasesStub.resolves(new Set([])); + getValidTsnsStub.resolves(['1']); + + const rows = [ + { + ITIS_TSN: 1, + SEX: undefined, + ALIAS: 'Carl', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 1, + SEX: 'NO', // invalid value + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + expect.fail(); + } else { + expect(validation.error.issues).to.deep.equal([ + { row: 0, message: 'Invalid SEX. Expecting: UNKNOWN, MALE, FEMALE, HERMAPHRODITIC.' }, + { row: 1, message: 'Invalid SEX. Expecting: UNKNOWN, MALE, FEMALE, HERMAPHRODITIC.' } + ]); + } + }); + + it('should return error when wlh_id invalid regex', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + + surveyAliasesStub.resolves(new Set([])); + getValidTsnsStub.resolves(['1']); + + const rows = [ + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl', + WLH_ID: '1-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl2', + WLH_ID: '101000', + DESCRIPTION: 'A' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + expect.fail(); + } else { + expect(validation.error.issues).to.deep.equal([ + { row: 0, message: `Invalid WLH_ID. Example format '10-1000R'.` }, + { row: 1, message: `Invalid WLH_ID. Example format '10-1000R'.` } + ]); + } + }); + + it('should return error when itis_tsn invalid option or undefined', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + + surveyAliasesStub.resolves(new Set([])); + getValidTsnsStub.resolves(['1']); + + const rows = [ + { + ITIS_TSN: undefined, + SEX: 'Male', + ALIAS: 'Carl', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 3, + SEX: 'Male', + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + expect.fail(); + } else { + expect(validation.error.issues).to.deep.equal([ + { row: 0, message: `Invalid ITIS_TSN.` }, + { row: 1, message: `Invalid ITIS_TSN.` } + ]); + } + }); + + it('should return error if alias undefined, duplicate or exists in surve', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + + surveyAliasesStub.resolves(new Set(['Carl3'])); + getValidTsnsStub.resolves(['1']); + + const rows = [ + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: undefined, + WLH_ID: '10-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + }, + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl3', + WLH_ID: '10-1000', + DESCRIPTION: 'A' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + expect.fail(); + } else { + expect(validation.error.issues).to.deep.equal([ + { row: 0, message: `Invalid ALIAS. Must be unique in Survey and CSV.` }, + { row: 1, message: `Invalid ALIAS. Must be unique in Survey and CSV.` }, + { row: 2, message: `Invalid ALIAS. Must be unique in Survey and CSV.` }, + { row: 3, message: `Invalid ALIAS. Must be unique in Survey and CSV.` } + ]); + } + }); + + it('should return error if collection unit invalid value', async () => { + const service = new ImportCrittersStrategy(mockConnection, 1); + + const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); + const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); + const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); + const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); + + surveyAliasesStub.resolves(new Set([])); + getValidTsnsStub.resolves(['1', '2']); + getColumnsStub.returns(['COLLECTION', 'HERD']); + collectionMapStub.resolves( + new Map([ + ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], + ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] + ]) + ); + + const rows = [ + { + ITIS_TSN: 1, + SEX: 'Male', + ALIAS: 'Carl', + WLH_ID: '10-1000', + DESCRIPTION: 'A', + COLLECTION: 'UNIT_C' + }, + { + ITIS_TSN: 2, + SEX: 'Male', + ALIAS: 'Carl2', + WLH_ID: '10-1000', + DESCRIPTION: 'A', + COLLECTION: 'UNIT_A' + } + ]; + + const validation = await service.validateRows(rows, {}); + + if (validation.success) { + expect.fail(); + } else { + expect(validation.error.issues).to.deep.equal([ + { row: 0, message: `Invalid COLLECTION. Cell value is not valid.` }, + { row: 1, message: `Invalid COLLECTION. Cell value not allowed for TSN.` } + ]); + } + }); + }); +}); diff --git a/api/src/services/import-services/import-critters-service.ts b/api/src/services/import-services/critter/import-critters-strategy.ts similarity index 62% rename from api/src/services/import-services/import-critters-service.ts rename to api/src/services/import-services/critter/import-critters-strategy.ts index 0c7a97550c..dbe0cf7bf7 100644 --- a/api/src/services/import-services/import-critters-service.ts +++ b/api/src/services/import-services/critter/import-critters-strategy.ts @@ -1,37 +1,24 @@ -import { capitalize, keys, omit, toUpper, uniq } from 'lodash'; +import { keys, omit, startCase, toUpper, uniq } from 'lodash'; import { v4 as uuid } from 'uuid'; import { WorkSheet } from 'xlsx'; -import { IDBConnection } from '../../database/db'; -import { ApiGeneralError } from '../../errors/api-error'; -import { getLogger } from '../../utils/logger'; -import { MediaFile } from '../../utils/media/media-file'; -import { - critterStandardColumnValidator, - getAliasFromRow, - getColumnValidatorSpecification, - getDescriptionFromRow, - getSexFromRow, - getTsnFromRow, - getWlhIdFromRow -} from '../../utils/xlsx-utils/column-cell-utils'; -import { - constructXLSXWorkbook, - getDefaultWorksheet, - getNonStandardColumnNamesFromWorksheet, - getWorksheetRowObjects, - validateCsvFile -} from '../../utils/xlsx-utils/worksheet-utils'; +import { IDBConnection } from '../../../database/db'; +import { ApiGeneralError } from '../../../errors/api-error'; +import { getLogger } from '../../../utils/logger'; +import { CSV_COLUMN_ALIASES } from '../../../utils/xlsx-utils/column-aliases'; +import { generateColumnCellGetterFromColumnValidator } from '../../../utils/xlsx-utils/column-validator-utils'; +import { getNonStandardColumnNamesFromWorksheet, IXLSXCSVValidator } from '../../../utils/xlsx-utils/worksheet-utils'; import { CritterbaseService, IBulkCreate, ICollection, ICollectionUnitWithCategory, ICreateCritter -} from '../critterbase-service'; -import { DBService } from '../db-service'; -import { PlatformService } from '../platform-service'; -import { SurveyCritterService } from '../survey-critter-service'; -import { CsvCritter, PartialCsvCritter, Row, Validation, ValidationError } from './import-critters-service.interface'; +} from '../../critterbase-service'; +import { DBService } from '../../db-service'; +import { PlatformService } from '../../platform-service'; +import { SurveyCritterService } from '../../survey-critter-service'; +import { CSVImportStrategy, Row, Validation, ValidationError } from '../import-csv.interface'; +import { CsvCritter, PartialCsvCritter } from './import-critters-strategy.interface'; const defaultLog = getLogger('services/import/import-critters-service'); @@ -39,20 +26,46 @@ const CSV_CRITTER_SEX_OPTIONS = ['UNKNOWN', 'MALE', 'FEMALE', 'HERMAPHRODITIC']; /** * - * @class ImportCrittersService + * ImportCrittersStrategy - Injected into CSVImportStrategy as the CSV import dependency + * + * @example new CSVImportStrategy(new ImportCrittersStrategy(connection, surveyId)).import(file); + * + * @class ImportCrittersStrategy * @extends DBService * */ -export class ImportCrittersService extends DBService { +export class ImportCrittersStrategy extends DBService implements CSVImportStrategy { platformService: PlatformService; critterbaseService: CritterbaseService; surveyCritterService: SurveyCritterService; - _rows?: PartialCsvCritter[]; + surveyId: number; - constructor(connection: IDBConnection) { + /** + * An XLSX validation config for the standard columns of a Critter CSV. + * + * Note: `satisfies` allows `keyof` to correctly infer key types, while also + * enforcing uppercase object keys. + */ + columnValidator = { + ITIS_TSN: { type: 'number', aliases: CSV_COLUMN_ALIASES.ITIS_TSN }, + SEX: { type: 'string' }, + ALIAS: { type: 'string', aliases: CSV_COLUMN_ALIASES.ALIAS }, + WLH_ID: { type: 'string' }, + DESCRIPTION: { type: 'string', aliases: CSV_COLUMN_ALIASES.DESCRIPTION } + } satisfies IXLSXCSVValidator; + + /** + * Instantiates an instance of ImportCrittersStrategy + * + * @param {IDBConnection} connection - Database connection + * @param {number} surveyId - Survey identifier + */ + constructor(connection: IDBConnection, surveyId: number) { super(connection); + this.surveyId = surveyId; + this.platformService = new PlatformService(connection); this.surveyCritterService = new SurveyCritterService(connection); this.critterbaseService = new CritterbaseService({ @@ -61,16 +74,6 @@ export class ImportCrittersService extends DBService { }); } - /** - * Get the worksheet from the CSV file. - * - * @param {MediaFile} critterCsv - CSV MediaFile - * @returns {WorkSheet} Xlsx worksheet - */ - _getWorksheet(critterCsv: MediaFile) { - return getDefaultWorksheet(constructXLSXWorkbook(critterCsv)); - } - /** * Get non-standard columns (collection unit columns) from worksheet. * @@ -78,57 +81,7 @@ export class ImportCrittersService extends DBService { * @returns {string[]} Array of non-standard headers from CSV (worksheet) */ _getNonStandardColumns(worksheet: WorkSheet) { - return uniq(getNonStandardColumnNamesFromWorksheet(worksheet, critterStandardColumnValidator)); - } - /** - * Parse the CSV rows into the Critterbase critter format. - * - * @param {Row[]} rows - CSV rows - * @returns {PartialCsvCritter[]} CSV critters before validation - */ - _getCritterRowsToValidate(rows: Row[], collectionUnitColumns: string[]): PartialCsvCritter[] { - return rows.map((row) => { - // Standard critter properties from CSV - const standardCritterRow: PartialCsvCritter = { - critter_id: uuid(), // Generate a uuid for each critter for convienence - sex: getSexFromRow(row), - itis_tsn: getTsnFromRow(row), - wlh_id: getWlhIdFromRow(row), - animal_id: getAliasFromRow(row), - critter_comment: getDescriptionFromRow(row) - }; - - // All other properties must be collection units ie: `population unit` or `herd unit` etc... - collectionUnitColumns.forEach((categoryHeader) => { - standardCritterRow[categoryHeader] = row[categoryHeader]; - }); - - return standardCritterRow; - }); - } - - /** - * Get the critter rows from the xlsx worksheet. - * - * @param {WorkSheet} worksheet - * @returns {PartialCsvCritter[]} List of partial CSV Critters - */ - _getRows(worksheet: WorkSheet) { - // Attempt to retrieve from rows property to prevent unnecessary parsing - if (this._rows) { - return this._rows; - } - - // Convert the worksheet into an array of records - const worksheetRows = getWorksheetRowObjects(worksheet); - - // Get the collection unit columns (all non standard columns) - const collectionUnitColumns = this._getNonStandardColumns(worksheet); - - // Pre parse the records into partial critter rows - this._rows = this._getCritterRowsToValidate(worksheetRows, collectionUnitColumns); - - return this._rows; + return uniq(getNonStandardColumnNamesFromWorksheet(worksheet, this.columnValidator)); } /** @@ -140,7 +93,7 @@ export class ImportCrittersService extends DBService { _getCritterFromRow(row: CsvCritter): ICreateCritter { return { critter_id: row.critter_id, - sex: capitalize(row.sex), + sex: row.sex, itis_tsn: row.itis_tsn, animal_id: row.animal_id, wlh_id: row.wlh_id, @@ -158,7 +111,7 @@ export class ImportCrittersService extends DBService { const critterId = row.critter_id; // Get portion of row object that is not a critter - const partialRow = omit(row, keys(this._getCritterFromRow(row))); + const partialRow: { [key: string]: any } = omit(row, keys(this._getCritterFromRow(row))); // Keys of collection units const collectionUnitKeys = keys(partialRow); @@ -170,22 +123,19 @@ export class ImportCrittersService extends DBService { } /** - * Get a Set of valid ITIS TSNS from xlsx worksheet. + * Get a Set of valid ITIS TSNS from xlsx worksheet rows. * * @async - * @param {WorkSheet} worksheet - Xlsx Worksheet * @returns {Promise} Unique Set of valid TSNS from worksheet. */ - async _getValidTsns(worksheet: WorkSheet): Promise { - const rows = this._getRows(worksheet); - + async _getValidTsns(rows: PartialCsvCritter[]): Promise { // Get a unique list of tsns from worksheet const critterTsns = uniq(rows.map((row) => String(row.itis_tsn))); // Query the platform service (taxonomy) for matching tsns const taxonomy = await this.platformService.getTaxonomyByTsns(critterTsns); - return taxonomy.map((taxon) => taxon.tsn); + return taxonomy.map((taxon) => String(taxon.tsn)); } /** @@ -223,33 +173,63 @@ export class ImportCrittersService extends DBService { return collectionUnitMap; } + /** + * Parse the CSV rows into the Critterbase critter format. + * + * @param {Row[]} rows - CSV rows + * @param {string[]} collectionUnitColumns - Non standard columns + * @returns {PartialCsvCritter[]} CSV critters before validation + */ + _getRowsToValidate(rows: Row[], collectionUnitColumns: string[]): PartialCsvCritter[] { + const getColumnCell = generateColumnCellGetterFromColumnValidator(this.columnValidator); + + return rows.map((row) => { + // Standard critter properties from CSV + const standardCritterRow = { + critter_id: uuid(), // Generate a uuid for each critter for convienence + sex: getColumnCell(row, 'SEX').cell, + itis_tsn: getColumnCell(row, 'ITIS_TSN').cell, + wlh_id: getColumnCell(row, 'WLH_ID').cell, + animal_id: getColumnCell(row, 'ALIAS').cell, + critter_comment: getColumnCell(row, 'DESCRIPTION').cell + }; + + // All other properties must be collection units ie: `population unit` or `herd unit` etc... + collectionUnitColumns.forEach((categoryHeader) => { + standardCritterRow[categoryHeader] = row[categoryHeader]; + }); + + return standardCritterRow; + }); + } + /** * Validate CSV worksheet rows against reference data. * * @async - * @param {number} surveyId - Survey identifier + * @param {Row[]} rows - Invalidated CSV rows * @param {WorkSheet} worksheet - Xlsx worksheet - * @returns {Promise} Conditional validation object + * @returns {Promise>} Conditional validation object */ - async _validateRows(surveyId: number, worksheet: WorkSheet): Promise { - const rows = this._getRows(worksheet); + async validateRows(rows: Row[], worksheet: WorkSheet): Promise> { const nonStandardColumns = this._getNonStandardColumns(worksheet); + const rowsToValidate = this._getRowsToValidate(rows, nonStandardColumns); // Retrieve the dynamic validation config const [validRowTsns, surveyCritterAliases] = await Promise.all([ - this._getValidTsns(worksheet), - this.surveyCritterService.getUniqueSurveyCritterAliases(surveyId) + this._getValidTsns(rowsToValidate), + this.surveyCritterService.getUniqueSurveyCritterAliases(this.surveyId) ]); const collectionUnitMap = await this._getCollectionUnitMap(worksheet, validRowTsns); // Parse reference data for validation const tsnSet = new Set(validRowTsns.map((tsn) => Number(tsn))); - const csvCritterAliases = rows.map((row) => row.animal_id); + const csvCritterAliases = rowsToValidate.map((row) => row.animal_id); // Track the row validation errors const errors: ValidationError[] = []; - const csvCritters = rows.map((row, index) => { + const csvCritters = rowsToValidate.map((row, index) => { /** * -------------------------------------------------------------------- * STANDARD ROW VALIDATION @@ -281,6 +261,9 @@ export class ImportCrittersService extends DBService { errors.push({ row: index, message: `Invalid ALIAS. Must be unique in Survey and CSV.` }); } + // Covert `sex` to expected casing for Critterbase + row.sex = startCase(row.sex?.toLowerCase()); + /** * -------------------------------------------------------------------- * NON-STANDARD ROW VALIDATION @@ -294,7 +277,6 @@ export class ImportCrittersService extends DBService { delete row[column]; return; } - // Attempt to find the collection unit with the cell value from the mapping const collectionUnitMatch = collectionUnitColumn.collectionUnits.find( (unit) => unit.unit_name.toLowerCase() === String(row[column]).toLowerCase() @@ -320,51 +302,18 @@ export class ImportCrittersService extends DBService { return { success: true, data: csvCritters as CsvCritter[] }; } - return { success: false, errors }; - } - - /** - * Validate the worksheet contains no errors within the data or structure of CSV. - * - * @async - * @param {number} surveyId - Survey identifier - * @param {WorkSheet} worksheet - Xlsx worksheet - * @throws {ApiGeneralError} - If validation fails - * @returns {Promise} Validated CSV rows - */ - async _validate(surveyId: number, worksheet: WorkSheet): Promise { - // Validate the standard columns in the CSV file - if (!validateCsvFile(worksheet, critterStandardColumnValidator)) { - throw new ApiGeneralError(`Column validator failed. Column headers or cell data types are incorrect.`, [ - { column_specification: getColumnValidatorSpecification(critterStandardColumnValidator) }, - 'importCrittersService->_validate->validateCsvFile' - ]); - } - - // Validate the CSV rows with reference data - const validation = await this._validateRows(surveyId, worksheet); - - // Throw error is row validation failed and inject validation errors - if (!validation.success) { - throw new ApiGeneralError(`Failed to import Critter CSV. Column data validator failed.`, [ - { column_validation: validation.errors }, - 'importCrittersService->_validate->_validateRows' - ]); - } - - return validation.data; + return { success: false, error: { issues: errors } }; } /** * Insert CSV critters into Critterbase and SIMS. * * @async - * @param {number} surveyId - Survey identifier * @param {CsvCritter[]} critterRows - CSV row critters * @throws {ApiGeneralError} - If unable to fully insert records into Critterbase * @returns {Promise} List of inserted survey critter ids */ - async _insertCsvCrittersIntoSimsAndCritterbase(surveyId: number, critterRows: CsvCritter[]): Promise { + async insert(critterRows: CsvCritter[]): Promise { const simsPayload: string[] = []; const critterbasePayload: IBulkCreate = { critters: [], collections: [] }; @@ -384,31 +333,12 @@ export class ImportCrittersService extends DBService { // In reality this error should not be triggered, safeguard to prevent floating critter ids in SIMS if (bulkResponse.created.critters !== simsPayload.length) { throw new ApiGeneralError('Unable to fully import critters from CSV', [ - 'importCrittersService -> insertCsvCrittersIntoSimsAndCritterbase', + 'importCrittersStrategy -> insertCsvCrittersIntoSimsAndCritterbase', 'critterbase bulk create response count !== critterIds.length' ]); } // Add Critters to SIMS survey - return this.surveyCritterService.addCrittersToSurvey(surveyId, simsPayload); - } - - /** - * Import the CSV into SIMS and Critterbase. - * - * @async - * @param {number} surveyId - Survey identifier - * @param {MediaFile} critterCsv - CSV MediaFile - * @returns {Promise} List of survey critter identifiers - */ - async import(surveyId: number, critterCsv: MediaFile): Promise { - // Get the worksheet from the CSV - const worksheet = this._getWorksheet(critterCsv); - - // Validate the standard columns and the data of the CSV - const critters = await this._validate(surveyId, worksheet); - - // Insert the data into SIMS and Critterbase - return this._insertCsvCrittersIntoSimsAndCritterbase(surveyId, critters); + return this.surveyCritterService.addCrittersToSurvey(this.surveyId, simsPayload); } } diff --git a/api/src/services/import-services/import-critters-service.interface.ts b/api/src/services/import-services/import-critters-service.interface.ts deleted file mode 100644 index 0a99524824..0000000000 --- a/api/src/services/import-services/import-critters-service.interface.ts +++ /dev/null @@ -1,42 +0,0 @@ -/** - * Type wrapper for unknown CSV rows/records - * - */ -export type Row = Record; - -/** - * A validated CSV Critter object - * - */ -export type CsvCritter = { - critter_id: string; - sex: string; - itis_tsn: number; - animal_id: string; - wlh_id?: string; - critter_comment?: string; -} & { - [collectionUnitColumn: string]: unknown; -}; - -/** - * Invalidated CSV Critter object - * - */ -export type PartialCsvCritter = Partial & { critter_id: string }; - -export type ValidationError = { row: number; message: string }; - -/** - * Conditional validation type similar to Zod SafeParseReturn - * - */ -export type Validation = - | { - success: true; - data: CsvCritter[]; - } - | { - success: false; - errors: ValidationError[]; - }; diff --git a/api/src/services/import-services/import-critters-service.test.ts b/api/src/services/import-services/import-critters-service.test.ts deleted file mode 100644 index 338e347a55..0000000000 --- a/api/src/services/import-services/import-critters-service.test.ts +++ /dev/null @@ -1,783 +0,0 @@ -import chai, { expect } from 'chai'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { WorkSheet } from 'xlsx'; -import { MediaFile } from '../../utils/media/media-file'; -import { critterStandardColumnValidator } from '../../utils/xlsx-utils/column-cell-utils'; -import * as xlsxUtils from '../../utils/xlsx-utils/worksheet-utils'; -import { getMockDBConnection } from '../../__mocks__/db'; -import { IBulkCreateResponse } from '../critterbase-service'; -import { ImportCrittersService } from './import-critters-service'; -import { CsvCritter, PartialCsvCritter } from './import-critters-service.interface'; - -chai.use(sinonChai); - -const mockConnection = getMockDBConnection(); - -describe('ImportCrittersService', () => { - describe('_getCritterRowsToValidate', () => { - it('it should correctly format rows', () => { - const rows = [ - { - SEX: 'Male', - ITIS_TSN: 1, - WLH_ID: '10-1000', - ALIAS: 'Carl', - COMMENT: 'Test', - COLLECTION: 'Unit', - BAD_COLLECTION: 'Bad' - } - ]; - const service = new ImportCrittersService(mockConnection); - - const parsedRow = service._getCritterRowsToValidate(rows, ['COLLECTION', 'TEST'])[0]; - - expect(parsedRow.sex).to.be.eq('Male'); - expect(parsedRow.itis_tsn).to.be.eq(1); - expect(parsedRow.wlh_id).to.be.eq('10-1000'); - expect(parsedRow.animal_id).to.be.eq('Carl'); - expect(parsedRow.critter_comment).to.be.eq('Test'); - expect(parsedRow.COLLECTION).to.be.eq('Unit'); - expect(parsedRow.TEST).to.be.undefined; - expect(parsedRow.BAD_COLLECTION).to.be.undefined; - }); - }); - - describe('_getCritterFromRow', () => { - it('should get all critter properties', () => { - const row: any = { - critter_id: 'id', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - extra_property: 'test' - }; - const service = new ImportCrittersService(mockConnection); - - const critter = service._getCritterFromRow(row); - - expect(critter).to.be.eql({ - critter_id: 'id', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment' - }); - }); - }); - - describe('_getCollectionUnitsFromRow', () => { - it('should get all collection unit properties', () => { - const row: any = { - critter_id: 'id', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'ID1', - HERD: 'ID2' - }; - const service = new ImportCrittersService(mockConnection); - - const collectionUnits = service._getCollectionUnitsFromRow(row); - - expect(collectionUnits).to.be.deep.equal([ - { collection_unit_id: 'ID1', critter_id: 'id' }, - { collection_unit_id: 'ID2', critter_id: 'id' } - ]); - }); - }); - - describe('_getValidTsns', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return unique list of tsns', async () => { - const service = new ImportCrittersService(mockConnection); - - const mockWorksheet = {} as unknown as WorkSheet; - - const getRowsStub = sinon - .stub(service, '_getRows') - .returns([{ itis_tsn: 1 }, { itis_tsn: 2 }, { itis_tsn: 2 }] as any); - - const getTaxonomyStub = sinon.stub(service.platformService, 'getTaxonomyByTsns').resolves([ - { tsn: '1', scientificName: 'a' }, - { tsn: '2', scientificName: 'b' } - ]); - const tsns = await service._getValidTsns(mockWorksheet); - expect(getRowsStub).to.have.been.calledWith(mockWorksheet); - expect(getTaxonomyStub).to.have.been.calledWith(['1', '2']); - expect(tsns).to.deep.equal(['1', '2']); - }); - }); - - describe('_getCollectionUnitMap', () => { - afterEach(() => { - sinon.restore(); - }); - - const collectionUnitsA = [ - { - collection_unit_id: '1', - collection_category_id: '2', - category_name: 'COLLECTION', - unit_name: 'UNIT_A', - description: 'description' - }, - { - collection_unit_id: '2', - collection_category_id: '3', - category_name: 'COLLECTION', - unit_name: 'UNIT_B', - description: 'description' - } - ]; - - const collectionUnitsB = [ - { - collection_unit_id: '1', - collection_category_id: '2', - category_name: 'HERD', - unit_name: 'UNIT_A', - description: 'description' - }, - { - collection_unit_id: '2', - collection_category_id: '3', - category_name: 'HERD', - unit_name: 'UNIT_B', - description: 'description' - } - ]; - - it('should return collection unit mapping', async () => { - const service = new ImportCrittersService(mockConnection); - - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const mockWorksheet = {} as unknown as WorkSheet; - - const findCollectionUnitsStub = sinon.stub(service.critterbaseService, 'findTaxonCollectionUnits'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - findCollectionUnitsStub.onCall(0).resolves(collectionUnitsA); - findCollectionUnitsStub.onCall(1).resolves(collectionUnitsB); - - const mapping = await service._getCollectionUnitMap(mockWorksheet, ['1', '2']); - expect(getColumnsStub).to.have.been.calledWith(mockWorksheet); - expect(findCollectionUnitsStub).to.have.been.calledTwice; - - expect(mapping).to.be.instanceof(Map); - expect(mapping.get('COLLECTION')).to.be.deep.equal({ collectionUnits: collectionUnitsA, tsn: 1 }); - expect(mapping.get('HERD')).to.be.deep.equal({ collectionUnits: collectionUnitsB, tsn: 2 }); - }); - - it('should return empty map when no collection unit columns', async () => { - const service = new ImportCrittersService(mockConnection); - - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const mockWorksheet = {} as unknown as WorkSheet; - - const findCollectionUnitsStub = sinon.stub(service.critterbaseService, 'findTaxonCollectionUnits'); - getColumnsStub.returns([]); - - const mapping = await service._getCollectionUnitMap(mockWorksheet, ['1', '2']); - expect(getColumnsStub).to.have.been.calledWith(mockWorksheet); - expect(findCollectionUnitsStub).to.have.not.been.called; - - expect(mapping).to.be.instanceof(Map); - }); - }); - - describe('_insertCsvCrittersIntoSimsAndCritterbase', () => { - afterEach(() => { - sinon.restore(); - }); - - const critters: CsvCritter[] = [ - { - critter_id: '1', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'Collection Unit' - }, - { - critter_id: '2', - sex: 'Female', - itis_tsn: 2, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - HERD: 'Herd Unit' - } - ]; - - it('should correctly parse collection units and critters and insert into sims / critterbase', async () => { - const service = new ImportCrittersService(mockConnection); - - const critterbaseBulkCreateStub = sinon.stub(service.critterbaseService, 'bulkCreate'); - const simsAddSurveyCrittersStub = sinon.stub(service.surveyCritterService, 'addCrittersToSurvey'); - - critterbaseBulkCreateStub.resolves({ created: { critters: 2, collections: 1 } } as IBulkCreateResponse); - simsAddSurveyCrittersStub.resolves([1]); - - const ids = await service._insertCsvCrittersIntoSimsAndCritterbase(1, critters); - - expect(critterbaseBulkCreateStub).to.have.been.calledWithExactly({ - critters: [ - { - critter_id: '1', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment' - }, - { - critter_id: '2', - sex: 'Female', - itis_tsn: 2, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment' - } - ], - collections: [ - { collection_unit_id: 'Collection Unit', critter_id: '1' }, - { collection_unit_id: 'Herd Unit', critter_id: '2' } - ] - }); - - expect(ids).to.be.deep.equal([1]); - }); - - it('should throw error if response from critterbase is less than provided critters', async () => { - const service = new ImportCrittersService(mockConnection); - - const critterbaseBulkCreateStub = sinon.stub(service.critterbaseService, 'bulkCreate'); - const simsAddSurveyCrittersStub = sinon.stub(service.surveyCritterService, 'addCrittersToSurvey'); - - critterbaseBulkCreateStub.resolves({ created: { critters: 1, collections: 1 } } as IBulkCreateResponse); - simsAddSurveyCrittersStub.resolves([1]); - - try { - await service._insertCsvCrittersIntoSimsAndCritterbase(1, critters); - expect.fail(); - } catch (err: any) { - expect(err.message).to.be.equal('Unable to fully import critters from CSV'); - } - - expect(simsAddSurveyCrittersStub).to.not.have.been.called; - }); - }); - - describe('_validateRows', () => { - afterEach(() => { - sinon.restore(); - }); - - const collectionUnitsA = [ - { - collection_unit_id: '1', - collection_category_id: '2', - category_name: 'COLLECTION', - unit_name: 'UNIT_A', - description: 'description' - }, - { - collection_unit_id: '2', - collection_category_id: '3', - category_name: 'COLLECTION', - unit_name: 'UNIT_B', - description: 'description' - } - ]; - - const collectionUnitsB = [ - { - collection_unit_id: '1', - collection_category_id: '2', - category_name: 'HERD', - unit_name: 'UNIT_A', - description: 'description' - }, - { - collection_unit_id: '2', - collection_category_id: '3', - category_name: 'HERD', - unit_name: 'UNIT_B', - description: 'description' - } - ]; - - it('should return successful', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const validRows: CsvCritter[] = [ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'B', - sex: 'Male', - itis_tsn: 2, - animal_id: 'Test', - wlh_id: '10-1000', - critter_comment: 'comment', - HERD: 'UNIT_B' - } - ]; - - getRowsStub.returns(validRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.true; - - if (validation.success) { - expect(validation.data).to.be.deep.equal([ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: '1' - }, - { - critter_id: 'B', - sex: 'Male', - itis_tsn: 2, - animal_id: 'Test', - wlh_id: '10-1000', - critter_comment: 'comment', - HERD: '2' - } - ]); - } - }); - - it('should push error when sex is undefined or invalid', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const invalidRows: PartialCsvCritter[] = [ - { - critter_id: 'A', - sex: undefined, - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'A', - sex: 'Whoops' as any, - itis_tsn: 1, - animal_id: 'Carl2', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - } - ]; - - getRowsStub.returns(invalidRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.false; - if (!validation.success) { - expect(validation.errors.length).to.be.eq(2); - expect(validation.errors).to.be.deep.equal([ - { - message: 'Invalid SEX. Expecting: UNKNOWN, MALE, FEMALE, HERMAPHRODITIC.', - row: 0 - }, - { - message: 'Invalid SEX. Expecting: UNKNOWN, MALE, FEMALE, HERMAPHRODITIC.', - row: 1 - } - ]); - } - }); - - it('should push error when wlh_id is invalid regex / shape', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const invalidRows: PartialCsvCritter[] = [ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '101000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl2', - wlh_id: '1-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - } - ]; - - getRowsStub.returns(invalidRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.false; - if (!validation.success) { - expect(validation.errors.length).to.be.eq(2); - expect(validation.errors).to.be.deep.equal([ - { - message: `Invalid WLH_ID. Example format '10-1000R'.`, - row: 0 - }, - { - message: `Invalid WLH_ID. Example format '10-1000R'.`, - row: 1 - } - ]); - } - }); - - it('should push error when itis_tsn undefined or invalid option', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const invalidRows: PartialCsvCritter[] = [ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: undefined, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 10, - animal_id: 'Carl2', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - } - ]; - - getRowsStub.returns(invalidRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.false; - if (!validation.success) { - expect(validation.errors.length).to.be.eq(4); - expect(validation.errors).to.be.deep.equal([ - { - message: `Invalid ITIS_TSN.`, - row: 0 - }, - { - message: `Invalid COLLECTION. Cell value not allowed for TSN.`, - row: 0 - }, - { - message: `Invalid ITIS_TSN.`, - row: 1 - }, - { - message: `Invalid COLLECTION. Cell value not allowed for TSN.`, - row: 1 - } - ]); - } - }); - - it('should push error when itis_tsn undefined or invalid option', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const invalidRows: PartialCsvCritter[] = [ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: undefined, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 10, - animal_id: 'Carl2', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - } - ]; - - getRowsStub.returns(invalidRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.false; - if (!validation.success) { - expect(validation.errors.length).to.be.eq(4); - expect(validation.errors).to.be.deep.equal([ - { - message: `Invalid ITIS_TSN.`, - row: 0 - }, - { - message: `Invalid COLLECTION. Cell value not allowed for TSN.`, - row: 0 - }, - { - message: `Invalid ITIS_TSN.`, - row: 1 - }, - { - message: `Invalid COLLECTION. Cell value not allowed for TSN.`, - row: 1 - } - ]); - } - }); - - it('should push error if alias undefined, duplicate or exists in survey', async () => { - const service = new ImportCrittersService(mockConnection); - const getRowsStub = sinon.stub(service, '_getRows'); - const getColumnsStub = sinon.stub(service, '_getNonStandardColumns'); - const surveyAliasesStub = sinon.stub(service.surveyCritterService, 'getUniqueSurveyCritterAliases'); - const getValidTsnsStub = sinon.stub(service, '_getValidTsns'); - const collectionMapStub = sinon.stub(service, '_getCollectionUnitMap'); - - getColumnsStub.returns(['COLLECTION', 'HERD']); - surveyAliasesStub.resolves(new Set(['Not Carl', 'Carlita'])); - getValidTsnsStub.resolves(['1', '2']); - collectionMapStub.resolves( - new Map([ - ['COLLECTION', { collectionUnits: collectionUnitsA, tsn: 1 }], - ['HERD', { collectionUnits: collectionUnitsB, tsn: 2 }] - ]) - ); - - const invalidRows: PartialCsvCritter[] = [ - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - }, - { - critter_id: 'A', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carlita', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'UNIT_A' - } - ]; - - getRowsStub.returns(invalidRows); - - const validation = await service._validateRows(1, {} as WorkSheet); - - expect(validation.success).to.be.false; - if (!validation.success) { - expect(validation.errors.length).to.be.eq(1); - expect(validation.errors).to.be.deep.equal([ - { - message: `Invalid ALIAS. Must be unique in Survey and CSV.`, - row: 1 - } - ]); - } - }); - }); - - describe('_validate', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw error when csv validation fails', async () => { - const validateCsvStub = sinon.stub(xlsxUtils, 'validateCsvFile').returns(false); - - const service = new ImportCrittersService(mockConnection); - - sinon.stub(service, '_validateRows'); - - try { - await service._validate(1, {} as WorkSheet); - expect.fail(); - } catch (err: any) { - expect(err.message).to.contain('Column validator failed.'); - } - expect(validateCsvStub).to.have.been.calledOnceWithExactly({}, critterStandardColumnValidator); - }); - - it('should call _validateRows if csv validation succeeds', async () => { - const validateCsvStub = sinon.stub(xlsxUtils, 'validateCsvFile'); - - const service = new ImportCrittersService(mockConnection); - - const validateRowsStub = sinon.stub(service, '_validateRows'); - - validateCsvStub.returns(true); - validateRowsStub.resolves({ success: true, data: [] }); - - const data = await service._validate(1, {} as WorkSheet); - expect(validateRowsStub).to.have.been.calledOnceWithExactly(1, {}); - expect(data).to.be.deep.equal([]); - }); - - it('should throw error if row validation fails', async () => { - const validateCsvStub = sinon.stub(xlsxUtils, 'validateCsvFile'); - - const service = new ImportCrittersService(mockConnection); - - const validateRowsStub = sinon.stub(service, '_validateRows'); - - validateCsvStub.returns(true); - validateRowsStub.resolves({ success: false, errors: [] }); - - try { - await service._validate(1, {} as WorkSheet); - - expect.fail(); - } catch (err: any) { - expect(err.message).to.contain('Failed to import Critter CSV.'); - } - expect(validateRowsStub).to.have.been.calledOnceWithExactly(1, {}); - }); - }); - - describe('import', () => { - it('should pass values to correct methods', async () => { - const service = new ImportCrittersService(mockConnection); - const csv = new MediaFile('file', 'mime', Buffer.alloc(1)); - - const critter: CsvCritter = { - critter_id: 'id', - sex: 'Male', - itis_tsn: 1, - animal_id: 'Carl', - wlh_id: '10-1000', - critter_comment: 'comment', - COLLECTION: 'Unit' - }; - - const getWorksheetStub = sinon.stub(service, '_getWorksheet').returns({} as unknown as WorkSheet); - const validateStub = sinon.stub(service, '_validate').resolves([critter]); - const insertStub = sinon.stub(service, '_insertCsvCrittersIntoSimsAndCritterbase').resolves([1]); - - const data = await service.import(1, csv); - - expect(getWorksheetStub).to.have.been.calledWithExactly(csv); - expect(validateStub).to.have.been.calledWithExactly(1, {}); - expect(insertStub).to.have.been.calledWithExactly(1, [critter]); - - expect(data).to.be.deep.equal([1]); - }); - }); -}); diff --git a/api/src/services/import-services/import-csv.interface.ts b/api/src/services/import-services/import-csv.interface.ts new file mode 100644 index 0000000000..6b843ab9e9 --- /dev/null +++ b/api/src/services/import-services/import-csv.interface.ts @@ -0,0 +1,102 @@ +import { WorkSheet } from 'xlsx'; +import { z } from 'zod'; +import { IXLSXCSVValidator } from '../../utils/xlsx-utils/worksheet-utils'; + +/** + * Type wrapper for unknown CSV rows/records + * + */ +export type Row = Record; + +/** + * Implementation for CSV Import Strategies. + * + * All CSV import strategies should implement this interface to be used with `CSVImport` function. + * + * Note: When implementing a strategy using this interface the generics will be inferred. + * + * @template ValidatedRow + * @template InsertReturn + */ +export interface CSVImportStrategy, InsertReturn = unknown> { + /** + * Standard column validator - used to validate the column headers and types. + * + * @see '../../utils/xlsx-utils/worksheet-utils.ts' + * @see '../../utils/xlsx-utils/column-cell-utils.ts' + */ + columnValidator: IXLSXCSVValidator; + + /** + * Pre parse the XLSX Worksheet before passing to `validateRows`. + * Optional method to implement if extra parsing needed for worksheet. + * + * @param {WorkSheet} worksheet - XLSX worksheet + * @returns {WorkSheet | Promise} + */ + preParseWorksheet?: (worksheet: WorkSheet) => WorkSheet | Promise; + + /** + * Validate the pre-parsed rows - return either custom Validation or Zod SafeParse. + * + * @param {Row[]} rows - Raw unparsed CSV rows + * @param {WorkSheet} [worksheet] - Xlsx worksheet - useful for calculating non-standard columns + * @returns {Promise | Validation>} Validation + */ + validateRows( + rows: Row[], + worksheet?: WorkSheet + ): Promise | Validation>; + + /** + * Insert the validated rows into database or send to external systems. + * + * @param {ValidatedRows[]} rows - Validated CSV rows + * @returns {Promise} + */ + insert(rows: ValidatedRow[]): Promise; +} + +/** + * CSV validation error + * + */ +export type ValidationError = { + /** + * CSV row index + * + */ + row: number; + /** + * CSV column header + * + */ + col?: string; + /** + * CSV row error message + * + */ + message: string; +}; + +/** + * Conditional validation type similar to Zod SafeParseReturn + * + */ +export type Validation = + /** + * On success (true) return the parsed CSV data + */ + | { + success: true; + data: T[]; + } + /** + * On failure (false) return the parsed CSV validation errors + */ + | { + success: false; + error: { + issues: ValidationError[]; + }; + }; diff --git a/api/src/services/import-services/import-csv.test.ts b/api/src/services/import-services/import-csv.test.ts new file mode 100644 index 0000000000..66955e21ee --- /dev/null +++ b/api/src/services/import-services/import-csv.test.ts @@ -0,0 +1,93 @@ +import chai, { expect } from 'chai'; +import { describe } from 'mocha'; +import sinon from 'sinon'; +import sinonChai from 'sinon-chai'; +import { MediaFile } from '../../utils/media/media-file'; +import * as worksheetUtils from '../../utils/xlsx-utils/worksheet-utils'; +import { importCSV } from './import-csv'; +import { CSVImportStrategy } from './import-csv.interface'; + +chai.use(sinonChai); + +describe('importCSV', () => { + beforeEach(() => { + sinon.restore(); + }); + + it('should pass correct values through chain', async () => { + const mockCsv = new MediaFile('file', 'file', Buffer.from('')); + const mockWorksheet = {}; + + const importer: CSVImportStrategy = { + columnValidator: { ID: { type: 'string' } }, + validateRows: sinon.stub().resolves({ success: true, data: true }), + insert: sinon.stub().resolves(true) + }; + + const getWorksheetStub = sinon.stub(worksheetUtils, 'getDefaultWorksheet').returns(mockWorksheet); + const validateCsvFileStub = sinon.stub(worksheetUtils, 'validateCsvFile').returns(true); + + const data = await importCSV(mockCsv, importer); + + expect(getWorksheetStub).to.have.been.called.calledOnceWithExactly(worksheetUtils.constructXLSXWorkbook(mockCsv)); + expect(validateCsvFileStub).to.have.been.called.calledOnceWithExactly(mockWorksheet, importer.columnValidator); + expect(importer.insert).to.have.been.called.calledOnceWithExactly(true); + expect(data).to.be.true; + }); + + it('should throw error if column validator fails', async () => { + const mockCsv = new MediaFile('file', 'file', Buffer.from('')); + + const importer: CSVImportStrategy = { + columnValidator: { ID: { type: 'string' } }, + validateRows: sinon.stub().resolves({ success: true, data: true }), + insert: sinon.stub().resolves(true) + }; + + sinon.stub(worksheetUtils, 'validateCsvFile').returns(false); + + try { + await importCSV(mockCsv, importer); + + expect.fail(); + } catch (err: any) { + expect(err.message).to.be.eql(`Column validator failed. Column headers or cell data types are incorrect.`); + expect(err.errors[0]).to.be.eql({ + csv_column_errors: [ + { + columnName: 'ID', + columnType: 'string', + columnAliases: undefined, + optional: undefined + } + ] + }); + } + }); + + it('should throw error if import strategy validateRows fails', async () => { + const mockCsv = new MediaFile('file', 'file', Buffer.from('')); + const mockWorksheet = {}; + const mockValidation = { success: false, error: { issues: [{ row: 1, message: 'invalidated' }] } }; + + const importer: CSVImportStrategy = { + columnValidator: { ID: { type: 'string' } }, + validateRows: sinon.stub().returns(mockValidation), + insert: sinon.stub().resolves(true) + }; + + sinon.stub(worksheetUtils, 'getDefaultWorksheet').returns(mockWorksheet); + sinon.stub(worksheetUtils, 'validateCsvFile').returns(true); + + try { + await importCSV(mockCsv, importer); + expect.fail(); + } catch (err: any) { + expect(importer.validateRows).to.have.been.calledOnceWithExactly([], mockWorksheet); + expect(err.message).to.be.eql(`Failed to import Critter CSV. Column data validator failed.`); + expect(err.errors[0]).to.be.eql({ + csv_row_errors: mockValidation.error.issues + }); + } + }); +}); diff --git a/api/src/services/import-services/import-csv.ts b/api/src/services/import-services/import-csv.ts new file mode 100644 index 0000000000..6cee607e8b --- /dev/null +++ b/api/src/services/import-services/import-csv.ts @@ -0,0 +1,66 @@ +import { ApiGeneralError } from '../../errors/api-error'; +import { MediaFile } from '../../utils/media/media-file'; +import { getColumnValidatorSpecification } from '../../utils/xlsx-utils/column-validator-utils'; +import { + constructXLSXWorkbook, + getDefaultWorksheet, + getWorksheetRowObjects, + validateCsvFile +} from '../../utils/xlsx-utils/worksheet-utils'; +import { CSVImportStrategy } from './import-csv.interface'; + +/** + * Import CSV - Used with `CSVImportStrategy` classes. + * + * How to?: Inject a media-file and import strategy that implements `CSVImportStrategy`. + * + * Flow: + * 1. Get the worksheet from the CSV MediaFile - _getWorksheet + * 2. Validate the standard columns with the `importCsvStrategy` column validator - _validate -> validateCsvFile + * 3. Validate row data with import strategy - _validate -> importCsvService.validateRows + * 4. Insert the data into database or send to external system - import -> importCsvStrategy.insert + * + * @async + * @template ValidatedRow - Validated row object + * @template InsertReturn - Return type of the importer insert method + * @param {MediaFile} csvMediaFile - CSV converted to MediaFile + * @param {CSVImportStrategy} importer - Import strategy + * @throws {ApiGeneralError} - If validation fails + * @returns {Promise} Generic return type + */ +export const importCSV = async ( + csvMediaFile: MediaFile, + importer: CSVImportStrategy +) => { + const _worksheet = getDefaultWorksheet(constructXLSXWorkbook(csvMediaFile)); + + // Optionally pre-parse the worksheet before passing to validator + // Usefull if needing to mutate incomming worksheet data before validation ie: time columns + const worksheet = importer.preParseWorksheet ? importer.preParseWorksheet(_worksheet) : _worksheet; + + // Validate the standard columns in the CSV file + if (!validateCsvFile(worksheet, importer.columnValidator)) { + throw new ApiGeneralError(`Column validator failed. Column headers or cell data types are incorrect.`, [ + { csv_column_errors: getColumnValidatorSpecification(importer.columnValidator) }, + 'importCSV->_validate->validateCsvFile' + ]); + } + + // Convert the worksheet into an array of records + const worksheetRows = getWorksheetRowObjects(worksheet); + + // Validate the CSV rows with reference data + const validation = await importer.validateRows(worksheetRows, worksheet); + + // Throw error is row validation failed and inject validation errors + // The validation errors can be either custom (Validation) or Zod (SafeParseReturn) + if (!validation.success) { + throw new ApiGeneralError(`Failed to import Critter CSV. Column data validator failed.`, [ + { csv_row_errors: validation.error.issues }, + 'importCSV->_validate->_validateRows' + ]); + } + + // Insert the data or send to external systems + return importer.insert(validation.data); +}; diff --git a/api/src/services/import-services/marking/import-markings-strategy.interface.ts b/api/src/services/import-services/marking/import-markings-strategy.interface.ts new file mode 100644 index 0000000000..0917f011b9 --- /dev/null +++ b/api/src/services/import-services/marking/import-markings-strategy.interface.ts @@ -0,0 +1,79 @@ +import { z } from 'zod'; +import { IAsSelectLookup } from '../../critterbase-service'; + +/** + * Get CSV Marking schema. + * + * Note: This getter allows custom values to be injected for validation. + * + * Note: This could be updated to transform the string values into the primary keys + * to prevent Critterbase from having to translate / patch in incomming bulk values. + * + * @param {IAsSelectLookup[]} colours - Array of supported Critterbase colours + * @returns {*} Custom Zod schema for CSV Markings + */ +export const getCsvMarkingSchema = ( + colours: IAsSelectLookup[], + markingTypes: IAsSelectLookup[], + critterBodyLocationsMap: Map +) => { + const colourNames = colours.map((colour) => colour.value.toLowerCase()); + const markingTypeNames = markingTypes.map((markingType) => markingType.value.toLowerCase()); + + const coloursSet = new Set(colourNames); + const markingTypesSet = new Set(markingTypeNames); + + return z + .object({ + critter_id: z.string({ required_error: 'Unable to find matching survey critter with alias' }).uuid(), + capture_id: z.string({ required_error: 'Unable to find matching capture with date and time' }).uuid(), + body_location: z.string(), + marking_type: z + .string() + .refine( + (val) => markingTypesSet.has(val.toLowerCase()), + `Marking type not supported. Allowed values: ${markingTypeNames.join(', ')}` + ) + .optional(), + identifier: z.string().optional(), + primary_colour: z + .string() + .refine( + (val) => coloursSet.has(val.toLowerCase()), + `Colour not supported. Allowed values: ${colourNames.join(', ')}` + ) + .optional(), + secondary_colour: z + .string() + .refine( + (val) => coloursSet.has(val.toLowerCase()), + `Colour not supported. Allowed values: ${colourNames.join(', ')}` + ) + .optional(), + comment: z.string().optional() + }) + .superRefine((schema, ctx) => { + const bodyLocations = critterBodyLocationsMap.get(schema.critter_id); + if (!bodyLocations) { + ctx.addIssue({ + code: z.ZodIssueCode.custom, + message: 'No taxon body locations found for Critter' + }); + } else if ( + !bodyLocations.filter((location) => location.value.toLowerCase() === schema.body_location.toLowerCase()).length + ) { + ctx.addIssue({ + code: z.ZodIssueCode.custom, + message: `Invalid body location for Critter. Allowed values: ${bodyLocations + .map((bodyLocation) => bodyLocation.value) + .join(', ')}` + }); + } + }); +}; + +/** + * A validated CSV Marking object + * + */ +export type CsvMarking = z.infer>; diff --git a/api/src/services/import-services/marking/import-markings-strategy.test.ts b/api/src/services/import-services/marking/import-markings-strategy.test.ts new file mode 100644 index 0000000000..4cfc6e192a --- /dev/null +++ b/api/src/services/import-services/marking/import-markings-strategy.test.ts @@ -0,0 +1,249 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { MediaFile } from '../../../utils/media/media-file'; +import * as worksheetUtils from '../../../utils/xlsx-utils/worksheet-utils'; +import { getMockDBConnection } from '../../../__mocks__/db'; +import { IBulkCreateResponse, ICritterDetailed } from '../../critterbase-service'; +import { importCSV } from '../import-csv'; +import { ImportMarkingsStrategy } from './import-markings-strategy'; +import { CsvMarking } from './import-markings-strategy.interface'; + +describe('ImportMarkingsStrategy', () => { + describe('importCSV marking worksheet', () => { + beforeEach(() => { + sinon.restore(); + }); + it('should validate successfully', async () => { + const worksheet = { + A1: { t: 's', v: 'CAPTURE_DATE' }, // testing order incorrect + B1: { t: 's', v: 'ALIAS' }, + C1: { t: 's', v: 'CAPTURE_TIME' }, + D1: { t: 's', v: 'BODY_LOCATION' }, + E1: { t: 's', v: 'MARKING_TYPE' }, + F1: { t: 's', v: 'IDENTIFIER' }, + G1: { t: 's', v: 'PRIMARY_COLOUR' }, + H1: { t: 's', v: 'SECONDARY_COLOUR' }, + I1: { t: 's', v: 'DESCRIPTION' }, // testing alias works + A2: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + B2: { t: 's', v: 'Carl' }, + C2: { t: 's', v: '10:10:12' }, + D2: { t: 's', v: 'Left ear' }, // testing case insensitivity + E2: { t: 's', v: 'Ear tag' }, + F2: { t: 's', v: 'asdfasdf' }, + G2: { t: 's', v: 'red' }, + H2: { t: 's', v: 'blue' }, + I2: { t: 's', v: 'tagged' }, + '!ref': 'A1:I2' + }; + + const mockDBConnection = getMockDBConnection(); + + const strategy = new ImportMarkingsStrategy(mockDBConnection, 1); + + const getDefaultWorksheetStub = sinon.stub(worksheetUtils, 'getDefaultWorksheet'); + const critterbaseInsertStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'bulkCreate'); + const aliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const colourStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'getColours'); + const markingTypeStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'getMarkingTypes'); + const taxonBodyLocationStub = sinon.stub(strategy, 'getTaxonBodyLocationsCritterIdMap'); + + colourStub.resolves([ + { id: 'A', key: 'colour', value: 'red' }, + { id: 'B', key: 'colour', value: 'blue' } + ]); + + markingTypeStub.resolves([ + { id: 'C', key: 'markingType', value: 'ear tag' }, + { id: 'D', key: 'markingType', value: 'nose band' } + ]); + + taxonBodyLocationStub.resolves( + new Map([ + ['3647cdc9-6fe9-4c32-acfa-6096fe123c4a', [{ id: 'D', key: 'bodylocation', value: 'left ear' }]], + ['4540d43a-7ced-4216-b49e-2a972d25dfdc', [{ id: 'E', key: 'bodylocation', value: 'tail' }]] + ]) + ); + + getDefaultWorksheetStub.returns(worksheet); + aliasMapStub.resolves( + new Map([ + [ + 'carl', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [ + { + capture_id: '4647cdc9-6fe9-4c32-acfa-6096fe123c4a', + capture_date: '2024-10-10', + capture_time: '10:10:12' + } + ] + } as ICritterDetailed + ], + [ + 'carlita', + { + critter_id: '3647cdc9-6fe9-4c32-acfa-6096fe123c4a', + captures: [ + { + capture_id: '5647cdc9-6fe9-4c32-acfa-6096fe123c4a', + capture_date: '2024-10-10', + capture_time: '10:10:10' + } + ] + } as ICritterDetailed + ] + ]) + ); + critterbaseInsertStub.resolves({ created: { markings: 2 } } as IBulkCreateResponse); + + try { + const data = await importCSV(new MediaFile('test', 'test', 'test' as unknown as Buffer), strategy); + expect(data).to.deep.equal(2); + } catch (err: any) { + expect.fail(); + } + }); + }); + describe('getTaxonBodyLocationsCritterIdMap', () => { + it('should return a critter_id mapping of body locations', async () => { + const mockDBConnection = getMockDBConnection(); + const strategy = new ImportMarkingsStrategy(mockDBConnection, 1); + + const taxonBodyLocationsStub = sinon.stub( + strategy.surveyCritterService.critterbaseService, + 'getTaxonBodyLocations' + ); + const mockBodyLocationsA = [ + { id: 'A', key: 'column', value: 'Right Ear' }, + { id: 'B', key: 'column', value: 'Antlers' } + ]; + + const mockBodyLocationsB = [ + { id: 'C', key: 'column', value: 'Nose' }, + { id: 'D', key: 'column', value: 'Tail' } + ]; + + taxonBodyLocationsStub.onCall(0).resolves(mockBodyLocationsA); + taxonBodyLocationsStub.onCall(1).resolves(mockBodyLocationsB); + + const critterMap = await strategy.getTaxonBodyLocationsCritterIdMap([ + { critter_id: 'ACRITTER', itis_tsn: 1 }, + { critter_id: 'BCRITTER', itis_tsn: 2 }, + { critter_id: 'CCRITTER', itis_tsn: 2 } + ] as ICritterDetailed[]); + + expect(taxonBodyLocationsStub).to.have.been.calledTwice; + expect(taxonBodyLocationsStub.getCall(0).args[0]).to.be.eql('1'); + expect(taxonBodyLocationsStub.getCall(1).args[0]).to.be.eql('2'); + expect(critterMap).to.be.deep.equal( + new Map([ + ['ACRITTER', mockBodyLocationsA], + ['BCRITTER', mockBodyLocationsB], + ['CCRITTER', mockBodyLocationsB] + ]) + ); + }); + }); + + describe('validateRows', () => { + it('should validate the rows successfully', async () => { + const mockDBConnection = getMockDBConnection(); + const strategy = new ImportMarkingsStrategy(mockDBConnection, 1); + + const mockCritterA = { + critter_id: '4df8fd4c-4d7b-4142-8f03-92d8bf52d8cb', + itis_tsn: 1, + captures: [ + { capture_id: 'e9087545-5b1f-4b86-bf1d-a3372a7b33c7', capture_date: '10-10-2024', capture_time: '10:10:10' } + ] + } as ICritterDetailed; + + const mockCritterB = { + critter_id: '4540d43a-7ced-4216-b49e-2a972d25dfdc', + itis_tsn: 1, + captures: [ + { capture_id: '21f3c699-9017-455b-bd7d-49110ca4b586', capture_date: '10-10-2024', capture_time: '10:10:10' } + ] + } as ICritterDetailed; + + const aliasStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const colourStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'getColours'); + const markingTypeStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'getMarkingTypes'); + const taxonBodyLocationStub = sinon.stub(strategy, 'getTaxonBodyLocationsCritterIdMap'); + + aliasStub.resolves( + new Map([ + ['carl', mockCritterA], + ['carlita', mockCritterB] + ]) + ); + + colourStub.resolves([ + { id: 'A', key: 'colour', value: 'red' }, + { id: 'B', key: 'colour', value: 'blue' } + ]); + + markingTypeStub.resolves([ + { id: 'C', key: 'markingType', value: 'ear tag' }, + { id: 'D', key: 'markingType', value: 'nose band' } + ]); + + taxonBodyLocationStub.resolves( + new Map([ + ['4df8fd4c-4d7b-4142-8f03-92d8bf52d8cb', [{ id: 'D', key: 'bodylocation', value: 'ear' }]], + ['4540d43a-7ced-4216-b49e-2a972d25dfdc', [{ id: 'E', key: 'bodylocation', value: 'tail' }]] + ]) + ); + + const rows = [ + { + CAPTURE_DATE: '10-10-2024', + CAPTURE_TIME: '10:10:10', + ALIAS: 'carl', + BODY_LOCATION: 'Ear', + MARKING_TYPE: 'ear tag', + IDENTIFIER: 'identifier', + PRIMARY_COLOUR: 'Red', + SECONDARY_COLOUR: 'blue', + DESCRIPTION: 'comment' + } + ]; + + const validation = await strategy.validateRows(rows); + + if (!validation.success) { + expect.fail(); + } else { + expect(validation.success).to.be.true; + expect(validation.data).to.be.deep.equal([ + { + critter_id: '4df8fd4c-4d7b-4142-8f03-92d8bf52d8cb', + capture_id: 'e9087545-5b1f-4b86-bf1d-a3372a7b33c7', + body_location: 'Ear', + marking_type: 'ear tag', + identifier: 'identifier', + primary_colour: 'Red', + secondary_colour: 'blue', + comment: 'comment' + } + ]); + } + }); + }); + describe('insert', () => { + it('should return the count of inserted markings', async () => { + const mockDBConnection = getMockDBConnection(); + const strategy = new ImportMarkingsStrategy(mockDBConnection, 1); + + const bulkCreateStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'bulkCreate'); + + bulkCreateStub.resolves({ created: { markings: 1 } } as IBulkCreateResponse); + + const data = await strategy.insert([{ critter_id: 'id' } as unknown as CsvMarking]); + + expect(bulkCreateStub).to.have.been.calledWith({ markings: [{ critter_id: 'id' }] }); + expect(data).to.be.eql(1); + }); + }); +}); diff --git a/api/src/services/import-services/marking/import-markings-strategy.ts b/api/src/services/import-services/marking/import-markings-strategy.ts new file mode 100644 index 0000000000..97dbf52237 --- /dev/null +++ b/api/src/services/import-services/marking/import-markings-strategy.ts @@ -0,0 +1,170 @@ +import { z } from 'zod'; +import { IDBConnection } from '../../../database/db'; +import { getLogger } from '../../../utils/logger'; +import { CSV_COLUMN_ALIASES } from '../../../utils/xlsx-utils/column-aliases'; +import { generateColumnCellGetterFromColumnValidator } from '../../../utils/xlsx-utils/column-validator-utils'; +import { IXLSXCSVValidator } from '../../../utils/xlsx-utils/worksheet-utils'; +import { IAsSelectLookup, ICritterDetailed } from '../../critterbase-service'; +import { DBService } from '../../db-service'; +import { SurveyCritterService } from '../../survey-critter-service'; +import { CSVImportStrategy, Row } from '../import-csv.interface'; +import { findCapturesFromDateTime } from '../utils/datetime'; +import { CsvMarking, getCsvMarkingSchema } from './import-markings-strategy.interface'; + +const defaultLog = getLogger('services/import/import-markings-strategy'); + +/** + * + * @class ImportMarkingsStrategy + * @extends DBService + * @see CSVImport + * + */ +export class ImportMarkingsStrategy extends DBService implements CSVImportStrategy { + surveyCritterService: SurveyCritterService; + surveyId: number; + + /** + * An XLSX validation config for the standard columns of a Critterbase Marking CSV. + * + * Note: `satisfies` allows `keyof` to correctly infer keyof type, while also + * enforcing uppercase object keys. + */ + columnValidator = { + ALIAS: { type: 'string', aliases: CSV_COLUMN_ALIASES.ALIAS }, + CAPTURE_DATE: { type: 'date' }, + CAPTURE_TIME: { type: 'string', optional: true }, + BODY_LOCATION: { type: 'string', optional: true }, + MARKING_TYPE: { type: 'string', optional: true }, + IDENTIFIER: { type: 'string', optional: true }, + PRIMARY_COLOUR: { type: 'string', optional: true }, + SECONDARY_COLOUR: { type: 'string', optional: true }, + DESCRIPTION: { type: 'string', aliases: CSV_COLUMN_ALIASES.DESCRIPTION, optional: true } + } satisfies IXLSXCSVValidator; + + /** + * Construct an instance of ImportMarkingsStrategy. + * + * @param {IDBConnection} connection - DB connection + * @param {string} surveyId + */ + constructor(connection: IDBConnection, surveyId: number) { + super(connection); + + this.surveyId = surveyId; + + this.surveyCritterService = new SurveyCritterService(connection); + } + + /** + * Get taxon body locations Map from a list of Critters. + * + * @async + * @param {ICritterDetailed[]} critters - List of detailed critters + * @returns {Promise>} Critter id -> taxon body locations Map + */ + async getTaxonBodyLocationsCritterIdMap(critters: ICritterDetailed[]): Promise> { + const tsnBodyLocationsMap = new Map(); + const critterBodyLocationsMap = new Map(); + + const uniqueTsns = Array.from(new Set(critters.map((critter) => critter.itis_tsn))); + + // Only fetch body locations for unique tsns + const bodyLocations = await Promise.all( + uniqueTsns.map((tsn) => this.surveyCritterService.critterbaseService.getTaxonBodyLocations(String(tsn))) + ); + + // Loop through the flattened responses and set the body locations for each tsn + bodyLocations.flatMap((bodyLocationValues, idx) => { + tsnBodyLocationsMap.set(uniqueTsns[idx], bodyLocationValues); + }); + + // Now loop through the critters and assign the body locations to the critter id + for (const critter of critters) { + const tsnBodyLocations = tsnBodyLocationsMap.get(critter.itis_tsn); + if (tsnBodyLocations) { + critterBodyLocationsMap.set(critter.critter_id, tsnBodyLocations); + } + } + + return critterBodyLocationsMap; + } + + /** + * Validate the CSV rows against zod schema. + * + * @param {Row[]} rows - CSV rows + * @returns {*} + */ + async validateRows(rows: Row[]) { + // Generate type-safe cell getter from column validator + const getColumnCell = generateColumnCellGetterFromColumnValidator(this.columnValidator); + + // Get validation reference data + const [critterAliasMap, colours, markingTypes] = await Promise.all([ + this.surveyCritterService.getSurveyCritterAliasMap(this.surveyId), + this.surveyCritterService.critterbaseService.getColours(), + this.surveyCritterService.critterbaseService.getMarkingTypes() + ]); + + // Used to find critter_id -> taxon body location [] map + const rowCritters: ICritterDetailed[] = []; + + // Rows passed to validator + const rowsToValidate: Partial[] = []; + + for (const row of rows) { + let critterId, captureId; + + const alias = getColumnCell(row, 'ALIAS'); + + // If the alias is included attempt to retrieve the critter_id and capture_id for the row + if (alias.cell) { + const captureDate = getColumnCell(row, 'CAPTURE_DATE'); + const captureTime = getColumnCell(row, 'CAPTURE_TIME'); + + const critter = critterAliasMap.get(alias.cell.toLowerCase()); + + if (critter) { + // Find the capture_id from the date time columns + const captures = findCapturesFromDateTime(critter.captures, captureDate.cell, captureTime.cell); + captureId = captures.length === 1 ? captures[0].capture_id : undefined; + critterId = critter.critter_id; + rowCritters.push(critter); + } + } + + rowsToValidate.push({ + critter_id: critterId, // Found using alias + capture_id: captureId, // Found using capture date and time + body_location: getColumnCell(row, 'BODY_LOCATION').cell, + marking_type: getColumnCell(row, 'MARKING_TYPE').cell, + identifier: getColumnCell(row, 'IDENTIFIER').cell, + primary_colour: getColumnCell(row, 'PRIMARY_COLOUR').cell, + secondary_colour: getColumnCell(row, 'SECONDARY_COLOUR').cell, + comment: getColumnCell(row, 'DESCRIPTION').cell + }); + } + // Get the critter_id -> taxonBodyLocations[] Map + const critterBodyLocationsMap = await this.getTaxonBodyLocationsCritterIdMap(rowCritters); + + // Generate the zod schema with injected reference values + // This allows the zod schema to validate against Critterbase lookup values + return z.array(getCsvMarkingSchema(colours, markingTypes, critterBodyLocationsMap)).safeParseAsync(rowsToValidate); + } + + /** + * Insert markings into Critterbase. + * + * @async + * @param {CsvCapture[]} markings - List of CSV markings to create + * @returns {Promise} Number of created markings + */ + async insert(markings: CsvMarking[]): Promise { + const response = await this.surveyCritterService.critterbaseService.bulkCreate({ markings }); + + defaultLog.debug({ label: 'import markings', markings, insertedCount: response.created.markings }); + + return response.created.markings; + } +} diff --git a/api/src/services/import-services/measurement/import-measurements-strategy.interface.ts b/api/src/services/import-services/measurement/import-measurements-strategy.interface.ts new file mode 100644 index 0000000000..2cfabf887f --- /dev/null +++ b/api/src/services/import-services/measurement/import-measurements-strategy.interface.ts @@ -0,0 +1,22 @@ +import { z } from 'zod'; + +export const CsvQualitativeMeasurementSchema = z.object({ + critter_id: z.string().uuid(), + capture_id: z.string().uuid(), + taxon_measurement_id: z.string().uuid(), + qualitative_option_id: z.string().uuid() +}); + +export const CsvQuantitativeMeasurementSchema = z.object({ + critter_id: z.string().uuid(), + capture_id: z.string().uuid(), + taxon_measurement_id: z.string().uuid(), + value: z.number() +}); + +export const CsvMeasurementSchema = CsvQualitativeMeasurementSchema.or(CsvQuantitativeMeasurementSchema); + +// Zod inferred types +export type CsvMeasurement = z.infer; +export type CsvQuantitativeMeasurement = z.infer; +export type CsvQualitativeMeasurement = z.infer; diff --git a/api/src/services/import-services/measurement/import-measurements-strategy.test.ts b/api/src/services/import-services/measurement/import-measurements-strategy.test.ts new file mode 100644 index 0000000000..9503e0569c --- /dev/null +++ b/api/src/services/import-services/measurement/import-measurements-strategy.test.ts @@ -0,0 +1,650 @@ +import { expect } from 'chai'; +import sinon from 'sinon'; +import { MediaFile } from '../../../utils/media/media-file'; +import * as worksheetUtils from '../../../utils/xlsx-utils/worksheet-utils'; +import { getMockDBConnection } from '../../../__mocks__/db'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition, + IBulkCreateResponse +} from '../../critterbase-service'; +import { importCSV } from '../import-csv'; +import { ImportMeasurementsStrategy } from './import-measurements-strategy'; + +describe('importMeasurementsStrategy', () => { + describe('importCSV', () => { + beforeEach(() => { + sinon.restore(); + }); + + it('should import the csv file correctly', async () => { + const worksheet = { + A1: { t: 's', v: 'ALIAS' }, + B1: { t: 's', v: 'CAPTURE_DATE' }, + C1: { t: 's', v: 'CAPTURE_TIME' }, + D1: { t: 's', v: 'tail length' }, + E1: { t: 's', v: 'skull condition' }, + F1: { t: 's', v: 'unknown' }, + A2: { t: 's', v: 'carl' }, + B2: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + C2: { t: 's', v: '10:10:12' }, + D2: { t: 'n', w: '2', v: 2 }, + E2: { t: 'n', w: '0', v: 'good' }, + A3: { t: 's', v: 'carlita' }, + B3: { z: 'm/d/yy', t: 'd', v: '2024-10-10T07:00:00.000Z', w: '10/10/24' }, + C3: { t: 's', v: '10:10:12' }, + D3: { t: 'n', w: '2', v: 2 }, + E3: { t: 'n', w: '0', v: 'good' }, + '!ref': 'A1:F3' + }; + + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const getDefaultWorksheetStub = sinon.stub(worksheetUtils, 'getDefaultWorksheet'); + const critterbaseInsertStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'bulkCreate'); + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + + const critterAliasMap = new Map([ + [ + 'carl', + { + critter_id: 'A', + animal_id: 'carl', + itis_tsn: 'tsn1', + captures: [{ capture_id: 'B', capture_date: '10/10/2024', capture_time: '10:10:12' }] + } as any + ], + [ + 'carlita', + { + critter_id: 'B', + animal_id: 'carlita', + itis_tsn: 'tsn2', + captures: [{ capture_id: 'B', capture_date: '10/10/2024', capture_time: '10:10:12' }] + } as any + ] + ]); + + getDefaultWorksheetStub.returns(worksheet); + nonStandardColumnsStub.returns(['TAIL LENGTH', 'SKULL CONDITION']); + critterAliasMapStub.resolves(critterAliasMap); + critterbaseInsertStub.resolves({ + created: { qualitative_measurements: 1, quantitative_measurements: 1 } + } as IBulkCreateResponse); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { + qualitative: [ + { + taxon_measurement_id: 'Z', + measurement_name: 'skull condition', + options: [{ qualitative_option_id: 'C', option_label: 'good' }] + } + ], + quantitative: [ + { taxon_measurement_id: 'Z', measurement_name: 'tail length', min_value: 0, max_value: 10 } + ] + } as any + ], + [ + 'tsn2', + { + qualitative: [ + { + taxon_measurement_id: 'Z', + measurement_name: 'skull condition', + + options: [{ qualitative_option_id: 'C', option_label: 'good' }] + } + ], + quantitative: [ + { taxon_measurement_id: 'Z', measurement_name: 'tail length', min_value: 0, max_value: 10 } + ] + } as any + ] + ]) + ); + + try { + const data = await importCSV(new MediaFile('test', 'test', 'test' as unknown as Buffer), strategy); + expect(data).to.be.eql(2); + expect(critterbaseInsertStub).to.have.been.calledOnceWithExactly({ + qualitative_measurements: [ + { + critter_id: 'A', + capture_id: 'B', + taxon_measurement_id: 'Z', + qualitative_option_id: 'C' + }, + { + critter_id: 'B', + capture_id: 'B', + taxon_measurement_id: 'Z', + qualitative_option_id: 'C' + } + ], + quantitative_measurements: [ + { + critter_id: 'A', + capture_id: 'B', + taxon_measurement_id: 'Z', + value: 2 + }, + { + critter_id: 'B', + capture_id: 'B', + taxon_measurement_id: 'Z', + value: 2 + } + ] + }); + } catch (e: any) { + expect.fail(); + } + }); + }); + describe('_getTsnsMeasurementMap', () => { + it('should return correct taxon measurement mapping', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const getTaxonMeasurementsStub = sinon.stub( + strategy.surveyCritterService.critterbaseService, + 'getTaxonMeasurements' + ); + + const measurementA: any = { qualitative: [{ tsn: 'tsn1', measurement: 'measurement1' }], quantitative: [] }; + const measurementB: any = { quantitative: [{ tsn: 'tsn2', measurement: 'measurement2', qualitative: [] }] }; + + getTaxonMeasurementsStub.onCall(0).resolves(measurementA); + + getTaxonMeasurementsStub.onCall(1).resolves(measurementB); + + const tsns = ['tsn1', 'tsn2', 'tsn2']; + + const result = await strategy._getTsnsMeasurementMap(tsns); + + const expectedResult = new Map([ + ['tsn1', measurementA], + ['tsn2', measurementB] + ]); + + expect(result).to.be.deep.equal(expectedResult); + }); + }); + + describe('_getRowMeta', () => { + it('should return correct row meta', () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const row = { ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10' }; + const critterAliasMap = new Map([ + [ + 'alias', + { + critter_id: 'A', + animal_id: 'alias', + itis_tsn: 'tsn1', + captures: [{ capture_id: 'B', capture_date: '10/10/2024', capture_time: '10:10:10' }] + } as any + ] + ]); + + const result = strategy._getRowMeta(row, critterAliasMap); + + expect(result).to.be.deep.equal({ critter_id: 'A', tsn: 'tsn1', capture_id: 'B' }); + }); + + it('should return all undefined properties if unable to match critter', () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const row = { ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10' }; + const critterAliasMap = new Map([ + [ + 'alias2', + { + critter_id: 'A', + animal_id: 'alias2', + itis_tsn: 'tsn1', + captures: [{ capture_id: 'B', capture_date: '10/10/2024', capture_time: '10:10:10' }] + } as any + ] + ]); + + const result = strategy._getRowMeta(row, critterAliasMap); + + expect(result).to.be.deep.equal({ critter_id: undefined, tsn: undefined, capture_id: undefined }); + }); + + it('should undefined capture_id if unable to match timestamps', () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const row = { ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10' }; + const critterAliasMap = new Map([ + [ + 'alias', + { + critter_id: 'A', + animal_id: 'alias', + itis_tsn: 'tsn1', + captures: [{ capture_id: 'B', capture_date: '11/11/2024', capture_time: '10:10:10' }] + } as any + ] + ]); + + const result = strategy._getRowMeta(row, critterAliasMap); + + expect(result).to.be.deep.equal({ critter_id: 'A', tsn: 'tsn1', capture_id: undefined }); + }); + }); + + describe('_validateQualitativeMeasurementCell', () => { + it('should return option_id when valid', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const measurement: CBQualitativeMeasurementTypeDefinition = { + itis_tsn: 1, + taxon_measurement_id: 'A', + measurement_name: 'measurement', + measurement_desc: null, + options: [{ qualitative_option_id: 'C', option_label: 'measurement', option_value: 0, option_desc: 'desc' }] + }; + + const result = strategy._validateQualitativeMeasurementCell('measurement', measurement); + + expect(result.error).to.be.undefined; + expect(result.optionId).to.be.equal('C'); + }); + + it('should return error when invalid value', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const measurement: CBQualitativeMeasurementTypeDefinition = { + itis_tsn: 1, + taxon_measurement_id: 'A', + measurement_name: 'measurement', + measurement_desc: null, + options: [{ qualitative_option_id: 'C', option_label: 'measurement', option_value: 0, option_desc: 'desc' }] + }; + + const result = strategy._validateQualitativeMeasurementCell('bad', measurement); + + expect(result.error).to.exist; + expect(result.optionId).to.be.undefined; + }); + }); + + describe('_validateQuantitativeMeasurementCell', () => { + it('should return value when valid', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const measurement: CBQuantitativeMeasurementTypeDefinition = { + itis_tsn: 1, + taxon_measurement_id: 'A', + measurement_name: 'measurement', + unit: 'centimeter', + min_value: 0, + max_value: 10, + measurement_desc: null + }; + + const resultA = strategy._validateQuantitativeMeasurementCell(0, measurement); + + expect(resultA.error).to.be.undefined; + expect(resultA.value).to.be.equal(0); + + const resultB = strategy._validateQuantitativeMeasurementCell(10, measurement); + + expect(resultB.error).to.be.undefined; + expect(resultB.value).to.be.equal(10); + }); + + it('should return error when invalid value', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const measurement: CBQuantitativeMeasurementTypeDefinition = { + itis_tsn: 1, + taxon_measurement_id: 'A', + measurement_name: 'measurement', + unit: 'centimeter', + min_value: 0, + max_value: 10, + measurement_desc: null + }; + + const resultA = strategy._validateQuantitativeMeasurementCell(-1, measurement); + + expect(resultA.error).to.exist; + expect(resultA.value).to.be.undefined; + + const resultB = strategy._validateQuantitativeMeasurementCell(11, measurement); + + expect(resultB.error).to.exist; + expect(resultB.value).to.be.undefined; + }); + }); + + describe('_validateMeasurementCell', () => { + const critterAliasMap = new Map([ + [ + 'alias', + { + critter_id: 'A', + animal_id: 'alias', + itis_tsn: 'tsn1', + captures: [{ capture_id: 'B', capture_date: '10/10/2024', capture_time: '10:10:10' }] + } as any + ] + ]); + + it('should return no errors and data when valid rows', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQualitativeMeasurementCellStub = sinon.stub(strategy, '_validateQualitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: 'B' }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { qualitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], quantitative: [] } as any + ] + ]) + ); + validateQualitativeMeasurementCellStub.returns({ error: undefined, optionId: 'C' }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect.fail(); + } else { + expect(result.data).to.be.deep.equal([ + { critter_id: 'A', capture_id: 'B', taxon_measurement_id: 'Z', qualitative_option_id: 'C' } + ]); + } + }); + + it('should return error when unable to map alias to critter', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQualitativeMeasurementCellStub = sinon.stub(strategy, '_validateQualitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: undefined, tsn: undefined, capture_id: undefined }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { qualitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], quantitative: [] } as any + ] + ]) + ); + validateQualitativeMeasurementCellStub.returns({ error: undefined, optionId: 'C' }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([ + { row: 0, message: 'Unable to find matching Critter with alias.' } + ]); + } else { + expect.fail(); + } + }); + + it('should return error when unable to map capture to critter', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQualitativeMeasurementCellStub = sinon.stub(strategy, '_validateQualitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: undefined }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { qualitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], quantitative: [] } as any + ] + ]) + ); + validateQualitativeMeasurementCellStub.returns({ error: undefined, optionId: 'C' }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([ + { row: 0, message: 'Unable to find matching Capture with date and time.' } + ]); + } else { + expect.fail(); + } + }); + + it('should return error when unable to map tsn to critter', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQualitativeMeasurementCellStub = sinon.stub(strategy, '_validateQualitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: undefined, capture_id: 'C' }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { qualitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], quantitative: [] } as any + ] + ]) + ); + validateQualitativeMeasurementCellStub.returns({ error: undefined, optionId: 'C' }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([{ row: 0, message: 'Unable to find ITIS TSN for Critter.' }]); + } else { + expect.fail(); + } + }); + + it('should return error when qualitative measurement validation fails', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQualitativeMeasurementCellStub = sinon.stub(strategy, '_validateQualitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: 'C' }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { qualitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], quantitative: [] } as any + ] + ]) + ); + validateQualitativeMeasurementCellStub.returns({ error: 'qualitative failed', optionId: undefined }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([{ row: 0, col: 'MEASUREMENT', message: 'qualitative failed' }]); + } else { + expect.fail(); + } + }); + + it('should return error when quantitative measurement validation fails', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + const validateQuantitativeMeasurementCellStub = sinon.stub(strategy, '_validateQuantitativeMeasurementCell'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: 'C' }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { quantitative: [{ taxon_measurement_id: 'Z', measurement_name: 'measurement' }], qualitative: [] } as any + ] + ]) + ); + validateQuantitativeMeasurementCellStub.returns({ error: 'quantitative failed', value: undefined }); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([{ row: 0, col: 'MEASUREMENT', message: 'quantitative failed' }]); + } else { + expect.fail(); + } + }); + + it('should return error when no measurements exist for taxon', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: 'C' }); + getTsnMeasurementMapStub.resolves(new Map([['tsn1', { quantitative: [], qualitative: [] } as any]])); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([ + { row: 0, col: 'MEASUREMENT', message: 'No measurements exist for this taxon.' } + ]); + } else { + expect.fail(); + } + }); + + it('should return error when no measurements exist for taxon', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const nonStandardColumnsStub = sinon.stub(strategy, '_getNonStandardColumns'); + const critterAliasMapStub = sinon.stub(strategy.surveyCritterService, 'getSurveyCritterAliasMap'); + const getRowMetaStub = sinon.stub(strategy, '_getRowMeta'); + const getTsnMeasurementMapStub = sinon.stub(strategy, '_getTsnsMeasurementMap'); + + nonStandardColumnsStub.returns(['MEASUREMENT']); + critterAliasMapStub.resolves(critterAliasMap); + getRowMetaStub.returns({ critter_id: 'A', tsn: 'tsn1', capture_id: 'C' }); + getTsnMeasurementMapStub.resolves( + new Map([ + [ + 'tsn1', + { quantitative: [{ measurement_name: 'notfound' }], qualitative: [{ measurement_name: 'notfound' }] } as any + ] + ]) + ); + + const rows = [{ ALIAS: 'alias', CAPTURE_DATE: '10/10/2024', CAPTURE_TIME: '10:10:10', measurement: 'length' }]; + + const result = await strategy.validateRows(rows, {}); + + if (!result.success) { + expect(result.error.issues).to.be.deep.equal([ + { row: 0, col: 'MEASUREMENT', message: 'Unable to match column name to an existing measurement.' } + ]); + } else { + expect.fail(); + } + }); + }); + describe('insert', () => { + it('should correctly format the insert payload for critterbase bulk insert', async () => { + const conn = getMockDBConnection(); + const strategy = new ImportMeasurementsStrategy(conn, 1); + + const bulkCreateStub = sinon.stub(strategy.surveyCritterService.critterbaseService, 'bulkCreate'); + + const rows = [ + { critter_id: 'A', capture_id: 'B', taxon_measurement_id: 'C', qualitative_option_id: 'D' }, + { critter_id: 'E', capture_id: 'F', taxon_measurement_id: 'G', value: 0 } + ]; + + bulkCreateStub.resolves({ + created: { qualitative_measurements: 1, quantitative_measurements: 1 } + } as IBulkCreateResponse); + + const result = await strategy.insert(rows); + + expect(bulkCreateStub).to.have.been.calledOnceWithExactly({ + qualitative_measurements: [ + { critter_id: 'A', capture_id: 'B', taxon_measurement_id: 'C', qualitative_option_id: 'D' } + ], + quantitative_measurements: [{ critter_id: 'E', capture_id: 'F', taxon_measurement_id: 'G', value: 0 }] + }); + expect(result).to.be.eql(2); + }); + }); +}); diff --git a/api/src/services/import-services/measurement/import-measurements-strategy.ts b/api/src/services/import-services/measurement/import-measurements-strategy.ts new file mode 100644 index 0000000000..d39e69f86c --- /dev/null +++ b/api/src/services/import-services/measurement/import-measurements-strategy.ts @@ -0,0 +1,344 @@ +import { uniq } from 'lodash'; +import { WorkSheet } from 'xlsx'; +import { IDBConnection } from '../../../database/db'; +import { getLogger } from '../../../utils/logger'; +import { CSV_COLUMN_ALIASES } from '../../../utils/xlsx-utils/column-aliases'; +import { generateColumnCellGetterFromColumnValidator } from '../../../utils/xlsx-utils/column-validator-utils'; +import { getNonStandardColumnNamesFromWorksheet, IXLSXCSVValidator } from '../../../utils/xlsx-utils/worksheet-utils'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition, + ICritterDetailed +} from '../../critterbase-service'; +import { DBService } from '../../db-service'; +import { SurveyCritterService } from '../../survey-critter-service'; +import { CSVImportStrategy, Row, Validation, ValidationError } from '../import-csv.interface'; +import { findCapturesFromDateTime } from '../utils/datetime'; +import { + CsvMeasurement, + CsvQualitativeMeasurement, + CsvQuantitativeMeasurement +} from './import-measurements-strategy.interface'; + +const defaultLog = getLogger('services/import/import-measurements-strategy'); + +/** + * + * ImportMeasurementsStrategy - Injected into importCSV as the CSV import dependency + * + * @example new CSVImport(new ImportMeasurementsStrategy(connection, surveyId)).import(file); + * + * @class ImportMeasurementsStrategy + * @extends DBService + * + */ +export class ImportMeasurementsStrategy extends DBService implements CSVImportStrategy { + surveyCritterService: SurveyCritterService; + + surveyId: number; + + /** + * An XLSX validation config for the standard columns of a Measurement CSV. + * + * Note: `satisfies` allows `keyof` to correctly infer key types, while also + * enforcing uppercase object keys. + */ + columnValidator = { + ALIAS: { type: 'string', aliases: CSV_COLUMN_ALIASES.ALIAS }, + CAPTURE_DATE: { type: 'date' }, + CAPTURE_TIME: { type: 'string', optional: true } + } satisfies IXLSXCSVValidator; + + /** + * Instantiates an instance of ImportMeasurementsStrategy + * + * @param {IDBConnection} connection - Database connection + * @param {number} surveyId - Survey identifier + */ + constructor(connection: IDBConnection, surveyId: number) { + super(connection); + + this.surveyId = surveyId; + + this.surveyCritterService = new SurveyCritterService(connection); + } + + /** + * Get non-standard columns (measurement columns) from worksheet. + * + * @param {WorkSheet} worksheet - Xlsx worksheet + * @returns {string[]} Array of non-standard headers from CSV (worksheet) + */ + _getNonStandardColumns(worksheet: WorkSheet) { + return uniq(getNonStandardColumnNamesFromWorksheet(worksheet, this.columnValidator)); + } + + /** + * Get TSN measurement map for validation. + * + * For a list of TSNS return all measurements inherited or directly assigned. + * + * @async + * @param {string[]} tsns - List of ITIS TSN's + * @returns {*} + */ + async _getTsnsMeasurementMap(tsns: string[]) { + const tsnMeasurementMap = new Map< + string, + { + qualitative: CBQualitativeMeasurementTypeDefinition[]; + quantitative: CBQuantitativeMeasurementTypeDefinition[]; + } + >(); + + const uniqueTsns = [...new Set(tsns)]; + + const measurements = await Promise.all( + uniqueTsns.map((tsn) => this.surveyCritterService.critterbaseService.getTaxonMeasurements(tsn)) + ); + + uniqueTsns.forEach((tsn, index) => { + tsnMeasurementMap.set(tsn, measurements[index]); + }); + + return tsnMeasurementMap; + } + + /** + * Get row meta data for validation. + * + * @param {Row} row - CSV row + * @param {Map} critterAliasMap - Survey critter alias mapping + * @returns {{ capture_id?: string; critter_id?: string; tsn?: string }} + */ + _getRowMeta( + row: Row, + critterAliasMap: Map + ): { capture_id?: string; critter_id?: string; tsn?: string } { + const getColumnCell = generateColumnCellGetterFromColumnValidator(this.columnValidator); + + const alias = getColumnCell(row, 'ALIAS'); + const captureDate = getColumnCell(row, 'CAPTURE_DATE'); + const captureTime = getColumnCell(row, 'CAPTURE_TIME'); + + let capture_id, critter_id, tsn; + + if (alias.cell) { + const critter = critterAliasMap.get(alias.cell.toLowerCase()); + + if (critter) { + const captures = findCapturesFromDateTime(critter.captures, captureDate.cell, captureTime.cell); + critter_id = critter.critter_id; + capture_id = captures.length === 1 ? captures[0].capture_id : undefined; + tsn = String(critter.itis_tsn); // Cast to string for convienience + } + } + + return { critter_id, capture_id, tsn }; + } + + /** + * Validate qualitative measurement. + * + * @param {string} cell - CSV measurement cell value + * @param {CBQualitativeMeasurementTypeDefinition} measurement - Found qualitative measurement match + * @returns {*} + */ + _validateQualitativeMeasurementCell(cell: string, measurement: CBQualitativeMeasurementTypeDefinition) { + if (typeof cell !== 'string') { + return { error: 'Qualitative measurement expecting text value.', optionId: undefined }; + } + + const matchingOptionValue = measurement.options.find( + (option) => option.option_label.toLowerCase() === cell.toLowerCase() + ); + + // Validate cell value is an alowed qualitative measurement option + if (!matchingOptionValue) { + return { + error: `Incorrect qualitative measurement value. Allowed: ${measurement.options.map((option) => + option.option_label.toLowerCase() + )}`, + optionId: undefined + }; + } + + return { error: undefined, optionId: matchingOptionValue.qualitative_option_id }; + } + + /** + * Validate quantitative measurement + * + * @param {number} cell - CSV measurement cell value + * @param {CBQuantitativeMeasurementTypeDefinition} measurement - Found quantitative measurement match + * @returns {*} + */ + _validateQuantitativeMeasurementCell(cell: number, measurement: CBQuantitativeMeasurementTypeDefinition) { + if (typeof cell !== 'number') { + return { error: 'Quantitative measurement expecting number value.', value: undefined }; + } + + // Validate cell value is withing the measurement min max bounds + if (measurement.max_value != null && cell > measurement.max_value) { + return { error: 'Quantitative measurement out of bounds. Too small.', value: undefined }; + } + + if (measurement.min_value != null && cell < measurement.min_value) { + return { error: 'Quantitative measurement out of bounds. Too small.' }; + } + + return { error: undefined, value: cell }; + } + + /** + * Validate CSV worksheet rows against reference data. + * + * Note: This function is longer than I would like, but moving logic into seperate methods + * made the flow more complex and equally as long. + * + * @async + * @param {Row[]} rows - Invalidated CSV rows + * @param {WorkSheet} worksheet - Xlsx worksheet + * @returns {*} + */ + async validateRows(rows: Row[], worksheet: WorkSheet): Promise> { + // Generate type-safe cell getter from column validator + const nonStandardColumns = this._getNonStandardColumns(worksheet); + + // Get Critterbase reference data + const critterAliasMap = await this.surveyCritterService.getSurveyCritterAliasMap(this.surveyId); + const rowTsns = rows.map((row) => this._getRowMeta(row, critterAliasMap).tsn).filter(Boolean) as string[]; + const tsnMeasurementsMap = await this._getTsnsMeasurementMap(rowTsns); + + const rowErrors: ValidationError[] = []; + const validatedRows: CsvMeasurement[] = []; + + rows.forEach((row, index) => { + const { critter_id, capture_id, tsn } = this._getRowMeta(row, critterAliasMap); + + // Validate critter can be matched via alias + if (!critter_id) { + rowErrors.push({ row: index, message: 'Unable to find matching Critter with alias.' }); + return; + } + + // Validate capture can be matched with date and time + if (!capture_id) { + rowErrors.push({ row: index, message: 'Unable to find matching Capture with date and time.' }); + return; + } + + // This will only be triggered with an invalid alias + if (!tsn) { + rowErrors.push({ row: index, message: 'Unable to find ITIS TSN for Critter.' }); + return; + } + + // Loop through all non-standard (measurement) columns + for (const column of nonStandardColumns) { + // Get the cell value from the row (case insensitive) + const cellValue = row[column] ?? row[column.toLowerCase()] ?? row[column.toUpperCase()]; + + // If the cell value is null or undefined - skip validation + if (cellValue == null) { + continue; + } + + const measurements = tsnMeasurementsMap.get(tsn); + + // Validate taxon has reference measurements in Critterbase + if (!measurements || (!measurements.quantitative.length && !measurements.qualitative.length)) { + rowErrors.push({ row: index, col: column, message: 'No measurements exist for this taxon.' }); + continue; + } + + const qualitativeMeasurement = measurements?.qualitative.find( + (measurement) => measurement.measurement_name.toLowerCase() === column.toLowerCase() + ); + + // QUALITATIVE MEASUREMENT VALIDATION + if (qualitativeMeasurement) { + const { error, optionId } = this._validateQualitativeMeasurementCell(cellValue, qualitativeMeasurement); + + if (error !== undefined) { + rowErrors.push({ row: index, col: column, message: error }); + } else { + // Assign qualitative measurement to validated rows + validatedRows.push({ + critter_id, + capture_id, + taxon_measurement_id: qualitativeMeasurement.taxon_measurement_id, + qualitative_option_id: optionId + }); + } + + continue; + } + + const quantitativeMeasurement = measurements?.quantitative.find( + (measurement) => measurement.measurement_name.toLowerCase() === column.toLowerCase() + ); + + // QUANTITATIVE MEASUREMENT VALIDATION + if (quantitativeMeasurement) { + const { error, value } = this._validateQuantitativeMeasurementCell(cellValue, quantitativeMeasurement); + + if (error !== undefined) { + rowErrors.push({ row: index, col: column, message: error }); + } else { + // Assign quantitative measurement to validated rows + validatedRows.push({ + critter_id, + capture_id, + taxon_measurement_id: quantitativeMeasurement.taxon_measurement_id, + value: value + }); + } + + continue; + } + + // Validate the column header is a known Critterbase measurement + rowErrors.push({ + row: index, + col: column, + message: 'Unable to match column name to an existing measurement.' + }); + } + }); + + if (!rowErrors.length) { + return { success: true, data: validatedRows }; + } + + return { success: false, error: { issues: rowErrors } }; + } + + /** + * Insert CSV measurements into Critterbase. + * + * @async + * @param {CsvCritter[]} measurements - CSV row measurements + * @returns {Promise} List of inserted measurements + */ + async insert(measurements: CsvMeasurement[]): Promise { + const qualitative_measurements = measurements.filter( + (measurement): measurement is CsvQualitativeMeasurement => 'qualitative_option_id' in measurement + ); + + const quantitative_measurements = measurements.filter( + (measurement): measurement is CsvQuantitativeMeasurement => 'value' in measurement + ); + + const response = await this.surveyCritterService.critterbaseService.bulkCreate({ + qualitative_measurements, + quantitative_measurements + }); + + const measurementCount = response.created.qualitative_measurements + response.created.quantitative_measurements; + + defaultLog.debug({ label: 'import measurements', measurements, insertedCount: measurementCount }); + + return measurementCount; + } +} diff --git a/api/src/services/import-services/utils/datetime.test.ts b/api/src/services/import-services/utils/datetime.test.ts new file mode 100644 index 0000000000..24e0452a13 --- /dev/null +++ b/api/src/services/import-services/utils/datetime.test.ts @@ -0,0 +1,38 @@ +import { expect } from 'chai'; +import { areDatesEqual, formatTimeString } from './datetime'; + +describe('formatTimeString', () => { + it('should correctly prepend leading 0 for 24 hour time', () => { + expect(formatTimeString('9:10:10')).to.be.eql('09:10:10'); + }); + + it('should correctly append 00 for missing seconds', () => { + expect(formatTimeString('10:10')).to.be.eql('10:10:00'); + }); + + it('should correctly append 00 for missing seconds and prepend 0 for 24 hour time', () => { + expect(formatTimeString('9:10')).to.be.eql('09:10:00'); + }); + + it('should return undefined if cannot format time', () => { + expect(formatTimeString('BLAH')).to.be.undefined; + }); + + it('should return undefined if dates are null', () => { + expect(formatTimeString(null)).to.be.undefined; + expect(formatTimeString(undefined)).to.be.undefined; + }); +}); + +describe('areDatesEqual', () => { + it('should be true when dates are equal in all formats', () => { + expect(areDatesEqual('10-10-2024', '10-10-2024')).to.be.true; + expect(areDatesEqual('10-10-2024', '10/10/2024')).to.be.true; + expect(areDatesEqual('10-10-2024', '10/10/24')).to.be.true; + expect(areDatesEqual('10-10-2024', '2024-10-10')).to.be.true; + }); + + it('should fail if dates are incorrect format', () => { + expect(areDatesEqual('BAD DATE BAD', '10/10/2024')).to.be.false; + }); +}); diff --git a/api/src/services/import-services/utils/datetime.ts b/api/src/services/import-services/utils/datetime.ts new file mode 100644 index 0000000000..8ab52447e4 --- /dev/null +++ b/api/src/services/import-services/utils/datetime.ts @@ -0,0 +1,70 @@ +import dayjs from 'dayjs'; +import customParseFormat from 'dayjs/plugin/customParseFormat'; + +dayjs.extend(customParseFormat); + +// Simplified Capture interface +interface ICaptureStub { + capture_id: string; + capture_date: string; + capture_time?: string | null; +} + +/** + * Format time strings to correct format for Zod and external systems. + * + * `10:10` -> `10:10:00` appends seconds if missing + * `9:10:10` -> `09:10:10` prepends `0` for 24 hour time + * `9:10` -> `09:10:00` does both + * + * @param {string} [time] - Time string + * @returns {string | undefined} + */ +export const formatTimeString = (time?: string | null): string | undefined => { + const fullTime = dayjs(time, 'HH:mm:ss'); + const shortTime = dayjs(time, 'HH:mm'); + + if (fullTime.isValid()) { + return fullTime.format('HH:mm:ss'); + } + + if (shortTime.isValid()) { + return shortTime.format('HH:mm:ss'); + } +}; + +/** + * Checks if two date strings are equal. + * + * Note: This will attempt to unify the formatting between the dates. + * ie: 2024-01-01 === 01-01-2024 + * + * @param {string} _dateA - Date string + * @param {string} _dateB - Date string + * @returns {string | undefined} + */ +export const areDatesEqual = (_dateA: string, _dateB: string): boolean => { + return dayjs(_dateA).isSame(dayjs(_dateB)); +}; + +/** + * Find Captures from Capture date and time fields. + * + * @template {T} Capture stub + * @param {ICapture[]} captures - Array of Critterbase captures + * @param {string} captureDate - String date + * @param {string} captureTime - String time + * @returns {T[]} Capture ID or undefined + */ +export const findCapturesFromDateTime = ( + captures: T[], + captureDate: string, + captureTime: string +): T[] => { + return captures.filter((capture) => { + return ( + formatTimeString(capture.capture_time) === formatTimeString(captureTime) && + areDatesEqual(capture.capture_date, captureDate) + ); + }); +}; diff --git a/api/src/services/observation-service.test.ts b/api/src/services/observation-service.test.ts index 157c613664..245df3f0b2 100644 --- a/api/src/services/observation-service.test.ts +++ b/api/src/services/observation-service.test.ts @@ -186,4 +186,25 @@ describe('ObservationService', () => { expect(response).to.eql(mockObservationCount); }); }); + + describe('getObservedSpeciesForSurvey', () => { + it('Gets the species observed in a survey', async () => { + const mockDBConnection = getMockDBConnection(); + + const mockTsns = [1, 2, 3]; + const surveyId = 1; + const mockSpecies = mockTsns.map((tsn) => ({ itis_tsn: tsn })); + + const getObservedSpeciesForSurveyStub = sinon + .stub(ObservationRepository.prototype, 'getObservedSpeciesForSurvey') + .resolves(mockSpecies); + + const observationService = new ObservationService(mockDBConnection); + + const response = await observationService.getObservedSpeciesForSurvey(surveyId); + + expect(getObservedSpeciesForSurveyStub).to.be.calledOnceWith(surveyId); + expect(response).to.eql(mockSpecies); + }); + }); }); diff --git a/api/src/services/observation-service.ts b/api/src/services/observation-service.ts index 5c0a660d26..3d44a837bd 100644 --- a/api/src/services/observation-service.ts +++ b/api/src/services/observation-service.ts @@ -7,6 +7,7 @@ import { ObservationRecord, ObservationRecordWithSamplingAndSubcountData, ObservationRepository, + ObservationSpecies, ObservationSubmissionRecord, UpdateObservation } from '../repositories/observation-repository/observation-repository'; @@ -41,20 +42,14 @@ import { TsnMeasurementTypeDefinitionMap, validateMeasurements } from '../utils/observation-xlsx-utils/measurement-column-utils'; -import { - getCountFromRow, - getDateFromRow, - getLatitudeFromRow, - getLongitudeFromRow, - getTimeFromRow, - getTsnFromRow, - observationStandardColumnValidator -} from '../utils/xlsx-utils/column-cell-utils'; +import { CSV_COLUMN_ALIASES } from '../utils/xlsx-utils/column-aliases'; +import { generateColumnCellGetterFromColumnValidator } from '../utils/xlsx-utils/column-validator-utils'; import { constructXLSXWorkbook, getDefaultWorksheet, getNonStandardColumnNamesFromWorksheet, getWorksheetRowObjects, + IXLSXCSVValidator, validateCsvFile } from '../utils/xlsx-utils/worksheet-utils'; import { ApiPaginationOptions } from '../zod-schema/pagination'; @@ -72,6 +67,23 @@ import { SubCountService } from './subcount-service'; const defaultLog = getLogger('services/observation-service'); +/** + * An XLSX validation config for the standard columns of an Observation CSV. + * + * Note: `satisfies` allows `keyof` to correctly infer key types, while also + * enforcing uppercase object keys. + */ +export const observationStandardColumnValidator = { + ITIS_TSN: { type: 'number', aliases: CSV_COLUMN_ALIASES.ITIS_TSN }, + COUNT: { type: 'number' }, + DATE: { type: 'date' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: CSV_COLUMN_ALIASES.LATITUDE }, + LONGITUDE: { type: 'number', aliases: CSV_COLUMN_ALIASES.LONGITUDE } +} satisfies IXLSXCSVValidator; + +export const getColumnCellValue = generateColumnCellGetterFromColumnValidator(observationStandardColumnValidator); + export interface InsertSubCount { observation_subcount_id: number | null; subcount: number; @@ -235,6 +247,17 @@ export class ObservationService extends DBService { return this.observationRepository.getAllSurveyObservations(surveyId); } + /** + * Retrieves all species observed in a given survey + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof ObservationRepository + */ + async getObservedSpeciesForSurvey(surveyId: number): Promise { + return this.observationRepository.getObservedSpeciesForSurvey(surveyId); + } + /** * Retrieves a single observation records by ID * @@ -567,7 +590,7 @@ export class ObservationService extends DBService { const newRowData: InsertUpdateObservations[] = worksheetRowObjects.map((row) => { const newSubcount: InsertSubCount = { observation_subcount_id: null, - subcount: getCountFromRow(row), + subcount: getColumnCellValue(row, 'COUNT').cell as number, qualitative_measurements: [], quantitative_measurements: [], qualitative_environments: [], @@ -593,16 +616,16 @@ export class ObservationService extends DBService { return { standardColumns: { survey_id: surveyId, - itis_tsn: getTsnFromRow(row), + itis_tsn: getColumnCellValue(row, 'ITIS_TSN').cell as number, itis_scientific_name: null, survey_sample_site_id: samplePeriodHierarchyIds?.survey_sample_site_id ?? null, survey_sample_method_id: samplePeriodHierarchyIds?.survey_sample_method_id ?? null, survey_sample_period_id: samplePeriodHierarchyIds?.survey_sample_period_id ?? null, - latitude: getLatitudeFromRow(row), - longitude: getLongitudeFromRow(row), - count: getCountFromRow(row), - observation_time: getTimeFromRow(row), - observation_date: getDateFromRow(row) + latitude: getColumnCellValue(row, 'LATITUDE').cell as number, + longitude: getColumnCellValue(row, 'LONGITUDE').cell as number, + count: getColumnCellValue(row, 'COUNT').cell as number, + observation_time: getColumnCellValue(row, 'TIME').cell as string, + observation_date: getColumnCellValue(row, 'DATE').cell as string }, subcounts: [newSubcount] }; @@ -648,7 +671,7 @@ export class ObservationService extends DBService { } const measurement = getMeasurementFromTsnMeasurementTypeDefinitionMap( - getTsnFromRow(row), + getColumnCellValue(row, 'ITIS_TSN').cell as string, mColumn, tsnMeasurements ); @@ -770,7 +793,7 @@ export class ObservationService extends DBService { return recordsToPatch.map((recordToPatch: RecordWithTaxonFields) => { recordToPatch.itis_scientific_name = - taxonomyResponse.find((taxonItem) => Number(taxonItem.tsn) === recordToPatch.itis_tsn)?.scientificName ?? null; + taxonomyResponse.find((taxonItem) => taxonItem.tsn === recordToPatch.itis_tsn)?.scientificName ?? null; return recordToPatch; }); diff --git a/api/src/services/platform-service.ts b/api/src/services/platform-service.ts index 5243bb7fe6..506c2d74ec 100644 --- a/api/src/services/platform-service.ts +++ b/api/src/services/platform-service.ts @@ -12,6 +12,7 @@ import { isFeatureFlagPresent } from '../utils/feature-flag-utils'; import { getFileFromS3 } from '../utils/file-utils'; import { getLogger } from '../utils/logger'; import { AttachmentService } from './attachment-service'; +import { IPostCollectionUnit } from './critterbase-service'; import { DBService } from './db-service'; import { HistoryPublishService } from './history-publish-service'; import { KeycloakService } from './keycloak-service'; @@ -44,7 +45,7 @@ export interface IArtifact { } export interface IItisSearchResult { - tsn: string; + tsn: number; commonNames?: string[]; scientificName: string; } @@ -57,6 +58,10 @@ export interface ITaxonomy { kingdom: string; } +export interface ITaxonomyWithEcologicalUnits extends ITaxonomy { + ecological_units: IPostCollectionUnit[]; +} + const getBackboneInternalApiHost = () => process.env.BACKBONE_INTERNAL_API_HOST || ''; const getBackboneArtifactIntakePath = () => process.env.BACKBONE_ARTIFACT_INTAKE_PATH || ''; const getBackboneSurveyIntakePath = () => process.env.BACKBONE_INTAKE_PATH || ''; diff --git a/api/src/services/project-service.test.ts b/api/src/services/project-service.test.ts index 7e1bd0722e..6147ca87e1 100644 --- a/api/src/services/project-service.test.ts +++ b/api/src/services/project-service.test.ts @@ -32,7 +32,8 @@ describe('ProjectService', () => { end_date: '2021-12-31', regions: [], focal_species: [], - types: [1, 2, 3] + types: [1, 2, 3], + members: [{ system_user_id: 1, display_name: 'John Doe' }] }, { project_id: 456, @@ -41,7 +42,8 @@ describe('ProjectService', () => { end_date: '2021-12-31', regions: [], focal_species: [], - types: [1, 2, 3] + types: [1, 2, 3], + members: [{ system_user_id: 1, display_name: 'John Doe' }] } ]; diff --git a/api/src/services/sample-location-service.test.ts b/api/src/services/sample-location-service.test.ts index c1b23aba2a..57a17b7dcc 100644 --- a/api/src/services/sample-location-service.test.ts +++ b/api/src/services/sample-location-service.test.ts @@ -173,10 +173,13 @@ describe('SampleLocationService', () => { .stub(SampleStratumService.prototype, 'deleteSampleStratumRecords') .resolves(); + const mockSurveySampleSiteId = 1; + const mockSurveyId = 1; + // Site sinon.stub(SampleLocationRepository.prototype, 'deleteSampleSiteRecord').resolves({ - survey_sample_site_id: 1, - survey_id: 1, + survey_sample_site_id: mockSurveySampleSiteId, + survey_id: mockSurveyId, name: 'Sample Site 1', description: '', geometry: null, @@ -189,18 +192,17 @@ describe('SampleLocationService', () => { revision_count: 0 }); - const mockSurveyId = 1; const { survey_sample_site_id } = await service.deleteSampleSiteRecord(mockSurveyId, 1); - expect(getSampleBlocksForSurveySampleSiteIdStub).to.be.calledOnceWith(survey_sample_site_id); - expect(deleteSampleBlockRecordsStub).to.be.calledOnceWith([survey_sample_site_id]); + expect(getSampleBlocksForSurveySampleSiteIdStub).to.be.calledOnceWith(mockSurveySampleSiteId); + expect(deleteSampleBlockRecordsStub).to.be.calledOnceWith([mockSurveySampleSiteId]); - expect(getSampleStratumsForSurveySampleSiteIdStub).to.be.calledOnceWith(survey_sample_site_id); - expect(deleteSampleStratumRecordsStub).to.be.calledOnceWith([survey_sample_site_id]); + expect(getSampleStratumsForSurveySampleSiteIdStub).to.be.calledOnceWith(mockSurveySampleSiteId); + expect(deleteSampleStratumRecordsStub).to.be.calledOnceWith([mockSurveySampleSiteId]); - expect(survey_sample_site_id).to.be.eq(survey_sample_site_id); - expect(getSampleMethodsForSurveySampleSiteIdStub).to.be.calledOnceWith(survey_sample_site_id); - expect(deleteSampleMethodRecordStub).to.be.calledOnceWith(survey_sample_site_id); + expect(survey_sample_site_id).to.be.eq(mockSurveySampleSiteId); + expect(getSampleMethodsForSurveySampleSiteIdStub).to.be.calledOnceWith(mockSurveySampleSiteId); + expect(deleteSampleMethodRecordStub).to.be.calledOnceWith(mockSurveySampleSiteId); }); }); diff --git a/api/src/services/sample-method-service.test.ts b/api/src/services/sample-method-service.test.ts index 496b03ead1..4ca9bf77b7 100644 --- a/api/src/services/sample-method-service.test.ts +++ b/api/src/services/sample-method-service.test.ts @@ -64,6 +64,28 @@ describe('SampleMethodService', () => { }); }); + describe('getSampleMethodsCountForTechniqueIds', () => { + afterEach(() => { + sinon.restore(); + }); + + it('Gets a count of sample methods for a method technique ID', async () => { + const mockDBConnection = getMockDBConnection(); + + const getSampleMethodsCountForTechniqueIdsStub = sinon + .stub(SampleMethodRepository.prototype, 'getSampleMethodsCountForTechniqueIds') + .resolves(0); + + const techniqueIds = [1, 2]; + const sampleMethodService = new SampleMethodService(mockDBConnection); + + const response = await sampleMethodService.getSampleMethodsCountForTechniqueIds(techniqueIds); + + expect(getSampleMethodsCountForTechniqueIdsStub).to.be.calledOnceWith(techniqueIds); + expect(response).to.eql(0); + }); + }); + describe('deleteSampleMethodRecord', () => { afterEach(() => { sinon.restore(); diff --git a/api/src/services/sample-method-service.ts b/api/src/services/sample-method-service.ts index 79cd434bd1..ad6e2f7a0f 100644 --- a/api/src/services/sample-method-service.ts +++ b/api/src/services/sample-method-service.ts @@ -40,6 +40,17 @@ export class SampleMethodService extends DBService { return this.sampleMethodRepository.getSampleMethodsForSurveySampleSiteId(surveyId, surveySampleSiteId); } + /** + * Gets count of sample methods associated with one or more method technique Ids + * + * @param {number[]} techniqueIds + * @return {*} {Promise} + * @memberof SampleMethodService + */ + async getSampleMethodsCountForTechniqueIds(techniqueIds: number[]): Promise { + return this.sampleMethodRepository.getSampleMethodsCountForTechniqueIds(techniqueIds); + } + /** * Deletes a survey Sample Method. * diff --git a/api/src/services/standards-service.test.ts b/api/src/services/standards-service.test.ts index aad35dfbd7..c59038faf4 100644 --- a/api/src/services/standards-service.test.ts +++ b/api/src/services/standards-service.test.ts @@ -27,11 +27,11 @@ describe('StandardsService', () => { const getTaxonomyByTsnsStub = sinon .stub(standardsService.platformService, 'getTaxonomyByTsns') - .resolves([{ tsn: String(mockTsn), scientificName: 'caribou' }]); + .resolves([{ tsn: mockTsn, scientificName: 'caribou' }]); const getTaxonBodyLocationsStub = sinon .stub(standardsService.critterbaseService, 'getTaxonBodyLocations') - .resolves({ markingBodyLocations: [{ id: '', key: '', value: 'left ear' }] }); + .resolves([{ id: '', key: '', value: 'left ear' }]); const getTaxonMeasurementsStub = sinon .stub(standardsService.critterbaseService, 'getTaxonMeasurements') @@ -68,4 +68,73 @@ describe('StandardsService', () => { expect(response.measurements.qualitative[0].measurement_desc).to.eql('description'); }); }); + + describe('getEnvironmentStandards', async () => { + const mockData = { + qualitative: [{ name: 'name', description: 'name', options: [{ name: 'name', description: 'description' }] }], + quantitative: [ + { name: 'name', description: 'description', unit: 'unit' }, + { name: 'name', description: 'description', unit: 'unit' } + ] + }; + const mockDbConnection = getMockDBConnection(); + + const standardsService = new StandardsService(mockDbConnection); + + const getEnvironmentStandardsStub = sinon + .stub(standardsService.standardsRepository, 'getEnvironmentStandards') + .resolves(mockData); + + const response = await standardsService.getEnvironmentStandards(); + + expect(getEnvironmentStandardsStub).to.be.calledOnce; + expect(response).to.eql(mockData); + }); + + describe('getMethodStandards', async () => { + const mockData = [ + { + method_lookup_id: 1, + name: 'Method 1', + description: ' Description 1', + attributes: { + quantitative: [ + { name: 'Method Standard 1', description: 'Description 1', unit: 'Unit 1' }, + { name: 'Method Standard 2', description: 'Description 2', unit: 'Unit 2' } + ], + qualitative: [ + { + name: 'Qualitative 1', + description: 'Description 1', + options: [ + { name: 'Option 1', description: 'Option 1 Description' }, + { name: 'Option 2', description: 'Option 2 Description' } + ] + }, + { + name: 'Qualitative 2', + description: 'Description 2', + options: [ + { name: 'Option 3', description: 'Option 3 Description' }, + { name: 'Option 4', description: 'Option 4 Description' } + ] + } + ] + } + } + ]; + + const mockDbConnection = getMockDBConnection(); + + const standardsService = new StandardsService(mockDbConnection); + + const getMethodStandardsStub = sinon + .stub(standardsService.standardsRepository, 'getMethodStandards') + .resolves(mockData); + + const response = await standardsService.getMethodStandards(); + + expect(getMethodStandardsStub).to.be.calledOnce; + expect(response).to.eql(mockData); + }); }); diff --git a/api/src/services/standards-service.ts b/api/src/services/standards-service.ts index 76bea02f87..eed1217efb 100644 --- a/api/src/services/standards-service.ts +++ b/api/src/services/standards-service.ts @@ -1,32 +1,21 @@ import { IDBConnection } from '../database/db'; -import { - CBQualitativeMeasurementTypeDefinition, - CBQuantitativeMeasurementTypeDefinition, - CritterbaseService -} from './critterbase-service'; +import { EnvironmentStandards, ISpeciesStandards, MethodStandard } from '../models/standards-view'; +import { StandardsRepository } from '../repositories/standards-repository'; +import { CritterbaseService } from './critterbase-service'; import { DBService } from './db-service'; import { PlatformService } from './platform-service'; -export interface ISpeciesStandardsResponse { - tsn: number; - scientificName: string; - measurements: { - quantitative: CBQuantitativeMeasurementTypeDefinition[]; - qualitative: CBQualitativeMeasurementTypeDefinition[]; - }; - markingBodyLocations: { id: string; key: string; value: string }[]; -} - /** - * Sample Stratum Repository + * Standards Repository * * @export - * @class SampleStratumService + * @class StandardsService * @extends {DBService} */ export class StandardsService extends DBService { platformService: PlatformService; critterbaseService: CritterbaseService; + standardsRepository: StandardsRepository; constructor(connection: IDBConnection) { super(connection); @@ -35,16 +24,17 @@ export class StandardsService extends DBService { keycloak_guid: this.connection.systemUserGUID(), username: this.connection.systemUserIdentifier() }); + this.standardsRepository = new StandardsRepository(connection); } /** - * Gets all survey Sample Stratums. + * Gets species standards * - * @param {number} surveySampleSiteId - * @return {*} {Promise} + * @param {number} tsn + * @return {ISpeciesStandards} * @memberof standardsService */ - async getSpeciesStandards(tsn: number): Promise { + async getSpeciesStandards(tsn: number): Promise { // Fetch all measurement type definitions from Critterbase for the unique taxon_measurement_ids const response = await Promise.all([ this.platformService.getTaxonomyByTsns([tsn]), @@ -59,4 +49,29 @@ export class StandardsService extends DBService { measurements: response[2] }; } + + /** + * Gets environment standards + * + * @param {string} keyword - search term for filtering the response based on environemntal variable name + * @return {EnvironmentStandard[]} + * @memberof standardsService + */ + async getEnvironmentStandards(keyword?: string): Promise { + const response = await this.standardsRepository.getEnvironmentStandards(keyword); + + return response; + } + + /** + * Gets standards for method lookups + * + * @param {string} keyword - search term for filtering the response based on method lookup name + * @return {MethodStandards} + * @memberof standardsService + */ + async getMethodStandards(keyword?: string): Promise { + const response = await this.standardsRepository.getMethodStandards(keyword); + return response; + } } diff --git a/api/src/services/survey-critter-service.test.ts b/api/src/services/survey-critter-service.test.ts index 0a3230b75a..352e24847b 100644 --- a/api/src/services/survey-critter-service.test.ts +++ b/api/src/services/survey-critter-service.test.ts @@ -62,20 +62,6 @@ describe('SurveyService', () => { }); }); - describe('addDeployment', () => { - it('returns the first row on success', async () => { - const dbConnection = getMockDBConnection(); - const service = new SurveyCritterService(dbConnection); - - const repoStub = sinon.stub(SurveyCritterRepository.prototype, 'upsertDeployment').resolves(); - - const response = await service.upsertDeployment(1, 'deployment_id'); - - expect(repoStub).to.be.calledOnce; - expect(response).to.be.undefined; - }); - }); - describe('updateCritter', () => { it('updates critter, returns nothing', async () => { const dbConnection = getMockDBConnection(); @@ -89,15 +75,4 @@ describe('SurveyService', () => { expect(response).to.be.undefined; }); }); - - describe('removeDeployment', () => { - it('removes deployment and returns void', async () => { - const dbConnection = getMockDBConnection(); - const service = new SurveyCritterService(dbConnection); - const repoStub = sinon.stub(SurveyCritterRepository.prototype, 'removeDeployment').resolves(); - const response = await service.removeDeployment(1, 'deployment_id'); - expect(repoStub).to.be.calledOnce; - expect(response).to.be.undefined; - }); - }); }); diff --git a/api/src/services/survey-critter-service.ts b/api/src/services/survey-critter-service.ts index fc1ac5c142..db5470df70 100644 --- a/api/src/services/survey-critter-service.ts +++ b/api/src/services/survey-critter-service.ts @@ -1,11 +1,14 @@ import { IDBConnection } from '../database/db'; import { IAnimalAdvancedFilters } from '../models/animal-view'; -import { ITelemetryAdvancedFilters } from '../models/telemetry-view'; +import { IAllTelemetryAdvancedFilters } from '../models/telemetry-view'; import { SurveyCritterRecord, SurveyCritterRepository } from '../repositories/survey-critter-repository'; +import { getLogger } from '../utils/logger'; import { ApiPaginationOptions } from '../zod-schema/pagination'; -import { CritterbaseService, ICritter } from './critterbase-service'; +import { CritterbaseService, ICritter, ICritterDetailed } from './critterbase-service'; import { DBService } from './db-service'; +const defaultLog = getLogger('SurveyCritterService'); + export type FindCrittersResponse = Pick< ICritter, 'wlh_id' | 'animal_id' | 'sex' | 'itis_tsn' | 'itis_scientific_name' | 'critter_comment' @@ -45,6 +48,19 @@ export class SurveyCritterService extends DBService { return this.critterRepository.getCrittersInSurvey(surveyId); } + /** + * Get all critter associations for the given survey. This only gets you critter ids, which can be used to fetch + * details from the external system. + * + * @param {number} surveyId + * @param {number} critterId + * @return {*} {Promise} + * @memberof SurveyCritterService + */ + async getCritterById(surveyId: number, critterId: number): Promise { + return this.critterRepository.getCritterById(surveyId, critterId); + } + /** * Retrieves all critters that are available to the user, based on their permissions. * @@ -115,14 +131,14 @@ export class SurveyCritterService extends DBService { * * @param {boolean} isUserAdmin * @param {(number | null)} systemUserId The system user id of the user making the request - * @param {ITelemetryAdvancedFilters} [filterFields] + * @param {IAllTelemetryAdvancedFilters} [filterFields] * @return {*} {Promise} * @memberof SurveyCritterService */ async findCrittersCount( isUserAdmin: boolean, systemUserId: number | null, - filterFields?: ITelemetryAdvancedFilters + filterFields?: IAllTelemetryAdvancedFilters ): Promise { return this.critterRepository.findCrittersCount(isUserAdmin, systemUserId, filterFields); } @@ -178,45 +194,74 @@ export class SurveyCritterService extends DBService { } /** - * Upsert a deployment row into SIMS. + * Get survey Critterbase critters. * - * @param {number} critterId - * @param {string} deplyomentId - * @return {*} {Promise} + * @param {number} surveyId + * @return {*} {Promise} * @memberof SurveyCritterService */ - async upsertDeployment(critterId: number, deplyomentId: string): Promise { - return this.critterRepository.upsertDeployment(critterId, deplyomentId); - } + async getCritterbaseSurveyCritters(surveyId: number): Promise { + const surveyCritters = await this.getCrittersInSurvey(surveyId); - /** - * Removes the deployment in SIMS. - * - * @param {number} critterId - * @param {string} deploymentId the bctw deployment uuid - * @return {*} {Promise} - * @memberof SurveyCritterService - */ - async removeDeployment(critterId: number, deploymentId: string): Promise { - return this.critterRepository.removeDeployment(critterId, deploymentId); + const critterbaseCritterIds = surveyCritters.map((critter) => critter.critterbase_critter_id); + + return this.critterbaseService.getMultipleCrittersByIdsDetailed(critterbaseCritterIds); } /** * Get unique Set of critter aliases (animal id / nickname) of a survey. * + * Note: Business expects unique critter alias' in Surveys effective 01/06/2024 + * * @param {number} surveyId * @return {*} {Promise} * @memberof SurveyCritterService */ async getUniqueSurveyCritterAliases(surveyId: number): Promise> { - const surveyCritters = await this.getCrittersInSurvey(surveyId); - - const critterbaseCritterIds = surveyCritters.map((critter) => critter.critterbase_critter_id); - - const critters = await this.critterbaseService.getMultipleCrittersByIds(critterbaseCritterIds); + const critters = await this.getCritterbaseSurveyCritters(surveyId); // Return a unique Set of non-null critterbase aliases of a Survey // Note: The type from filtered critters should be Set not Set return new Set(critters.filter(Boolean).map((critter) => critter.animal_id)) as Set; } + + /** + * Get mapping of `alias` (animal_id) -> critterbase critter for a survey. + * + * Note: Aliases are converted to lowercase, when accessing the value use .toLowerCase() + * Note: Business expects unique critter alias' in Surveys effective 01/06/2024 + * + * TODO: Update this function to handle duplicate, not found and found critter aliases ie: `alias -> critter[]` + * + * @async + * @param {number} surveyId + * @returns {Promise>} Critter alias -> Detailed critter + */ + async getSurveyCritterAliasMap(surveyId: number): Promise> { + const critters = await this.getCritterbaseSurveyCritters(surveyId); + + // Create mapping of alias -> critter_id + const critterAliasMap = new Map(); + + for (const critter of critters) { + if (critter.animal_id) { + const alias = critter.animal_id.toLowerCase(); + // Do not allow existing duplicate aliases to map over eachother + if (critterAliasMap.get(alias)) { + defaultLog.debug({ + label: 'critter alias map', + message: 'duplicate critter alias for survey', + details: { surveyId: surveyId, critter: critter } + }); + + // Duplicate alias found, overwrite as undefined + critterAliasMap.set(alias, undefined); + } else { + critterAliasMap.set(alias, critter); + } + } + } + + return critterAliasMap; + } } diff --git a/api/src/services/survey-service.test.ts b/api/src/services/survey-service.test.ts index 1fca184b50..b10e809880 100644 --- a/api/src/services/survey-service.test.ts +++ b/api/src/services/survey-service.test.ts @@ -10,7 +10,6 @@ import { GetReportAttachmentsData } from '../models/project-view'; import { PostProprietorData, PostSurveyObject } from '../models/survey-create'; import { PostSurveyLocationData, PutSurveyObject, PutSurveyPermitData } from '../models/survey-update'; import { - GetAncillarySpeciesData, GetAttachmentsData, GetFocalSpeciesData, GetSurveyData, @@ -22,10 +21,10 @@ import { FundingSourceRepository } from '../repositories/funding-source-reposito import { IPermitModel } from '../repositories/permit-repository'; import { SurveyLocationRecord, SurveyLocationRepository } from '../repositories/survey-location-repository'; import { - IGetSpeciesData, ISurveyProprietorModel, SurveyRecord, SurveyRepository, + SurveyTaxonomyWithEcologicalUnits, SurveyTypeRecord } from '../repositories/survey-repository'; import { getMockDBConnection } from '../__mocks__/db'; @@ -143,9 +142,6 @@ describe('SurveyService', () => { const dbConnectionObj = getMockDBConnection(); const updateSurveyDetailsDataStub = sinon.stub(SurveyService.prototype, 'updateSurveyDetailsData').resolves(); - const updateSurveyVantageCodesDataStub = sinon - .stub(SurveyService.prototype, 'updateSurveyVantageCodesData') - .resolves(); const updateSurveySpeciesDataStub = sinon.stub(SurveyService.prototype, 'updateSurveySpeciesData').resolves(); const updateSurveyPermitDataStub = sinon.stub(SurveyService.prototype, 'updateSurveyPermitData').resolves(); const upsertSurveyFundingSourceDataStub = sinon @@ -173,7 +169,6 @@ describe('SurveyService', () => { await surveyService.updateSurvey(surveyId, putSurveyData); expect(updateSurveyDetailsDataStub).not.to.have.been.called; - expect(updateSurveyVantageCodesDataStub).not.to.have.been.called; expect(updateSurveySpeciesDataStub).not.to.have.been.called; expect(updateSurveyPermitDataStub).not.to.have.been.called; expect(upsertSurveyFundingSourceDataStub).to.have.been.calledOnce; @@ -188,9 +183,6 @@ describe('SurveyService', () => { const updateSurveyDetailsDataStub = sinon.stub(SurveyService.prototype, 'updateSurveyDetailsData').resolves(); const updateSurveyTypesDataStub = sinon.stub(SurveyService.prototype, 'updateSurveyTypesData').resolves(); - const updateSurveyVantageCodesDataStub = sinon - .stub(SurveyService.prototype, 'updateSurveyVantageCodesData') - .resolves(); const updateSurveyIntendedOutcomesStub = sinon .stub(SurveyService.prototype, 'updateSurveyIntendedOutcomes') .resolves(); @@ -236,7 +228,6 @@ describe('SurveyService', () => { expect(updateSurveyDetailsDataStub).to.have.been.calledOnce; expect(updateSurveyTypesDataStub).to.have.been.calledOnce; - expect(updateSurveyVantageCodesDataStub).to.have.been.calledOnce; expect(updateSurveySpeciesDataStub).to.have.been.calledOnce; expect(updateSurveyPermitDataStub).to.have.been.calledOnce; expect(upsertSurveyFundingSourceDataStub).to.have.been.calledOnce; @@ -367,23 +358,44 @@ describe('SurveyService', () => { }); describe('getSpeciesData', () => { - it('returns the first row on success', async () => { + it('returns combined species and taxonomy data on success', async () => { const dbConnection = getMockDBConnection(); const service = new SurveyService(dbConnection); - const data = { id: 1 } as unknown as IGetSpeciesData; + const mockEcologicalUnits = [ + { critterbase_collection_category_id: 'abc', critterbase_collection_unit_id: 'xyz' } + ]; + const mockSpeciesData = [ + { itis_tsn: 123, ecological_units: [] }, + { + itis_tsn: 456, + ecological_units: mockEcologicalUnits + } + ] as unknown as SurveyTaxonomyWithEcologicalUnits[]; + const mockTaxonomyData = [ + { tsn: 123, scientificName: 'Species 1' }, + { tsn: 456, scientificName: 'Species 2' } + ]; + const mockResponse = new GetFocalSpeciesData([ + { tsn: 123, scientificName: 'Species 1', ecological_units: [] }, + { + tsn: 456, + scientificName: 'Species 2', + ecological_units: mockEcologicalUnits + } + ]); - const repoStub = sinon.stub(SurveyRepository.prototype, 'getSpeciesData').resolves([data]); - const getTaxonomyByTsnsStub = sinon.stub(PlatformService.prototype, 'getTaxonomyByTsns').resolves([]); + const repoStub = sinon.stub(SurveyRepository.prototype, 'getSpeciesData').resolves(mockSpeciesData); + const getTaxonomyByTsnsStub = sinon + .stub(PlatformService.prototype, 'getTaxonomyByTsns') + .resolves(mockTaxonomyData); const response = await service.getSpeciesData(1); + // Assertions expect(repoStub).to.be.calledOnce; - expect(getTaxonomyByTsnsStub).to.be.calledTwice; - expect(response).to.eql({ - ...new GetFocalSpeciesData([]), - ...new GetAncillarySpeciesData([]) - }); + expect(getTaxonomyByTsnsStub).to.be.calledOnceWith([123, 456]); + expect(response.focal_species).to.eql(mockResponse.focal_species); }); }); @@ -585,35 +597,32 @@ describe('SurveyService', () => { }); }); - describe('insertAncillarySpecies', () => { + describe('insertFocalSpeciesWithUnits', () => { it('returns the first row on success', async () => { const dbConnection = getMockDBConnection(); const service = new SurveyService(dbConnection); - const data = 1; - - const repoStub = sinon.stub(SurveyRepository.prototype, 'insertAncillarySpecies').resolves(data); - - const response = await service.insertAncillarySpecies(1, 1); - - expect(repoStub).to.be.calledOnce; - expect(response).to.eql(data); - }); - }); - - describe('insertVantageCodes', () => { - it('returns the first row on success', async () => { - const dbConnection = getMockDBConnection(); - const service = new SurveyService(dbConnection); - - const data = 1; - - const repoStub = sinon.stub(SurveyRepository.prototype, 'insertVantageCodes').resolves(data); - - const response = await service.insertVantageCodes(1, 1); - - expect(repoStub).to.be.calledOnce; - expect(response).to.eql(data); + const mockFocalSpeciesId = 1; + const mockFocalSpeciesData = { + tsn: mockFocalSpeciesId, + scientificName: 'name', + commonNames: [], + rank: 'species', + kingdom: 'Animalia', + ecological_units: [{ critterbase_collection_category_id: 'abc', critterbase_collection_unit_id: 'xyz' }] + }; + const insertFocalSpeciesStub = sinon + .stub(SurveyRepository.prototype, 'insertFocalSpecies') + .resolves(mockFocalSpeciesId); + const insertFocalSpeciesUnitsStub = sinon + .stub(SurveyRepository.prototype, 'insertFocalSpeciesUnits') + .resolves(mockFocalSpeciesId); + + const response = await service.insertFocalSpeciesWithUnits(mockFocalSpeciesData, 1); + + expect(insertFocalSpeciesStub).to.be.calledOnce; + expect(insertFocalSpeciesUnitsStub).to.be.calledOnce; + expect(response).to.eql(mockFocalSpeciesId); }); }); @@ -726,9 +735,9 @@ describe('SurveyService', () => { }); it('returns data if response is not null', async () => { + sinon.stub(SurveyService.prototype, 'deleteSurveySpeciesUnitData').resolves(); sinon.stub(SurveyService.prototype, 'deleteSurveySpeciesData').resolves(); - sinon.stub(SurveyService.prototype, 'insertFocalSpecies').resolves(1); - sinon.stub(SurveyService.prototype, 'insertAncillarySpecies').resolves(1); + sinon.stub(SurveyService.prototype, 'insertFocalSpeciesWithUnits').resolves(1); const mockQueryResponse = { response: 'something', rowCount: 1 } as unknown as QueryResult; @@ -737,10 +746,10 @@ describe('SurveyService', () => { const response = await surveyService.updateSurveySpeciesData(1, { survey_details: 'details', - species: { focal_species: [1], ancillary_species: [1] } + species: { focal_species: [1] } } as unknown as PutSurveyObject); - expect(response).to.eql([1, 1]); + expect(response).to.eql([1]); }); }); @@ -912,60 +921,6 @@ describe('SurveyService', () => { }); }); - describe('updateSurveyVantageCodesData', () => { - afterEach(() => { - sinon.restore(); - }); - - it('returns [] if not vantage_code_ids is given', async () => { - sinon.stub(SurveyService.prototype, 'deleteSurveyVantageCodes').resolves(); - - const mockQueryResponse = undefined as unknown as QueryResult; - - const mockDBConnection = getMockDBConnection({ sql: async () => mockQueryResponse }); - const surveyService = new SurveyService(mockDBConnection); - - const response = await surveyService.updateSurveyVantageCodesData(1, { - permit: { permit_number: '1', permit_type: 'type' }, - purpose_and_methodology: { vantage_code_ids: undefined } - } as unknown as PutSurveyObject); - - expect(response).to.eql([]); - }); - - it('returns data if response is not null', async () => { - sinon.stub(SurveyService.prototype, 'deleteSurveyVantageCodes').resolves(); - sinon.stub(SurveyService.prototype, 'insertVantageCodes').resolves(1); - - const mockQueryResponse = undefined as unknown as QueryResult; - - const mockDBConnection = getMockDBConnection({ sql: async () => mockQueryResponse }); - const surveyService = new SurveyService(mockDBConnection); - - const response = await surveyService.updateSurveyVantageCodesData(1, { - permit: { permit_number: '1', permit_type: 'type' }, - proprietor: { survey_data_proprietary: 'asd' }, - purpose_and_methodology: { vantage_code_ids: [1] } - } as unknown as PutSurveyObject); - - expect(response).to.eql([1]); - }); - }); - - describe('deleteSurveyVantageCodes', () => { - it('returns the first row on success', async () => { - const dbConnection = getMockDBConnection(); - const service = new SurveyService(dbConnection); - - const repoStub = sinon.stub(SurveyRepository.prototype, 'deleteSurveyVantageCodes').resolves(); - - const response = await service.deleteSurveyVantageCodes(1); - - expect(repoStub).to.be.calledOnce; - expect(response).to.eql(undefined); - }); - }); - describe('deleteSurvey', () => { it('should delete the survey and return nothing', async () => { const dbConnection = getMockDBConnection(); diff --git a/api/src/services/survey-service.ts b/api/src/services/survey-service.ts index ccba496253..c414dbf420 100644 --- a/api/src/services/survey-service.ts +++ b/api/src/services/survey-service.ts @@ -4,7 +4,6 @@ import { PostProprietorData, PostSurveyObject } from '../models/survey-create'; import { PostSurveyLocationData, PutPartnershipsData, PutSurveyObject } from '../models/survey-update'; import { FindSurveysResponse, - GetAncillarySpeciesData, GetAttachmentsData, GetFocalSpeciesData, GetPermitData, @@ -18,7 +17,6 @@ import { SurveyObject, SurveySupplementaryData } from '../models/survey-view'; -import { AttachmentRepository } from '../repositories/attachment-repository'; import { PostSurveyBlock, SurveyBlockRecordWithCount } from '../repositories/survey-block-repository'; import { SurveyLocationRecord } from '../repositories/survey-location-repository'; import { ISurveyProprietorModel, SurveyBasicFields, SurveyRepository } from '../repositories/survey-repository'; @@ -27,7 +25,7 @@ import { DBService } from './db-service'; import { FundingSourceService } from './funding-source-service'; import { HistoryPublishService } from './history-publish-service'; import { PermitService } from './permit-service'; -import { ITaxonomy, PlatformService } from './platform-service'; +import { ITaxonomyWithEcologicalUnits, PlatformService } from './platform-service'; import { RegionService } from './region-service'; import { SiteSelectionStrategyService } from './site-selection-strategy-service'; import { SurveyBlockService } from './survey-block-service'; @@ -35,7 +33,6 @@ import { SurveyLocationService } from './survey-location-service'; import { SurveyParticipationService } from './survey-participation-service'; export class SurveyService extends DBService { - attachmentRepository: AttachmentRepository; surveyRepository: SurveyRepository; platformService: PlatformService; historyPublishService: HistoryPublishService; @@ -47,7 +44,6 @@ export class SurveyService extends DBService { constructor(connection: IDBConnection) { super(connection); - this.attachmentRepository = new AttachmentRepository(connection); this.surveyRepository = new SurveyRepository(connection); this.platformService = new PlatformService(connection); this.historyPublishService = new HistoryPublishService(connection); @@ -168,33 +164,27 @@ export class SurveyService extends DBService { * Get associated species data for a survey from the taxonomic service for a given Survey ID * * @param {number} surveyId - * @returns {*} {Promise} + * @returns {*} {Promise} * @memberof SurveyService */ - async getSpeciesData(surveyId: number): Promise { + async getSpeciesData(surveyId: number): Promise { + // Fetch species data for the survey const studySpeciesResponse = await this.surveyRepository.getSpeciesData(surveyId); - const [focalSpeciesIds, ancillarySpeciesIds] = studySpeciesResponse.reduce( - ([focal, ancillary]: [number[], number[]], studySpecies) => { - if (studySpecies.is_focal) { - focal.push(studySpecies.itis_tsn); - } else { - ancillary.push(studySpecies.itis_tsn); - } - - return [focal, ancillary]; - }, - [[], []] + // Fetch taxonomy data for each survey species + const taxonomyResponse = await this.platformService.getTaxonomyByTsns( + studySpeciesResponse.map((species) => species.itis_tsn) ); - const platformService = new PlatformService(this.connection); + const focalSpecies = []; - const [focalSpecies, ancillarySpecies] = await Promise.all([ - platformService.getTaxonomyByTsns(focalSpeciesIds), - platformService.getTaxonomyByTsns(ancillarySpeciesIds) - ]); + for (const species of studySpeciesResponse) { + const taxon = taxonomyResponse.find((taxonomy) => Number(taxonomy.tsn) === species.itis_tsn) ?? {}; + focalSpecies.push({ ...taxon, tsn: species.itis_tsn, ecological_units: species.ecological_units }); + } - return { ...new GetFocalSpeciesData(focalSpecies), ...new GetAncillarySpeciesData(ancillarySpecies) }; + // Return the combined data + return new GetFocalSpeciesData(focalSpecies); } /** @@ -310,7 +300,7 @@ export class SurveyService extends DBService { const decoratedSurveys: SurveyBasicFields[] = []; for (const survey of surveys) { const matchingFocalSpeciesNames = focalSpecies - .filter((item) => survey.focal_species.includes(Number(item.tsn))) + .filter((item) => survey.focal_species.includes(item.tsn)) .map((item) => [item.commonNames, `(${item.scientificName})`].filter(Boolean).join(' ')); decoratedSurveys.push({ ...survey, focal_species_names: matchingFocalSpeciesNames }); @@ -390,18 +380,16 @@ export class SurveyService extends DBService { ); // Handle focal species associated to this survey + // If there are ecological units, insert them promises.push( Promise.all( - postSurveyData.species.focal_species.map((species: ITaxonomy) => this.insertFocalSpecies(species.tsn, surveyId)) - ) - ); - - // Handle ancillary species associated to this survey - promises.push( - Promise.all( - postSurveyData.species.ancillary_species.map((species: ITaxonomy) => - this.insertAncillarySpecies(species.tsn, surveyId) - ) + postSurveyData.species.focal_species.map((species: ITaxonomyWithEcologicalUnits) => { + if (species.ecological_units.length) { + this.insertFocalSpeciesWithUnits(species, surveyId); + } else { + this.insertFocalSpecies(species.tsn, surveyId); + } + }) ) ); @@ -454,15 +442,6 @@ export class SurveyService extends DBService { // Handle survey proprietor data postSurveyData.proprietor && promises.push(this.insertSurveyProprietor(postSurveyData.proprietor, surveyId)); - //Handle vantage codes associated to this survey - promises.push( - Promise.all( - postSurveyData.purpose_and_methodology.vantage_code_ids.map((vantageCode: number) => - this.insertVantageCodes(vantageCode, surveyId) - ) - ) - ); - if (postSurveyData.locations) { // Insert survey locations promises.push(Promise.all(postSurveyData.locations.map((item) => this.insertSurveyLocations(surveyId, item)))); @@ -584,27 +563,23 @@ export class SurveyService extends DBService { } /** - * Inserts a new record and associates ancillary species to a survey + * Inserts a new focal species record and associates it with ecological units for a survey. * - * @param {number} ancillary_species_id - * @param {number} surveyId - * @returns {*} {Promise} + * @param {ITaxonomyWithEcologicalUnits[]} taxonWithUnits - Array of species with ecological unit objects to associate. + * @param {number} surveyId - ID of the survey. + * @returns {Promise} - The ID of the newly created focal species. * @memberof SurveyService */ - async insertAncillarySpecies(ancillary_species_id: number, surveyId: number): Promise { - return this.surveyRepository.insertAncillarySpecies(ancillary_species_id, surveyId); - } + async insertFocalSpeciesWithUnits(taxonWithUnits: ITaxonomyWithEcologicalUnits, surveyId: number): Promise { + // Insert the new focal species and get its ID + const studySpeciesId = await this.surveyRepository.insertFocalSpecies(taxonWithUnits.tsn, surveyId); - /** - * Inserts new record and associated a vantage code to a survey - * - * @param {number} vantage_code_id - * @param {number} surveyId - * @returns {*} {Promise} - * @memberof SurveyService - */ - async insertVantageCodes(vantage_code_id: number, surveyId: number): Promise { - return this.surveyRepository.insertVantageCodes(vantage_code_id, surveyId); + // Insert ecological units associated with the newly created focal species + await Promise.all( + taxonWithUnits.ecological_units.map((unit) => this.surveyRepository.insertFocalSpeciesUnits(unit, studySpeciesId)) + ); + + return studySpeciesId; } /** @@ -673,7 +648,6 @@ export class SurveyService extends DBService { } if (putSurveyData?.purpose_and_methodology) { - promises.push(this.updateSurveyVantageCodesData(surveyId, putSurveyData)); promises.push(this.updateSurveyIntendedOutcomes(surveyId, putSurveyData)); } @@ -827,16 +801,14 @@ export class SurveyService extends DBService { * @memberof SurveyService */ async updateSurveySpeciesData(surveyId: number, surveyData: PutSurveyObject) { + // Delete any ecological units associated with the focal species record + await this.deleteSurveySpeciesUnitData(surveyId); await this.deleteSurveySpeciesData(surveyId); const promises: Promise[] = []; - surveyData.species.focal_species.forEach((focalSpecies: ITaxonomy) => - promises.push(this.insertFocalSpecies(focalSpecies.tsn, surveyId)) - ); - - surveyData.species.ancillary_species.forEach((ancillarySpecies: ITaxonomy) => - promises.push(this.insertAncillarySpecies(ancillarySpecies.tsn, surveyId)) + surveyData.species.focal_species.forEach((focalSpecies: ITaxonomyWithEcologicalUnits) => + promises.push(this.insertFocalSpeciesWithUnits(focalSpecies, surveyId)) ); return Promise.all(promises); @@ -853,6 +825,17 @@ export class SurveyService extends DBService { return this.surveyRepository.deleteSurveySpeciesData(surveyId); } + /** + * Delete focal ecological units for a given survey ID + * + * @param {number} surveyId + * @returns {*} {Promise} + * @memberof SurveyService + */ + async deleteSurveySpeciesUnitData(surveyId: number) { + return this.surveyRepository.deleteSurveySpeciesUnitData(surveyId); + } + /** * Updates survey participants * @@ -1148,39 +1131,6 @@ export class SurveyService extends DBService { return this.surveyRepository.insertStakeholderPartnerships(stakeholderPartners, surveyId); } - /** - * Updates vantage codes associated to a survey - * - * @param {number} surveyId - * @param {PutSurveyObject} surveyData - * @returns {*} {Promise} - * @memberof SurveyService - */ - async updateSurveyVantageCodesData(surveyId: number, surveyData: PutSurveyObject) { - await this.deleteSurveyVantageCodes(surveyId); - - const promises: Promise[] = []; - - if (surveyData.purpose_and_methodology.vantage_code_ids) { - surveyData.purpose_and_methodology.vantage_code_ids.forEach((vantageCodeId: number) => - promises.push(this.insertVantageCodes(vantageCodeId, surveyId)) - ); - } - - return Promise.all(promises); - } - - /** - * Breaks link between vantage codes and a survey fora given survey Id - * - * @param {number} surveyId - * @returns {*} {Promise} - * @memberof SurveyService - */ - async deleteSurveyVantageCodes(surveyId: number): Promise { - return this.surveyRepository.deleteSurveyVantageCodes(surveyId); - } - /** * Deletes a survey for a given ID * diff --git a/api/src/services/telemetry-service.ts b/api/src/services/telemetry-service.ts index a064741af2..1d235ca823 100644 --- a/api/src/services/telemetry-service.ts +++ b/api/src/services/telemetry-service.ts @@ -1,11 +1,12 @@ import { default as dayjs } from 'dayjs'; import { IDBConnection } from '../database/db'; import { ApiGeneralError } from '../errors/api-error'; -import { ITelemetryAdvancedFilters } from '../models/telemetry-view'; +import { IAllTelemetryAdvancedFilters } from '../models/telemetry-view'; import { SurveyCritterRecord } from '../repositories/survey-critter-repository'; import { Deployment, TelemetryRepository, TelemetrySubmissionRecord } from '../repositories/telemetry-repository'; import { generateS3FileKey, getFileFromS3 } from '../utils/file-utils'; import { parseS3File } from '../utils/media/media-utils'; +import { CSV_COLUMN_ALIASES } from '../utils/xlsx-utils/column-aliases'; import { constructXLSXWorkbook, getDefaultWorksheet, @@ -14,35 +15,42 @@ import { validateCsvFile } from '../utils/xlsx-utils/worksheet-utils'; import { ApiPaginationOptions } from '../zod-schema/pagination'; -import { BctwService, IAllTelemetry, ICreateManualTelemetry, IDeploymentRecord } from './bctw-service'; +import { AttachmentService } from './attachment-service'; +import { BctwDeploymentRecord, BctwDeploymentService } from './bctw-service/bctw-deployment-service'; +import { BctwTelemetryService, IAllTelemetry, ICreateManualTelemetry } from './bctw-service/bctw-telemetry-service'; import { ICritter, ICritterbaseUser } from './critterbase-service'; import { DBService } from './db-service'; +import { DeploymentService } from './deployment-service'; import { SurveyCritterService } from './survey-critter-service'; export type FindTelemetryResponse = { telemetry_id: string } & Pick< IAllTelemetry, 'acquisition_date' | 'latitude' | 'longitude' | 'telemetry_type' > & - Pick & + Pick & Pick & Pick & Pick; const telemetryCSVColumnValidator: IXLSXCSVValidator = { - columnNames: ['DEVICE_ID', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'], - columnTypes: ['number', 'date', 'string', 'number', 'number'], - columnAliases: { - LATITUDE: ['LAT'], - LONGITUDE: ['LON', 'LONG', 'LNG'] - } + DEVICE_ID: { type: 'number' }, + DATE: { type: 'date' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: CSV_COLUMN_ALIASES.LATITUDE }, + LONGITUDE: { type: 'number', aliases: CSV_COLUMN_ALIASES.LONGITUDE } }; export class TelemetryService extends DBService { telemetryRepository: TelemetryRepository; + attachmentService: AttachmentService; + constructor(connection: IDBConnection) { super(connection); + this.telemetryRepository = new TelemetryRepository(connection); + + this.attachmentService = new AttachmentService(connection); } /** @@ -101,13 +109,13 @@ export class TelemetryService extends DBService { const worksheetRowObjects = getWorksheetRowObjects(xlsxWorksheet); // step 7 fetch survey deployments - const bctwService = new BctwService(user); - const critterService = new SurveyCritterService(this.connection); - - const critters = await critterService.getCrittersInSurvey(submission.survey_id); - const critterIds = critters.map((item) => item.critterbase_critter_id); + const deploymentService = new DeploymentService(this.connection); + const bctwDeploymentService = new BctwDeploymentService(user); - const deployments = await bctwService.getDeploymentsByCritterId(critterIds); + const surveyDeployments = await deploymentService.getDeploymentsForSurveyId(submission.survey_id); + const deployments = await bctwDeploymentService.getDeploymentsByIds( + surveyDeployments.map((deployment) => deployment.bctw_deployment_id) + ); // step 8 parse file data and find deployment ids based on device id and attachment dates const itemsToAdd: ICreateManualTelemetry[] = []; @@ -153,9 +161,12 @@ export class TelemetryService extends DBService { }); // step 9 create telemetries + + const bctwTelemetryService = new BctwTelemetryService(user); + if (itemsToAdd.length > 0) { try { - return bctwService.createManualTelemetry(itemsToAdd); + return await bctwTelemetryService.createManualTelemetry(itemsToAdd); } catch (error) { throw new ApiGeneralError('Error adding Manual Telemetry'); } @@ -182,13 +193,27 @@ export class TelemetryService extends DBService { return this.telemetryRepository.getDeploymentsByCritterIds(critterIds); } + /** + * Get deployments for the provided survey id. + * + * Note: SIMS does not store deployment information, beyond an ID. Deployment details must be fetched from the + * external BCTW API. + * + * @param {number} surveyId + * @return {*} {Promise} + * @memberof TelemetryService + */ + async getDeploymentsBySurveyId(surveyId: number): Promise { + return this.telemetryRepository.getDeploymentsBySurveyId(surveyId); + } + /** * Retrieves the paginated list of all telemetry records that are available to the user, based on their permissions * and provided filter criteria. * * @param {boolean} isUserAdmin * @param {(number | null)} systemUserId The system user id of the user making the request - * @param {ITelemetryAdvancedFilters} [filterFields] + * @param {IAllTelemetryAdvancedFilters} [filterFields] * @param {ApiPaginationOptions} [pagination] * @return {*} {Promise} * @memberof TelemetryService @@ -196,7 +221,7 @@ export class TelemetryService extends DBService { async findTelemetry( isUserAdmin: boolean, systemUserId: number | null, - filterFields?: ITelemetryAdvancedFilters, + filterFields?: IAllTelemetryAdvancedFilters, pagination?: ApiPaginationOptions ): Promise { // --- Step 1 ----------------------------- @@ -248,14 +273,18 @@ export class TelemetryService extends DBService { return []; } - const bctwService = new BctwService({ + const user = { keycloak_guid: this.connection.systemUserGUID(), username: this.connection.systemUserIdentifier() - }); + }; + + const bctwDeploymentService = new BctwDeploymentService(user); + const bctwTelemetryService = new BctwTelemetryService(user); + // The detailed deployment records from BCTW // Note: This may include records the user does not have acces to (A critter may have multiple deployments over its // lifespan, but the user may only have access to a subset of them). - const allBctwDeploymentsForCritters = await bctwService.getDeploymentsByCritterId(critterbaseCritterIds); + const allBctwDeploymentsForCritters = await bctwDeploymentService.getDeploymentsByCritterId(critterbaseCritterIds); // Remove records the user does not have access to const usersBctwDeployments = allBctwDeploymentsForCritters.filter((deployment) => @@ -271,7 +300,7 @@ export class TelemetryService extends DBService { // --- Step 4 ------------------------------ // The telemetry records for the deployments the user has access to - const allTelemetryRecords = await bctwService.getAllTelemetryByDeploymentIds(usersBctwDeploymentIds); + const allTelemetryRecords = await bctwTelemetryService.getAllTelemetryByDeploymentIds(usersBctwDeploymentIds); // --- Step 5 ------------------------------ @@ -309,7 +338,7 @@ export class TelemetryService extends DBService { latitude: telemetryRecord.latitude, longitude: telemetryRecord.longitude, telemetry_type: telemetryRecord.telemetry_type, - // IDeploymentRecord + // BctwDeploymentRecord device_id: usersBctwDeployment.device_id, // Deployment bctw_deployment_id: telemetryRecord.deployment_id, diff --git a/api/src/utils/file-utils.test.ts b/api/src/utils/file-utils.test.ts index 84c4cf315e..4783d97742 100644 --- a/api/src/utils/file-utils.test.ts +++ b/api/src/utils/file-utils.test.ts @@ -55,17 +55,22 @@ describe('generateS3FileKey', () => { it('returns project folder file path', async () => { process.env.S3_KEY_PREFIX = 'some/s3/prefix'; - const result = generateS3FileKey({ projectId: 1, folder: 'folder', fileName: 'testFileName' }); + const result = generateS3FileKey({ projectId: 1, folder: 'reports', fileName: 'testFileName' }); - expect(result).to.equal('some/s3/prefix/projects/1/folder/testFileName'); + expect(result).to.equal('some/s3/prefix/projects/1/reports/testFileName'); }); it('returns survey folder file path', async () => { process.env.S3_KEY_PREFIX = 'some/s3/prefix'; - const result = generateS3FileKey({ projectId: 1, surveyId: 2, folder: 'folder', fileName: 'testFileName' }); + const result = generateS3FileKey({ + projectId: 1, + surveyId: 2, + folder: 'telemetry-credentials', + fileName: 'testFileName' + }); - expect(result).to.equal('some/s3/prefix/projects/1/surveys/2/folder/testFileName'); + expect(result).to.equal('some/s3/prefix/projects/1/surveys/2/telemetry-credentials/testFileName'); }); it('returns survey submission folder file path when a submission ID is passed', async () => { diff --git a/api/src/utils/file-utils.ts b/api/src/utils/file-utils.ts index dc4e661f91..63f2c1f49a 100644 --- a/api/src/utils/file-utils.ts +++ b/api/src/utils/file-utils.ts @@ -253,10 +253,32 @@ export async function getS3SignedURL(key: string): Promise { } export interface IS3FileKey { + /** + * The project ID the file is associated with. + */ projectId: number; + /** + * The survey ID the file is associated with. + */ surveyId?: number; + /** + * The template submission ID the file is associated with. + * + * @deprecated + */ submissionId?: number; - folder?: string; + /** + * The sub-folder in the project/survey where the file is stored. + * + * Note: For regular/generic file attachments, leave this undefined. + */ + folder?: 'reports' | 'telemetry-credentials'; + /** + * The name of the file. + * + * @type {string} + * @memberof IS3FileKey + */ fileName: string; } diff --git a/api/src/utils/logger.test.ts b/api/src/utils/logger.test.ts index 1af556d09f..1fc7585831 100644 --- a/api/src/utils/logger.test.ts +++ b/api/src/utils/logger.test.ts @@ -1,6 +1,6 @@ import { expect } from 'chai'; import { describe } from 'mocha'; -import { getLogger, setLogLevel } from './logger'; +import { getLogger, setLogLevel, setLogLevelFile } from './logger'; describe('logger', () => { describe('getLogger', () => { @@ -12,18 +12,62 @@ describe('logger', () => { }); describe('setLogLevel', () => { - it('sets the log level for all loggers', () => { - const myLogger1 = getLogger('myLogger'); - expect(myLogger1.transports[0].level).to.equal('info'); + let currentLogLevel: string | undefined; + + beforeEach(() => { + currentLogLevel = process.env.LOG_LEVEL; + + // Set initial log level value + process.env.LOG_LEVEL = 'info'; + }); + + afterEach(() => { + // Restore the original log level + process.env.LOG_LEVEL = currentLogLevel; + }); + + it('sets the log level for the console transport', () => { + const myLogger1 = getLogger('myLoggerA'); + expect(myLogger1.transports[1].level).to.equal('info'); setLogLevel('debug'); - const myLogger2 = getLogger('myLogger'); - expect(myLogger2.transports[0].level).to.equal('debug'); + const myLogger2 = getLogger('myLoggerA'); + expect(myLogger2.transports[1].level).to.equal('debug'); + + const myNewLogger3 = getLogger('myNewLoggerA'); + + expect(myNewLogger3.transports[1].level).to.equal('debug'); + }); + }); + + describe('setLogLevelFile', () => { + let currentLogLevelFile: string | undefined; + + beforeEach(() => { + currentLogLevelFile = process.env.LOG_LEVEL_FILE; + + // Set initial log level file value + process.env.LOG_LEVEL_FILE = 'warn'; + }); + + afterEach(() => { + // Restore the original log level + process.env.LOG_LEVEL_FILE = currentLogLevelFile; + }); + + it('sets the log level for the file transport', () => { + const myLogger4 = getLogger('myLoggerB'); + expect(myLogger4.transports[0].level).to.equal('warn'); + + setLogLevelFile('error'); + + const myLogger5 = getLogger('myLoggerB'); + expect(myLogger5.transports[0].level).to.equal('error'); - const myNewLogger = getLogger('myNewLogger'); + const myNewLogger6 = getLogger('myNewLoggerB'); - expect(myNewLogger.transports[0].level).to.equal('debug'); + expect(myNewLogger6.transports[0].level).to.equal('error'); }); }); }); diff --git a/api/src/utils/logger.ts b/api/src/utils/logger.ts index e9d493fb21..cefe86ba19 100644 --- a/api/src/utils/logger.ts +++ b/api/src/utils/logger.ts @@ -1,4 +1,5 @@ import winston from 'winston'; +import DailyRotateFile from 'winston-daily-rotate-file'; /** * Get or create a logger for the given `logLabel`. @@ -43,17 +44,46 @@ import winston from 'winston'; * * ...etc * - * Valid `LOG_LEVEL` values (from least logging to most logging) (default: info): - * silent, error, warn, info, debug, silly + * Environment Variables: + * + * LOG_LEVEL - Defines the level of logging that the logger will output to the console. (default: debug) + * + * LOG_LEVEL_FILE - Defines the level of logging that the logger will output to persistent log files. (default: debug) + * + * Valid logging level values (from least logging to most logging) - silent, error, warn, info, debug, silly * * @param {string} logLabel common label for the instance of the logger. * @returns */ export const getLogger = function (logLabel: string) { - return winston.loggers.get(logLabel || 'default', { - transports: [ + const transports = []; + + // Output logs to file + transports.push( + new DailyRotateFile({ + dirname: process.env.LOG_FILE_DIR || 'data/logs', + filename: process.env.LOG_FILE_NAME || 'sims-api-%DATE%.log', + datePattern: process.env.LOG_FILE_DATE_PATTERN || 'YYYY-MM-DD-HH', + maxSize: process.env.LOG_FILE_MAX_SIZE || '50m', + maxFiles: process.env.LOG_FILE_MAX_FILES || '10', + level: process.env.LOG_LEVEL_FILE || 'debug', + format: winston.format.combine( + winston.format((info) => { + const { timestamp, level, ...rest } = info; + // Return the properties of info in a specific order + return { timestamp, level, logger: logLabel, ...rest }; + })(), + winston.format.timestamp({ format: 'YYYY-MM-DD HH:mm:ss' }), + winston.format.prettyPrint({ colorize: false, depth: 10 }) + ) + }) + ); + + if (process.env.NODE_ENV !== 'production') { + // Additionally output logs to console in non-production environments + transports.push( new winston.transports.Console({ - level: process.env.LOG_LEVEL || 'info', + level: process.env.LOG_LEVEL || 'debug', format: winston.format.combine( winston.format((info) => { const { timestamp, level, ...rest } = info; @@ -61,11 +91,13 @@ export const getLogger = function (logLabel: string) { return { timestamp, level, logger: logLabel, ...rest }; })(), winston.format.timestamp({ format: 'YYYY-MM-DD HH:mm:ss' }), - winston.format.prettyPrint({ colorize: true, depth: 5 }) + winston.format.prettyPrint({ colorize: true, depth: 10 }) ) }) - ] - }); + ); + } + + return winston.loggers.get(logLabel || 'default', { transports: transports }); }; export const WinstonLogLevels = ['silent', 'error', 'warn', 'info', 'debug', 'silly'] as const; @@ -73,7 +105,7 @@ export const WinstonLogLevels = ['silent', 'error', 'warn', 'info', 'debug', 'si export type WinstonLogLevel = (typeof WinstonLogLevels)[number]; /** - * Set the winston logger log level. + * Set the winston logger log level for the console transport * * @param {WinstonLogLevel} logLevel */ @@ -81,8 +113,25 @@ export const setLogLevel = (logLevel: WinstonLogLevel) => { // Update env var for future loggers process.env.LOG_LEVEL = logLevel; - // Update existing loggers + if (process.env.NODE_ENV !== 'production') { + // Update console transport log level, which is the second transport in non-production environments + winston.loggers.loggers.forEach((logger) => { + logger.transports[1].level = logLevel; + }); + } +}; + +/** + * Set the winston logger log level for the file transport. + * + * @param {WinstonLogLevel} logLevel + */ +export const setLogLevelFile = (logLevelFile: WinstonLogLevel) => { + // Update env var for future loggers + process.env.LOG_LEVEL_FILE = logLevelFile; + + // Update file transport log level, which is the first transport in all environments winston.loggers.loggers.forEach((logger) => { - logger.transports[0].level = logLevel; + logger.transports[0].level = logLevelFile; }); }; diff --git a/api/src/utils/media/media-utils.test.ts b/api/src/utils/media/media-utils.test.ts index 7300f60996..2ccef9cd5b 100644 --- a/api/src/utils/media/media-utils.test.ts +++ b/api/src/utils/media/media-utils.test.ts @@ -4,6 +4,7 @@ import chai, { expect } from 'chai'; import { describe } from 'mocha'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; +import { TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE } from '../../constants/attachments'; import { ArchiveFile, MediaFile } from './media-file'; import * as media_utils from './media-utils'; @@ -212,51 +213,296 @@ describe('parseS3File', () => { }); }); -describe('checkFileForKeyx', () => { - const validKeyxFile = { - originalname: 'test.keyx', - mimetype: 'application/octet-stream', - buffer: Buffer.alloc(0) - } as unknown as Express.Multer.File; - - const invalidFile = { - originalname: 'test.txt', - mimetype: 'text/plain', - buffer: Buffer.alloc(0) - } as unknown as Express.Multer.File; - - const zipFile = { - originalname: 'test.zip', - mimetype: 'application/zip', - buffer: Buffer.alloc(0) - } as unknown as Express.Multer.File; +describe('isValidTelementryCredentialFile', () => { + it('should return true if the file extension is .keyx', () => { + const validKeyxFile = { + originalname: 'test.keyx', + mimetype: 'application/octet-stream', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + expect(media_utils.checkFileForKeyx(validKeyxFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX + }); + }); + + it('should return false if the file is not a .keyx or zip mimetype', () => { + const invalidFile = { + originalname: 'test.txt', + mimetype: 'text/plain', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const multerFile = { ...invalidFile, buffer: Buffer.alloc(0) }; + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is neither a .keyx file, nor an archive containing only .keyx files' + }); + }); + + it('should return false if the file is an empty zip file', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const emptyZipFile = new AdmZip(); + const multerFile = { ...zipFile, buffer: emptyZipFile.toBuffer() }; + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains no content' + }); + }); + + it('should return false if the zip file contains any non .keyx files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const invalidZipFile = new AdmZip(); + invalidZipFile.addFile('test.txt', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: invalidZipFile.toBuffer() }; + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains non .keyx files' + }); + }); + + it('should return true if the zip file contains only .keyx files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const validZipFile = new AdmZip(); + validZipFile.addFile('test.keyx', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: validZipFile.toBuffer() }; + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX + }); + }); + + it('should return true if the file extension is .cfg', () => { + const validCfgFile = { + originalname: 'test.cfg', + mimetype: 'application/octet-stream', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + expect(media_utils.checkFileForCfg(validCfgFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG + }); + }); + + it('should return false if the file is not a .cfg or zip mimetype', () => { + const invalidFile = { + originalname: 'test.txt', + mimetype: 'text/plain', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const multerFile = { ...invalidFile, buffer: Buffer.alloc(0) }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is neither a .cfg file, nor an archive containing only .cfg files' + }); + }); + + it('should return false if the file is an empty zip file', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const emptyZipFile = new AdmZip(); + const multerFile = { ...zipFile, buffer: emptyZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains no content' + }); + }); + + it('should return false if the zip file contains any non .cfg files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const invalidZipFile = new AdmZip(); + invalidZipFile.addFile('test.txt', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: invalidZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains non .cfg files' + }); + }); + it('should return true if the zip file contains only .cfg files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const validZipFile = new AdmZip(); + validZipFile.addFile('test.cfg', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: validZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG + }); + }); +}); + +describe('checkFileForKeyx', () => { it('should return true if the file extension is .keyx', () => { - expect(media_utils.checkFileForKeyx(validKeyxFile)).to.equal(true); + const validKeyxFile = { + originalname: 'test.keyx', + mimetype: 'application/octet-stream', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + expect(media_utils.checkFileForKeyx(validKeyxFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX + }); }); it('should return false if the file is not a .keyx or zip mimetype', () => { + const invalidFile = { + originalname: 'test.txt', + mimetype: 'text/plain', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + const multerFile = { ...invalidFile, buffer: Buffer.alloc(0) }; - expect(media_utils.checkFileForKeyx(multerFile)).to.equal(false); + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is neither a .keyx file, nor an archive containing only .keyx files' + }); }); it('should return false if the file is an empty zip file', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + const emptyZipFile = new AdmZip(); const multerFile = { ...zipFile, buffer: emptyZipFile.toBuffer() }; - expect(media_utils.checkFileForKeyx(multerFile)).to.equal(false); + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains no content' + }); }); - it('should return false if the zip file contains any non-keyx files', () => { + it('should return false if the zip file contains any non .keyx files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + const invalidZipFile = new AdmZip(); invalidZipFile.addFile('test.txt', Buffer.alloc(0)); const multerFile = { ...zipFile, buffer: invalidZipFile.toBuffer() }; - expect(media_utils.checkFileForKeyx(multerFile)).to.equal(false); + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains non .keyx files' + }); }); it('should return true if the zip file contains only .keyx files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + const validZipFile = new AdmZip(); validZipFile.addFile('test.keyx', Buffer.alloc(0)); const multerFile = { ...zipFile, buffer: validZipFile.toBuffer() }; - expect(media_utils.checkFileForKeyx(multerFile)).to.equal(true); + expect(media_utils.checkFileForKeyx(multerFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX + }); + }); +}); + +describe('checkFileForCfg', () => { + it('should return true if the file extension is .cfg', () => { + const validCfgFile = { + originalname: 'test.cfg', + mimetype: 'application/octet-stream', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + expect(media_utils.checkFileForCfg(validCfgFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG + }); + }); + + it('should return false if the file is not a .cfg or zip mimetype', () => { + const invalidFile = { + originalname: 'test.txt', + mimetype: 'text/plain', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const multerFile = { ...invalidFile, buffer: Buffer.alloc(0) }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is neither a .cfg file, nor an archive containing only .cfg files' + }); + }); + + it('should return false if the file is an empty zip file', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const emptyZipFile = new AdmZip(); + const multerFile = { ...zipFile, buffer: emptyZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains no content' + }); + }); + + it('should return false if the zip file contains any non .cfg files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const invalidZipFile = new AdmZip(); + invalidZipFile.addFile('test.txt', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: invalidZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: 'unknown', + error: 'File is an archive that contains non .cfg files' + }); + }); + + it('should return true if the zip file contains only .cfg files', () => { + const zipFile = { + originalname: 'test.zip', + mimetype: 'application/zip', + buffer: Buffer.alloc(0) + } as unknown as Express.Multer.File; + + const validZipFile = new AdmZip(); + validZipFile.addFile('test.cfg', Buffer.alloc(0)); + const multerFile = { ...zipFile, buffer: validZipFile.toBuffer() }; + expect(media_utils.checkFileForCfg(multerFile)).to.eql({ + type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG + }); }); }); diff --git a/api/src/utils/media/media-utils.ts b/api/src/utils/media/media-utils.ts index 8f6f724051..72487a5627 100644 --- a/api/src/utils/media/media-utils.ts +++ b/api/src/utils/media/media-utils.ts @@ -1,6 +1,7 @@ import { GetObjectCommandOutput } from '@aws-sdk/client-s3'; import AdmZip from 'adm-zip'; import mime from 'mime'; +import { TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE } from '../../constants/attachments'; import { ArchiveFile, MediaFile } from './media-file'; /** @@ -125,30 +126,127 @@ export const isZipMimetype = (mimetype: string): boolean => { ); }; +/** + * Checks if the file is a valid telemetry credential file. + * + * @param {Express.Multer.File} file + * @return {*} {({ + * type: 'unknown' | TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE; + * error?: string; + * })} + */ +export const isValidTelementryCredentialFile = ( + file: Express.Multer.File +): { + type: 'unknown' | TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE; + error?: string; +} => { + const isKeyX = checkFileForKeyx(file); + + if (isKeyX.error === undefined) { + return isKeyX; + } + + const isCfg = checkFileForCfg(file); + + if (isCfg.error === undefined) { + return isCfg; + } + + return { + type: 'unknown', + error: 'The file is neither a .keyx or .cfg file, nor is it an archive containing only files of these types.' + }; +}; + /** * Returns true if the file is a keyx file, or a zip that contains only keyx files. * * @export * @param {Express.Multer.File} file - * @return {*} {boolean} + * @return {*} {({ + * type: 'unknown' | 'keyx'; + * error?: string; + * })} */ -export function checkFileForKeyx(file: Express.Multer.File): boolean { +export const checkFileForKeyx = ( + file: Express.Multer.File +): { + type: 'unknown' | TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX; + error?: string; +} => { // File is a KeyX file if it ends in '.keyx' - if (file?.originalname.endsWith('.keyx')) { - return true; + if (file.originalname.endsWith('.keyx')) { + return { type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX }; } + const mimeType = mime.getType(file.originalname) ?? ''; if (!isZipMimetype(mimeType)) { // File cannot be a KeyX file, since it is not an archive nor does it have a .keyx extension - return false; + return { + type: 'unknown', + error: 'File is neither a .keyx file, nor an archive containing only .keyx files' + }; } const zipEntries = parseUnknownZipFile(file.buffer); if (zipEntries.length === 0) { // File is a zip file, but it is empty - return false; + return { type: 'unknown', error: 'File is an archive that contains no content' }; } // Return false if any of the files in the zip are not keyx files - return zipEntries.every((zipEntry) => zipEntry.fileName.endsWith('.keyx')); -} + const result = zipEntries.every((zipEntry) => zipEntry.fileName.endsWith('.keyx')); + + if (!result) { + return { type: 'unknown', error: 'File is an archive that contains non .keyx files' }; + } + + return { type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.KEYX }; +}; + +/** + * Returns true if the file is a cfg file, or a zip that contains only cfg files. + * + * @export + * @param {Express.Multer.File} file + * @return {*} {({ + * type: 'unknown' | TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG; + * error?: string; + * })} + */ +export const checkFileForCfg = ( + file: Express.Multer.File +): { + type: 'unknown' | TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG; + error?: string; +} => { + // File is a Cfg file if it ends in '.cfg' + if (file?.originalname.endsWith('.cfg')) { + return { type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG }; + } + + const mimeType = mime.getType(file.originalname) ?? ''; + if (!isZipMimetype(mimeType)) { + // File cannot be a Cfg file, since it is not an archive nor does it have a .cfg extension + return { + type: 'unknown', + error: 'File is neither a .cfg file, nor an archive containing only .cfg files' + }; + } + + const zipEntries = parseUnknownZipFile(file.buffer); + if (zipEntries.length === 0) { + // File is a zip file, but it is empty + return { type: 'unknown', error: 'File is an archive that contains no content' }; + } + + // Return false if any of the files in the zip are not cfg files + const result = zipEntries.every((zipEntry) => zipEntry.fileName.endsWith('.cfg')); + + if (!result) { + return { type: 'unknown', error: 'File is an archive that contains non .cfg files' }; + } + + return { type: TELEMETRY_CREDENTIAL_ATTACHMENT_TYPE.CFG }; +}; diff --git a/api/src/utils/spatial-utils.test.ts b/api/src/utils/spatial-utils.test.ts index e602ac6384..fd03427cd9 100644 --- a/api/src/utils/spatial-utils.test.ts +++ b/api/src/utils/spatial-utils.test.ts @@ -1,6 +1,6 @@ import { expect } from 'chai'; import { describe } from 'mocha'; -import { parseLatLongString, parseUTMString, utmToLatLng } from './spatial-utils'; +import { parseUTMString, utmToLatLng } from './spatial-utils'; describe('parseUTMString', () => { it('returns null when no UTM string provided', async () => { @@ -95,53 +95,6 @@ describe('parseUTMString', () => { }); }); -describe('parseLatLongString', () => { - it('returns null when no LatLong string provided', async () => { - expect(parseLatLongString(null as unknown as string)).to.be.null; - expect(parseLatLongString('')).to.be.null; - }); - - it('returns null when provided LatLong string has invalid format', () => { - expect(parseLatLongString('49.1.2 -120')).to.be.null; - expect(parseLatLongString('49.49 -120.1.2')).to.be.null; - expect(parseLatLongString('badLatitude 120')).to.be.null; - expect(parseLatLongString('-49 badLongitude')).to.be.null; - expect(parseLatLongString('49 -120 extra')).to.be.null; - expect(parseLatLongString('')).to.be.null; - expect(parseLatLongString('not a lat long string')).to.be.null; - }); - - it('returns null when latitude is too small', async () => { - const result = parseLatLongString('-91 0'); - - expect(result).to.be.null; - }); - - it('returns null when latitude is too large', async () => { - const result = parseLatLongString('91 0'); - - expect(result).to.be.null; - }); - - it('returns null when longitude is too small', async () => { - const result = parseLatLongString('0 -181'); - - expect(result).to.be.null; - }); - - it('returns null when longitude is too large', async () => { - const result = parseLatLongString('0 181'); - - expect(result).to.be.null; - }); - - it('returns parsed lat long when lat long string is valid', async () => { - const result = parseLatLongString('49.123 -120.123'); - - expect(result).to.eql({ lat: 49.123, long: -120.123 }); - }); -}); - describe('utmToLatLng', () => { it('returns lat, long when zone_letter is provided', async () => { const verbatimCoordinates = { diff --git a/api/src/utils/spatial-utils.ts b/api/src/utils/spatial-utils.ts index c25d6cb12d..8aa377022c 100644 --- a/api/src/utils/spatial-utils.ts +++ b/api/src/utils/spatial-utils.ts @@ -90,38 +90,6 @@ export interface ILatLong { long: number; } -const LAT_LONG_STRING_FORMAT = RegExp(/^[+-]?(\d*[.])?\d+ [+-]?(\d*[.])?\d+$/i); - -/** - * Parses a `latitude longitude` string of the form: `49.116906 -122.62887` - * - * @export - * @param {string} latLong - * @return {*} {(ILatLong | null)} - */ -export function parseLatLongString(latLong: string): ILatLong | null { - if (!latLong || !LAT_LONG_STRING_FORMAT.test(latLong)) { - // latLong string is null or does not match the expected format - return null; - } - - const latLongParts = latLong.split(' '); - - const lat = Number(latLongParts[0]); - if (lat < -90 || lat > 90) { - // latitude is invalid - return null; - } - - const long = Number(latLongParts[1]); - if (long < -180 || long > 180) { - // longitude is invalid - return null; - } - - return { lat, long }; -} - /** * Function to generate the SQL for insertion of a geometry collection * diff --git a/api/src/utils/xlsx-utils/cell-utils.ts b/api/src/utils/xlsx-utils/cell-utils.ts index d6ef3b16ab..eb2e75f704 100644 --- a/api/src/utils/xlsx-utils/cell-utils.ts +++ b/api/src/utils/xlsx-utils/cell-utils.ts @@ -51,7 +51,7 @@ export function replaceCellDates(cell: CellObject) { } if (isTimeFormatCell(cell)) { - const TimeFormat = 'HH:mm'; + const TimeFormat = 'HH:mm:ss'; cell.v = cellDate.format(TimeFormat); return cell; } diff --git a/api/src/utils/xlsx-utils/column-aliases.ts b/api/src/utils/xlsx-utils/column-aliases.ts new file mode 100644 index 0000000000..6ea8db046f --- /dev/null +++ b/api/src/utils/xlsx-utils/column-aliases.ts @@ -0,0 +1,8 @@ +export const CSV_COLUMN_ALIASES: Record, Uppercase[]> = { + ITIS_TSN: ['TAXON', 'SPECIES', 'TSN'], + LATITUDE: ['LAT'], + LONGITUDE: ['LON', 'LONG', 'LNG'], + DESCRIPTION: ['COMMENT'], + ALIAS: ['NICKNAME'], + MARKING_TYPE: ['TYPE'] +}; diff --git a/api/src/utils/xlsx-utils/column-cell-utils.test.ts b/api/src/utils/xlsx-utils/column-cell-utils.test.ts deleted file mode 100644 index 58afdc0730..0000000000 --- a/api/src/utils/xlsx-utils/column-cell-utils.test.ts +++ /dev/null @@ -1,64 +0,0 @@ -import { expect } from 'chai'; -import { generateCellValueGetter, getColumnValidatorSpecification } from './column-cell-utils'; -import { IXLSXCSVValidator } from './worksheet-utils'; - -describe('column-validators', () => { - describe('generateCellValueGetter', () => { - it('should return value if property exists in object', () => { - const getValue = generateCellValueGetter('test', 'property'); - const object = { property: true }; - expect(getValue(object)).to.be.true; - }); - - it('should return undefined if property does not exist in object', () => { - const getValue = generateCellValueGetter('test', 'property'); - const object = { bad: true }; - expect(getValue(object)).to.be.undefined; - }); - }); - - describe('getColumnValidatorSpecification', () => { - it('should return specification format', () => { - const columnValidator: IXLSXCSVValidator = { - columnNames: ['TEST', 'COLUMN'], - columnTypes: ['number', 'string'], - columnAliases: { - TEST: ['ALSO TEST'], - COLUMN: ['ALSO COLUMN'] - } - }; - - const spec = getColumnValidatorSpecification(columnValidator); - - expect(spec).to.be.deep.equal([ - { - columnName: 'TEST', - columnType: 'number', - columnAliases: ['ALSO TEST'] - }, - { - columnName: 'COLUMN', - columnType: 'string', - columnAliases: ['ALSO COLUMN'] - } - ]); - }); - - it('should return specification format without aliases if not defined', () => { - const columnValidator: IXLSXCSVValidator = { - columnNames: ['TEST'], - columnTypes: ['number'] - }; - - const spec = getColumnValidatorSpecification(columnValidator); - - expect(spec).to.be.deep.equal([ - { - columnAliases: undefined, - columnName: 'TEST', - columnType: 'number' - } - ]); - }); - }); -}); diff --git a/api/src/utils/xlsx-utils/column-cell-utils.ts b/api/src/utils/xlsx-utils/column-cell-utils.ts deleted file mode 100644 index b90218609f..0000000000 --- a/api/src/utils/xlsx-utils/column-cell-utils.ts +++ /dev/null @@ -1,123 +0,0 @@ -import { IXLSXCSVValidator } from './worksheet-utils'; - -type Row = Record; - -// Taxon / species aliases -const ITIS_TSN = 'ITIS_TSN'; -const TAXON = 'TAXON'; -const SPECIES = 'SPECIES'; -const TSN = 'TSN'; - -// DateTime -const DATE = 'DATE'; -const TIME = 'TIME'; - -// Latitude and aliases -const LATITUDE = 'LATITUDE'; -const LAT = 'LAT'; - -// Longitude and aliases -const LONGITUDE = 'LONGITUDE'; -const LON = 'LON'; -const LONG = 'LONG'; -const LNG = 'LNG'; - -// Comment aliases -const COMMENT = 'COMMENT'; -const DESCRIPTION = 'DESCRIPTION'; - -// Critter nickname and aliases -const ALIAS = 'ALIAS'; -const NICKNAME = 'NICKNAME'; - -// Critter sex -const SEX = 'SEX'; - -// Critter Wildlife Health ID and aliases -const WLH_ID = 'WLH_ID'; -const WILDLIFE_HEALTH_ID = 'WILDLIFE_HEALTH_ID'; - -// Observation sub-count -const COUNT = 'COUNT'; - -/** - * An XLSX validation config for the standard columns of an observation CSV. - */ -export const observationStandardColumnValidator: IXLSXCSVValidator = { - columnNames: [ITIS_TSN, COUNT, DATE, TIME, LATITUDE, LONGITUDE], - columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'], - columnAliases: { - ITIS_TSN: [TAXON, SPECIES, TSN], - LATITUDE: [LAT], - LONGITUDE: [LON, LONG, LNG] - } -}; - -/** - * An XLSX validation config for the standard columns of a critter CSV. - */ -export const critterStandardColumnValidator: IXLSXCSVValidator = { - columnNames: [ITIS_TSN, SEX, ALIAS, WLH_ID, DESCRIPTION], - columnTypes: ['number', 'string', 'string', 'string', 'string'], - columnAliases: { - ITIS_TSN: [TAXON, SPECIES, TSN], - DESCRIPTION: [COMMENT], - ALIAS: [NICKNAME] - } -}; - -/** - * Get column validator specification as a readable format. Useful for error handling and logging. - * - * @param {IXLSXCSVValidator} columnValidator - Standard column validator - * @returns {*} - */ -export const getColumnValidatorSpecification = (columnValidator: IXLSXCSVValidator) => { - return columnValidator.columnNames.map((column, index) => ({ - columnName: column, - columnType: columnValidator.columnTypes[index], - columnAliases: columnValidator.columnAliases?.[column] - })); -}; - -/** - * Generate a row value getter function from array of allowed column values. - * - * @example const getTsnFromRow = generateCellValueGetter(ITIS_TSN, TSN, TAXON, SPECIES); - * - * @param {...string[]} headers - Column headers - * @returns {(row: Row) => T | undefined} Row value getter function - */ -export const generateCellValueGetter = (...headers: string[]) => { - return (row: Row) => { - for (const header of headers) { - if (row[header]) { - return row[header] as T; - } - } - }; -}; - -/** - * Row cell value getters. Attempt to retrive a cell value from a list of known column headers. - * - */ -export const getTsnFromRow = generateCellValueGetter(ITIS_TSN, TSN, TAXON, SPECIES); - -export const getCountFromRow = generateCellValueGetter(COUNT); - -export const getDateFromRow = generateCellValueGetter(DATE); - -export const getTimeFromRow = generateCellValueGetter(TIME); - -export const getLatitudeFromRow = generateCellValueGetter(LATITUDE, LAT); - -export const getLongitudeFromRow = generateCellValueGetter(LONGITUDE, LONG, LON, LNG); - -export const getDescriptionFromRow = generateCellValueGetter(DESCRIPTION, COMMENT); - -export const getAliasFromRow = generateCellValueGetter(ALIAS, NICKNAME); - -export const getWlhIdFromRow = generateCellValueGetter(WLH_ID, WILDLIFE_HEALTH_ID); - -export const getSexFromRow = generateCellValueGetter(SEX); diff --git a/api/src/utils/xlsx-utils/column-validator-utils.test.ts b/api/src/utils/xlsx-utils/column-validator-utils.test.ts new file mode 100644 index 0000000000..46ff4044b0 --- /dev/null +++ b/api/src/utils/xlsx-utils/column-validator-utils.test.ts @@ -0,0 +1,52 @@ +import { expect } from 'chai'; +import { + generateColumnCellGetterFromColumnValidator, + getColumnAliasesFromValidator, + getColumnNamesFromValidator +} from './column-validator-utils'; +import { IXLSXCSVValidator } from './worksheet-utils'; + +const columnValidator = { + NAME: { type: 'string' }, + ID: { type: 'number', aliases: ['IDENTIFIER'] }, + AGE: { type: 'number' }, + BIRTH_DATE: { type: 'date' } +} satisfies IXLSXCSVValidator; + +describe('column-validator-utils', () => { + describe('getColumnNamesFromValidator', () => { + it('should return all column names from validator', () => { + expect(getColumnNamesFromValidator(columnValidator)).to.be.eql(['NAME', 'ID', 'AGE', 'BIRTH_DATE']); + }); + }); + + describe('getColumnAliasesFromValidator', () => { + it('should return all column aliases from validator', () => { + expect(getColumnAliasesFromValidator(columnValidator)).to.be.eql(['IDENTIFIER']); + }); + }); + + describe('generateColumnCellGetterFromColumnValidator', () => { + const getCellValue = generateColumnCellGetterFromColumnValidator(columnValidator); + + it('should return the cell value for a known column name', () => { + expect(getCellValue({ NAME: 'Dr. Steve Brule' }, 'NAME').cell).to.be.eql('Dr. Steve Brule'); + }); + + it('should return the cell value for a known alias name', () => { + expect(getCellValue({ IDENTIFIER: 1 }, 'ID').cell).to.be.eql(1); + }); + + it('should return undefined if row cannot find cell value', () => { + expect(getCellValue({ BAD_NAME: 1 }, 'NAME').cell).to.be.eql(undefined); + }); + + it('should return column name', () => { + expect(getCellValue({ NAME: 1 }, 'NAME').column).to.be.eql('NAME'); + }); + + it('should return column alias name', () => { + expect(getCellValue({ IDENTIFIER: 1 }, 'ID').column).to.be.eql('IDENTIFIER'); + }); + }); +}); diff --git a/api/src/utils/xlsx-utils/column-validator-utils.ts b/api/src/utils/xlsx-utils/column-validator-utils.ts new file mode 100644 index 0000000000..c1f4ff5384 --- /dev/null +++ b/api/src/utils/xlsx-utils/column-validator-utils.ts @@ -0,0 +1,94 @@ +import { Row } from '../../services/import-services/import-csv.interface'; +import { IXLSXCSVColumn, IXLSXCSVValidator } from './worksheet-utils'; + +// TODO: Move the IXLSXCSVValidator type to this file + +/** + * Get column names / headers from column validator. + * + * Note: This actually returns Uppercase[] but for convenience we define the return as string[] + * + * @param {IXLSXCSVValidator} columnValidator + * @returns {*} {string[]} Column names / headers + */ +export const getColumnNamesFromValidator = (columnValidator: IXLSXCSVValidator): string[] => { + return Object.keys(columnValidator); +}; + +/** + * Get flattened list of ALL column aliases from column validator. + * + * Note: This actually returns Uppercase[] but for convenience we define the return as string[] + * + * @param {IXLSXCSVValidator} columnValidator + * @returns {*} {string[]} Column aliases + */ +export const getColumnAliasesFromValidator = (columnValidator: IXLSXCSVValidator): string[] => { + const columnNames = getColumnNamesFromValidator(columnValidator); + + // Return flattened list of column validator aliases + return columnNames.flatMap((columnName) => (columnValidator[columnName] as IXLSXCSVColumn).aliases ?? []); +}; + +/** + * Get column validator specification as a readable format. Useful for error handling and logging. + * + * @param {IXLSXCSVValidator} columnValidator - Standard column validator + * @returns {*} + */ +export const getColumnValidatorSpecification = (columnValidator: IXLSXCSVValidator) => { + // Expected formats of date/time columns + + return Object.keys(columnValidator).map((columnName) => { + const columnSpec: IXLSXCSVColumn = columnValidator[columnName]; + return { + columnName: columnName, + columnType: columnSpec.type, + columnAliases: columnSpec.aliases, + optional: columnSpec.optional + }; + }); +}; + +/** + * Generate a column + cell getter from a column validator. + * + * Note: This will attempt to retrive the column header and cell value from the row by the known header first. + * If not found, it will then attempt to retrieve the value by the column header aliases. + * + * @example + * const getColumnCell = generateColumnCellGetterFromColumnValidator(columnValidator) + * + * const itis_tsn = getColumnCell(row, 'ITIS_TSN').cell + * const tsnColumn = getColumnCell(row, 'ITIS_TSN').column + * + * @template T + * @param {T} columnValidator - Column validator + * @returns {*} + */ +export const generateColumnCellGetterFromColumnValidator = (columnValidator: T) => { + return (row: Row, validatorKey: keyof T): { column: string; cell: J | undefined } => { + // Cast the columnValidatorKey to a string for convienience + const key = validatorKey as string; + + // Attempt to retrieve the column and cell value from the default column name + if (row[key]) { + return { column: key, cell: row[key] }; + } + + const columnSpec = columnValidator[validatorKey] as IXLSXCSVColumn; + + // Get the column aliases + const aliases = columnSpec.aliases ?? []; + + // Loop through the aliases and attempt to retrieve the column and cell value + for (const alias of aliases) { + if (row[alias]) { + return { column: alias, cell: row[alias] }; + } + } + + // Returning the provided key when no match + return { column: key, cell: undefined }; + }; +}; diff --git a/api/src/utils/xlsx-utils/worksheet-utils.test.ts b/api/src/utils/xlsx-utils/worksheet-utils.test.ts index f358b99c3e..067e1c9063 100644 --- a/api/src/utils/xlsx-utils/worksheet-utils.test.ts +++ b/api/src/utils/xlsx-utils/worksheet-utils.test.ts @@ -5,43 +5,43 @@ import xlsx from 'xlsx'; import { IXLSXCSVValidator } from '../xlsx-utils/worksheet-utils'; import * as worksheet_utils from './worksheet-utils'; +const xlsxWorksheet: xlsx.WorkSheet = { + A1: { t: 's', v: 'Species' }, + B1: { t: 's', v: 'Count' }, + C1: { t: 's', v: 'Date' }, + D1: { t: 's', v: 'Time' }, + E1: { t: 's', v: 'Latitude' }, + F1: { t: 's', v: 'Longitude' }, + G1: { t: 's', v: 'Antler Configuration' }, + H1: { t: 's', v: 'Wind Direction' }, + A2: { t: 'n', w: '180703', v: 180703 }, + B2: { t: 'n', w: '1', v: 1 }, + C2: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, + D2: { t: 's', v: '9:01' }, + E2: { t: 'n', w: '-58', v: -58 }, + F2: { t: 'n', w: '-123', v: -123 }, + G2: { t: 's', v: 'more than 3 points' }, + H2: { t: 's', v: 'North' }, + A3: { t: 'n', w: '180596', v: 180596 }, + B3: { t: 'n', w: '2', v: 2 }, + C3: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, + D3: { t: 's', v: '9:02' }, + E3: { t: 'n', w: '-57', v: -57 }, + F3: { t: 'n', w: '-122', v: -122 }, + H3: { t: 's', v: 'North' }, + A4: { t: 'n', w: '180713', v: 180713 }, + B4: { t: 'n', w: '3', v: 3 }, + C4: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, + D4: { t: 's', v: '9:03' }, + E4: { t: 'n', w: '-56', v: -56 }, + F4: { t: 'n', w: '-121', v: -121 }, + H4: { t: 's', v: 'North' }, + '!ref': 'A1:H9' +}; + describe('worksheet-utils', () => { describe('getHeadersUpperCase', () => { it('returns the column headers in UPPERCASE', () => { - const xlsxWorksheet: xlsx.WorkSheet = { - A1: { t: 's', v: 'Species' }, - B1: { t: 's', v: 'Count' }, - C1: { t: 's', v: 'Date' }, - D1: { t: 's', v: 'Time' }, - E1: { t: 's', v: 'Latitude' }, - F1: { t: 's', v: 'Longitude' }, - G1: { t: 's', v: 'Antler Configuration' }, - H1: { t: 's', v: 'Wind Direction' }, - A2: { t: 'n', w: '180703', v: 180703 }, - B2: { t: 'n', w: '1', v: 1 }, - C2: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, - D2: { t: 's', v: '9:01' }, - E2: { t: 'n', w: '-58', v: -58 }, - F2: { t: 'n', w: '-123', v: -123 }, - G2: { t: 's', v: 'more than 3 points' }, - H2: { t: 's', v: 'North' }, - A3: { t: 'n', w: '180596', v: 180596 }, - B3: { t: 'n', w: '2', v: 2 }, - C3: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, - D3: { t: 's', v: '9:02' }, - E3: { t: 'n', w: '-57', v: -57 }, - F3: { t: 'n', w: '-122', v: -122 }, - H3: { t: 's', v: 'North' }, - A4: { t: 'n', w: '180713', v: 180713 }, - B4: { t: 'n', w: '3', v: 3 }, - C4: { z: 'm/d/yy', t: 'd', v: '1970-01-01T08:00:00.000Z', w: '1/1/70' }, - D4: { t: 's', v: '9:03' }, - E4: { t: 'n', w: '-56', v: -56 }, - F4: { t: 'n', w: '-121', v: -121 }, - H4: { t: 's', v: 'North' }, - '!ref': 'A1:H9' - }; - const result = worksheet_utils.getHeadersUpperCase(xlsxWorksheet); expect(result).to.eql([ @@ -64,13 +64,56 @@ describe('worksheet-utils', () => { it('should validate aliases', () => { const observationCSVColumnValidator: IXLSXCSVValidator = { - columnNames: ['SPECIES', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'], - columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'], - columnAliases: { - LATITUDE: ['LAT'], - LONGITUDE: ['LON', 'LONG', 'LNG'], - SPECIES: ['TAXON'] - } + SPECIES: { type: 'string', aliases: ['TAXON'] }, + COUNT: { type: 'number' }, + DATE: { type: 'string' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: ['LAT'] }, + LONGITUDE: { type: 'number', aliases: ['LON', 'LONG', 'LNG'] } + }; + + const mockWorksheet = {} as unknown as xlsx.WorkSheet; + + const getHeadersUpperCaseStub = sinon + .stub(worksheet_utils, 'getHeadersUpperCase') + .callsFake(() => ['TAXON', 'COUNT', 'DATE', 'TIME', 'LAT', 'LON']); + + const result = worksheet_utils.validateWorksheetHeaders(mockWorksheet, observationCSVColumnValidator); + + expect(getHeadersUpperCaseStub).to.be.calledOnce; + expect(result).to.equal(true); + }); + + it('should validate for missing optional headers', () => { + const observationCSVColumnValidator: IXLSXCSVValidator = { + SPECIES: { type: 'string', aliases: ['TAXON'], optional: true }, + COUNT: { type: 'number', optional: true }, + DATE: { type: 'string' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: ['LAT'] }, + LONGITUDE: { type: 'number', aliases: ['LON', 'LONG', 'LNG'] } + }; + + const mockWorksheet = {} as unknown as xlsx.WorkSheet; + + const getHeadersUpperCaseStub = sinon + .stub(worksheet_utils, 'getHeadersUpperCase') + .callsFake(() => ['DATE', 'TIME', 'LAT', 'LON']); + + const result = worksheet_utils.validateWorksheetHeaders(mockWorksheet, observationCSVColumnValidator); + + expect(getHeadersUpperCaseStub).to.be.calledOnce; + expect(result).to.equal(true); + }); + + it('should succeed for header thats optional but provided', () => { + const observationCSVColumnValidator: IXLSXCSVValidator = { + SPECIES: { type: 'string', aliases: ['TAXON'], optional: true }, + COUNT: { type: 'number' }, + DATE: { type: 'string' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: ['LAT'] }, + LONGITUDE: { type: 'number', aliases: ['LON', 'LONG', 'LNG'] } }; const mockWorksheet = {} as unknown as xlsx.WorkSheet; @@ -87,12 +130,12 @@ describe('worksheet-utils', () => { it('should fail for unknown aliases', () => { const observationCSVColumnValidator: IXLSXCSVValidator = { - columnNames: ['SPECIES', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'], - columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'], - columnAliases: { - LATITUDE: ['LAT'], - LONGITUDE: ['LON', 'LONG', 'LNG'] - } + SPECIES: { type: 'string', aliases: ['TAXON'] }, + COUNT: { type: 'number' }, + DATE: { type: 'string' }, + TIME: { type: 'string' }, + LATITUDE: { type: 'number', aliases: ['LAT'] }, + LONGITUDE: { type: 'number', aliases: ['LON', 'LONG', 'LNG'] } }; const mockWorksheet = {} as unknown as xlsx.WorkSheet; diff --git a/api/src/utils/xlsx-utils/worksheet-utils.ts b/api/src/utils/xlsx-utils/worksheet-utils.ts index 45b68e460b..2023fb46af 100644 --- a/api/src/utils/xlsx-utils/worksheet-utils.ts +++ b/api/src/utils/xlsx-utils/worksheet-utils.ts @@ -1,35 +1,48 @@ import { default as dayjs } from 'dayjs'; +import customParseFormat from 'dayjs/plugin/customParseFormat'; +import { intersection, isUndefined } from 'lodash'; import xlsx, { CellObject } from 'xlsx'; import { getLogger } from '../logger'; import { MediaFile } from '../media/media-file'; import { DEFAULT_XLSX_SHEET_NAME } from '../media/xlsx/xlsx-file'; import { safeToLowerCase } from '../string-utils'; import { replaceCellDates, trimCellWhitespace } from './cell-utils'; +import { + generateColumnCellGetterFromColumnValidator, + getColumnAliasesFromValidator, + getColumnNamesFromValidator +} from './column-validator-utils'; + +dayjs.extend(customParseFormat); const defaultLog = getLogger('src/utils/xlsx-utils/worksheet-utils'); -export interface IXLSXCSVValidator { +export interface IXLSXCSVColumn { /** - * Uppercase column headers - * - * @see column-cell-utils.ts + * Supported column cell types * + * time: HH:mm:ss */ - columnNames: Uppercase[]; + type: 'string' | 'number' | 'date'; /** - * Supported column cell types + * Allowed aliases / mappings for column headers. * */ - columnTypes: Array<'string' | 'number' | 'date'>; + aliases?: Uppercase[]; /** - * Allowed aliases / mappings for column headers. + * Column is optional. * */ - columnAliases?: Record, Uppercase[]>; + optional?: true; +} + +// Record with column name and column spec +export interface IXLSXCSVValidator { + [columnName: Uppercase]: IXLSXCSVColumn; } /** - * Returns true if the given cell is a date type cell. + * Construct the XLSX workbook. * * @export * @param {MediaFile} file @@ -195,15 +208,21 @@ export const getWorksheetRowObjects = (worksheet: xlsx.WorkSheet): Record { - const { columnNames, columnAliases } = columnValidator; + // Get column names and aliases from validator + const validatorHeaders = getColumnNamesFromValidator(columnValidator); + // Get column names from actual worksheet const worksheetHeaders = getHeadersUpperCase(worksheet); - return columnNames.every((expectedHeader) => { - return ( - columnAliases?.[expectedHeader]?.some((alias) => worksheetHeaders.includes(alias)) || - worksheetHeaders.includes(expectedHeader) - ); + // Check that every validator header has matching header or alias in worksheet + return validatorHeaders.every((header) => { + const columnSpec = columnValidator[header as keyof typeof columnValidator]; + + const aliases = columnSpec?.aliases ?? []; + const columnHeaderAndAliases = [header, ...aliases]; + + // All column headers exist or only missing optional headers + return intersection(columnHeaderAndAliases, worksheetHeaders).length || columnSpec.optional; }); }; @@ -219,22 +238,44 @@ export const validateWorksheetColumnTypes = ( worksheet: xlsx.WorkSheet, columnValidator: IXLSXCSVValidator ): boolean => { - const rowValueTypes: string[] = columnValidator.columnTypes; - const worksheetRows = getWorksheetRows(worksheet); + const worksheetRows = getWorksheetRowObjects(worksheet); + const columnNames = getColumnNamesFromValidator(columnValidator); + const getCellValue = generateColumnCellGetterFromColumnValidator(columnValidator); return worksheetRows.every((row) => { - return Object.values(columnValidator.columnNames).every((_, index) => { - const value = row[index]; + return columnNames.every((columnName, index) => { + const value = getCellValue(row, columnName.toUpperCase() as Uppercase).cell; const type = typeof value; - if (rowValueTypes[index] === 'date') { - return dayjs(value).isValid(); + const columnSpec: IXLSXCSVColumn = columnValidator[columnName]; + + let validated = false; + + if (columnSpec.type === 'date') { + validated = dayjs(value).isValid(); + } + + if (columnSpec.type === type) { + validated = true; + } + + // Undefined values only allowed if column spec is set to optional + if (isUndefined(value)) { + validated = Boolean(columnSpec.optional); } - if (rowValueTypes[index] === type) { - return true; + if (!validated) { + defaultLog.debug({ + label: 'validateWorksheetColumnTypes', + details: { + columnName, + columnType: columnSpec.type, + cellValue: value, + rowIndex: index + } + }); } - return false; + return validated; }); }); }; @@ -280,13 +321,16 @@ export const getWorksheetRange = (worksheet: xlsx.WorkSheet): xlsx.Range | undef return xlsx.utils.decode_range(ref); }; + /** * Iterates over the cells in the worksheet and: * - Trims whitespace from cell values. * - Converts `Date` objects to ISO strings. * * https://stackoverflow.com/questions/61789174/how-can-i-remove-all-the-spaces-in-the-cells-of-excelsheet-using-nodejs-code - * @param worksheet + * + * @param {xlsx.WorkSheet} worksheet + * @returns {xlsx.WorkSheet} */ export const prepareWorksheetCells = (worksheet: xlsx.WorkSheet) => { const range = getWorksheetRange(worksheet); @@ -305,11 +349,14 @@ export const prepareWorksheetCells = (worksheet: xlsx.WorkSheet) => { continue; } + // Replace date and time cells cell = replaceCellDates(cell); cell = trimCellWhitespace(cell); } } + + return worksheet; }; /** @@ -349,16 +396,13 @@ export function getNonStandardColumnNamesFromWorksheet( ): string[] { const columns = getHeadersUpperCase(xlsxWorksheet); - let aliasColumns: string[] = []; - - // Create a list of all column names and aliases - if (columnValidator.columnAliases) { - aliasColumns = Object.values(columnValidator.columnAliases).flat(); - } + // Get column headers and aliases + const columnValidatorHeaders = getColumnNamesFromValidator(columnValidator); + const columnValidatorAliases = getColumnAliasesFromValidator(columnValidator); // Combine the column validator headers and all aliases - const standardColumNames = [...columnValidator.columnNames, ...aliasColumns]; + const standardColumnNames = new Set([...columnValidatorHeaders, ...columnValidatorAliases]); // Only return column names not in the validation CSV Column validator (ie: only return the non-standard columns) - return columns.filter((column) => !standardColumNames.includes(column)); + return columns.filter((column) => !standardColumnNames.has(column)); } diff --git a/app/.docker/app/Dockerfile b/app/.docker/app/Dockerfile index e77e9cf6f9..2b4f6e4c55 100644 --- a/app/.docker/app/Dockerfile +++ b/app/.docker/app/Dockerfile @@ -1,5 +1,5 @@ # ######################################################################################################## -# This DockerFile is used for local development (via docker-compose) only. +# This DockerFile is used for local development (via compose.yml) only. # ######################################################################################################## FROM node:20 diff --git a/app/.pipeline/config.js b/app/.pipeline/config.js index dc8b453bc6..df25c0403c 100644 --- a/app/.pipeline/config.js +++ b/app/.pipeline/config.js @@ -121,6 +121,33 @@ const phases = { biohubTaxonPath: '/api/taxonomy/taxon', biohubTaxonTsnPath: '/api/taxonomy/taxon/tsn' }, + 'test-spi': { + namespace: 'af2668-test', + name: `${name}-spi`, + phase: 'test-spi', + changeId: deployChangeId, + suffix: `-test-spi`, + instance: `${name}-test-spi`, + version: `${version}`, + tag: `test-spi-${version}`, + host: staticUrls['test-spi'], + apiHost: staticUrlsAPI['test-spi'], + siteminderLogoutURL: config.siteminderLogoutURL['test-spi'], + maxUploadNumFiles, + maxUploadFileSize, + nodeEnv: 'production', + sso: config.sso['test-spi'], + featureFlags: '', + cpuRequest: '50m', + cpuLimit: '500m', + memoryRequest: '100Mi', + memoryLimit: '500Mi', + replicas: '2', + replicasMax: '2', + backbonePublicApiHost: 'https://api-test-biohub-platform.apps.silver.devops.gov.bc.ca', + biohubTaxonPath: '/api/taxonomy/taxon', + biohubTaxonTsnPath: '/api/taxonomy/taxon/tsn' + }, prod: { namespace: 'af2668-prod', name: `${name}`, diff --git a/app/.vscode/settings.json b/app/.vscode/settings.json index 65a1965328..5e59a3ee78 100644 --- a/app/.vscode/settings.json +++ b/app/.vscode/settings.json @@ -1,3 +1,4 @@ { + "typescript.preferences.importModuleSpecifier": "non-relative", "editor.defaultFormatter": "esbenp.prettier-vscode" } diff --git a/app/package-lock.json b/app/package-lock.json index 7aeb9f5dd4..f114441c7b 100644 --- a/app/package-lock.json +++ b/app/package-lock.json @@ -30,6 +30,7 @@ "@turf/center-of-mass": "^6.5.0", "@turf/centroid": "^6.5.0", "@turf/truncate": "^6.5.0", + "ajv": "^8.16.0", "axios": "^1.6.8", "dayjs": "^1.11.10", "express": "^4.19.2", @@ -55,7 +56,7 @@ "react-router-dom": "^5.3.3", "react-window": "^1.8.6", "request": "^2.88.2", - "shpjs": "^3.6.3", + "shpjs": "^5.0.2", "typescript": "^4.7.4", "uuid": "^8.3.2", "yup": "^0.32.9" @@ -81,7 +82,7 @@ "@types/react-router": "^5.1.20", "@types/react-router-dom": "^5.3.3", "@types/react-window": "^1.8.2", - "@types/shpjs": "^3.4.0", + "@types/shpjs": "^3.4.7", "@types/uuid": "^8.3.0", "@typescript-eslint/eslint-plugin": "~7.6.0", "@typescript-eslint/parser": "~7.6.0", @@ -108,19 +109,10 @@ "npm": ">= 10.0.0" } }, - "node_modules/@aashutoshrathi/word-wrap": { - "version": "1.2.6", - "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", - "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==", - "dev": true, - "engines": { - "node": ">=0.10.0" - } - }, "node_modules/@adobe/css-tools": { - "version": "4.3.3", - "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.3.tgz", - "integrity": "sha512-rE0Pygv0sEZ4vBWHlAgJLGDU7Pm8xoO6p3wsEceb7GYAjScrOHpEo8KK/eVkAcnSM+slAEtXjA2JpdjLp4fJQQ==", + "version": "4.4.0", + "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.4.0.tgz", + "integrity": "sha512-Ff9+ksdQQB3rMncgqDK78uLznstjyfIf2Arnh22pW8kBpLs6rpKDwgnZT46hin5Hl1WzazzK64DOrhSwYpS7bQ==", "dev": true }, "node_modules/@alloc/quick-lru": { @@ -147,12 +139,29 @@ "node": ">=6.0.0" } }, + "node_modules/@apideck/better-ajv-errors": { + "version": "0.3.6", + "resolved": "https://registry.npmjs.org/@apideck/better-ajv-errors/-/better-ajv-errors-0.3.6.tgz", + "integrity": "sha512-P+ZygBLZtkp0qqOAJJVX4oX/sFo5JR3eBWwwuqHHhK0GIgQOKWrAfiAaWX0aArHkRWHMuggFEgAZNxVPwPZYaA==", + "dev": true, + "dependencies": { + "json-schema": "^0.4.0", + "jsonpointer": "^5.0.0", + "leven": "^3.1.0" + }, + "engines": { + "node": ">=10" + }, + "peerDependencies": { + "ajv": ">=8" + } + }, "node_modules/@babel/code-frame": { - 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} - }, "node_modules/workbox-build/node_modules/fs-extra": { "version": "9.1.0", "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-9.1.0.tgz", @@ -26392,12 +26049,6 @@ "node": ">=10" } }, - "node_modules/workbox-build/node_modules/json-schema-traverse": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz", - "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==", - "dev": true - }, "node_modules/workbox-build/node_modules/source-map": { "version": "0.8.0-beta.0", "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.8.0-beta.0.tgz", @@ -26716,9 +26367,9 @@ } }, "node_modules/ws": { - "version": "8.16.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.16.0.tgz", - "integrity": "sha512-HS0c//TP7Ina87TfiPUz1rQzMhHrl/SG2guqRcTOIUYD2q8uhUdNHZYJUaQ8aTGPzCh+c6oawMKW35nFl1dxyQ==", + "version": "8.18.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", + "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", "dev": true, "engines": { "node": ">=10.0.0" diff --git a/app/package.json b/app/package.json index 95b9e6668a..05208cad7d 100644 --- a/app/package.json +++ b/app/package.json @@ -46,6 +46,7 @@ "@turf/center-of-mass": "^6.5.0", "@turf/centroid": "^6.5.0", "@turf/truncate": "^6.5.0", + "ajv": "^8.16.0", "axios": "^1.6.8", "dayjs": "^1.11.10", "express": "^4.19.2", @@ -71,7 +72,7 @@ "react-router-dom": "^5.3.3", "react-window": "^1.8.6", "request": "^2.88.2", - "shpjs": "^3.6.3", + "shpjs": "^5.0.2", "typescript": "^4.7.4", "uuid": "^8.3.2", "yup": "^0.32.9" @@ -97,7 +98,7 @@ "@types/react-router": "^5.1.20", "@types/react-router-dom": "^5.3.3", "@types/react-window": "^1.8.2", - "@types/shpjs": "^3.4.0", + "@types/shpjs": "^3.4.7", "@types/uuid": "^8.3.0", "@typescript-eslint/eslint-plugin": "~7.6.0", "@typescript-eslint/parser": "~7.6.0", diff --git a/app/server/index.js b/app/server/index.js index 020eeb4532..bb903d2809 100644 --- a/app/server/index.js +++ b/app/server/index.js @@ -28,7 +28,7 @@ const request = require('request'); * This includes a health check endpoint that OpenShift uses to determine if the app is healthy. * * This file is only used when serving the app in OpenShift. - * When running the app locally, the app is served by docker-compose, and doesn't use this file at all. + * When running the app locally, the app is served by compose.yml, and doesn't use this file at all. * * Note: All changes to env vars here must also be reflected in the `app/src/contexts/configContext.tsx` file, so that * the app has access to the same env vars when running in both OpenShift and local development. diff --git a/app/src/App.tsx b/app/src/App.tsx index a22693d7ea..3097514ba3 100644 --- a/app/src/App.tsx +++ b/app/src/App.tsx @@ -28,6 +28,8 @@ const App = () => { authority: `${config.KEYCLOAK_CONFIG.authority}/realms/${config.KEYCLOAK_CONFIG.realm}/`, client_id: config.KEYCLOAK_CONFIG.clientId, resource: config.KEYCLOAK_CONFIG.clientId, + // Automatically renew the access token before it expires + automaticSilentRenew: true, // Default sign in redirect redirect_uri: buildUrl(window.location.origin), // Default sign out redirect diff --git a/app/src/AppRouter.tsx b/app/src/AppRouter.tsx index 4728f20175..5e09060113 100644 --- a/app/src/AppRouter.tsx +++ b/app/src/AppRouter.tsx @@ -6,7 +6,7 @@ import AdminUsersRouter from 'features/admin/AdminUsersRouter'; import FundingSourcesRouter from 'features/funding-sources/FundingSourcesRouter'; import ProjectsRouter from 'features/projects/ProjectsRouter'; import ResourcesPage from 'features/resources/ResourcesPage'; -import SpeciesStandardsPage from 'features/standards/SpeciesStandardsPage'; +import StandardsPage from 'features/standards/StandardsPage'; import SummaryRouter from 'features/summary/SummaryRouter'; import BaseLayout from 'layouts/BaseLayout'; import AccessDenied from 'pages/403/AccessDenied'; @@ -83,7 +83,9 @@ const AppRouter: React.FC = () => { - + + + @@ -112,7 +114,7 @@ const AppRouter: React.FC = () => { - + diff --git a/app/src/components/accordion/AccordionCard.tsx b/app/src/components/accordion/AccordionCard.tsx deleted file mode 100644 index 2a604276b7..0000000000 --- a/app/src/components/accordion/AccordionCard.tsx +++ /dev/null @@ -1,92 +0,0 @@ -import { mdiChevronDown, mdiDotsVertical } from '@mdi/js'; -import { Icon } from '@mdi/react'; -import Accordion from '@mui/material/Accordion'; -import AccordionDetails from '@mui/material/AccordionDetails'; -import AccordionSummary from '@mui/material/AccordionSummary'; -import Box from '@mui/material/Box'; -import IconButton from '@mui/material/IconButton'; -import Paper from '@mui/material/Paper'; - -interface IAccordionCardProps { - /** - * The content to display in the non-collapsible portion of the card. - */ - summaryContent: JSX.Element; - /** - * The content to display in the collapsible portion of the card, when expanded. - */ - detailsContent: JSX.Element; - /** - * Callback for when the menu button is clicked. - * If not provided, the menu button will not be rendered. - */ - onMenuClick?: (event: React.MouseEvent) => void; - /** - * Icon to display in the menu button. - * Defaults to three vertical dots. - */ - menuIcon?: JSX.Element; - /** - * If true, the accordion will be expanded by default. - */ - expanded?: boolean; -} - -/** - * General purpose accordion card component. - * - * @param {IAccordionCardProps} props - * @return {*} - */ -export const AccordionCard = (props: IAccordionCardProps) => { - const { summaryContent, detailsContent, onMenuClick, menuIcon, expanded } = props; - - return ( - - - } - aria-controls="panel1bh-content" - sx={{ - flex: '1 1 auto', - mr: 1, - pr: 8.5, - minHeight: 55, - overflow: 'hidden', - border: 0, - '& .MuiAccordionSummary-content': { - flex: '1 1 auto', - py: 0, - pl: 0, - overflow: 'hidden', - whiteSpace: 'nowrap' - } - }}> - {summaryContent} - - {onMenuClick && ( - - {menuIcon || } - - )} - - {detailsContent} - - ); -}; diff --git a/app/src/components/alert/FormikErrorSnackbar.tsx b/app/src/components/alert/FormikErrorSnackbar.tsx index b62d93cb0f..97d749ff18 100644 --- a/app/src/components/alert/FormikErrorSnackbar.tsx +++ b/app/src/components/alert/FormikErrorSnackbar.tsx @@ -4,6 +4,23 @@ import { useFormikContext } from 'formik'; import { useEffect, useState } from 'react'; import { logIfDevelopment } from 'utils/developer-utils'; +/** + * Plug-and-play Formik error snackbar component. + * + * Adds a snackbar that displays when there are form validation errors. + * + * Additionally, when in NODE_ENV=development, logs the formik values and errors to the console. + * + * @example + * ```tsx + * + * + *
+ * + * ``` + * + * @return {*} + */ const FormikErrorSnackbar = () => { const formikProps = useFormikContext(); const { values, errors, submitCount, isSubmitting } = formikProps; diff --git a/app/src/components/attachments/FileUploadWithMeta.tsx b/app/src/components/attachments/FileUploadWithMeta.tsx index c16676baa6..7d7574a94c 100644 --- a/app/src/components/attachments/FileUploadWithMeta.tsx +++ b/app/src/components/attachments/FileUploadWithMeta.tsx @@ -8,12 +8,12 @@ import { IUploadHandler, UploadFileStatus } from 'components/file-upload/FileUploadItem'; -import { AttachmentType, ProjectSurveyAttachmentValidExtensions } from 'constants/attachments'; +import { AttachmentType, AttachmentTypeFileExtensions } from 'constants/attachments'; import { useFormikContext } from 'formik'; import React from 'react'; export interface IFileUploadWithMetaProps { - attachmentType: AttachmentType.REPORT | AttachmentType.KEYX | AttachmentType.OTHER; + attachmentType: AttachmentType.REPORT | AttachmentType.KEYX | AttachmentType.CFG | AttachmentType.OTHER; uploadHandler: IUploadHandler; fileHandler?: IFileHandler; onSuccess?: IOnUploadSuccess; @@ -52,7 +52,7 @@ export const FileUploadWithMeta: React.FC = (props) => dropZoneProps={{ maxNumFiles: 1, multiple: false, - acceptedFileExtensions: ProjectSurveyAttachmentValidExtensions.REPORT + acceptedFileExtensions: AttachmentTypeFileExtensions.REPORT }} status={UploadFileStatus.STAGED} replace={true} @@ -71,7 +71,7 @@ export const FileUploadWithMeta: React.FC = (props) => fileHandler={fileHandler} onSuccess={props.onSuccess} dropZoneProps={{ - acceptedFileExtensions: ProjectSurveyAttachmentValidExtensions.KEYX + acceptedFileExtensions: AttachmentTypeFileExtensions.KEYX }} enableErrorDetails={true} /> diff --git a/app/src/components/chips/AccessStatusChip.tsx b/app/src/components/chips/AccessStatusChip.tsx index 111240bf07..c9ca012592 100644 --- a/app/src/components/chips/AccessStatusChip.tsx +++ b/app/src/components/chips/AccessStatusChip.tsx @@ -9,15 +9,18 @@ const useStyles = () => { return { chipPending: { color: '#fff', - backgroundColor: theme.palette.error.main + backgroundColor: theme.palette.error.main, + userSelect: 'none' }, chipActioned: { color: '#fff', - backgroundColor: theme.palette.success.main + backgroundColor: theme.palette.success.main, + userSelect: 'none' }, chipRejected: { color: '#fff', - backgroundColor: theme.palette.error.main + backgroundColor: theme.palette.error.main, + userSelect: 'none' } }; }; diff --git a/app/src/components/chips/ColouredRectangleChip.tsx b/app/src/components/chips/ColouredRectangleChip.tsx index 8cc7716d45..9baf0282f0 100644 --- a/app/src/components/chips/ColouredRectangleChip.tsx +++ b/app/src/components/chips/ColouredRectangleChip.tsx @@ -27,7 +27,8 @@ const ColouredRectangleChip = (props: IColouredRectangleChipProps) => { fontSize: '0.75rem', p: 1, textTransform: 'uppercase' - } + }, + ...props.sx }} /> ); diff --git a/app/src/components/data-grid/GenericGridColumnDefinitions.tsx b/app/src/components/data-grid/GenericGridColumnDefinitions.tsx index e6711ec818..f432551087 100644 --- a/app/src/components/data-grid/GenericGridColumnDefinitions.tsx +++ b/app/src/components/data-grid/GenericGridColumnDefinitions.tsx @@ -1,8 +1,5 @@ -import { mdiTrashCanOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import IconButton from '@mui/material/IconButton'; import Typography from '@mui/material/Typography'; -import { GridCellParams, GridColDef, GridRowParams, GridValidRowModel } from '@mui/x-data-grid'; +import { GridCellParams, GridColDef, GridValidRowModel } from '@mui/x-data-grid'; import TextFieldDataGrid from 'components/data-grid/TextFieldDataGrid'; import TimePickerDataGrid from 'components/data-grid/TimePickerDataGrid'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; @@ -13,13 +10,15 @@ import { getFormattedDate } from 'utils/Utils'; export const GenericDateColDef = (props: { field: string; headerName: string; + description?: string; hasError: (params: GridCellParams) => boolean; }): GridColDef => { - const { field, headerName, hasError } = props; + const { field, headerName, hasError, description } = props; return { field, headerName, + description: description ?? undefined, editable: true, hideable: true, type: 'date', @@ -62,15 +61,17 @@ export const GenericDateColDef = (props: { export const GenericTimeColDef = (props: { field: string; headerName: string; + description?: string; hasError: (params: GridCellParams) => boolean; }): GridColDef => { - const { hasError, field, headerName } = props; + const { hasError, field, headerName, description } = props; return { field, headerName, editable: true, hideable: true, + description: description ?? undefined, type: 'string', width: 150, disableColumnMenu: true, @@ -124,13 +125,15 @@ export const GenericTimeColDef = (props: { export const GenericLatitudeColDef = (props: { field: string; headerName: string; + description?: string; hasError: (params: GridCellParams) => boolean; }): GridColDef => { - const { hasError, field, headerName } = props; + const { hasError, field, headerName, description } = props; return { field, headerName, + description: description ?? undefined, editable: true, hideable: true, width: 120, @@ -183,13 +186,15 @@ export const GenericLatitudeColDef = (props: { export const GenericLongitudeColDef = (props: { field: string; headerName: string; + description?: string; hasError: (params: GridCellParams) => boolean; }): GridColDef => { - const { hasError, field, headerName } = props; + const { hasError, field, headerName, description } = props; return { field, headerName, + description: description ?? undefined, editable: true, hideable: true, width: 120, @@ -238,29 +243,3 @@ export const GenericLongitudeColDef = (props: { } }; }; - -export const GenericActionsColDef = (props: { - disabled: boolean | ((params: GridRowParams) => boolean); - onDelete: (records: T[]) => void; -}): GridColDef => { - return { - field: 'actions', - headerName: '', - type: 'actions', - width: 70, - disableColumnMenu: true, - align: 'right', - resizable: false, - cellClassName: 'pinnedColumn', - getActions: (params) => [ - { - props.onDelete([params.row]); - }} - disabled={typeof props.disabled === 'function' ? props.disabled(params) : props.disabled} - key={`actions[${params.id}].handleDeleteRow`}> - - - ] - }; -}; diff --git a/app/src/components/data-grid/StyledDataGrid.tsx b/app/src/components/data-grid/StyledDataGrid.tsx index ba283d3a8c..566f929745 100644 --- a/app/src/components/data-grid/StyledDataGrid.tsx +++ b/app/src/components/data-grid/StyledDataGrid.tsx @@ -49,9 +49,21 @@ export const StyledDataGrid = (props: StyledD '& .MuiDataGrid-columnHeader:last-of-type, .MuiDataGrid-cell:last-of-type': { pr: 2 }, - '&.MuiDataGrid-root--densityCompact .MuiDataGrid-cell': { py: '8px' }, - '&.MuiDataGrid-root--densityStandard .MuiDataGrid-cell': { py: '15px' }, - '&.MuiDataGrid-root--densityComfortable .MuiDataGrid-cell': { py: '22px' }, + '&.MuiDataGrid-root--densityCompact .MuiDataGrid-cell': { + py: '8px', + wordWrap: 'anywhere' + }, + '&.MuiDataGrid-root--densityStandard .MuiDataGrid-cell': { + py: '15px', + wordWrap: 'anywhere' + }, + '&.MuiDataGrid-root--densityComfortable .MuiDataGrid-cell': { + py: '22px', + wordWrap: 'anywhere' + }, + '& .MuiDataGrid-columnHeaderDraggableContainer': { + minWidth: '50px' + }, ...props.sx }} /> diff --git a/app/src/components/data-grid/autocomplete/AsyncAutocompleteDataGridEditCell.tsx b/app/src/components/data-grid/autocomplete/AsyncAutocompleteDataGridEditCell.tsx index a46027a4c2..91a244b3b9 100644 --- a/app/src/components/data-grid/autocomplete/AsyncAutocompleteDataGridEditCell.tsx +++ b/app/src/components/data-grid/autocomplete/AsyncAutocompleteDataGridEditCell.tsx @@ -1,46 +1,40 @@ import { Paper } from '@mui/material'; -import Autocomplete from '@mui/material/Autocomplete'; +import Autocomplete, { AutocompleteProps } from '@mui/material/Autocomplete'; import Box from '@mui/material/Box'; import CircularProgress from '@mui/material/CircularProgress'; -import { grey } from '@mui/material/colors'; +import ListItemText from '@mui/material/ListItemText'; import TextField from '@mui/material/TextField'; import useEnhancedEffect from '@mui/material/utils/useEnhancedEffect'; -import { GridRenderCellParams, GridValidRowModel } from '@mui/x-data-grid'; -import { - IAutocompleteDataGridOption, - IAutocompleteDataGridTaxonomyOption -} from 'components/data-grid/autocomplete/AutocompleteDataGrid.interface'; -import SpeciesCard from 'components/species/components/SpeciesCard'; +import { GridRenderEditCellParams, GridValidRowModel } from '@mui/x-data-grid'; +import { IAutocompleteDataGridOption } from 'components/data-grid/autocomplete/AutocompleteDataGrid.interface'; import { DebouncedFunc } from 'lodash-es'; import { useEffect, useRef, useState } from 'react'; export interface IAsyncAutocompleteDataGridEditCell< DataGridType extends GridValidRowModel, + AutocompleteOptionType extends IAutocompleteDataGridOption, ValueType extends string | number > { /** * Data grid props for the cell. * - * @type {GridRenderCellParams} + * @type {GridRenderEditCellParams} * @memberof IAsyncAutocompleteDataGridEditCell */ - dataGridProps: GridRenderCellParams; + dataGridProps: GridRenderEditCellParams; /** * Function that returns a single option. Used to translate an existing value to its matching option. * * @memberof IAsyncAutocompleteDataGridEditCell */ - getCurrentOption: (value: ValueType) => Promise | null>; + getCurrentOption: (value: ValueType) => Promise; /** * Search function that returns an array of options to choose from. * * @memberof IAsyncAutocompleteDataGridEditCell */ getOptions: DebouncedFunc< - ( - searchTerm: string, - onSearchResults: (searchResults: IAutocompleteDataGridTaxonomyOption[]) => void - ) => Promise + (searchTerm: string, onSearchResults: (searchResults: AutocompleteOptionType[]) => void) => Promise >; /** * Indicates if there is an error with the control @@ -51,21 +45,26 @@ export interface IAsyncAutocompleteDataGridEditCell< /** * Optional function to render the autocomplete option. */ - renderOption?: (option: IAutocompleteDataGridOption) => JSX.Element; + renderOption?: AutocompleteProps['renderOption']; } /** * Data grid single value asynchronous autocomplete component for edit. * * @template DataGridType + * @template AutocompleteOptionType * @template ValueType - * @param {IAsyncAutocompleteDataGridEditCell} props + * @param {IAsyncAutocompleteDataGridEditCell} props * @return {*} */ -const AsyncAutocompleteDataGridEditCell = ( - props: IAsyncAutocompleteDataGridEditCell +const AsyncAutocompleteDataGridEditCell = < + DataGridType extends GridValidRowModel, + AutocompleteOptionType extends IAutocompleteDataGridOption, + ValueType extends string | number +>( + props: IAsyncAutocompleteDataGridEditCell ) => { - const { dataGridProps, getCurrentOption, getOptions } = props; + const { dataGridProps, getCurrentOption, getOptions, error, renderOption } = props; const ref = useRef(); @@ -78,11 +77,11 @@ const AsyncAutocompleteDataGridEditCell = ['label']>(''); + const [inputValue, setInputValue] = useState(''); // The currently selected option - const [currentOption, setCurrentOption] = useState | null>(null); + const [currentOption, setCurrentOption] = useState(null); // The array of options to choose from - const [options, setOptions] = useState[]>([]); + const [options, setOptions] = useState([]); // Is control loading (search in progress) const [isLoading, setIsLoading] = useState(false); @@ -187,9 +186,9 @@ const AsyncAutocompleteDataGridEditCell = @@ -200,23 +199,16 @@ const AsyncAutocompleteDataGridEditCell = )} - renderOption={(renderProps, renderOption) => { - return ( - - - + renderOption={ + renderOption ?? + ((renderProps, renderOption) => { + return ( + + - - ); - }} + ); + }) + } data-testid={dataGridProps.id} /> ); diff --git a/app/src/components/data-grid/autocomplete/AutocompleteDataGrid.interface.ts b/app/src/components/data-grid/autocomplete/AutocompleteDataGrid.interface.ts index fd0f1183d1..48d7dea057 100644 --- a/app/src/components/data-grid/autocomplete/AutocompleteDataGrid.interface.ts +++ b/app/src/components/data-grid/autocomplete/AutocompleteDataGrid.interface.ts @@ -1,5 +1,3 @@ -import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; - /** * Defines a single option for a data grid autocomplete control. * @@ -12,16 +10,3 @@ export interface IAutocompleteDataGridOption label: string; subtext?: string; } - -/** - * Defines a single option for a data grid taxonomy autocomplete control. - * - * @export - * @interface IAutocompleteDataGridTaxonomyOption - * @extends {ITaxonomy} - * @template ValueType - */ -export interface IAutocompleteDataGridTaxonomyOption extends IPartialTaxonomy { - value: ValueType; - label: string; -} diff --git a/app/src/components/data-grid/taxonomy/TaxonomyDataGrid.interface.ts b/app/src/components/data-grid/taxonomy/TaxonomyDataGrid.interface.ts new file mode 100644 index 0000000000..4e3542ccbe --- /dev/null +++ b/app/src/components/data-grid/taxonomy/TaxonomyDataGrid.interface.ts @@ -0,0 +1,13 @@ +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; + +/** + * Defines a single option for a data grid taxonomy autocomplete control. + * + * @export + * @interface IAutocompleteDataGridTaxonomyOption + * @extends {IPartialTaxonomy} + */ +export interface IAutocompleteDataGridTaxonomyOption extends IPartialTaxonomy { + value: number; + label: string; +} diff --git a/app/src/components/data-grid/taxonomy/TaxonomyDataGridEditCell.tsx b/app/src/components/data-grid/taxonomy/TaxonomyDataGridEditCell.tsx index d08377ea24..ba47cfd44f 100644 --- a/app/src/components/data-grid/taxonomy/TaxonomyDataGridEditCell.tsx +++ b/app/src/components/data-grid/taxonomy/TaxonomyDataGridEditCell.tsx @@ -1,10 +1,13 @@ +import Box from '@mui/material/Box'; +import { grey } from '@mui/material/colors'; import { GridRenderEditCellParams, GridValidRowModel } from '@mui/x-data-grid'; import AsyncAutocompleteDataGridEditCell from 'components/data-grid/autocomplete/AsyncAutocompleteDataGridEditCell'; +import { IAutocompleteDataGridTaxonomyOption } from 'components/data-grid/taxonomy/TaxonomyDataGrid.interface'; +import SpeciesCard from 'components/species/components/SpeciesCard'; import { useBiohubApi } from 'hooks/useBioHubApi'; import { useTaxonomyContext } from 'hooks/useContext'; import debounce from 'lodash-es/debounce'; import { useMemo } from 'react'; -import { IAutocompleteDataGridTaxonomyOption } from '../autocomplete/AutocompleteDataGrid.interface'; export interface ITaxonomyDataGridCellProps { dataGridProps: GridRenderEditCellParams; @@ -19,7 +22,7 @@ export interface ITaxonomyDataGridCellProps} props * @return {*} */ -const TaxonomyDataGridEditCell = ( +const TaxonomyDataGridEditCell = ( props: ITaxonomyDataGridCellProps ) => { const { dataGridProps } = props; @@ -27,9 +30,7 @@ const TaxonomyDataGridEditCell = | null> => { + const getCurrentOption = async (speciesId: string | number): Promise => { if (!speciesId) { return null; } @@ -47,7 +48,7 @@ const TaxonomyDataGridEditCell = []) => void + onSearchResults: (searchedValues: IAutocompleteDataGridTaxonomyOption[]) => void ) => { if (!searchTerm) { onSearchResults([]); @@ -72,7 +73,7 @@ const TaxonomyDataGridEditCell = ({ - value: item.tsn as ValueType, + value: item.tsn, label: item.scientificName, tsn: item.tsn, commonNames: item.commonNames, @@ -93,6 +94,21 @@ const TaxonomyDataGridEditCell = ( + + + + + + )} /> ); }; diff --git a/app/src/components/dialog/YesNoDialog.tsx b/app/src/components/dialog/YesNoDialog.tsx index 757ca9130a..4703a2973d 100644 --- a/app/src/components/dialog/YesNoDialog.tsx +++ b/app/src/components/dialog/YesNoDialog.tsx @@ -52,7 +52,7 @@ export interface IYesNoDialogProps { * * @memberof IYesNoDialogProps */ - onYes: () => void; + onYes: () => Promise | void; /** * The yes button label. diff --git a/app/src/components/dialog/attachments/FileUploadWithMetaDialog.tsx b/app/src/components/dialog/attachments/FileUploadWithMetaDialog.tsx index b8264c57f4..c95f8c8a21 100644 --- a/app/src/components/dialog/attachments/FileUploadWithMetaDialog.tsx +++ b/app/src/components/dialog/attachments/FileUploadWithMetaDialog.tsx @@ -34,10 +34,10 @@ export interface IFileUploadWithMetaDialogProps { /** * The type of attachment. * - * @type {('Report' | 'KeyX' | 'Other')} + * @type {('Report' | 'KeyX' | 'Cfg' | 'Other')} * @memberof IFileUploadWithMetaDialogProps */ - attachmentType: AttachmentType.REPORT | AttachmentType.KEYX | AttachmentType.OTHER; + attachmentType: AttachmentType.REPORT | AttachmentType.KEYX | AttachmentType.CFG | AttachmentType.OTHER; /** * Set to `true` to open the dialog, `false` to close the dialog. * diff --git a/app/src/components/fields/AnimalAutocompleteField.tsx b/app/src/components/fields/AnimalAutocompleteField.tsx new file mode 100644 index 0000000000..755212e5c9 --- /dev/null +++ b/app/src/components/fields/AnimalAutocompleteField.tsx @@ -0,0 +1,177 @@ +import Autocomplete from '@mui/material/Autocomplete'; +import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; +import grey from '@mui/material/colors/grey'; +import TextField from '@mui/material/TextField'; +import Typography from '@mui/material/Typography'; +import { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { useFormikContext } from 'formik'; +import { useSurveyContext } from 'hooks/useContext'; +import { ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; +import { get } from 'lodash-es'; +import { useState } from 'react'; + +export interface IAnimalAutocompleteFieldProps { + /** + * Formik field name. + * + * @type {string} + * @memberof IAnimalAutocompleteFieldProps + */ + formikFieldName: string; + /** + * The field label. + * + * @type {string} + * @memberof IAnimalAutocompleteFieldProps + */ + label: string; + /** + * Callback fired on option selection. + * + * @memberof IAnimalAutocompleteFieldProps + */ + onSelect: (animal: ICritterSimpleResponse) => void; + /** + * Optional callback fired on option de-selected/cleared. + * + * @memberof IAnimalAutocompleteFieldProps + */ + onClear?: () => void; + /** + * Default animal to render for input and options. + * + * @type {ICritterSimpleResponse} + * @memberof IAnimalAutocompleteFieldProps + */ + defaultAnimal?: ICritterSimpleResponse; + /** + * If field is required. + * + * @type {boolean} + * @memberof IAnimalAutocompleteFieldProps + */ + required?: boolean; + /** + * If field is disabled. + * + * @type {boolean} + * @memberof IAnimalAutocompleteFieldProps + */ + disabled?: boolean; + /** + * If `true`, clears the input field after a selection is made. + * + * @type {ICritterSimpleResponse} + * @memberof IAnimalAutocompleteFieldProps + */ + clearOnSelect?: boolean; + /** + * Placeholder text for the TextField + * + * @type {string} + * @memberof IAnimalAutocompleteFieldProps + */ + placeholder?: string; +} + +/** + * An autocomplete field for selecting an existing animal from the Survey. + * + * @template T + * @param {IAnimalAutocompleteFieldProps} props + * @return {*} + */ +export const AnimalAutocompleteField = (props: IAnimalAutocompleteFieldProps) => { + const { formikFieldName, label, onSelect, defaultAnimal, required, disabled, clearOnSelect, placeholder } = props; + + const { touched, errors, setFieldValue } = useFormikContext>(); + + const surveyContext = useSurveyContext(); + + // The input field value + const [inputValue, setInputValue] = useState(defaultAnimal?.animal_id ?? ''); + + // Survey animals to choose from + const options = surveyContext.critterDataLoader.data; + + return ( + option.animal_id ?? String(option.critter_id)} + isOptionEqualToValue={(option, value) => { + return option.critter_id === value.critter_id; + }} + filterOptions={(item) => item} + inputValue={inputValue} + onInputChange={(_, _value, reason) => { + if (clearOnSelect && reason === 'clear') { + setFieldValue(formikFieldName, ''); + setInputValue(''); + } + }} + onChange={(_, option) => { + if (option) { + onSelect(option); + setInputValue(option.animal_id ?? String(option.critter_id)); //startCase(option?.commonNames?.length ? option.commonNames[0] : option.scientificName)); + } + }} + renderOption={(renderProps, renderOption) => { + return ( + + + + + {renderOption.animal_id}  + + {renderOption.wlh_id} + + + {renderOption.critter_id} + + + + + ); + }} + renderInput={(params) => ( + setInputValue(event.currentTarget.value)} + required={required} + sx={{ opacity: props?.disabled ? 0.25 : 1 }} + error={get(touched, formikFieldName) && Boolean(get(errors, formikFieldName))} + helperText={get(touched, formikFieldName) && get(errors, formikFieldName)} + fullWidth + placeholder={placeholder || 'Search for an animal in the Survey'} + InputProps={{ + ...params.InputProps, + endAdornment: ( + <> + {surveyContext.critterDataLoader.isLoading ? : null} + {params.InputProps.endAdornment} + + ) + }} + /> + )} + /> + ); +}; diff --git a/app/src/components/fields/AutocompleteField.tsx b/app/src/components/fields/AutocompleteField.tsx index 974d0ccddd..421c969c23 100644 --- a/app/src/components/fields/AutocompleteField.tsx +++ b/app/src/components/fields/AutocompleteField.tsx @@ -71,7 +71,7 @@ const AutocompleteField = (props: IAutocompleteField< getOptionDisabled={props.getOptionDisabled} filterOptions={createFilterOptions({ limit: props.filterLimit })} disabled={props?.disabled || false} - sx={props.sx} + sx={{ flex: '1 1 auto', ...props.sx }} loading={props.loading} onInputChange={(_event, _value, reason) => { if (reason === 'reset') { diff --git a/app/src/components/fields/CbSelectField.tsx b/app/src/components/fields/CbSelectField.tsx deleted file mode 100644 index 1619510292..0000000000 --- a/app/src/components/fields/CbSelectField.tsx +++ /dev/null @@ -1,100 +0,0 @@ -import { FormControlProps } from '@mui/material/FormControl'; -import MenuItem from '@mui/material/MenuItem'; -import { SelectChangeEvent } from '@mui/material/Select'; -import { useFormikContext } from 'formik'; -import { ICbSelectRows, SelectOptionsProps } from 'hooks/cb_api/useLookupApi'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { startCase } from 'lodash-es'; -import get from 'lodash-es/get'; -import { useEffect, useMemo } from 'react'; -import { CbSelectWrapper } from './CbSelectFieldWrapper'; - -export interface ICbSelectSharedProps { - name: string; - label: string; - controlProps?: FormControlProps; -} - -export type ICbSelectField = ICbSelectSharedProps & - SelectOptionsProps & { - id: string; - disabledValues?: Record; - handleChangeSideEffect?: (value: string, label: string) => void; - }; - -interface ICbSelectOption { - value: string | number; - label: string; -} -/** - * Critterbase Select Field. Handles data retrieval, formatting and error handling. - * - * @param {ICbSelectField} props - * @return {*} - * - */ -const CbSelectField = (props: ICbSelectField) => { - const { name, orderBy, label, route, query, handleChangeSideEffect, controlProps, disabledValues } = props; - - const critterbaseApi = useCritterbaseApi(); - - const { data, refresh } = useDataLoader(critterbaseApi.lookup.getSelectOptions); - const { values, handleChange } = useFormikContext(); - - const val = get(values, name) ?? ''; - - const selectParams = { route, query, orderBy }; - - useEffect(() => { - // Skip fetching if route ends with an undefined id - // example: /xref/collection-units/{undefined} - if (route.endsWith('/')) { - return; - } - refresh(selectParams); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [JSON.stringify(selectParams)]); - - const isValueInRange = useMemo(() => { - if (val === '') { - return true; - } - if (!data) { - return false; - } - const inRange = data.some((d) => (typeof d === 'string' ? d === val : d.id === val)); - - return inRange; - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [data, val, name]); - - const innerChangeHandler = (e: SelectChangeEvent) => { - handleChange(e); - // useful for when the select item label is needed in parent component - if (handleChangeSideEffect) { - const item = data?.find((a) => typeof a !== 'string' && a.id === e.target.value); - handleChangeSideEffect(e.target.value, (item as ICbSelectRows).value); - } - }; - - return ( - - {data?.map((a) => { - const item = typeof a === 'string' ? { label: a, value: a } : { label: a.value, value: a.id }; - return ( - - {startCase(item.label)} - - ); - })} - - ); -}; - -export default CbSelectField; diff --git a/app/src/components/fields/CbSelectFieldWrapper.tsx b/app/src/components/fields/CbSelectFieldWrapper.tsx deleted file mode 100644 index 19ed62ff19..0000000000 --- a/app/src/components/fields/CbSelectFieldWrapper.tsx +++ /dev/null @@ -1,43 +0,0 @@ -import FormControl from '@mui/material/FormControl'; -import FormHelperText from '@mui/material/FormHelperText'; -import InputLabel from '@mui/material/InputLabel'; -import Select, { SelectProps } from '@mui/material/Select'; -import { useFormikContext } from 'formik'; -import { get } from 'lodash-es'; -import { ReactNode } from 'react'; -import { ICbSelectSharedProps } from './CbSelectField'; - -interface CbSelectWrapperProps extends ICbSelectSharedProps { - children?: ReactNode; - onChange?: SelectProps['onChange']; - value?: SelectProps['value']; -} - -/** - * - * Wrapper for cb selects to handle all errors / onChange / onBlur - * - * @return {*} - * - **/ - -export const CbSelectWrapper = ({ children, name, label, controlProps, onChange, value }: CbSelectWrapperProps) => { - const { values, touched, errors, handleBlur, handleChange } = useFormikContext(); - const val = get(values, name) ?? ''; - const err = get(touched, name) && get(errors, name); - return ( - - {label} - - {err} - - ); -}; diff --git a/app/src/components/fields/CustomTextField.tsx b/app/src/components/fields/CustomTextField.tsx index 38744291fd..4f50ed4ae3 100644 --- a/app/src/components/fields/CustomTextField.tsx +++ b/app/src/components/fields/CustomTextField.tsx @@ -9,6 +9,13 @@ export interface ICustomTextField { * @memberof ICustomTextField */ label: string; + /** + * Placeholder for the text field + * + * @type {string} + * @memberof ICustomTextField + */ + placeholder?: string; /** * Name of the text field, typically this is used to identify the field in the formik context. * @@ -34,13 +41,14 @@ export interface ICustomTextField { const CustomTextField = (props: React.PropsWithChildren) => { const { touched, errors, values, handleChange, handleBlur } = useFormikContext(); - const { name, label, other } = props; + const { name, label, other, placeholder } = props; return ( { + label: string; + name: string; + id: string; + required: boolean; + formikProps: FormikContextType; +} + +export const DateField = (props: IDateFieldProps) => { + const { + formikProps: { values, errors, touched, setFieldValue }, + label, + name, + id, + required + } = props; + + const rawDateValue = get(values, name); + const formattedDateValue = + (rawDateValue && + dayjs(rawDateValue, DATE_FORMAT.ShortDateFormat).isValid() && + dayjs(rawDateValue, DATE_FORMAT.ShortDateFormat)) || + null; + + return ( + + + }} + slotProps={{ + textField: { + id: id, + name: name, + required: required, + variant: 'outlined', + error: get(touched, name) && Boolean(get(errors, name)), + helperText: get(touched, name) && get(errors, name), + inputProps: { + 'data-testid': name + }, + InputLabelProps: { + shrink: true + }, + fullWidth: true + } + }} + label={label} + format={DATE_FORMAT.ShortDateFormat} + minDate={dayjs(DATE_LIMIT.min)} + maxDate={dayjs(DATE_LIMIT.max)} + value={formattedDateValue} + onChange={(value) => { + if (!value || value === 'Invalid Date') { + // The creation input value will be 'Invalid Date' when the date field is cleared (empty), and will + // contain an actual date string value if the field is not empty but is invalid. + setFieldValue(name, null); + return; + } + + setFieldValue(name, dayjs(value).format(DATE_FORMAT.ShortDateFormat)); + }} + /> + + ); +}; diff --git a/app/src/components/fields/StartEndDateFields.tsx b/app/src/components/fields/StartEndDateFields.tsx index ccd12b51a7..6efcaad1af 100644 --- a/app/src/components/fields/StartEndDateFields.tsx +++ b/app/src/components/fields/StartEndDateFields.tsx @@ -6,11 +6,11 @@ import { AdapterDayjs } from '@mui/x-date-pickers/AdapterDayjs'; import { LocalizationProvider } from '@mui/x-date-pickers/LocalizationProvider'; import { DATE_FORMAT, DATE_LIMIT } from 'constants/dateTimeFormats'; import { default as dayjs } from 'dayjs'; +import { useFormikContext } from 'formik'; import get from 'lodash-es/get'; import React from 'react'; interface IStartEndDateFieldsProps { - formikProps: any; startName: string; endName: string; startRequired: boolean; @@ -30,13 +30,9 @@ const CalendarEndIcon = () => { * */ const StartEndDateFields: React.FC = (props) => { - const { - formikProps: { values, errors, touched, setFieldValue }, - startName, - endName, - startRequired, - endRequired - } = props; + const { startName, endName, startRequired, endRequired } = props; + + const { values, errors, touched, setFieldValue } = useFormikContext(); const rawStartDateValue = get(values, startName); const rawEndDateValue = get(values, endName); diff --git a/app/src/components/fields/SystemUserAutocompleteField.tsx b/app/src/components/fields/SystemUserAutocompleteField.tsx index 1af9a1cc89..be2e133998 100644 --- a/app/src/components/fields/SystemUserAutocompleteField.tsx +++ b/app/src/components/fields/SystemUserAutocompleteField.tsx @@ -182,8 +182,8 @@ export const SystemUserAutocompleteField = (props: ISystemUserAutocompleteFieldP borderTop: '1px solid' + grey[300] } }} - key={renderOption.system_user_id} - {...renderProps}> + {...renderProps} + key={renderOption.system_user_id}> = (props) => { +const TelemetrySelectField: React.FC = (props) => { const bctwLookupLoader = useDataLoader(() => props.fetchData()); const { values, touched, errors, handleChange, handleBlur } = useFormikContext(); diff --git a/app/src/components/fields/TimeField.tsx b/app/src/components/fields/TimeField.tsx new file mode 100644 index 0000000000..23772bbfab --- /dev/null +++ b/app/src/components/fields/TimeField.tsx @@ -0,0 +1,83 @@ +import { mdiClockOutline } from '@mdi/js'; +import Icon from '@mdi/react'; +import { TimePicker } from '@mui/x-date-pickers'; +import { AdapterDayjs } from '@mui/x-date-pickers/AdapterDayjs'; +import { LocalizationProvider } from '@mui/x-date-pickers/LocalizationProvider'; +import { TIME_FORMAT } from 'constants/dateTimeFormats'; +import { default as dayjs } from 'dayjs'; +import { FormikContextType } from 'formik'; +import get from 'lodash-es/get'; + +interface ITimeFieldProps { + label: string; + name: string; + id: string; + required: boolean; + formikProps: FormikContextType; +} + +export const TimeField = (props: ITimeFieldProps) => { + const { + formikProps: { values, errors, touched, setFieldValue }, + label, + name, + id, + required + } = props; + + const rawTimeValue = get(values, name); + const formattedTimeValue = + (rawTimeValue && + dayjs(rawTimeValue, TIME_FORMAT.LongTimeFormat24Hour).isValid() && + dayjs(rawTimeValue, TIME_FORMAT.LongTimeFormat24Hour)) || + null; + + return ( + + + }} + slotProps={{ + textField: { + id: id, + name: name, + required: required, + variant: 'outlined', + error: get(touched, name) && Boolean(get(errors, name)), + helperText: get(touched, name) && get(errors, name), + inputProps: { + 'data-testid': id, + 'aria-label': 'Time (optional)' + }, + InputLabelProps: { + shrink: true + }, + fullWidth: true + } + }} + label={label} + format={TIME_FORMAT.LongTimeFormat24Hour} + value={formattedTimeValue} + onChange={(value: dayjs.Dayjs | null) => { + if (!value || !dayjs(value).isValid()) { + // Check if the value is null or invalid, and if so, clear the field. + setFieldValue(name, null); + return; + } + + setFieldValue(name, dayjs(value).format(TIME_FORMAT.LongTimeFormat24Hour)); + }} + views={['hours', 'minutes', 'seconds']} + timeSteps={{ hours: 1, minutes: 1, seconds: 1 }} + ampm={false} + /> + + ); +}; diff --git a/app/src/components/file-upload/DropZone.tsx b/app/src/components/file-upload/DropZone.tsx index 953b49c418..2fa5c2bdbf 100644 --- a/app/src/components/file-upload/DropZone.tsx +++ b/app/src/components/file-upload/DropZone.tsx @@ -48,12 +48,13 @@ export interface IDropZoneConfigProps { /** * Comma separated list of allowed file extensions. * - * Example: `'.pdf, .txt'` + * @example '.pdf, .txt' + * @example ['.pdf', '.txt'] * - * @type {string} + * @type {(string | string[])} * @memberof IDropZoneConfigProps */ - acceptedFileExtensions?: string; + acceptedFileExtensions?: string | string[]; } export const DropZone: React.FC = (props) => { diff --git a/app/src/components/layout/Header.tsx b/app/src/components/layout/Header.tsx index 3366c386fa..0e52a07142 100644 --- a/app/src/components/layout/Header.tsx +++ b/app/src/components/layout/Header.tsx @@ -277,11 +277,9 @@ const Header: React.FC = () => { Funding Sources - - - Standards - - + + Standards + Support @@ -354,11 +352,9 @@ const Header: React.FC = () => { Funding Sources - - - Standards - - + + Standards + - - - )} - /> - - ); -}; - -export default AddSystemUsersForm; diff --git a/app/src/features/admin/users/ManageUsersPage.test.tsx b/app/src/features/admin/users/ManageUsersPage.test.tsx index 3cd33589cc..ea17d4e119 100644 --- a/app/src/features/admin/users/ManageUsersPage.test.tsx +++ b/app/src/features/admin/users/ManageUsersPage.test.tsx @@ -1,8 +1,11 @@ import { AuthStateContext } from 'contexts/authStateContext'; +import { CodesContext, ICodesContext } from 'contexts/codesContext'; import { createMemoryHistory } from 'history'; import { useBiohubApi } from 'hooks/useBioHubApi'; +import { DataLoader } from 'hooks/useDataLoader'; import { Router } from 'react-router'; import { getMockAuthState, SystemAdminAuthState } from 'test-helpers/auth-helpers'; +import { codes } from 'test-helpers/code-helpers'; import { cleanup, render, waitFor } from 'test-helpers/test-utils'; import ManageUsersPage from './ManageUsersPage'; @@ -11,11 +14,20 @@ const history = createMemoryHistory(); const renderContainer = () => { const authState = getMockAuthState({ base: SystemAdminAuthState }); + const mockCodesContext: ICodesContext = { + codesDataLoader: { + data: codes, + load: () => {} + } as DataLoader + }; + return render( - - - + + + + + ); }; @@ -74,7 +86,7 @@ describe('ManageUsersPage', () => { const { getByText } = renderContainer(); await waitFor(() => { - expect(getByText('No Access Requests')).toBeVisible(); + expect(getByText('No Pending Access Requests')).toBeVisible(); expect(getByText('No Active Users')).toBeVisible(); }); }); diff --git a/app/src/features/admin/users/ManageUsersPage.tsx b/app/src/features/admin/users/ManageUsersPage.tsx index 69afec4863..9c11f7e044 100644 --- a/app/src/features/admin/users/ManageUsersPage.tsx +++ b/app/src/features/admin/users/ManageUsersPage.tsx @@ -3,13 +3,13 @@ import CircularProgress from '@mui/material/CircularProgress'; import Container from '@mui/material/Container'; import PageHeader from 'components/layout/PageHeader'; import { AdministrativeActivityStatusType, AdministrativeActivityType } from 'constants/misc'; -import AccessRequestList from 'features/admin/users/AccessRequestList'; import { useBiohubApi } from 'hooks/useBioHubApi'; import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; import { ISystemUser } from 'interfaces/useUserApi.interface'; import React, { useEffect, useState } from 'react'; -import ActiveUsersList from './ActiveUsersList'; +import AccessRequestContainer from './access-requests/AccessRequestContainer'; +import ActiveUsersList from './active/ActiveUsersList'; /** * Page to display user management data/functionality. @@ -33,7 +33,11 @@ const ManageUsersPage: React.FC = () => { const refreshAccessRequests = async () => { const accessResponse = await biohubApi.admin.getAdministrativeActivities( [AdministrativeActivityType.SYSTEM_ACCESS], - [AdministrativeActivityStatusType.PENDING, AdministrativeActivityStatusType.REJECTED] + [ + AdministrativeActivityStatusType.PENDING, + AdministrativeActivityStatusType.REJECTED, + AdministrativeActivityStatusType.ACTIONED + ] ); setAccessRequests(accessResponse); @@ -43,7 +47,11 @@ const ManageUsersPage: React.FC = () => { const getAccessRequests = async () => { const accessResponse = await biohubApi.admin.getAdministrativeActivities( [AdministrativeActivityType.SYSTEM_ACCESS], - [AdministrativeActivityStatusType.PENDING, AdministrativeActivityStatusType.REJECTED] + [ + AdministrativeActivityStatusType.PENDING, + AdministrativeActivityStatusType.REJECTED, + AdministrativeActivityStatusType.ACTIONED + ] ); setAccessRequests(() => { @@ -120,7 +128,7 @@ const ManageUsersPage: React.FC = () => { <> - { diff --git a/app/src/features/admin/users/access-requests/AccessRequestContainer.tsx b/app/src/features/admin/users/access-requests/AccessRequestContainer.tsx new file mode 100644 index 0000000000..051a9616ce --- /dev/null +++ b/app/src/features/admin/users/access-requests/AccessRequestContainer.tsx @@ -0,0 +1,123 @@ +import { mdiCancel, mdiCheck, mdiExclamationThick } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import Divider from '@mui/material/Divider'; +import Paper from '@mui/material/Paper'; +import ToggleButton from '@mui/material/ToggleButton'; +import ToggleButtonGroup from '@mui/material/ToggleButtonGroup/ToggleButtonGroup'; +import Toolbar from '@mui/material/Toolbar'; +import Typography from '@mui/material/Typography'; +import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; +import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; +import { useState } from 'react'; +import AccessRequestActionedList from './list/actioned/AccessRequestActionedList'; +import AccessRequestPendingList from './list/pending/AccessRequestPendingList'; +import AccessRequestRejectedList from './list/rejected/AccessRequestRejectedList'; + +export interface IAccessRequestContainerProps { + accessRequests: IGetAccessRequestsListResponse[]; + codes: IGetAllCodeSetsResponse; + refresh: () => void; +} + +enum AccessRequestViewEnum { + ACTIONED = 'ACTIONED', + PENDING = 'PENDING', + REJECTED = 'REJECTED' +} + +/** + * Container for displaying a list of user access requests. + * + */ +const AccessRequestContainer = (props: IAccessRequestContainerProps) => { + const { accessRequests, codes, refresh } = props; + const [activeView, setActiveView] = useState(AccessRequestViewEnum.PENDING); + + const views = [ + { value: AccessRequestViewEnum.PENDING, label: 'Pending', icon: mdiExclamationThick }, + { value: AccessRequestViewEnum.ACTIONED, label: 'Approved', icon: mdiCheck }, + { value: AccessRequestViewEnum.REJECTED, label: 'Rejected', icon: mdiCancel } + ]; + + const pendingRequests = accessRequests.filter((request) => request.status_name === 'Pending'); + const actionedRequests = accessRequests.filter((request) => request.status_name === 'Actioned'); + const rejectedRequests = accessRequests.filter((request) => request.status_name === 'Rejected'); + + return ( + + + + Access Requests + + + + + { + if (!view) { + // An active view must be selected at all times + return; + } + + setActiveView(view); + }} + exclusive + sx={{ + width: '100%', + gap: 1, + '& Button': { + py: 0.5, + px: 1.5, + border: 'none !important', + fontWeight: 700, + borderRadius: '4px !important', + fontSize: '0.875rem', + letterSpacing: '0.02rem' + } + }}> + {views.map((view) => { + const getCount = () => { + switch (view.value) { + case AccessRequestViewEnum.PENDING: + return pendingRequests.length; + case AccessRequestViewEnum.ACTIONED: + return actionedRequests.length; + case AccessRequestViewEnum.REJECTED: + return rejectedRequests.length; + default: + return 0; + } + }; + return ( + }> + {view.label} ({getCount()}) + + ); + })} + + + + + {activeView === AccessRequestViewEnum.PENDING && ( + + )} + {activeView === AccessRequestViewEnum.ACTIONED && ( + + )} + {activeView === AccessRequestViewEnum.REJECTED && ( + + )} + + + ); +}; + +export default AccessRequestContainer; diff --git a/app/src/features/admin/users/ReviewAccessRequestForm.test.tsx b/app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.test.tsx similarity index 95% rename from app/src/features/admin/users/ReviewAccessRequestForm.test.tsx rename to app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.test.tsx index 1c4c5a2c36..4041c0f84a 100644 --- a/app/src/features/admin/users/ReviewAccessRequestForm.test.tsx +++ b/app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.test.tsx @@ -1,12 +1,12 @@ import { SYSTEM_IDENTITY_SOURCE } from 'constants/auth'; -import ReviewAccessRequestForm, { - ReviewAccessRequestFormInitialValues, - ReviewAccessRequestFormYupSchema -} from 'features/admin/users/ReviewAccessRequestForm'; import { Formik } from 'formik'; import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; import { codes } from 'test-helpers/code-helpers'; import { render, waitFor } from 'test-helpers/test-utils'; +import ReviewAccessRequestForm, { + ReviewAccessRequestFormInitialValues, + ReviewAccessRequestFormYupSchema +} from './ReviewAccessRequestForm'; describe('ReviewAccessRequestForm', () => { describe('IDIR Request', () => { @@ -20,6 +20,8 @@ describe('ReviewAccessRequestForm', () => { description: 'test description', notes: 'test node', create_date: '2021-04-18', + updated_by: 'Doe, John WLRS:EX', + update_date: '2021-04-20', data: { name: 'test data name', username: 'test data username', @@ -54,7 +56,6 @@ describe('ReviewAccessRequestForm', () => { expect(getByText('test data name')).toBeVisible(); expect(getByText('IDIR/test data username')).toBeVisible(); expect(getByText('test data email')).toBeVisible(); - expect(getByText('04/18/2021')).toBeVisible(); }); }); }); @@ -70,6 +71,8 @@ describe('ReviewAccessRequestForm', () => { description: 'test description', notes: 'test node', create_date: '2021-04-18', + updated_by: 'Doe, John WLRS:EX', + update_date: '2021-04-20', data: { name: 'test data name', username: 'test data username', @@ -105,7 +108,6 @@ describe('ReviewAccessRequestForm', () => { expect(getByText('test data name')).toBeVisible(); expect(getByText('BCeID Basic/test data username')).toBeVisible(); expect(getByText('test data email')).toBeVisible(); - expect(getByText('04/18/2021')).toBeVisible(); expect(getByText('test company')).toBeVisible(); }); }); diff --git a/app/src/features/admin/users/ReviewAccessRequestForm.tsx b/app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.tsx similarity index 95% rename from app/src/features/admin/users/ReviewAccessRequestForm.tsx rename to app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.tsx index 51f4f2c7b9..5aee63c3f7 100644 --- a/app/src/features/admin/users/ReviewAccessRequestForm.tsx +++ b/app/src/features/admin/users/access-requests/components/ReviewAccessRequestForm.tsx @@ -4,10 +4,11 @@ import Typography from '@mui/material/Typography'; import AutocompleteField, { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; import { SYSTEM_IDENTITY_SOURCE } from 'constants/auth'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; import { useFormikContext } from 'formik'; import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; import React from 'react'; -import { getFormattedDate, getFormattedIdentitySource } from 'utils/Utils'; +import { getFormattedIdentitySource } from 'utils/Utils'; import yup from 'utils/YupSchema'; export interface IReviewAccessRequestForm { @@ -79,7 +80,7 @@ const ReviewAccessRequestForm: React.FC = (props) Date of Request - {getFormattedDate(DATE_FORMAT.ShortDateFormatMonthFirst, props.request.create_date)} + {dayjs(props.request.create_date).format(DATE_FORMAT.ShortMediumDateTimeFormat)} @@ -109,7 +110,7 @@ const ReviewAccessRequestForm: React.FC = (props) sx={{ marginBottom: '18px' }}> - Requested System Role + System Role
diff --git a/app/src/features/admin/users/access-requests/components/ViewAccessRequestForm.tsx b/app/src/features/admin/users/access-requests/components/ViewAccessRequestForm.tsx new file mode 100644 index 0000000000..49ee184853 --- /dev/null +++ b/app/src/features/admin/users/access-requests/components/ViewAccessRequestForm.tsx @@ -0,0 +1,93 @@ +import { mdiInformationOutline } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import { blue } from '@mui/material/colors'; +import Grid from '@mui/material/Grid'; +import Typography from '@mui/material/Typography'; +import { SYSTEM_IDENTITY_SOURCE } from 'constants/auth'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; +import React from 'react'; +import { getFormattedIdentitySource } from 'utils/Utils'; + +export interface IViewAccessReuqestFormProps { + request: IGetAccessRequestsListResponse; + bannerText: string; +} + +/** + * Component to view system access requests without the ability to edit the user's system role + * + * @return {*} + */ +export const ViewAccessRequestForm: React.FC = (props: IViewAccessReuqestFormProps) => { + const formattedUsername = [ + getFormattedIdentitySource(props.request.data.identitySource as SYSTEM_IDENTITY_SOURCE), + props.request.data.username + ] + .filter(Boolean) + .join('/'); + + return ( + <> + + + + + {props.bannerText} + + + + + + User Details + +
+ + + + Name + + {props.request.data.name} + + + + Username + + {formattedUsername} + + + + Email Address + + {props.request.data.email} + + + + Date of Request + + + {dayjs(props.request.create_date).format(DATE_FORMAT.ShortMediumDateTimeFormat)} + + + + + Company + + + {('company' in props.request.data && props.request.data.company) || 'Not Applicable'} + + + + + Reason for Request + + {props.request.data.reason} + + +
+ + + ); +}; diff --git a/app/src/features/admin/users/access-requests/list/actioned/AccessRequestActionedList.tsx b/app/src/features/admin/users/access-requests/list/actioned/AccessRequestActionedList.tsx new file mode 100644 index 0000000000..c16d0bc61a --- /dev/null +++ b/app/src/features/admin/users/access-requests/list/actioned/AccessRequestActionedList.tsx @@ -0,0 +1,128 @@ +import Button from '@mui/material/Button'; +import Dialog from '@mui/material/Dialog'; +import DialogContent from '@mui/material/DialogContent'; +import DialogTitle from '@mui/material/DialogTitle'; +import { GridColDef } from '@mui/x-data-grid'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { getAccessRequestStatusColour } from 'constants/colours'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; +import { useState } from 'react'; +import { ViewAccessRequestForm } from '../../components/ViewAccessRequestForm'; + +interface IAccessRequestActionedListProps { + accessRequests: IGetAccessRequestsListResponse[]; +} + +/** + * Returns a data grid component displaying approved access requests + * + * @param props {IAccessRequestActionedListProps} + * @returns + */ +const AccessRequestActionedList = (props: IAccessRequestActionedListProps) => { + const { accessRequests } = props; + + const [showViewDialog, setShowViewDialog] = useState(false); + const [activeReview, setActiveReview] = useState(null); + + const accessRequestsColumnDefs: GridColDef[] = [ + { + field: 'display_name', + headerName: 'Display Name', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.data?.displayName; + } + }, + { + field: 'username', + headerName: 'Username', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.data?.username; + } + }, + { + field: 'create_date', + flex: 1, + headerName: 'Date of Request', + disableColumnMenu: true, + valueFormatter: (params) => { + return dayjs(params.value).format(DATE_FORMAT.ShortMediumDateTimeFormat); + } + }, + { + field: 'status_name', + width: 170, + headerName: 'Status', + disableColumnMenu: true, + renderCell: (params) => { + return ( + + ); + } + }, + { + field: 'actions', + headerName: '', + type: 'actions', + flex: 1, + sortable: false, + disableColumnMenu: true, + resizable: false, + align: 'right', + renderCell: (params) => ( + + ) + } + ]; + + return ( + <> + {activeReview && ( + setShowViewDialog(false)}> + Access Request + + + + + )} + + + ); +}; + +export default AccessRequestActionedList; diff --git a/app/src/features/admin/users/AccessRequestList.tsx b/app/src/features/admin/users/access-requests/list/pending/AccessRequestPendingList.tsx similarity index 59% rename from app/src/features/admin/users/AccessRequestList.tsx rename to app/src/features/admin/users/access-requests/list/pending/AccessRequestPendingList.tsx index fbd0ac607a..8144e3da8c 100644 --- a/app/src/features/admin/users/AccessRequestList.tsx +++ b/app/src/features/admin/users/access-requests/list/pending/AccessRequestPendingList.tsx @@ -1,88 +1,60 @@ -import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; -import Divider from '@mui/material/Divider'; -import Paper from '@mui/material/Paper'; -import Toolbar from '@mui/material/Toolbar'; import Typography from '@mui/material/Typography'; import { GridColDef } from '@mui/x-data-grid'; -import { AccessStatusChip } from 'components/chips/AccessStatusChip'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; import RequestDialog from 'components/dialog/RequestDialog'; +import { getAccessRequestStatusColour } from 'constants/colours'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; -import { AccessApprovalDispatchI18N, AccessDenialDispatchI18N, ReviewAccessRequestI18N } from 'constants/i18n'; -import { AdministrativeActivityStatusType } from 'constants/misc'; -import { DialogContext } from 'contexts/dialogContext'; +import { ReviewAccessRequestI18N } from 'constants/i18n'; +import { DialogContext, ISnackbarProps } from 'contexts/dialogContext'; +import dayjs from 'dayjs'; import { APIError } from 'hooks/api/useAxios'; import { useBiohubApi } from 'hooks/useBioHubApi'; import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; import { useContext, useState } from 'react'; -import { getFormattedDate } from 'utils/Utils'; import ReviewAccessRequestForm, { IReviewAccessRequestForm, ReviewAccessRequestFormInitialValues, ReviewAccessRequestFormYupSchema -} from './ReviewAccessRequestForm'; +} from '../../components/ReviewAccessRequestForm'; -export interface IAccessRequestListProps { +interface IAccessRequestPendingListProps { accessRequests: IGetAccessRequestsListResponse[]; codes: IGetAllCodeSetsResponse; refresh: () => void; } -const pageSizeOptions = [10, 25, 50]; - /** - * Page to display a list of user access. + * Returns a data grid component displaying pending access requests * + * @param props {IAccessRequestPendingListProps} + * @returns */ -const AccessRequestList = (props: IAccessRequestListProps) => { +const AccessRequestPendingList = (props: IAccessRequestPendingListProps) => { const { accessRequests, codes, refresh } = props; const biohubApi = useBiohubApi(); + const dialogContext = useContext(DialogContext); const [showReviewDialog, setShowReviewDialog] = useState(false); const [activeReview, setActiveReview] = useState(null); - const dialogContext = useContext(DialogContext); - - const defaultErrorDialogProps = { - dialogTitle: ReviewAccessRequestI18N.reviewErrorTitle, - dialogText: ReviewAccessRequestI18N.reviewErrorText, - open: false, - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - } - }; - - const dispatchApprovalErrorDialogProps = { - dialogTitle: AccessApprovalDispatchI18N.reviewErrorTitle, - dialogText: AccessApprovalDispatchI18N.reviewErrorText, - open: false, - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - } - }; - - const dispatchDenialErrorDialogProps = { - dialogTitle: AccessDenialDispatchI18N.reviewErrorTitle, - dialogText: AccessDenialDispatchI18N.reviewErrorText, - open: false, - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - } + const showSnackBar = (textDialogProps?: Partial) => { + dialogContext.setSnackbar({ ...textDialogProps, open: true }); }; const accessRequestsColumnDefs: GridColDef[] = [ + { + field: 'display_name', + headerName: 'Display Name', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.data?.displayName; + } + }, { field: 'username', headerName: 'Username', @@ -98,7 +70,7 @@ const AccessRequestList = (props: IAccessRequestListProps) => { headerName: 'Date of Request', disableColumnMenu: true, valueFormatter: (params) => { - return getFormattedDate(DATE_FORMAT.ShortMediumDateFormat, params.value); + return dayjs(params.value).format(DATE_FORMAT.ShortMediumDateTimeFormat); } }, { @@ -107,7 +79,12 @@ const AccessRequestList = (props: IAccessRequestListProps) => { headerName: 'Status', disableColumnMenu: true, renderCell: (params) => { - return ; + return ( + + ); } }, { @@ -119,26 +96,32 @@ const AccessRequestList = (props: IAccessRequestListProps) => { disableColumnMenu: true, resizable: false, align: 'right', - renderCell: (params) => { - if (params.row.status_name !== AdministrativeActivityStatusType.PENDING) { - return <>; - } - - return ( - - ); - } + renderCell: (params) => ( + + ) } ]; + const defaultErrorDialogProps = { + dialogTitle: ReviewAccessRequestI18N.reviewErrorTitle, + dialogText: ReviewAccessRequestI18N.reviewErrorText, + open: false, + onClose: () => { + dialogContext.setErrorDialog({ open: false }); + }, + onOk: () => { + dialogContext.setErrorDialog({ open: false }); + } + }; + const handleReviewDialogApprove = async (values: IReviewAccessRequestForm) => { if (!activeReview) { return; @@ -156,6 +139,14 @@ const AccessRequestList = (props: IAccessRequestListProps) => { roleIds: (values.system_role && [values.system_role]) || [] }); + showSnackBar({ + snackbarMessage: ( + + Approved access request + + ) + }); + try { await biohubApi.admin.sendGCNotification( { @@ -166,16 +157,18 @@ const AccessRequestList = (props: IAccessRequestListProps) => { { subject: 'SIMS: Your request for access has been approved.', header: 'Your request for access to the Species Inventory Management System has been approved.', - main_body1: 'This is an automated message from the BioHub Species Inventory Management System', + main_body1: 'This is an automated message from the Species Inventory Management System', main_body2: '', footer: '' } ); } catch (error) { - dialogContext.setErrorDialog({ - ...dispatchApprovalErrorDialogProps, - open: true, - dialogErrorDetails: (error as APIError).errors + showSnackBar({ + snackbarMessage: ( + + Approved access request, but failed to send notification + + ) }); } finally { refresh(); @@ -199,6 +192,14 @@ const AccessRequestList = (props: IAccessRequestListProps) => { try { await biohubApi.admin.denyAccessRequest(activeReview.id); + showSnackBar({ + snackbarMessage: ( + + Approved access request + + ) + }); + try { await biohubApi.admin.sendGCNotification( { @@ -209,16 +210,18 @@ const AccessRequestList = (props: IAccessRequestListProps) => { { subject: 'SIMS: Your request for access has been denied.', header: 'Your request for access to the Species Inventory Management System has been denied.', - main_body1: 'This is an automated message from the BioHub Species Inventory Management System', + main_body1: 'This is an automated message from the Species Inventory Management System', main_body2: '', footer: '' } ); } catch (error) { - dialogContext.setErrorDialog({ - ...dispatchDenialErrorDialogProps, - open: true, - dialogErrorDetails: (error as APIError).errors + showSnackBar({ + snackbarMessage: ( + + Denied access request, but failed to send notification + + ) }); } finally { refresh(); @@ -246,51 +249,28 @@ const AccessRequestList = (props: IAccessRequestListProps) => { element: activeReview ? ( { - return { value: item.id, label: item.name }; - }) || [] - } + system_roles={codes?.system_roles?.map((item: any) => ({ value: item.id, label: item.name })) || []} /> ) : ( <> ) }} /> - - - - Access Requests{' '} - - ({Number(accessRequests?.length ?? 0).toLocaleString()}) - - - - - - - - + ); }; -export default AccessRequestList; +export default AccessRequestPendingList; diff --git a/app/src/features/admin/users/access-requests/list/rejected/AccessRequestRejectedList.tsx b/app/src/features/admin/users/access-requests/list/rejected/AccessRequestRejectedList.tsx new file mode 100644 index 0000000000..b22d0ddab8 --- /dev/null +++ b/app/src/features/admin/users/access-requests/list/rejected/AccessRequestRejectedList.tsx @@ -0,0 +1,128 @@ +import Button from '@mui/material/Button'; +import Dialog from '@mui/material/Dialog'; +import DialogContent from '@mui/material/DialogContent'; +import DialogTitle from '@mui/material/DialogTitle'; +import { GridColDef } from '@mui/x-data-grid'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { getAccessRequestStatusColour } from 'constants/colours'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { IGetAccessRequestsListResponse } from 'interfaces/useAdminApi.interface'; +import { useState } from 'react'; +import { ViewAccessRequestForm } from '../../components/ViewAccessRequestForm'; + +interface IAccessRequestRejectedListProps { + accessRequests: IGetAccessRequestsListResponse[]; +} + +/** + * Returns a data grid component displaying denied access requests + * + * @param props {IAccessRequestRejectedListProps} + * @returns + */ +const AccessRequestRejectedList = (props: IAccessRequestRejectedListProps) => { + const { accessRequests } = props; + + const [showReviewDialog, setShowReviewDialog] = useState(false); + const [activeReview, setActiveReview] = useState(null); + + const accessRequestsColumnDefs: GridColDef[] = [ + { + field: 'display_name', + headerName: 'Display Name', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.data?.displayName; + } + }, + { + field: 'username', + headerName: 'Username', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.data?.username; + } + }, + { + field: 'create_date', + flex: 1, + headerName: 'Date of Request', + disableColumnMenu: true, + valueFormatter: (params) => { + return dayjs(params.value).format(DATE_FORMAT.ShortMediumDateTimeFormat); + } + }, + { + field: 'status_name', + width: 170, + headerName: 'Status', + disableColumnMenu: true, + renderCell: (params) => { + return ( + + ); + } + }, + { + field: 'actions', + headerName: '', + type: 'actions', + flex: 1, + sortable: false, + disableColumnMenu: true, + resizable: false, + align: 'right', + renderCell: (params) => ( + + ) + } + ]; + + return ( + <> + {activeReview && ( + setShowReviewDialog(false)}> + Access Request + + + + + )} + + + ); +}; + +export default AccessRequestRejectedList; diff --git a/app/src/features/admin/users/ActiveUsersList.test.tsx b/app/src/features/admin/users/active/ActiveUsersList.test.tsx similarity index 53% rename from app/src/features/admin/users/ActiveUsersList.test.tsx rename to app/src/features/admin/users/active/ActiveUsersList.test.tsx index ece9f2f459..272db2df25 100644 --- a/app/src/features/admin/users/ActiveUsersList.test.tsx +++ b/app/src/features/admin/users/active/ActiveUsersList.test.tsx @@ -1,6 +1,8 @@ import { AuthStateContext } from 'contexts/authStateContext'; +import { CodesContext, ICodesContext } from 'contexts/codesContext'; import { createMemoryHistory } from 'history'; import { useBiohubApi } from 'hooks/useBioHubApi'; +import { DataLoader } from 'hooks/useDataLoader'; import { Router } from 'react-router'; import { getMockAuthState, SystemAdminAuthState } from 'test-helpers/auth-helpers'; import { codes } from 'test-helpers/code-helpers'; @@ -9,7 +11,7 @@ import ActiveUsersList, { IActiveUsersListProps } from './ActiveUsersList'; const history = createMemoryHistory(); -jest.mock('../../../hooks/useBioHubApi'); +jest.mock('../../../../hooks/useBioHubApi'); const mockBiohubApi = useBiohubApi as jest.Mock; const mockUseApi = { @@ -19,17 +21,29 @@ const mockUseApi = { }, admin: { addSystemUser: jest.fn() + }, + codes: { + getAllCodeSets: jest.fn() } }; +const mockCodesContext: ICodesContext = { + codesDataLoader: { + data: codes, + load: () => {} + } as DataLoader +}; + const renderContainer = (props: IActiveUsersListProps) => { const authState = getMockAuthState({ base: SystemAdminAuthState }); return render( - - - + + + + + ); }; @@ -55,57 +69,6 @@ describe('ActiveUsersList', () => { }); }); - it('shows a table row for an active user with all fields having values', async () => { - const { getByText } = renderContainer({ - activeUsers: [ - { - system_user_id: 1, - user_identifier: 'username', - user_guid: 'user-guid', - record_end_date: '2020-10-10', - role_names: ['role 1'], - identity_source: 'idir', - role_ids: [1], - email: '', - display_name: '', - agency: '' - } - ], - codes: codes, - refresh: () => {} - }); - - await waitFor(() => { - expect(getByText('username')).toBeVisible(); - expect(getByText('role 1')).toBeVisible(); - }); - }); - - it('shows a table row for an active user with fields not having values', async () => { - const { getByTestId } = renderContainer({ - activeUsers: [ - { - system_user_id: 1, - user_identifier: 'username', - user_guid: 'user-guid', - record_end_date: '2020-10-10', - role_names: [], - identity_source: 'idir', - role_ids: [], - email: '', - display_name: '', - agency: '' - } - ], - codes: codes, - refresh: () => {} - }); - - await waitFor(() => { - expect(getByTestId('custom-menu-button-NotApplicable')).toBeInTheDocument(); - }); - }); - it('renders the add new users button correctly', async () => { const { getByTestId } = renderContainer({ activeUsers: [], diff --git a/app/src/features/admin/users/ActiveUsersList.tsx b/app/src/features/admin/users/active/ActiveUsersList.tsx similarity index 82% rename from app/src/features/admin/users/ActiveUsersList.tsx rename to app/src/features/admin/users/active/ActiveUsersList.tsx index d6e48eabd0..f6380948e2 100644 --- a/app/src/features/admin/users/ActiveUsersList.tsx +++ b/app/src/features/admin/users/active/ActiveUsersList.tsx @@ -2,6 +2,7 @@ import { mdiAccountDetailsOutline, mdiChevronDown, mdiDotsVertical, mdiPlus, mdi import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; +import grey from '@mui/material/colors/grey'; import Divider from '@mui/material/Divider'; import Link from '@mui/material/Link'; import Paper from '@mui/material/Paper'; @@ -16,16 +17,18 @@ import { DialogContext, ISnackbarProps } from 'contexts/dialogContext'; import { APIError } from 'hooks/api/useAxios'; import { useAuthStateContext } from 'hooks/useAuthStateContext'; import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useCodesContext } from 'hooks/useContext'; import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; import { ISystemUser } from 'interfaces/useUserApi.interface'; -import { useContext, useState } from 'react'; +import { useContext, useEffect, useState } from 'react'; import { useHistory } from 'react-router'; import { Link as RouterLink } from 'react-router-dom'; +import { getCodesName } from 'utils/Utils'; import AddSystemUsersForm, { AddSystemUsersFormInitialValues, AddSystemUsersFormYupSchema, IAddSystemUsersForm -} from './AddSystemUsersForm'; +} from '../add/AddSystemUsersForm'; export interface IActiveUsersListProps { activeUsers: ISystemUser[]; @@ -50,10 +53,32 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { const [openAddUserDialog, setOpenAddUserDialog] = useState(false); + const codesContext = useCodesContext(); + + useEffect(() => { + codesContext.codesDataLoader.load(); + }, [codesContext.codesDataLoader]); + const activeUsersColumnDefs: GridColDef[] = [ { - field: 'user_identifier', - headerName: 'Username', + field: 'system_user_id', + headerName: 'ID', + width: 70, + minWidth: 70, + renderHeader: () => ( + + ID + + ), + renderCell: (params) => ( + + {params.row.system_user_id} + + ) + }, + { + field: 'display_name', + headerName: 'Display Name', flex: 1, disableColumnMenu: true, renderCell: (params) => { @@ -63,11 +88,29 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { underline="always" to={`/admin/users/${params.row.system_user_id}`} component={RouterLink}> - {params.row.user_identifier || 'No identifier'} + {params.row.display_name || 'No identifier'} ); } }, + { + field: 'identity_source', + headerName: 'Account Type', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.identity_source; + } + }, + { + field: 'user_identifier', + headerName: 'Username', + flex: 1, + disableColumnMenu: true, + valueGetter: (params) => { + return params.row.user_identifier; + } + }, { field: 'role_names', flex: 1, @@ -279,16 +322,16 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { const handleAddSystemUsersSave = async (values: IAddSystemUsersForm) => { setOpenAddUserDialog(false); + const systemUser = values.systemUser; + try { - for (const systemUser of values.systemUsers) { - await biohubApi.admin.addSystemUser( - systemUser.userIdentifier, - systemUser.identitySource, - systemUser.displayName, - systemUser.email, - systemUser.systemRole - ); - } + await biohubApi.admin.addSystemUser( + systemUser.userIdentifier, + systemUser.identitySource, + systemUser.displayName, + systemUser.email, + systemUser.systemRole + ); // Refresh users list refresh(); @@ -297,7 +340,7 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { open: true, snackbarMessage: ( - {values.systemUsers.length} system {values.systemUsers.length > 1 ? 'users' : 'user'} added. + Successfully added {systemUser.displayName} ) }); @@ -307,8 +350,12 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { if (apiError.status === 409) { dialogContext.setErrorDialog({ open: true, - dialogTitle: 'Failed to create users', - dialogText: 'One of the users you added already exists.', + dialogTitle: 'User already exists', + dialogText: `${systemUser.displayName} already exists as a ${getCodesName( + codesContext.codesDataLoader.data, + 'system_roles', + systemUser.systemRole + )}`, onClose: () => { dialogContext.setErrorDialog({ open: false }); }, @@ -339,7 +386,7 @@ const ActiveUsersList = (props: IActiveUsersListProps) => { - Active Users{' '} + Active Users  { { - return { value: item.id, label: item.name }; - }) || [] - } - /> + <> + + This form creates a new user that will be linked to an IDIR/BCeID when an account with a matching + username, email, and account type logs in. + + { + return { value: item.id, label: item.name }; + }) || [] + } + /> + ), initialValues: AddSystemUsersFormInitialValues, - validationSchema: AddSystemUsersFormYupSchema + validationSchema: AddSystemUsersFormYupSchema, + validateOnBlur: false }} onCancel={() => setOpenAddUserDialog(false)} onSave={(values) => { diff --git a/app/src/features/admin/users/add/AddSystemUsersForm.tsx b/app/src/features/admin/users/add/AddSystemUsersForm.tsx new file mode 100644 index 0000000000..2f13b1d813 --- /dev/null +++ b/app/src/features/admin/users/add/AddSystemUsersForm.tsx @@ -0,0 +1,136 @@ +import Box from '@mui/material/Box'; +import Stack from '@mui/material/Stack'; +import AutocompleteField, { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; +import CustomTextField from 'components/fields/CustomTextField'; +import { SYSTEM_IDENTITY_SOURCE } from 'constants/auth'; +import { useFormikContext } from 'formik'; +import React from 'react'; +import yup from 'utils/YupSchema'; + +export interface IAddSystemUsersFormArrayItem { + userIdentifier: string; + displayName: string; + email: string; + identitySource: string; + systemRole: number; +} + +export interface IAddSystemUsersForm { + systemUser: IAddSystemUsersFormArrayItem; +} + +export const AddSystemUsersFormArrayItemInitialValues: IAddSystemUsersFormArrayItem = { + userIdentifier: '', + displayName: '', + email: '', + identitySource: '', + systemRole: '' as unknown as number +}; + +export const AddSystemUsersFormInitialValues: IAddSystemUsersForm = { + systemUser: AddSystemUsersFormArrayItemInitialValues +}; + +export const AddSystemUsersFormYupSchema = yup.object().shape({ + systemUser: yup.object().shape({ + userIdentifier: yup.string().required('Username is required'), + displayName: yup.string().required('Display Name is required'), + email: yup.string().email('Must be a valid email').required('Email is required'), + identitySource: yup.string().required('Account Type is required'), + systemRole: yup.number().required('System Role is required') + }) +}); + +export interface AddSystemUsersFormProps { + systemRoles: IAutocompleteFieldOption[]; +} + +/** + * Returns form component for manually adding system users before access is requested + * + * @param props + * @returns + */ +const AddSystemUsersForm: React.FC = (props) => { + const { values, handleSubmit, getFieldMeta } = useFormikContext(); + + const userIdentifierMeta = getFieldMeta('systemUser.userIdentifier'); + const displayNameMeta = getFieldMeta('systemUser.displayName'); + const emailMeta = getFieldMeta('systemUser.email'); + + const { systemRoles } = props; + const identitySources: IAutocompleteFieldOption[] = [ + { value: SYSTEM_IDENTITY_SOURCE.IDIR as string, label: SYSTEM_IDENTITY_SOURCE.IDIR }, + { value: SYSTEM_IDENTITY_SOURCE.BCEID_BASIC as string, label: SYSTEM_IDENTITY_SOURCE.BCEID_BASIC }, + { value: SYSTEM_IDENTITY_SOURCE.BCEID_BUSINESS as string, label: SYSTEM_IDENTITY_SOURCE.BCEID_BUSINESS }, + { value: SYSTEM_IDENTITY_SOURCE.UNVERIFIED as string, label: SYSTEM_IDENTITY_SOURCE.UNVERIFIED } + ]; + + return ( + + + + + + + + + + + + + + + + + + + + ); +}; + +export default AddSystemUsersForm; diff --git a/app/src/features/admin/users/UsersDetailHeader.test.tsx b/app/src/features/admin/users/projects/UsersDetailHeader.test.tsx similarity index 97% rename from app/src/features/admin/users/UsersDetailHeader.test.tsx rename to app/src/features/admin/users/projects/UsersDetailHeader.test.tsx index 1e24966b8b..cda6451ea1 100644 --- a/app/src/features/admin/users/UsersDetailHeader.test.tsx +++ b/app/src/features/admin/users/projects/UsersDetailHeader.test.tsx @@ -1,14 +1,14 @@ import { DialogContextProvider } from 'contexts/dialogContext'; import { createMemoryHistory } from 'history'; +import { useBiohubApi } from 'hooks/useBioHubApi'; import { ISystemUser } from 'interfaces/useUserApi.interface'; import { Router } from 'react-router'; import { cleanup, fireEvent, render, waitFor } from 'test-helpers/test-utils'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; import UsersDetailHeader from './UsersDetailHeader'; const history = createMemoryHistory(); -jest.mock('../../../hooks/useBioHubApi'); +jest.mock('../../../../hooks/useBioHubApi'); const mockBiohubApi = useBiohubApi as jest.Mock; diff --git a/app/src/features/admin/users/UsersDetailHeader.tsx b/app/src/features/admin/users/projects/UsersDetailHeader.tsx similarity index 88% rename from app/src/features/admin/users/UsersDetailHeader.tsx rename to app/src/features/admin/users/projects/UsersDetailHeader.tsx index 8e096f2741..48d73acebd 100644 --- a/app/src/features/admin/users/UsersDetailHeader.tsx +++ b/app/src/features/admin/users/projects/UsersDetailHeader.tsx @@ -4,17 +4,17 @@ import Breadcrumbs from '@mui/material/Breadcrumbs'; import Button from '@mui/material/Button'; import Link from '@mui/material/Link'; import Typography from '@mui/material/Typography'; +import { IErrorDialogProps } from 'components/dialog/ErrorDialog'; +import { IYesNoDialogProps } from 'components/dialog/YesNoDialog'; import PageHeader from 'components/layout/PageHeader'; +import { SystemUserI18N } from 'constants/i18n'; +import { DialogContext } from 'contexts/dialogContext'; +import { APIError } from 'hooks/api/useAxios'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { ISystemUser } from 'interfaces/useUserApi.interface'; import React, { useCallback, useContext, useMemo } from 'react'; import { useHistory } from 'react-router'; import { Link as RouterLink } from 'react-router-dom'; -import { IErrorDialogProps } from '../../../components/dialog/ErrorDialog'; -import { IYesNoDialogProps } from '../../../components/dialog/YesNoDialog'; -import { SystemUserI18N } from '../../../constants/i18n'; -import { DialogContext } from '../../../contexts/dialogContext'; -import { APIError } from '../../../hooks/api/useAxios'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; -import { ISystemUser } from '../../../interfaces/useUserApi.interface'; export interface IUsersHeaderProps { userDetails: ISystemUser; @@ -97,11 +97,11 @@ const UsersDetailHeader: React.FC = (props) => { Manage Users - {userDetails.user_identifier} + {userDetails.display_name} } - title={userDetails.user_identifier} + title={userDetails.display_name} subTitleJSX={ {userDetails.role_names[0]} diff --git a/app/src/features/admin/users/UsersDetailPage.test.tsx b/app/src/features/admin/users/projects/UsersDetailPage.test.tsx similarity index 90% rename from app/src/features/admin/users/UsersDetailPage.test.tsx rename to app/src/features/admin/users/projects/UsersDetailPage.test.tsx index 1de69e46d3..e12cf2326b 100644 --- a/app/src/features/admin/users/UsersDetailPage.test.tsx +++ b/app/src/features/admin/users/projects/UsersDetailPage.test.tsx @@ -1,15 +1,15 @@ import { createMemoryHistory } from 'history'; +import { useBiohubApi } from 'hooks/useBioHubApi'; import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; +import { IGetUserProjectsListResponse } from 'interfaces/useProjectApi.interface'; +import { ISystemUser } from 'interfaces/useUserApi.interface'; import { Router } from 'react-router'; import { cleanup, render, waitFor } from 'test-helpers/test-utils'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; -import { IGetUserProjectsListResponse } from '../../../interfaces/useProjectApi.interface'; -import { ISystemUser } from '../../../interfaces/useUserApi.interface'; import UsersDetailPage from './UsersDetailPage'; const history = createMemoryHistory(); -jest.mock('../../../hooks/useBioHubApi'); +jest.mock('../../../../hooks/useBioHubApi'); const mockBiohubApi = useBiohubApi as jest.Mock; diff --git a/app/src/features/admin/users/UsersDetailPage.tsx b/app/src/features/admin/users/projects/UsersDetailPage.tsx similarity index 90% rename from app/src/features/admin/users/UsersDetailPage.tsx rename to app/src/features/admin/users/projects/UsersDetailPage.tsx index 5a0dd9b5e6..a9785a8da2 100644 --- a/app/src/features/admin/users/UsersDetailPage.tsx +++ b/app/src/features/admin/users/projects/UsersDetailPage.tsx @@ -1,9 +1,9 @@ import CircularProgress from '@mui/material/CircularProgress'; import Container from '@mui/material/Container'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { ISystemUser } from 'interfaces/useUserApi.interface'; import React, { useEffect, useState } from 'react'; import { useParams } from 'react-router'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; -import { ISystemUser } from '../../../interfaces/useUserApi.interface'; import UsersDetailHeader from './UsersDetailHeader'; import UsersDetailProjects from './UsersDetailProjects'; diff --git a/app/src/features/admin/users/UsersDetailProjects.test.tsx b/app/src/features/admin/users/projects/UsersDetailProjects.test.tsx similarity index 98% rename from app/src/features/admin/users/UsersDetailProjects.test.tsx rename to app/src/features/admin/users/projects/UsersDetailProjects.test.tsx index 4759fcb244..ebac9cf029 100644 --- a/app/src/features/admin/users/UsersDetailProjects.test.tsx +++ b/app/src/features/admin/users/projects/UsersDetailProjects.test.tsx @@ -1,16 +1,16 @@ import { DialogContextProvider } from 'contexts/dialogContext'; import { createMemoryHistory } from 'history'; +import { useBiohubApi } from 'hooks/useBioHubApi'; import { IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; +import { IGetUserProjectsListResponse } from 'interfaces/useProjectApi.interface'; import { ISystemUser } from 'interfaces/useUserApi.interface'; import { Router } from 'react-router'; import { cleanup, fireEvent, render, waitFor } from 'test-helpers/test-utils'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; -import { IGetUserProjectsListResponse } from '../../../interfaces/useProjectApi.interface'; import UsersDetailProjects from './UsersDetailProjects'; const history = createMemoryHistory(); -jest.mock('../../../hooks/useBioHubApi'); +jest.mock('../../../../hooks/useBioHubApi'); const mockBiohubApi = useBiohubApi as jest.Mock; diff --git a/app/src/features/admin/users/UsersDetailProjects.tsx b/app/src/features/admin/users/projects/UsersDetailProjects.tsx similarity index 93% rename from app/src/features/admin/users/UsersDetailProjects.tsx rename to app/src/features/admin/users/projects/UsersDetailProjects.tsx index 7000e425e0..47e7827515 100644 --- a/app/src/features/admin/users/UsersDetailProjects.tsx +++ b/app/src/features/admin/users/projects/UsersDetailProjects.tsx @@ -13,19 +13,19 @@ import TableHead from '@mui/material/TableHead'; import TableRow from '@mui/material/TableRow'; import Toolbar from '@mui/material/Toolbar'; import Typography from '@mui/material/Typography'; +import { IErrorDialogProps } from 'components/dialog/ErrorDialog'; +import { IYesNoDialogProps } from 'components/dialog/YesNoDialog'; +import { CustomMenuButton } from 'components/toolbar/ActionToolbars'; +import { ProjectParticipantsI18N, SystemUserI18N } from 'constants/i18n'; +import { DialogContext } from 'contexts/dialogContext'; +import { APIError } from 'hooks/api/useAxios'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { CodeSet, IGetAllCodeSetsResponse } from 'interfaces/useCodesApi.interface'; +import { IGetUserProjectsListResponse } from 'interfaces/useProjectApi.interface'; +import { ISystemUser } from 'interfaces/useUserApi.interface'; import React, { useCallback, useContext, useEffect, useMemo, useState } from 'react'; import { useParams } from 'react-router'; import { Link as RouterLink } from 'react-router-dom'; -import { IErrorDialogProps } from '../../../components/dialog/ErrorDialog'; -import { IYesNoDialogProps } from '../../../components/dialog/YesNoDialog'; -import { CustomMenuButton } from '../../../components/toolbar/ActionToolbars'; -import { ProjectParticipantsI18N, SystemUserI18N } from '../../../constants/i18n'; -import { DialogContext } from '../../../contexts/dialogContext'; -import { APIError } from '../../../hooks/api/useAxios'; -import { useBiohubApi } from '../../../hooks/useBioHubApi'; -import { CodeSet, IGetAllCodeSetsResponse } from '../../../interfaces/useCodesApi.interface'; -import { IGetUserProjectsListResponse } from '../../../interfaces/useProjectApi.interface'; -import { ISystemUser } from '../../../interfaces/useUserApi.interface'; export interface IProjectDetailsProps { userDetails: ISystemUser; diff --git a/app/src/features/funding-sources/components/FundingSourceForm.tsx b/app/src/features/funding-sources/components/FundingSourceForm.tsx index 8bffd0db04..569a8f3cc6 100644 --- a/app/src/features/funding-sources/components/FundingSourceForm.tsx +++ b/app/src/features/funding-sources/components/FundingSourceForm.tsx @@ -2,7 +2,6 @@ import Box from '@mui/material/Box'; import Typography from '@mui/material/Typography'; import CustomTextField from 'components/fields/CustomTextField'; import StartEndDateFields from 'components/fields/StartEndDateFields'; -import { useFormikContext } from 'formik'; import React from 'react'; export interface IFundingSourceData { @@ -15,8 +14,6 @@ export interface IFundingSourceData { } const FundingSourceForm: React.FC = () => { - const formikProps = useFormikContext(); - return (
@@ -41,13 +38,7 @@ const FundingSourceForm: React.FC = () => { Effective Dates - + diff --git a/app/src/features/funding-sources/details/FundingSourceSurveyReferences.tsx b/app/src/features/funding-sources/details/FundingSourceSurveyReferences.tsx index d6bd0126c3..a1b544e47a 100644 --- a/app/src/features/funding-sources/details/FundingSourceSurveyReferences.tsx +++ b/app/src/features/funding-sources/details/FundingSourceSurveyReferences.tsx @@ -8,6 +8,7 @@ import Paper from '@mui/material/Paper'; import TextField from '@mui/material/TextField'; import Typography from '@mui/material/Typography'; import { DataGrid, GridColDef, GridOverlay } from '@mui/x-data-grid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; import { IGetFundingSourceResponse } from 'interfaces/useFundingSourceApi.interface'; import { debounce } from 'lodash'; import { useCallback, useMemo, useState } from 'react'; @@ -149,22 +150,24 @@ const FundingSourceSurveyReferences = (props: IFundingSourceSurveyReferencesProp fullWidth={true} /> - {fundingSourceSurveyReferences.length === 0 ? ( - - - - No surveys found - - - - ) : ( + + + + No surveys found + + + + }> - )} + ); diff --git a/app/src/features/projects/ProjectsRouter.tsx b/app/src/features/projects/ProjectsRouter.tsx index fd59a5f8a4..671a54c9e2 100644 --- a/app/src/features/projects/ProjectsRouter.tsx +++ b/app/src/features/projects/ProjectsRouter.tsx @@ -5,7 +5,6 @@ import { ObservationsContextProvider } from 'contexts/observationsContext'; import { ProjectAuthStateContextProvider } from 'contexts/projectAuthStateContext'; import { ProjectContextProvider } from 'contexts/projectContext'; import { SurveyContextProvider } from 'contexts/surveyContext'; -import { TelemetryDataContextProvider } from 'contexts/telemetryDataContext'; import ProjectPage from 'features/projects/view/ProjectPage'; import CreateSurveyPage from 'features/surveys/CreateSurveyPage'; import SurveyRouter from 'features/surveys/SurveyRouter'; @@ -95,9 +94,7 @@ const ProjectsRouter: React.FC = () => { validSystemRoles={[SYSTEM_ROLE.SYSTEM_ADMIN, SYSTEM_ROLE.DATA_ADMINISTRATOR]}> - - - + diff --git a/app/src/features/projects/components/ProjectUserForm.tsx b/app/src/features/projects/components/ProjectUserForm.tsx index 6baa68ebb4..08474c0236 100644 --- a/app/src/features/projects/components/ProjectUserForm.tsx +++ b/app/src/features/projects/components/ProjectUserForm.tsx @@ -218,8 +218,8 @@ const ProjectUserForm = (props: IProjectUserFormProps) => { borderTop: '1px solid' + grey[300] } }} - key={renderOption.system_user_id} - {...renderProps}> + {...renderProps} + key={renderOption.system_user_id}> { const mockProjectContext: IProjectContext = { artifactDataLoader: { data: null, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, projectId: 1, projectDataLoader: { @@ -119,7 +121,7 @@ describe('ProjectAttachments', () => { hasLoadedParticipantInfo: true }; - const { getByText } = render( + const { getByTestId } = render( @@ -133,7 +135,7 @@ describe('ProjectAttachments', () => { ); await waitFor(() => { - expect(getByText('No shared files found')).toBeInTheDocument(); + expect(getByTestId('project-attachments-list-no-data-overlay')).toBeInTheDocument(); }); }); @@ -155,7 +157,9 @@ describe('ProjectAttachments', () => { projectId: 1, projectDataLoader: { data: { projectData: { project: { project_name: 'name' } } }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader } as unknown as IProjectContext; @@ -361,12 +365,16 @@ describe('ProjectAttachments', () => { } ] }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, projectId: 1, projectDataLoader: { data: { projectData: { project: { project_name: 'name' } } }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader } as unknown as IProjectContext; diff --git a/app/src/features/projects/view/ProjectAttachmentsList.tsx b/app/src/features/projects/view/ProjectAttachmentsList.tsx index f2fdbeb13f..f272a12b99 100644 --- a/app/src/features/projects/view/ProjectAttachmentsList.tsx +++ b/app/src/features/projects/view/ProjectAttachmentsList.tsx @@ -1,6 +1,10 @@ +import { mdiArrowTopRight } from '@mdi/js'; import Typography from '@mui/material/Typography'; import AttachmentsList from 'components/attachments/list/AttachmentsList'; import ProjectReportAttachmentDialog from 'components/dialog/attachments/project/ProjectReportAttachmentDialog'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { AttachmentType } from 'constants/attachments'; import { AttachmentsI18N } from 'constants/i18n'; import { DialogContext, ISnackbarProps } from 'contexts/dialogContext'; @@ -120,13 +124,29 @@ const ProjectAttachmentsList = () => { open={!!currentAttachment && currentAttachment?.fileType === AttachmentType.REPORT} onClose={handleViewDetailsClose} /> - - attachments={attachmentsList} - handleDownload={handleDownload} - handleDelete={handleDelete} - handleViewDetails={handleViewDetailsOpen} - emptyStateText="No shared files found" - /> + } + isLoadingFallbackDelay={100} + hasNoData={!attachmentsList.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + attachments={attachmentsList} + handleDownload={handleDownload} + handleDelete={handleDelete} + handleViewDetails={handleViewDetailsOpen} + emptyStateText="No shared files found" + /> + ); }; diff --git a/app/src/features/projects/view/components/TeamMember.tsx b/app/src/features/projects/view/components/TeamMember.tsx index 08b47ebba7..381f9e865d 100644 --- a/app/src/features/projects/view/components/TeamMember.tsx +++ b/app/src/features/projects/view/components/TeamMember.tsx @@ -8,6 +8,7 @@ import { PROJECT_ROLE_ICONS } from 'constants/roles'; import { ProjectContext } from 'contexts/projectContext'; import { useContext, useMemo } from 'react'; import { getRandomHexColor } from 'utils/Utils'; +import { TeamMemberAvatar } from './TeamMemberAvatar'; interface IProjectParticipantsRoles { display_name: string; @@ -59,32 +60,20 @@ const TeamMembers = () => { return ( {/* Avatar Box */} - - {member.initials} + + - {/* Member Display Name and Roles */} + {/* Member Display Name */} {member.display_name} - - {/* Roles with Icons */} - {member.roles.map((role) => ( - - - - ))} + {/* Member Roles with Icons */} + {member.roles.map((role) => ( + + + + ))} ); })} diff --git a/app/src/features/projects/view/components/TeamMemberAvatar.tsx b/app/src/features/projects/view/components/TeamMemberAvatar.tsx new file mode 100644 index 0000000000..4b07c16059 --- /dev/null +++ b/app/src/features/projects/view/components/TeamMemberAvatar.tsx @@ -0,0 +1,33 @@ +import Box from '@mui/material/Box'; +import Typography from '@mui/material/Typography'; + +interface ITeamMemberAvatarProps { + color: string; + label: string; + title?: string; +} + +/** + * Returns a circular icon representing a user, typically displaying their initials as the label + * @param props + * @returns + */ +export const TeamMemberAvatar = (props: ITeamMemberAvatarProps) => { + const { color, label, title } = props; + return ( + + {label} + + ); +}; diff --git a/app/src/features/standards/SpeciesStandardsPage.tsx b/app/src/features/standards/SpeciesStandardsPage.tsx deleted file mode 100644 index 881d08a1aa..0000000000 --- a/app/src/features/standards/SpeciesStandardsPage.tsx +++ /dev/null @@ -1,50 +0,0 @@ -import { Box, Container, Paper, Toolbar, Typography } from '@mui/material'; -import PageHeader from 'components/layout/PageHeader'; -import SpeciesAutocompleteField from 'components/species/components/SpeciesAutocompleteField'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; -import SpeciesStandardsResults from './view/SpeciesStandardsResults'; - -/** - * Page to display species standards, which describes what data can be entered and in what structure - * - * @return {*} - */ -const SpeciesStandardsPage = () => { - const biohubApi = useBiohubApi(); - const standardsDataLoader = useDataLoader((species: IPartialTaxonomy) => - biohubApi.standards.getSpeciesStandards(species.tsn) - ); - - return ( - <> - - - - - - Discover data standards for species - - - - { - if (value) { - standardsDataLoader.refresh(value); - } - }} - /> - - - - - - - - ); -}; - -export default SpeciesStandardsPage; diff --git a/app/src/features/standards/StandardsPage.tsx b/app/src/features/standards/StandardsPage.tsx new file mode 100644 index 0000000000..038479645e --- /dev/null +++ b/app/src/features/standards/StandardsPage.tsx @@ -0,0 +1,60 @@ +import { mdiLeaf, mdiPaw, mdiToolbox } from '@mdi/js'; +import Box from '@mui/material/Box'; +import Container from '@mui/material/Container'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import PageHeader from 'components/layout/PageHeader'; +import { useState } from 'react'; +import { StandardsToolbar } from './components/StandardsToolbar'; +import { EnvironmentStandards } from './view/environment/EnvironmentStandards'; +import { MethodStandards } from './view/methods/MethodStandards'; +import { SpeciesStandards } from './view/species/SpeciesStandards'; + +export enum StandardsPageView { + SPECIES = 'SPECIES', + METHODS = 'METHODS', + ENVIRONMENT = 'ENVIRONMENT' +} + +export interface IStandardsPageView { + label: string; + value: StandardsPageView; + icon: string; +} + +const StandardsPage = () => { + const [currentView, setCurrentView] = useState(StandardsPageView.SPECIES); + + const views: IStandardsPageView[] = [ + { label: 'Species', value: StandardsPageView.SPECIES, icon: mdiPaw }, + { label: 'Sampling Methods', value: StandardsPageView.METHODS, icon: mdiToolbox }, + { label: 'Environment variables', value: StandardsPageView.ENVIRONMENT, icon: mdiLeaf } + ]; + + return ( + <> + + + + {/* TOOLBAR FOR SWITCHING VIEWS */} + + + + + + {/* SPECIES STANDARDS */} + {currentView === StandardsPageView.SPECIES && } + + {/* METHOD STANDARDS */} + {currentView === StandardsPageView.METHODS && } + + {/* ENVIRONMENT STANDARDS */} + {currentView === StandardsPageView.ENVIRONMENT && } + + + + + ); +}; + +export default StandardsPage; diff --git a/app/src/features/standards/components/StandardsToolbar.tsx b/app/src/features/standards/components/StandardsToolbar.tsx new file mode 100644 index 0000000000..44ff76623c --- /dev/null +++ b/app/src/features/standards/components/StandardsToolbar.tsx @@ -0,0 +1,64 @@ +import Icon from '@mdi/react'; +import Button from '@mui/material/Button'; +import ToggleButton from '@mui/material/ToggleButton/ToggleButton'; +import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; +import Typography from '@mui/material/Typography'; +import React, { SetStateAction } from 'react'; +import { IStandardsPageView, StandardsPageView } from '../StandardsPage'; + +interface IStandardsToolbar { + views: IStandardsPageView[]; + currentView: StandardsPageView; + setCurrentView: React.Dispatch>; +} + +/** + * Toolbar for setting the standards page view + * + * @param props + * @returns + */ +export const StandardsToolbar = (props: IStandardsToolbar) => { + const { views, currentView, setCurrentView } = props; + + return ( + <> + Data types + , view: StandardsPageView | null) => { + if (view) { + setCurrentView(view); + } + }} + exclusive + sx={{ + display: 'flex', + gap: 1, + '& Button': { + py: 1.25, + px: 2.5, + border: 'none', + borderRadius: '4px !important', + fontSize: '0.875rem', + fontWeight: 700, + letterSpacing: '0.02rem', + textAlign: 'left', + justifyContent: 'flex-start' + } + }}> + {views.map((view) => ( + } + key={view.value} + value={view.value} + color="primary"> + {view.label} + + ))} + + + ); +}; diff --git a/app/src/features/standards/view/SpeciesStandardsResults.tsx b/app/src/features/standards/view/SpeciesStandardsResults.tsx deleted file mode 100644 index 520adc80e7..0000000000 --- a/app/src/features/standards/view/SpeciesStandardsResults.tsx +++ /dev/null @@ -1,96 +0,0 @@ -import { mdiRuler, mdiTag } from '@mdi/js'; -import { Box, CircularProgress, Divider, Stack, Typography } from '@mui/material'; -import { IGetSpeciesStandardsResponse } from 'interfaces/useStandardsApi.interface'; -import { useState } from 'react'; -import MarkingBodyLocationStandardCard from './components/MarkingBodyLocationStandardCard'; -import MeasurementStandardCard from './components/MeasurementStandardCard'; -import SpeciesStandardsToolbar, { SpeciesStandardsViewEnum } from './components/SpeciesStandardsToolbar'; - -interface ISpeciesStandardsResultsProps { - data?: IGetSpeciesStandardsResponse; - isLoading: boolean; -} - -/** - * Component to display species standards results - * - * @return {*} - */ -const SpeciesStandardsResults = (props: ISpeciesStandardsResultsProps) => { - const [activeView, setActiveView] = useState(SpeciesStandardsViewEnum.MEASUREMENTS); - - if (props.isLoading) { - return ( - - - - ); - } - - if (!props.data) { - return <>; - } - - return ( - <> - - - Showing results for{' '} - {props.data.scientificName.split(' ').length >= 2 ? ( - {props.data.scientificName} - ) : ( - props.data.scientificName - )} - - - - - - - - {activeView === 'MEASUREMENTS' && ( - - {props.data.measurements.qualitative.map((measurement) => ( - - ))} - {props.data.measurements.quantitative.map((measurement) => ( - - ))} - - )} - {activeView === 'MARKING BODY LOCATIONS' && ( - - {props.data.markingBodyLocations.map((location) => ( - - ))} - - )} - - ); -}; - -export default SpeciesStandardsResults; diff --git a/app/src/features/standards/view/components/AccordionStandardCard.tsx b/app/src/features/standards/view/components/AccordionStandardCard.tsx new file mode 100644 index 0000000000..1779b4841a --- /dev/null +++ b/app/src/features/standards/view/components/AccordionStandardCard.tsx @@ -0,0 +1,71 @@ +import { mdiChevronDown, mdiChevronUp } from '@mdi/js'; +import { Icon } from '@mdi/react'; +import { Collapse } from '@mui/material'; +import Box, { BoxProps } from '@mui/material/Box'; +import Paper from '@mui/material/Paper'; +import Typography from '@mui/material/Typography'; +import { useState } from 'react'; + +interface IAccordionStandardCardProps extends BoxProps { + label: string; + subtitle?: string | null; + ornament?: JSX.Element; + children?: JSX.Element; + colour: string; + disableCollapse?: boolean; +} + +/** + * Returns a collapsible paper component for displaying lookup values + * @param props + * @returns + */ +export const AccordionStandardCard = (props: IAccordionStandardCardProps) => { + const { label, subtitle, children, colour, ornament, disableCollapse } = props; + + const [isCollapsed, setIsCollapsed] = useState(true); + + const expandable = (children || subtitle) && !disableCollapse; + + const handleHeaderClick = () => { + if (expandable) { + setIsCollapsed(!isCollapsed); + } + }; + + return ( + + + + + {label} + + {ornament} + + {expandable && } + + + + {subtitle && ( + + {subtitle} + + )} + {children} + + + + ); +}; diff --git a/app/src/features/standards/view/components/EnvironmentStandardCard.tsx b/app/src/features/standards/view/components/EnvironmentStandardCard.tsx deleted file mode 100644 index 036309e7c5..0000000000 --- a/app/src/features/standards/view/components/EnvironmentStandardCard.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import { mdiChevronDown, mdiChevronUp } from '@mdi/js'; -import Icon from '@mdi/react'; -import { Box, Card, Collapse, Paper, Stack, Typography } from '@mui/material'; -import { grey } from '@mui/material/colors'; -import { EnvironmentQualitativeOption } from 'interfaces/useReferenceApi.interface'; -import { useState } from 'react'; - -interface IEnvironmentStandardCard { - label: string; - description?: string; - options?: EnvironmentQualitativeOption[]; - unit?: string; - small?: boolean; -} - -/** - * Card to display environment information. - * - * @return {*} - */ -const EnvironmentStandardCard = (props: IEnvironmentStandardCard) => { - const [isCollapsed, setIsCollapsed] = useState(true); - const { small } = props; - - return ( - setIsCollapsed(!isCollapsed)}> - - - {props.label} - - - - - - - {props.description ? props.description : 'No description'} - - - - {props.options?.map((option) => ( - - - {option.name} - - - {option?.description} - - - ))} - - - - ); -}; - -export default EnvironmentStandardCard; diff --git a/app/src/features/standards/view/components/MarkingBodyLocationStandardCard.tsx b/app/src/features/standards/view/components/MarkingBodyLocationStandardCard.tsx deleted file mode 100644 index d271785418..0000000000 --- a/app/src/features/standards/view/components/MarkingBodyLocationStandardCard.tsx +++ /dev/null @@ -1,29 +0,0 @@ -import { Paper, Typography } from '@mui/material'; -import { grey } from '@mui/material/colors'; - -interface IMarkingBodyLocationStandardCard { - label: string; -} - -/** - * Card to display marking body location for species standards - * - * @return {*} - */ -const MarkingBodyLocationStandardCard = (props: IMarkingBodyLocationStandardCard) => { - return ( - - - {props.label} - - - ); -}; - -export default MarkingBodyLocationStandardCard; diff --git a/app/src/features/standards/view/components/MeasurementStandardCard.tsx b/app/src/features/standards/view/components/MeasurementStandardCard.tsx deleted file mode 100644 index 095031a323..0000000000 --- a/app/src/features/standards/view/components/MeasurementStandardCard.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import { mdiChevronDown, mdiChevronUp } from '@mdi/js'; -import Icon from '@mdi/react'; -import { Box, Card, Collapse, Paper, Stack, Typography } from '@mui/material'; -import { grey } from '@mui/material/colors'; -import { CBQualitativeOption } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; - -interface IMeasurementStandardCard { - label: string; - description?: string; - options?: CBQualitativeOption[]; - unit?: string; - small?: boolean; -} - -/** - * Card to display measurements information for species standards - * - * @return {*} - */ -const MeasurementStandardCard = (props: IMeasurementStandardCard) => { - const [isCollapsed, setIsCollapsed] = useState(true); - const { small } = props; - - return ( - setIsCollapsed(!isCollapsed)}> - - - {props.label} - - - - - - - {props.description ? props.description : 'No description'} - - - - {props.options?.map((option) => ( - - - {option.option_label} - - - {option?.option_desc} - - - ))} - - - - ); -}; - -export default MeasurementStandardCard; diff --git a/app/src/features/standards/view/environment/EnvironmentStandards.tsx b/app/src/features/standards/view/environment/EnvironmentStandards.tsx new file mode 100644 index 0000000000..b273a903eb --- /dev/null +++ b/app/src/features/standards/view/environment/EnvironmentStandards.tsx @@ -0,0 +1,64 @@ +import Box from '@mui/material/Box'; +import Skeleton from '@mui/material/Skeleton'; +import Stack from '@mui/material/Stack'; +import TextField from '@mui/material/TextField'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { debounce } from 'lodash-es'; +import { useEffect, useMemo } from 'react'; +import { EnvironmentStandardsResults } from './EnvironmentStandardsResults'; + +/** + * Returns environmental variable lookup values for the standards page + * + * @returns + */ +export const EnvironmentStandards = () => { + const biohubApi = useBiohubApi(); + + const environmentsDataLoader = useDataLoader((keyword?: string) => + biohubApi.standards.getEnvironmentStandards(keyword) + ); + + const debouncedRefresh = useMemo( + () => + debounce((value: string) => { + environmentsDataLoader.refresh(value); + }, 500), + // eslint-disable-next-line react-hooks/exhaustive-deps + [] + ); + + useEffect(() => { + environmentsDataLoader.load(); + }, [environmentsDataLoader]); + + return ( + <> + { + const value = event.currentTarget.value; + debouncedRefresh(value); + }} + /> + + {environmentsDataLoader.data ? ( + + ) : ( + + + + + + + + + )} + + + ); +}; diff --git a/app/src/features/standards/view/environment/EnvironmentStandardsResults.tsx b/app/src/features/standards/view/environment/EnvironmentStandardsResults.tsx new file mode 100644 index 0000000000..d4d22d0e57 --- /dev/null +++ b/app/src/features/standards/view/environment/EnvironmentStandardsResults.tsx @@ -0,0 +1,38 @@ +import { grey } from '@mui/material/colors'; +import Stack from '@mui/material/Stack'; +import { AccordionStandardCard } from 'features/standards/view/components/AccordionStandardCard'; +import { IEnvironmentStandards } from 'interfaces/useStandardsApi.interface'; + +interface ISpeciesStandardsResultsProps { + data: IEnvironmentStandards; +} + +/** + * Component to display environments standards results + * + * @return {*} + */ +export const EnvironmentStandardsResults = (props: ISpeciesStandardsResultsProps) => { + const { data } = props; + + return ( + + {data.quantitative.map((environment) => ( + + ))} + {data.qualitative.map((environment) => ( + + ))} + + ); +}; diff --git a/app/src/features/standards/view/methods/MethodStandards.tsx b/app/src/features/standards/view/methods/MethodStandards.tsx new file mode 100644 index 0000000000..2d540e13a9 --- /dev/null +++ b/app/src/features/standards/view/methods/MethodStandards.tsx @@ -0,0 +1,61 @@ +import { Skeleton, Stack, TextField } from '@mui/material'; +import Box from '@mui/material/Box'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { debounce } from 'lodash-es'; +import { useEffect, useMemo } from 'react'; +import { MethodStandardsResults } from './MethodStandardsResults'; + +/** + * + * Returns information about method lookup options + * + * @returns + */ +export const MethodStandards = () => { + const biohubApi = useBiohubApi(); + + const methodDataLoader = useDataLoader((keyword?: string) => biohubApi.standards.getMethodStandards(keyword)); + + const debouncedRefresh = useMemo( + () => + debounce((value: string) => { + methodDataLoader.refresh(value); + }, 500), + // eslint-disable-next-line react-hooks/exhaustive-deps + [] + ); + + useEffect(() => { + methodDataLoader.load(); + }, [methodDataLoader]); + + return ( + <> + { + const value = event.currentTarget.value; + debouncedRefresh(value); + }} + /> + + {methodDataLoader.data ? ( + + ) : ( + + + + + + + + + )} + + + ); +}; diff --git a/app/src/features/standards/view/methods/MethodStandardsResults.tsx b/app/src/features/standards/view/methods/MethodStandardsResults.tsx new file mode 100644 index 0000000000..001e9bb640 --- /dev/null +++ b/app/src/features/standards/view/methods/MethodStandardsResults.tsx @@ -0,0 +1,66 @@ +import { blueGrey, grey } from '@mui/material/colors'; +import Stack from '@mui/material/Stack'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; +import { IMethodStandard } from 'interfaces/useStandardsApi.interface'; +import { AccordionStandardCard } from '../components/AccordionStandardCard'; + +interface ISpeciesStandardsResultsProps { + data: IMethodStandard[]; +} + +/** + * Component to display methods standards results + * + * @return {*} + */ +export const MethodStandardsResults = (props: ISpeciesStandardsResultsProps) => { + const { data } = props; + + return ( + + {data.map((method) => ( + + {method.attributes.qualitative.map((attribute) => ( + + {attribute.options.map((option) => ( + + ))} + + } + /> + ))} + {method.attributes.quantitative.map((attribute) => ( + } + /> + ))} + + } + /> + ))} + + ); +}; + +export default MethodStandardsResults; diff --git a/app/src/features/standards/view/species/SpeciesStandards.tsx b/app/src/features/standards/view/species/SpeciesStandards.tsx new file mode 100644 index 0000000000..44602950d5 --- /dev/null +++ b/app/src/features/standards/view/species/SpeciesStandards.tsx @@ -0,0 +1,63 @@ +import { mdiArrowTopRight } from '@mdi/js'; +import { Skeleton } from '@mui/material'; +import Box from '@mui/material/Box'; +import Stack from '@mui/material/Stack'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import SpeciesAutocompleteField from 'components/species/components/SpeciesAutocompleteField'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import SpeciesStandardsResults from './SpeciesStandardsResults'; + +/** + * Returns species standards page for searching species and viewing lookup values available for selected species. + * This component handles the data request, then passes the data to its children components. + * + * @returns + */ +export const SpeciesStandards = () => { + const biohubApi = useBiohubApi(); + + const standardsDataLoader = useDataLoader((species: IPartialTaxonomy) => + biohubApi.standards.getSpeciesStandards(species.tsn) + ); + + return ( + <> + { + standardsDataLoader.clearData(); + }} + handleSpecies={(value) => { + if (value) { + standardsDataLoader.refresh(value); + } + }} + /> + + {standardsDataLoader.data && } + {standardsDataLoader.isLoading ? ( + + + + + + + + + + ) : ( + + + + )} + + + ); +}; diff --git a/app/src/features/standards/view/species/SpeciesStandardsResults.tsx b/app/src/features/standards/view/species/SpeciesStandardsResults.tsx new file mode 100644 index 0000000000..92ca47e97b --- /dev/null +++ b/app/src/features/standards/view/species/SpeciesStandardsResults.tsx @@ -0,0 +1,97 @@ +import { mdiRuler, mdiTag } from '@mdi/js'; +import { Box, Divider, Stack, Typography } from '@mui/material'; +import { grey } from '@mui/material/colors'; +import { AccordionStandardCard } from 'features/standards/view/components/AccordionStandardCard'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { ISpeciesStandards } from 'interfaces/useStandardsApi.interface'; +import { useState } from 'react'; +import SpeciesStandardsToolbar, { SpeciesStandardsViewEnum } from './components/SpeciesStandardsToolbar'; + +interface ISpeciesStandardsResultsProps { + data: ISpeciesStandards; +} + +/** + * Component to display species standards results + * + * @return {*} + */ +const SpeciesStandardsResults = (props: ISpeciesStandardsResultsProps) => { + const [activeView, setActiveView] = useState(SpeciesStandardsViewEnum.MEASUREMENTS); + + return ( + <> + + + Showing results for  + + + + + + + + + {activeView === SpeciesStandardsViewEnum.MEASUREMENTS && ( + <> + {props.data.measurements.qualitative.map((measurement) => ( + + {measurement.options.map((option) => ( + + ))} + + } + /> + ))} + {props.data.measurements.quantitative.map((measurement) => ( + + ))} + + )} + {activeView === SpeciesStandardsViewEnum.MARKING_BODY_LOCATIONS && ( + <> + {props.data.markingBodyLocations.map((location) => ( + + ))} + + )} + + + ); +}; + +export default SpeciesStandardsResults; diff --git a/app/src/features/standards/view/components/SpeciesStandardsToolbar.tsx b/app/src/features/standards/view/species/components/SpeciesStandardsToolbar.tsx similarity index 100% rename from app/src/features/standards/view/components/SpeciesStandardsToolbar.tsx rename to app/src/features/standards/view/species/components/SpeciesStandardsToolbar.tsx diff --git a/app/src/features/summary/components/FilterFieldsContainer.tsx b/app/src/features/summary/components/FilterFieldsContainer.tsx index df6086cc96..9400c2706c 100644 --- a/app/src/features/summary/components/FilterFieldsContainer.tsx +++ b/app/src/features/summary/components/FilterFieldsContainer.tsx @@ -44,8 +44,8 @@ export const FilterFieldsContainer = { const { showSearch } = props; const biohubApi = useBiohubApi(); - const codesContext = useCodesContext(); - const taxonomyContext = useTaxonomyContext(); const { searchParams, setSearchParams } = useSearchParams>(); - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - const [paginationModel, setPaginationModel] = useState({ pageSize: Number(searchParams.get('p_limit') ?? ApiPaginationRequestOptionsInitialValues.limit), page: Number(searchParams.get('p_page') ?? ApiPaginationRequestOptionsInitialValues.page) @@ -104,17 +100,17 @@ const ProjectsListContainer = (props: IProjectsListContainerProps) => { [paginationModel.page, paginationModel.pageSize, sort?.field, sort?.sort] ); - const { refresh, isReady, data } = useDataLoader( + const projectsDataLoader = useDataLoader( (pagination: ApiPaginationRequestOptions, filter?: IProjectAdvancedFilters) => biohubApi.project.findProjects(pagination, filter) ); // Fetch projects when either the pagination, sort, or advanced filters change useDeepCompareEffect(() => { - refresh(paginationSort, advancedFiltersModel); + projectsDataLoader.refresh(paginationSort, advancedFiltersModel); }, [advancedFiltersModel, paginationSort]); - const rows = data?.projects ?? []; + const rows = projectsDataLoader.data?.projects ?? []; // Define the columns for the DataGrid const columns: GridColDef[] = [ @@ -140,18 +136,6 @@ const ProjectsListContainer = (props: IProjectsListContainerProps) => { flex: 1, disableColumnMenu: true, renderCell: (params) => { - const focalSpecies = params.row.focal_species - .map((species) => taxonomyContext.getCachedSpeciesTaxonomyById(species)?.commonNames) - .filter(Boolean) - .join(' \u2013 '); // n-dash with spaces - - const types = params.row.types - .map((type) => getCodesName(codesContext.codesDataLoader.data, 'type', type || 0)) - .filter(Boolean) - .join(' \u2013 '); // n-dash with spaces - - const detailsArray = [focalSpecies, types].filter(Boolean).join(' \u2013 '); - return ( { to={`/admin/projects/${params.row.project_id}`} children={params.row.name} /> - {/* Only administrators see the second title to help them find Projects with a standard naming convention */} - - {detailsArray.length > 0 ? ( - - {detailsArray} - - ) : ( - - There are no Surveys in this Project - - )} - ); } }, + { + field: 'members', + headerName: 'Members', + flex: 0.4, + renderCell: (params) => ( + + {params.row.members.map((member) => ( + name.trim().slice(0, 1).toUpperCase()) + .reverse() + .join('')} + color={getRandomHexColor(member.system_user_id)} + /> + ))} + + ) + }, { field: 'regions', headerName: 'Region', type: 'string', - flex: 0.4, + flex: 0.5, renderCell: (params) => ( {params.row.regions.map((region) => { @@ -200,7 +193,7 @@ const ProjectsListContainer = (props: IProjectsListContainerProps) => { return ( <> - + { @@ -216,63 +209,67 @@ const ProjectsListContainer = (props: IProjectsListContainerProps) => { - - row.project_id} - // Pagination - paginationMode="server" - paginationModel={paginationModel} - pageSizeOptions={pageSizeOptions} - onPaginationModelChange={(model) => { - if (!model) { - return; - } - setSearchParams(searchParams.set('p_page', String(model.page)).set('p_limit', String(model.pageSize))); - setPaginationModel(model); - }} - // Sorting - sortingMode="server" - sortModel={sortModel} - sortingOrder={['asc', 'desc']} - onSortModelChange={(model) => { - if (!model.length) { - return; - } - setSearchParams(searchParams.set('p_sort', model[0].field).set('p_order', model[0].sort ?? 'desc')); - setSortModel(model); - }} - // Row options - rowSelection={false} - checkboxSelection={false} - disableRowSelectionOnClick - // Column options - disableColumnSelector - disableColumnFilter - disableColumnMenu - // Styling - rowHeight={70} - getRowHeight={() => 'auto'} - autoHeight={false} - sx={{ - '& .MuiDataGrid-overlay': { - background: grey[50] - }, - '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' + + + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.project_id} + // Pagination + paginationMode="server" + paginationModel={paginationModel} + pageSizeOptions={pageSizeOptions} + onPaginationModelChange={(model) => { + if (!model) { + return; } - } - }} - /> + setSearchParams(searchParams.set('p_page', String(model.page)).set('p_limit', String(model.pageSize))); + setPaginationModel(model); + }} + // Sorting + sortingMode="server" + sortModel={sortModel} + sortingOrder={['asc', 'desc']} + onSortModelChange={(model) => { + if (!model.length) { + return; + } + setSearchParams(searchParams.set('p_sort', model[0].field).set('p_order', model[0].sort ?? 'desc')); + setSortModel(model); + }} + // Row options + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + // Column options + disableColumnSelector + disableColumnFilter + disableColumnMenu + // Styling + rowHeight={70} + getRowHeight={() => 'auto'} + autoHeight={false} + /> + ); diff --git a/app/src/features/summary/list-data/survey/SurveysListContainer.tsx b/app/src/features/summary/list-data/survey/SurveysListContainer.tsx index 0f9dccb619..5226ea5e04 100644 --- a/app/src/features/summary/list-data/survey/SurveysListContainer.tsx +++ b/app/src/features/summary/list-data/survey/SurveysListContainer.tsx @@ -1,3 +1,4 @@ +import { mdiArrowTopRight } from '@mdi/js'; import Box from '@mui/material/Box'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; @@ -8,23 +9,23 @@ import Typography from '@mui/material/Typography'; import { GridColDef, GridPaginationModel, GridSortDirection, GridSortModel } from '@mui/x-data-grid'; import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; -import { SystemRoleGuard } from 'components/security/Guards'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { getNrmRegionColour, NrmRegionKeys } from 'constants/colours'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; import { NRM_REGION_APPENDED_TEXT } from 'constants/regions'; -import { SYSTEM_ROLE } from 'constants/roles'; import dayjs from 'dayjs'; +import { SurveyProgressChip } from 'features/surveys/components/SurveyProgressChip'; import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCodesContext, useTaxonomyContext } from 'hooks/useContext'; import useDataLoader from 'hooks/useDataLoader'; import { useDeepCompareEffect } from 'hooks/useDeepCompareEffect'; import { useSearchParams } from 'hooks/useSearchParams'; import { SurveyBasicFieldsObject } from 'interfaces/useSurveyApi.interface'; -import { useEffect, useState } from 'react'; +import { useState } from 'react'; import { Link as RouterLink } from 'react-router-dom'; import { ApiPaginationRequestOptions, StringValues } from 'types/misc'; -import { firstOrNull, getCodesName } from 'utils/Utils'; -import { SurveyProgressChip } from '../../../surveys/components/SurveyProgressChip'; +import { firstOrNull } from 'utils/Utils'; import SurveysListFilterForm, { ISurveyAdvancedFilters, SurveyAdvancedFiltersInitialValues @@ -67,15 +68,9 @@ const SurveysListContainer = (props: ISurveysListContainerProps) => { const { showSearch } = props; const biohubApi = useBiohubApi(); - const codesContext = useCodesContext(); - const taxonomyContext = useTaxonomyContext(); const { searchParams, setSearchParams } = useSearchParams>(); - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - const [paginationModel, setPaginationModel] = useState({ pageSize: Number(searchParams.get('s_limit') ?? initialPaginationParams.limit), page: Number(searchParams.get('s_page') ?? initialPaginationParams.page) @@ -138,22 +133,6 @@ const SurveysListContainer = (props: ISurveysListContainerProps) => { flex: 1, disableColumnMenu: true, renderCell: (params) => { - const dates = [params.row.start_date?.split('-')[0], params.row.end_date?.split('-')[0]] - .filter(Boolean) - .join(' \u2013 '); // n-dash with spaces - - const focalSpecies = params.row.focal_species - .map((species) => taxonomyContext.getCachedSpeciesTaxonomyById(species)?.commonNames) - .filter(Boolean) - .join(' \u2013 '); // n-dash with spaces - - const types = params.row.types - .map((type) => getCodesName(codesContext.codesDataLoader.data, 'type', type || 0)) - .filter(Boolean) - .join(' \u2013 '); // n-dash with spaces - - const detailsArray = [dates, focalSpecies, types].filter(Boolean).join(' \u2013 '); - return ( { to={`/admin/projects/${params.row.project_id}/surveys/${params.row.survey_id}`} children={params.row.name} /> - {/* Only administrators see the second title to help them find Projects with a standard naming convention */} - - - {detailsArray} - - ); } @@ -227,7 +200,7 @@ const SurveysListContainer = (props: ISurveysListContainerProps) => { return ( <> - + { @@ -243,63 +216,67 @@ const SurveysListContainer = (props: ISurveysListContainerProps) => { - - row.survey_id} - // Pagination - paginationMode="server" - paginationModel={paginationModel} - pageSizeOptions={pageSizeOptions} - onPaginationModelChange={(model) => { - if (!model) { - return; - } - setSearchParams(searchParams.set('s_page', String(model.page)).set('s_limit', String(model.pageSize))); - setPaginationModel(model); - }} - // Sorting - sortingMode="server" - sortModel={sortModel} - sortingOrder={['asc', 'desc']} - onSortModelChange={(model) => { - if (!model.length) { - return; - } - setSearchParams(searchParams.set('s_sort', model[0].field).set('s_order', model[0].sort ?? 'desc')); - setSortModel(model); - }} - // Row options - checkboxSelection={false} - disableRowSelectionOnClick - rowSelection={false} - // Column options - disableColumnSelector - disableColumnFilter - disableColumnMenu - // Styling - rowHeight={70} - getRowHeight={() => 'auto'} - autoHeight={false} - sx={{ - '& .MuiDataGrid-overlay': { - background: grey[50] - }, - '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' + + + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.survey_id} + // Pagination + paginationMode="server" + paginationModel={paginationModel} + pageSizeOptions={pageSizeOptions} + onPaginationModelChange={(model) => { + if (!model) { + return; + } + setSearchParams(searchParams.set('s_page', String(model.page)).set('s_limit', String(model.pageSize))); + setPaginationModel(model); + }} + // Sorting + sortingMode="server" + sortModel={sortModel} + sortingOrder={['asc', 'desc']} + onSortModelChange={(model) => { + if (!model.length) { + return; } - } - }} - /> + setSearchParams(searchParams.set('s_sort', model[0].field).set('s_order', model[0].sort ?? 'desc')); + setSortModel(model); + }} + // Row options + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + // Column options + disableColumnSelector + disableColumnFilter + disableColumnMenu + // Styling + rowHeight={70} + getRowHeight={() => 'auto'} + autoHeight={false} + /> + ); diff --git a/app/src/features/summary/list-data/survey/SurveysListFilterForm.tsx b/app/src/features/summary/list-data/survey/SurveysListFilterForm.tsx index d015ca82c1..8f1adefade 100644 --- a/app/src/features/summary/list-data/survey/SurveysListFilterForm.tsx +++ b/app/src/features/summary/list-data/survey/SurveysListFilterForm.tsx @@ -71,7 +71,6 @@ const SurveysListFilterForm = (props: ISurveysListFilterFormProps) => { { if (value?.system_user_id) { formikProps.setFieldValue('system_user_id', value.system_user_id); diff --git a/app/src/features/summary/tabular-data/TabularDataTableContainer.tsx b/app/src/features/summary/tabular-data/TabularDataTableContainer.tsx index 7f34f51b7d..ba9e879dc1 100644 --- a/app/src/features/summary/tabular-data/TabularDataTableContainer.tsx +++ b/app/src/features/summary/tabular-data/TabularDataTableContainer.tsx @@ -1,10 +1,12 @@ -import { mdiEye, mdiMagnify, mdiPaw, mdiWifiMarker } from '@mdi/js'; +import { mdiEye, mdiPaw, mdiWifiMarker } from '@mdi/js'; import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; import Divider from '@mui/material/Divider'; +import Stack from '@mui/material/Stack'; import ToggleButton from '@mui/material/ToggleButton'; import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; -import Toolbar from '@mui/material/Toolbar'; +import Typography from '@mui/material/Typography'; import AnimalsListContainer from 'features/summary/tabular-data/animal/AnimalsListContainer'; import ObservationsListContainer from 'features/summary/tabular-data/observation/ObservationsListContainer'; import TelemetryListContainer from 'features/summary/tabular-data/telemetry/TelemetryListContainer'; @@ -32,12 +34,14 @@ type TabularDataTableURLParams = { const buttonSx = { py: 0.5, - px: 1.5, + px: 2, border: 'none', fontWeight: 700, borderRadius: '4px !important', fontSize: '0.875rem', - letterSpacing: '0.02rem' + letterSpacing: '0.02rem', + minHeight: '35px', + justifyContent: 'flex-start' }; /** @@ -49,7 +53,7 @@ export const TabularDataTableContainer = () => { const { searchParams, setSearchParams } = useSearchParams(); const [activeView, setActiveView] = useState(searchParams.get(ACTIVE_VIEW_KEY) ?? ACTIVE_VIEW_VALUE.observations); - const [showSearch, setShowSearch] = useState(searchParams.get(SHOW_SEARCH_KEY) === SHOW_SEARCH_VALUE.true); + const showSearch = true; const views = [ { value: ACTIVE_VIEW_VALUE.observations, label: 'observations', icon: mdiEye }, @@ -68,47 +72,37 @@ export const TabularDataTableContainer = () => { }; return ( - <> - - - {views.map((view) => ( - } - value={view.value}> - {view.label} - - ))} - - - - - - {activeView === ACTIVE_VIEW_VALUE.observations && } - {activeView === ACTIVE_VIEW_VALUE.animals && } - {activeView === ACTIVE_VIEW_VALUE.telemetry && } - + + + Data + {views.map((view) => ( + } + value={view.value}> + {view.label} + + ))} + + + + {activeView === ACTIVE_VIEW_VALUE.observations && } + {activeView === ACTIVE_VIEW_VALUE.animals && } + {activeView === ACTIVE_VIEW_VALUE.telemetry && } + + ); }; diff --git a/app/src/features/summary/tabular-data/animal/AnimalsListContainer.tsx b/app/src/features/summary/tabular-data/animal/AnimalsListContainer.tsx index fc53dd8b74..dcafbcd54d 100644 --- a/app/src/features/summary/tabular-data/animal/AnimalsListContainer.tsx +++ b/app/src/features/summary/tabular-data/animal/AnimalsListContainer.tsx @@ -1,3 +1,4 @@ +import { mdiArrowTopRight } from '@mdi/js'; import Box from '@mui/material/Box'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; @@ -5,6 +6,9 @@ import Divider from '@mui/material/Divider'; import Typography from '@mui/material/Typography'; import { GridColDef, GridPaginationModel, GridSortDirection, GridSortModel } from '@mui/x-data-grid'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { useBiohubApi } from 'hooks/useBioHubApi'; import useDataLoader from 'hooks/useDataLoader'; import { useDeepCompareEffect } from 'hooks/useDeepCompareEffect'; @@ -91,7 +95,7 @@ const AnimalsListContainer = (props: IAnimalsListContainerProps) => { animalsDataLoader.refresh(paginationSort, advancedFiltersModel); }, [advancedFiltersModel, paginationSort]); - const animalRows = animalsDataLoader.data?.animals ?? []; + const rows = animalsDataLoader.data?.animals ?? []; const columns: GridColDef[] = [ { @@ -141,7 +145,7 @@ const AnimalsListContainer = (props: IAnimalsListContainerProps) => { return ( <> - + { @@ -152,63 +156,67 @@ const AnimalsListContainer = (props: IAnimalsListContainerProps) => { - - row.critter_id} - // Pagination - paginationMode="server" - pageSizeOptions={pageSizeOptions} - paginationModel={paginationModel} - onPaginationModelChange={(model) => { - if (!model) { - return; - } - setSearchParams(searchParams.set('a_page', String(model.page)).set('a_limit', String(model.pageSize))); - setPaginationModel(model); - }} - // Sorting - sortingMode="server" - sortModel={sortModel} - sortingOrder={['asc', 'desc']} - onSortModelChange={(model) => { - if (!model.length) { - return; - } - setSearchParams(searchParams.set('a_sort', model[0].field).set('a_order', model[0].sort ?? 'desc')); - setSortModel(model); - }} - // Row options - checkboxSelection={false} - disableRowSelectionOnClick - rowSelection={false} - // Column options - disableColumnSelector - disableColumnFilter - disableColumnMenu - // Styling - rowHeight={70} - getRowHeight={() => 'auto'} - autoHeight={false} - sx={{ - '& .MuiDataGrid-overlay': { - background: grey[50] - }, - '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' + + + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.critter_id} + // Pagination + paginationMode="server" + paginationModel={paginationModel} + pageSizeOptions={pageSizeOptions} + onPaginationModelChange={(model) => { + if (!model) { + return; + } + setSearchParams(searchParams.set('a_page', String(model.page)).set('a_limit', String(model.pageSize))); + setPaginationModel(model); + }} + // Sorting + sortingMode="server" + sortModel={sortModel} + sortingOrder={['asc', 'desc']} + onSortModelChange={(model) => { + if (!model.length) { + return; } - } - }} - /> + setSearchParams(searchParams.set('a_sort', model[0].field).set('a_order', model[0].sort ?? 'desc')); + setSortModel(model); + }} + // Row options + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + // Column options + disableColumnSelector + disableColumnFilter + disableColumnMenu + // Styling + rowHeight={70} + getRowHeight={() => 'auto'} + autoHeight={false} + /> + ); diff --git a/app/src/features/summary/tabular-data/observation/ObservationsListContainer.tsx b/app/src/features/summary/tabular-data/observation/ObservationsListContainer.tsx index 4b4667a275..5f43fff388 100644 --- a/app/src/features/summary/tabular-data/observation/ObservationsListContainer.tsx +++ b/app/src/features/summary/tabular-data/observation/ObservationsListContainer.tsx @@ -1,3 +1,4 @@ +import { mdiArrowTopRight } from '@mdi/js'; import Box from '@mui/material/Box'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; @@ -5,16 +6,18 @@ import Divider from '@mui/material/Divider'; import Typography from '@mui/material/Typography'; import { GridColDef, GridPaginationModel, GridSortDirection, GridSortModel } from '@mui/x-data-grid'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; import { IObservationTableRow } from 'contexts/observationsTableContext'; import dayjs from 'dayjs'; import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCodesContext } from 'hooks/useContext'; import useDataLoader from 'hooks/useDataLoader'; import { useDeepCompareEffect } from 'hooks/useDeepCompareEffect'; import { useSearchParams } from 'hooks/useSearchParams'; import { IGetSurveyObservationsResponse } from 'interfaces/useObservationApi.interface'; -import { useCallback, useEffect, useState } from 'react'; +import { useCallback, useState } from 'react'; import { ApiPaginationRequestOptions, StringValues } from 'types/misc'; import { firstOrNull } from 'utils/Utils'; import { @@ -53,7 +56,7 @@ const initialPaginationParams: Required = { page: 0, limit: 10, sort: 'survey_observation_id', - order: 'desc' + order: 'asc' }; /** @@ -65,14 +68,9 @@ const ObservationsListContainer = (props: IObservationsListContainerProps) => { const { showSearch } = props; const biohubApi = useBiohubApi(); - const codesContext = useCodesContext(); const { searchParams, setSearchParams } = useSearchParams>(); - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - const [paginationModel, setPaginationModel] = useState({ pageSize: Number(searchParams.get('o_limit') ?? initialPaginationParams.limit), page: Number(searchParams.get('o_page') ?? initialPaginationParams.page) @@ -163,7 +161,7 @@ const ObservationsListContainer = (props: IObservationsListContainerProps) => { [] ); - const observationRows = observationsDataLoader.data ? getRowsFromObservations(observationsDataLoader.data) : []; + const rows = observationsDataLoader.data ? getRowsFromObservations(observationsDataLoader.data) : []; const columns: GridColDef[] = [ { @@ -226,7 +224,7 @@ const ObservationsListContainer = (props: IObservationsListContainerProps) => { return ( <> - + { @@ -247,63 +245,67 @@ const ObservationsListContainer = (props: IObservationsListContainerProps) => { - - row.observation_subcount_id} - // Pagination - paginationMode="server" - pageSizeOptions={pageSizeOptions} - paginationModel={paginationModel} - onPaginationModelChange={(model) => { - if (!model) { - return; - } - setSearchParams(searchParams.set('o_page', String(model.page)).set('o_limit', String(model.pageSize))); - setPaginationModel(model); - }} - // Sorting - sortingMode="server" - sortModel={sortModel} - sortingOrder={['asc', 'desc']} - onSortModelChange={(model) => { - if (!model.length) { - return; - } - setSearchParams(searchParams.set('o_sort', model[0].field).set('o_order', model[0].sort ?? 'desc')); - setSortModel(model); - }} - // Row options - checkboxSelection={false} - disableRowSelectionOnClick - rowSelection={false} - // Column options - disableColumnSelector - disableColumnFilter - disableColumnMenu - // Styling - rowHeight={70} - getRowHeight={() => 'auto'} - autoHeight={false} - sx={{ - '& .MuiDataGrid-overlay': { - background: grey[50] - }, - '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' + + + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.observation_subcount_id} + // Pagination + paginationMode="server" + paginationModel={paginationModel} + pageSizeOptions={pageSizeOptions} + onPaginationModelChange={(model) => { + if (!model) { + return; + } + setSearchParams(searchParams.set('o_page', String(model.page)).set('o_limit', String(model.pageSize))); + setPaginationModel(model); + }} + // Sorting + sortingMode="server" + sortModel={sortModel} + sortingOrder={['asc', 'desc']} + onSortModelChange={(model) => { + if (!model.length) { + return; } - } - }} - /> + setSearchParams(searchParams.set('o_sort', model[0].field).set('o_order', model[0].sort ?? 'desc')); + setSortModel(model); + }} + // Row options + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + // Column options + disableColumnSelector + disableColumnFilter + disableColumnMenu + // Styling + rowHeight={70} + getRowHeight={() => 'auto'} + autoHeight={false} + /> + ); diff --git a/app/src/features/summary/tabular-data/telemetry/TelemetryListContainer.tsx b/app/src/features/summary/tabular-data/telemetry/TelemetryListContainer.tsx index 843ed8ffa1..1609839ea1 100644 --- a/app/src/features/summary/tabular-data/telemetry/TelemetryListContainer.tsx +++ b/app/src/features/summary/tabular-data/telemetry/TelemetryListContainer.tsx @@ -1,3 +1,4 @@ +import { mdiArrowTopRight } from '@mdi/js'; import Box from '@mui/material/Box'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; @@ -5,6 +6,9 @@ import Divider from '@mui/material/Divider'; import Typography from '@mui/material/Typography'; import { GridColDef, GridPaginationModel, GridSortDirection, GridSortModel } from '@mui/x-data-grid'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; import dayjs from 'dayjs'; import { useBiohubApi } from 'hooks/useBioHubApi'; @@ -16,7 +20,7 @@ import { useState } from 'react'; import { ApiPaginationRequestOptions, StringValues } from 'types/misc'; import { firstOrNull } from 'utils/Utils'; import TelemetryListFilterForm, { - ITelemetryAdvancedFilters, + IAllTelemetryAdvancedFilters, TelemetryAdvancedFiltersInitialValues } from './TelemetryListFilterForm'; @@ -34,7 +38,7 @@ type TelemetryDataTableURLParams = { const pageSizeOptions = [10, 25, 50]; -interface ITelemetryListContainerProps { +interface IAllTelemetryListContainerProps { showSearch: boolean; } @@ -51,7 +55,7 @@ const initialPaginationParams: ApiPaginationRequestOptions = { * * @return {*} */ -const TelemetryListContainer = (props: ITelemetryListContainerProps) => { +const TelemetryListContainer = (props: IAllTelemetryListContainerProps) => { const { showSearch } = props; const biohubApi = useBiohubApi(); @@ -70,7 +74,7 @@ const TelemetryListContainer = (props: ITelemetryListContainerProps) => { } ]); - const [advancedFiltersModel, setAdvancedFiltersModel] = useState({ + const [advancedFiltersModel, setAdvancedFiltersModel] = useState({ itis_tsn: searchParams.get('t_itis_tsn') ? Number(searchParams.get('t_itis_tsn')) : TelemetryAdvancedFiltersInitialValues.itis_tsn @@ -85,7 +89,7 @@ const TelemetryListContainer = (props: ITelemetryListContainerProps) => { }; const telemetryDataLoader = useDataLoader( - (pagination?: ApiPaginationRequestOptions, filter?: ITelemetryAdvancedFilters) => + (pagination?: ApiPaginationRequestOptions, filter?: IAllTelemetryAdvancedFilters) => biohubApi.telemetry.findTelemetry(pagination, filter) ); @@ -93,14 +97,13 @@ const TelemetryListContainer = (props: ITelemetryListContainerProps) => { telemetryDataLoader.refresh(paginationSort, advancedFiltersModel); }, [advancedFiltersModel, paginationSort]); - const telemetryRows = telemetryDataLoader.data?.telemetry ?? []; + const rows = telemetryDataLoader.data?.telemetry ?? []; const columns: GridColDef[] = [ { field: 'telemetry_id', headerName: 'ID', - width: 50, - minWidth: 50, + minWidth: 200, sortable: false, renderHeader: () => ( @@ -145,7 +148,7 @@ const TelemetryListContainer = (props: ITelemetryListContainerProps) => { return ( <> - + { @@ -156,63 +159,67 @@ const TelemetryListContainer = (props: ITelemetryListContainerProps) => { - - row.telemetry_id} - // Pagination - paginationMode="server" - pageSizeOptions={pageSizeOptions} - paginationModel={paginationModel} - onPaginationModelChange={(model) => { - if (!model) { - return; - } - setSearchParams(searchParams.set('t_page', String(model.page)).set('t_limit', String(model.pageSize))); - setPaginationModel(model); - }} - // Sorting - sortingMode="server" - sortModel={sortModel} - sortingOrder={['asc', 'desc']} - onSortModelChange={(model) => { - if (!model[0]) { - return; - } - setSearchParams(searchParams.set('t_sort', model[0].field).set('t_order', model[0].sort ?? 'desc')); - setSortModel(model); - }} - // Row options - checkboxSelection={false} - disableRowSelectionOnClick - rowSelection={false} - // Column options - disableColumnSelector - disableColumnFilter - disableColumnMenu - // Styling - rowHeight={70} - getRowHeight={() => 'auto'} - autoHeight={false} - sx={{ - '& .MuiDataGrid-overlay': { - background: grey[50] - }, - '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' + + + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.telemetry_id} + // Pagination + paginationMode="server" + paginationModel={paginationModel} + pageSizeOptions={pageSizeOptions} + onPaginationModelChange={(model) => { + if (!model) { + return; + } + setSearchParams(searchParams.set('t_page', String(model.page)).set('t_limit', String(model.pageSize))); + setPaginationModel(model); + }} + // Sorting + sortingMode="server" + sortModel={sortModel} + sortingOrder={['asc', 'desc']} + onSortModelChange={(model) => { + if (!model.length) { + return; } - } - }} - /> + setSearchParams(searchParams.set('t_sort', model[0].field).set('t_order', model[0].sort ?? 'desc')); + setSortModel(model); + }} + // Row options + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + // Column options + disableColumnSelector + disableColumnFilter + disableColumnMenu + // Styling + rowHeight={70} + getRowHeight={() => 'auto'} + autoHeight={false} + /> + ); diff --git a/app/src/features/summary/tabular-data/telemetry/TelemetryListFilterForm.tsx b/app/src/features/summary/tabular-data/telemetry/TelemetryListFilterForm.tsx index 34fdc80766..d16e02529d 100644 --- a/app/src/features/summary/tabular-data/telemetry/TelemetryListFilterForm.tsx +++ b/app/src/features/summary/tabular-data/telemetry/TelemetryListFilterForm.tsx @@ -4,17 +4,17 @@ import { FilterFieldsContainer } from 'features/summary/components/FilterFieldsC import { Formik } from 'formik'; import { useTaxonomyContext } from 'hooks/useContext'; -export type ITelemetryAdvancedFilters = { +export type IAllTelemetryAdvancedFilters = { itis_tsn?: number; }; -export const TelemetryAdvancedFiltersInitialValues: ITelemetryAdvancedFilters = { +export const TelemetryAdvancedFiltersInitialValues: IAllTelemetryAdvancedFilters = { itis_tsn: undefined }; -export interface ITelemetryListFilterFormProps { - handleSubmit: (filterValues: ITelemetryAdvancedFilters) => void; - initialValues?: ITelemetryAdvancedFilters; +export interface IAllTelemetryListFilterFormProps { + handleSubmit: (filterValues: IAllTelemetryAdvancedFilters) => void; + initialValues?: IAllTelemetryAdvancedFilters; } /** @@ -23,10 +23,10 @@ export interface ITelemetryListFilterFormProps { * TODO: The filter fields are disabled for now. The fields are functional (the values are captured and passed to the * backend), but the backend does not currently use them for filtering. * - * @param {ITelemetryListFilterFormProps} props + * @param {IAllTelemetryListFilterFormProps} props * @return {*} */ -const TelemetryListFilterForm = (props: ITelemetryListFilterFormProps) => { +const TelemetryListFilterForm = (props: IAllTelemetryListFilterFormProps) => { const { handleSubmit, initialValues } = props; const taxonomyContext = useTaxonomyContext(); diff --git a/app/src/features/surveys/CreateSurveyPage.tsx b/app/src/features/surveys/CreateSurveyPage.tsx index 4212920be8..54436b3f8d 100644 --- a/app/src/features/surveys/CreateSurveyPage.tsx +++ b/app/src/features/surveys/CreateSurveyPage.tsx @@ -13,6 +13,7 @@ import { CreateSurveyI18N } from 'constants/i18n'; import { CodesContext } from 'contexts/codesContext'; import { DialogContext } from 'contexts/dialogContext'; import { ProjectContext } from 'contexts/projectContext'; +import { ISurveyPermitForm, SurveyPermitFormInitialValues } from 'features/surveys/components/permit/SurveyPermitForm'; import { SurveyPartnershipsFormInitialValues } from 'features/surveys/view/components/SurveyPartnershipsForm'; import { FormikProps } from 'formik'; import { APIError } from 'hooks/api/useAxios'; @@ -24,17 +25,22 @@ import { Prompt, useHistory } from 'react-router'; import { Link as RouterLink } from 'react-router-dom'; import { AgreementsInitialValues } from './components/agreements/AgreementsForm'; import { ProprietaryDataInitialValues } from './components/agreements/ProprietaryDataForm'; -import { SurveyFundingSourceFormInitialValues } from './components/funding/SurveyFundingSourceForm'; +import { + ISurveyFundingSourceForm, + SurveyFundingSourceFormInitialValues +} from './components/funding/SurveyFundingSourceForm'; import { GeneralInformationInitialValues } from './components/general-information/GeneralInformationForm'; import { SurveyLocationInitialValues } from './components/locations/StudyAreaForm'; import { PurposeAndMethodologyInitialValues } from './components/methodology/PurposeAndMethodologyForm'; import { SurveyUserJobFormInitialValues } from './components/participants/SurveyUserForm'; import { SurveyBlockInitialValues } from './components/sampling-strategy/blocks/SurveyBlockForm'; import { SurveySiteSelectionInitialValues } from './components/sampling-strategy/SurveySiteSelectionForm'; +import { SpeciesInitialValues } from './components/species/SpeciesForm'; import EditSurveyForm from './edit/EditSurveyForm'; -export const defaultSurveyDataFormValues: ICreateSurveyRequest = { +export const defaultSurveyDataFormValues: ICreateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm = { ...GeneralInformationInitialValues, + ...SurveyPermitFormInitialValues, ...PurposeAndMethodologyInitialValues, ...SurveyFundingSourceFormInitialValues, ...SurveyPartnershipsFormInitialValues, @@ -43,7 +49,8 @@ export const defaultSurveyDataFormValues: ICreateSurveyRequest = { ...SurveyLocationInitialValues, ...SurveySiteSelectionInitialValues, ...SurveyUserJobFormInitialValues, - ...SurveyBlockInitialValues + ...SurveyBlockInitialValues, + ...SpeciesInitialValues }; /** @@ -101,10 +108,39 @@ const CreateSurveyPage = () => { * * @return {*} */ - const handleSubmit = async (values: ICreateSurveyRequest) => { + const handleSubmit = async (values: ICreateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) => { setIsSaving(true); try { - const response = await biohubApi.survey.createSurvey(Number(projectData?.project.project_id), values); + // Remove the permit_used and funding_used properties + const response = await biohubApi.survey.createSurvey(Number(projectData?.project.project_id), { + blocks: values.blocks, + funding_sources: values.funding_sources, + locations: values.locations.map((location) => ({ + survey_location_id: location.survey_location_id, + geojson: location.geojson, + name: location.name, + description: location.description, + revision_count: location.revision_count + })), + participants: values.participants, + partnerships: values.partnerships, + permit: { + permits: values.permit.permits + }, + proprietor: values.proprietor, + site_selection: { + stratums: values.site_selection.stratums.map((stratum) => ({ + survey_stratum_id: stratum.survey_stratum_id, + name: stratum.name, + description: stratum.description + })), + strategies: values.site_selection.strategies + }, + species: values.species, + survey_details: values.survey_details, + purpose_and_methodology: values.purpose_and_methodology, + agreements: values.agreements + }); if (!response?.id) { showCreateErrorDialog({ @@ -170,7 +206,9 @@ const CreateSurveyPage = () => { handleSubmit(formikData as unknown as ICreateSurveyRequest)} + handleSubmit={(formikData) => + handleSubmit(formikData as unknown as ICreateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) + } formikRef={formikRef} /> diff --git a/app/src/features/surveys/SurveyRouter.tsx b/app/src/features/surveys/SurveyRouter.tsx index cb3c251cfe..1ee306311c 100644 --- a/app/src/features/surveys/SurveyRouter.tsx +++ b/app/src/features/surveys/SurveyRouter.tsx @@ -2,16 +2,17 @@ import { ProjectRoleRouteGuard } from 'components/security/RouteGuards'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; import { AnimalPageContextProvider } from 'contexts/animalPageContext'; import { DialogContextProvider } from 'contexts/dialogContext'; +import { TelemetryDataContextProvider } from 'contexts/telemetryDataContext'; import { AnimalRouter } from 'features/surveys/animals/AnimalRouter'; import EditSurveyPage from 'features/surveys/edit/EditSurveyPage'; import { SurveyObservationPage } from 'features/surveys/observations/SurveyObservationPage'; import { SamplingRouter } from 'features/surveys/sampling-information/SamplingRouter'; -import ManualTelemetryPage from 'features/surveys/telemetry/ManualTelemetryPage'; import SurveyPage from 'features/surveys/view/SurveyPage'; import React from 'react'; import { Redirect, Switch } from 'react-router'; import RouteWithTitle from 'utils/RouteWithTitle'; import { getTitle } from 'utils/Utils'; +import { TelemetryRouter } from './telemetry/TelemetryRouter'; /** * Router for all `/admin/projects/:id/surveys/:survey_id/*` pages. @@ -53,26 +54,28 @@ const SurveyRouter: React.FC = () => { - {/* Observations Routes */} - + {/* Telemetry Routes */} + - + + + + + - {/* Telemetry Routes */} - + {/* Observations Routes */} + - - - + diff --git a/app/src/features/surveys/animals/AnimalRouter.tsx b/app/src/features/surveys/animals/AnimalRouter.tsx index 0bb7eb1d39..6ca4d02e44 100644 --- a/app/src/features/surveys/animals/AnimalRouter.tsx +++ b/app/src/features/surveys/animals/AnimalRouter.tsx @@ -56,7 +56,7 @@ export const AnimalRouter: React.FC = () => { { { { { { unit.collection_category_id)} + ecologicalUnits={ecologicalUnitsDataLoader?.data ?? []} arrayHelpers={arrayHelpers} index={index} /> diff --git a/app/src/features/surveys/animals/animal-form/components/ecological-units/components/EcologicalUnitsSelect.tsx b/app/src/features/surveys/animals/animal-form/components/ecological-units/components/EcologicalUnitsSelect.tsx deleted file mode 100644 index da703dbe1f..0000000000 --- a/app/src/features/surveys/animals/animal-form/components/ecological-units/components/EcologicalUnitsSelect.tsx +++ /dev/null @@ -1,130 +0,0 @@ -import { mdiClose } from '@mdi/js'; -import { Icon } from '@mdi/react'; -import Card from '@mui/material/Card'; -import grey from '@mui/material/colors/grey'; -import IconButton from '@mui/material/IconButton'; -import Stack from '@mui/material/Stack'; -import AutocompleteField from 'components/fields/AutocompleteField'; -import { FieldArrayRenderProps, useFormikContext } from 'formik'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { ICollectionCategory, ICreateEditAnimalRequest } from 'interfaces/useCritterApi.interface'; -import { useEffect, useMemo, useState } from 'react'; -import { EcologicalUnitsOptionSelect } from './EcologicalUnitsOptionSelect'; - -interface IEcologicalUnitsSelect { - // The collection units (categories) available to select from - ecologicalUnits: ICollectionCategory[]; - // Formik field array helpers - arrayHelpers: FieldArrayRenderProps; - // The index of the field array for these controls - index: number; -} - -/** - * Returns a component for selecting ecological (ie. collection) units for a given species. - * - * @param {IEcologicalUnitsSelect} props - * @return {*} - */ -export const EcologicalUnitsSelect = (props: IEcologicalUnitsSelect) => { - const { index, ecologicalUnits } = props; - - const { values, setFieldValue } = useFormikContext(); - - const critterbaseApi = useCritterbaseApi(); - - // Get the collection category ID for the selected ecological unit - const selectedEcologicalUnitId: string | undefined = values.ecological_units[index]?.collection_category_id; - - const ecologicalUnitOptionDataLoader = useDataLoader((collection_category_id: string) => - critterbaseApi.xref.getCollectionUnits(collection_category_id) - ); - - useEffect(() => { - // If a collection category is already selected, load the collection units for that category - if (!selectedEcologicalUnitId) { - return; - } - - ecologicalUnitOptionDataLoader.load(selectedEcologicalUnitId); - }, [ecologicalUnitOptionDataLoader, selectedEcologicalUnitId]); - - // Set the label for the ecological unit options autocomplete field - const [ecologicalUnitOptionLabel, setEcologicalUnitOptionLabel] = useState( - ecologicalUnits.find((ecologicalUnit) => ecologicalUnit.collection_category_id === selectedEcologicalUnitId) - ?.category_name ?? '' - ); - - // Filter out the categories that are already selected so they can't be selected again - const filteredCategories = useMemo( - () => - ecologicalUnits - .filter( - (ecologicalUnit) => - !values.ecological_units.some( - (existing) => - existing.collection_category_id === ecologicalUnit.collection_category_id && - existing.collection_category_id !== selectedEcologicalUnitId - ) - ) - .map((option) => { - return { - value: option.collection_category_id, - label: option.category_name - }; - }) ?? [], - [ecologicalUnits, selectedEcologicalUnitId, values.ecological_units] - ); - - // Map the collection unit options to the format required by the AutocompleteField - const ecologicalUnitOptions = useMemo( - () => - ecologicalUnitOptionDataLoader.data?.map((option) => ({ - value: option.collection_unit_id, - label: option.unit_name - })) ?? [], - [ecologicalUnitOptionDataLoader.data] - ); - - return ( - - { - if (option?.value) { - setFieldValue(`ecological_units.[${index}].collection_category_id`, option.value); - setEcologicalUnitOptionLabel(option.label); - } - }} - required - sx={{ - flex: '1 1 auto' - }} - /> - - props.arrayHelpers.remove(index)} - sx={{ mt: 1.125 }}> - - - - ); -}; diff --git a/app/src/features/surveys/animals/animal-form/components/general-information/AnimalGeneralInformationForm.tsx b/app/src/features/surveys/animals/animal-form/components/general-information/AnimalGeneralInformationForm.tsx index d89ec8cb5d..6bf20c9e5f 100644 --- a/app/src/features/surveys/animals/animal-form/components/general-information/AnimalGeneralInformationForm.tsx +++ b/app/src/features/surveys/animals/animal-form/components/general-information/AnimalGeneralInformationForm.tsx @@ -2,10 +2,10 @@ import Collapse from '@mui/material/Collapse'; import Grid from '@mui/material/Grid'; import Box from '@mui/system/Box'; import CustomTextField from 'components/fields/CustomTextField'; -import SelectedSpecies from 'components/species/components/SelectedSpecies'; import SpeciesAutocompleteField from 'components/species/components/SpeciesAutocompleteField'; import { useFormikContext } from 'formik'; import { ICreateEditAnimalRequest } from 'interfaces/useCritterApi.interface'; +import SelectedAnimalSpecies from './components/SelectedAnimalSpecies'; export interface IAnimalGeneralInformationFormProps { isEdit?: boolean; @@ -41,7 +41,7 @@ export const AnimalGeneralInformationForm = (props: IAnimalGeneralInformationFor /> {values.species && ( - setFieldValue('species', null)} diff --git a/app/src/features/surveys/animals/animal-form/components/general-information/components/SelectedAnimalSpecies.tsx b/app/src/features/surveys/animals/animal-form/components/general-information/components/SelectedAnimalSpecies.tsx new file mode 100644 index 0000000000..122d0f7b15 --- /dev/null +++ b/app/src/features/surveys/animals/animal-form/components/general-information/components/SelectedAnimalSpecies.tsx @@ -0,0 +1,38 @@ +import Collapse from '@mui/material/Collapse'; +import grey from '@mui/material/colors/grey'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import SpeciesSelectedCard from 'components/species/components/SpeciesSelectedCard'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import { TransitionGroup } from 'react-transition-group'; + +export interface ISelectedAnimalSpeciesProps { + selectedSpecies: IPartialTaxonomy[]; + handleRemoveSpecies?: (species_id: number) => void; +} + +/** + * Returns a stack of selected species cards. + * + * @param props {ISelectedAnimalSpeciesProps} + * @returns + */ +const SelectedAnimalSpecies = (props: ISelectedAnimalSpeciesProps) => { + const { selectedSpecies, handleRemoveSpecies } = props; + + return ( + + {selectedSpecies.map((species, speciesIndex) => { + return ( + + + + + + ); + })} + + ); +}; + +export default SelectedAnimalSpecies; diff --git a/app/src/features/surveys/animals/animal-form/create/CreateAnimalPage.tsx b/app/src/features/surveys/animals/animal-form/create/CreateAnimalPage.tsx index 3f8ed2659d..b0e84cd94f 100644 --- a/app/src/features/surveys/animals/animal-form/create/CreateAnimalPage.tsx +++ b/app/src/features/surveys/animals/animal-form/create/CreateAnimalPage.tsx @@ -25,6 +25,7 @@ import { Link as RouterLink } from 'react-router-dom'; export const defaultAnimalDataFormValues: ICreateEditAnimalRequest = { nickname: '', species: null, + sex: AnimalSex.UNKNOWN, ecological_units: [], wildlife_health_id: '', critter_comment: '' @@ -91,7 +92,7 @@ export const CreateAnimalPage = () => { itis_tsn: values.species.tsn, wlh_id: undefined, animal_id: values.nickname, - sex: AnimalSex.UNKNOWN, + sex: values.sex, critter_comment: values.critter_comment }); @@ -118,7 +119,7 @@ export const CreateAnimalPage = () => { animalPageContext.setSelectedAnimal({ critterbase_critter_id: response.critterbase_critter_id, - survey_critter_id: response.survey_critter_id + critter_id: response.critter_id }); // Refresh the context, so the next page loads with the latest data diff --git a/app/src/features/surveys/animals/animal-form/edit/EditAnimalPage.tsx b/app/src/features/surveys/animals/animal-form/edit/EditAnimalPage.tsx index a38fb4d213..2a33aa80f0 100644 --- a/app/src/features/surveys/animals/animal-form/edit/EditAnimalPage.tsx +++ b/app/src/features/surveys/animals/animal-form/edit/EditAnimalPage.tsx @@ -44,7 +44,7 @@ export const EditAnimalPage = () => { const taxonomyContext = useTaxonomyContext(); const urlParams: Record = useParams(); - const surveyCritterId: number | undefined = Number(urlParams['survey_critter_id']); + const surveyCritterId: number | undefined = Number(urlParams['critter_id']); const { locationChangeInterceptor } = useUnsavedChangesDialog(); @@ -70,7 +70,7 @@ export const EditAnimalPage = () => { }, [critter?.itis_tsn, taxonomyContext]); // Loading spinner if the data later hasn't updated to the selected animal yet - if (!critter || animalPageContext.selectedAnimal?.critterbase_critter_id !== critter.critter_id) { + if (!critter || animalPageContext.selectedAnimal?.critterbase_critter_id !== critter.critterbase_critter_id) { return ; } @@ -107,11 +107,11 @@ export const EditAnimalPage = () => { } const response = await critterbaseApi.critters.updateCritter({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, itis_tsn: values.species.tsn, wlh_id: values.wildlife_health_id, animal_id: values.nickname, - sex: AnimalSex.UNKNOWN, + sex: values.sex, critter_comment: values.critter_comment }); @@ -130,13 +130,13 @@ export const EditAnimalPage = () => { .filter((unit) => unit.collection_category_id !== null && unit.collection_unit_id !== null) .map((unit) => ({ critter_collection_unit_id: unit.critter_collection_unit_id, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, collection_category_id: unit.collection_category_id as string, collection_unit_id: unit.collection_unit_id as string })), ...collectionsForDelete.map((collection) => ({ ...collection, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, _delete: true })) ] @@ -150,8 +150,8 @@ export const EditAnimalPage = () => { } // Refresh the context, so the next page loads with the latest data - surveyContext.critterDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - animalPageContext.critterDataLoader.refresh(critter.critter_id); + surveyContext.critterDataLoader.refresh(projectId, surveyId); + animalPageContext.critterDataLoader.refresh(projectId, surveyId, critter.critter_id); history.push(`/admin/projects/${projectId}/surveys/${surveyId}/animals`, SKIP_CONFIRMATION_DIALOG); } catch (error) { @@ -216,8 +216,9 @@ export const EditAnimalPage = () => { { tsn: critter.itis_tsn, scientificName: critter.itis_scientific_name }, - ecological_units: critter.collection_units.map((unit) => ({ ...unit, critter_id: critter.critter_id })), + ecological_units: critter.collection_units.map((unit) => ({ + ...unit, + critter_id: critter.critterbase_critter_id + })), wildlife_health_id: critter.wlh_id, critter_comment: critter.critter_comment }} diff --git a/app/src/features/surveys/animals/components/ScientificNameTypography.tsx b/app/src/features/surveys/animals/components/ScientificNameTypography.tsx index 405e137848..f4d0f9d851 100644 --- a/app/src/features/surveys/animals/components/ScientificNameTypography.tsx +++ b/app/src/features/surveys/animals/components/ScientificNameTypography.tsx @@ -16,7 +16,7 @@ export const ScientificNameTypography = (props: IScientificNameTypographyProps) if (terms.length > 1) { return ( - + {props.name} ); diff --git a/app/src/features/surveys/animals/list/AnimalListContainer.tsx b/app/src/features/surveys/animals/list/AnimalListContainer.tsx index 1d1accf6a1..a65ae523c8 100644 --- a/app/src/features/surveys/animals/list/AnimalListContainer.tsx +++ b/app/src/features/surveys/animals/list/AnimalListContainer.tsx @@ -113,7 +113,7 @@ export const AnimalListContainer = () => { dialogContext.setYesNoDialog({ open: false }); // If the selected animal is the deleted animal, unset the selected animal - if (checkboxSelectedIds.some((id) => id == selectedAnimal?.survey_critter_id)) { + if (checkboxSelectedIds.some((id) => id == selectedAnimal?.critter_id)) { setSelectedAnimal(); } @@ -164,11 +164,11 @@ export const AnimalListContainer = () => { }, open: true, onYes: () => { - if (selectedCritterMenu?.survey_critter_id) { - handleDeleteCritter(selectedCritterMenu?.survey_critter_id); + if (selectedCritterMenu?.critter_id) { + handleDeleteCritter(selectedCritterMenu?.critter_id); } // If the selected animal is the deleted animal, unset the selected animal - if (selectedCritterMenu?.survey_critter_id == selectedAnimal?.survey_critter_id) { + if (selectedCritterMenu?.critter_id == selectedAnimal?.critter_id) { setSelectedAnimal(); } } @@ -234,7 +234,7 @@ export const AnimalListContainer = () => { } }}> { setSelectedAnimal(selectedCritterMenu); }}> @@ -323,7 +323,7 @@ export const AnimalListContainer = () => { return; } - const critterIds = critters.map((critter) => critter.survey_critter_id); + const critterIds = critters.map((critter) => critter.critter_id); setCheckboxSelectedIds(critterIds); }} inputProps={{ 'aria-label': 'controlled' }} @@ -355,7 +355,7 @@ export const AnimalListContainer = () => { )} {critters.map((critter) => ( { }}> { edge="end" onClick={(event: React.MouseEvent) => handleCritterMenuClick(event, { - critterbase_critter_id: critter.critter_id, - survey_critter_id: critter.survey_critter_id + critterbase_critter_id: critter.critterbase_critter_id, + critter_id: critter.critter_id }) } aria-label="animal-settings"> diff --git a/app/src/features/surveys/animals/list/components/CritterListItem.tsx b/app/src/features/surveys/animals/list/components/CritterListItem.tsx index 459e0f2681..297c4c547b 100644 --- a/app/src/features/surveys/animals/list/components/CritterListItem.tsx +++ b/app/src/features/surveys/animals/list/components/CritterListItem.tsx @@ -5,12 +5,12 @@ import IconButton from '@mui/material/IconButton'; import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; import { useAnimalPageContext, useSurveyContext } from 'hooks/useContext'; -import { ISimpleCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; +import { ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; import { useEffect } from 'react'; import { ScientificNameTypography } from '../../components/ScientificNameTypography'; interface ICritterListItemProps { - critter: ISimpleCritterWithInternalId; + critter: ICritterSimpleResponse; isChecked: boolean; handleCheckboxChange: (surveyCritterId: number) => void; } @@ -45,10 +45,10 @@ export const CritterListItem = (props: ICritterListItemProps) => { }}> { - if (critter.survey_critter_id !== selectedAnimal?.survey_critter_id) + if (critter.critter_id !== selectedAnimal?.critter_id) setSelectedAnimal({ - survey_critter_id: critter.survey_critter_id, - critterbase_critter_id: critter.critter_id + critter_id: critter.critter_id, + critterbase_critter_id: critter.critterbase_critter_id }); }} sx={{ @@ -63,7 +63,7 @@ export const CritterListItem = (props: ICritterListItemProps) => { '& .MuiTypography-root': { color: 'text.primary' }, - bgcolor: selectedAnimal?.survey_critter_id === critter.survey_critter_id ? grey[100] : undefined + bgcolor: selectedAnimal?.critter_id === critter.critter_id ? grey[100] : undefined }}> { checked={isChecked} onClick={(event) => { event.stopPropagation(); - handleCheckboxChange(critter.survey_critter_id); + handleCheckboxChange(critter.critter_id); }} inputProps={{ 'aria-label': 'controlled' }} /> diff --git a/app/src/features/surveys/animals/profile/captures/AnimalCaptureContainer.tsx b/app/src/features/surveys/animals/profile/captures/AnimalCaptureContainer.tsx index aed46f7446..5e9f2d0c0a 100644 --- a/app/src/features/surveys/animals/profile/captures/AnimalCaptureContainer.tsx +++ b/app/src/features/surveys/animals/profile/captures/AnimalCaptureContainer.tsx @@ -72,7 +72,7 @@ export const AnimalCaptureContainer = () => { } })) || []; - const handleDelete = async (selectedCapture: string, critterbase_critter_id: string) => { + const handleDelete = async (selectedCapture: string, critter_id: number) => { // Delete markings and measurements associated with the capture to avoid foreign key constraint error await critterbaseApi.critters.bulkUpdate({ markings: data?.markings @@ -102,7 +102,7 @@ export const AnimalCaptureContainer = () => { await critterbaseApi.capture.deleteCapture(selectedCapture); // Refresh capture container - animalPageContext.critterDataLoader.refresh(critterbase_critter_id); + animalPageContext.critterDataLoader.refresh(projectId, surveyId, critter_id); }; const capturesWithLocation = captures.filter((capture) => capture.capture_location); @@ -113,7 +113,7 @@ export const AnimalCaptureContainer = () => { capturesCount={captures.length} onAddAnimalCapture={() => { history.push( - `/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.survey_critter_id}/capture/create` + `/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.critter_id}/capture/create` ); }} /> diff --git a/app/src/features/surveys/animals/profile/captures/capture-form/components/location/CaptureLocationMapControl.tsx b/app/src/features/surveys/animals/profile/captures/capture-form/components/location/CaptureLocationMapControl.tsx index fb775a470a..6520df756d 100644 --- a/app/src/features/surveys/animals/profile/captures/capture-form/components/location/CaptureLocationMapControl.tsx +++ b/app/src/features/surveys/animals/profile/captures/capture-form/components/location/CaptureLocationMapControl.tsx @@ -29,6 +29,7 @@ import { useEffect, useMemo, useRef, useState } from 'react'; import { FeatureGroup, LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; import { calculateUpdatedMapBounds } from 'utils/mapBoundaryUploadHelpers'; import { getCoordinatesFromGeoJson, isGeoJsonPointFeature, isValidCoordinates } from 'utils/spatial-utils'; +import { v4 as uuid } from 'uuid'; export interface ICaptureLocationMapControlProps { name: string; @@ -277,7 +278,15 @@ export const CaptureLocationMapControl = diff --git a/app/src/features/surveys/animals/profile/captures/capture-form/create/CreateCapturePage.tsx b/app/src/features/surveys/animals/profile/captures/capture-form/create/CreateCapturePage.tsx index 46c26a7d6c..903c9154ac 100644 --- a/app/src/features/surveys/animals/profile/captures/capture-form/create/CreateCapturePage.tsx +++ b/app/src/features/surveys/animals/profile/captures/capture-form/create/CreateCapturePage.tsx @@ -58,7 +58,7 @@ export const CreateCapturePage = () => { const animalPageContext = useAnimalPageContext(); const urlParams: Record = useParams(); - const surveyCritterId: number | undefined = Number(urlParams['survey_critter_id']); + const surveyCritterId: number | undefined = Number(urlParams['critter_id']); const { locationChangeInterceptor } = useUnsavedChangesDialog(); @@ -106,6 +106,7 @@ export const CreateCapturePage = () => { setIsSaving(true); try { + const surveyCritterId = animalPageContext.selectedAnimal?.critter_id; const critterbaseCritterId = animalPageContext.selectedAnimal?.critterbase_critter_id; if (!values || !critterbaseCritterId || values.capture.capture_location?.geometry.type !== 'Point') { @@ -190,7 +191,10 @@ export const CreateCapturePage = () => { } // Refresh page - animalPageContext.critterDataLoader.refresh(critterbaseCritterId); + + if (surveyCritterId) { + animalPageContext.critterDataLoader.refresh(projectId, surveyId, surveyCritterId); + } history.push(`/admin/projects/${projectId}/surveys/${surveyId}/animals/details`, SKIP_CONFIRMATION_DIALOG); } catch (error) { diff --git a/app/src/features/surveys/animals/profile/captures/capture-form/edit/EditCapturePage.tsx b/app/src/features/surveys/animals/profile/captures/capture-form/edit/EditCapturePage.tsx index bb78fc28a1..688e0dcf9a 100644 --- a/app/src/features/surveys/animals/profile/captures/capture-form/edit/EditCapturePage.tsx +++ b/app/src/features/surveys/animals/profile/captures/capture-form/edit/EditCapturePage.tsx @@ -40,7 +40,7 @@ export const EditCapturePage = () => { const urlParams: Record = useParams(); - const surveyCritterId: number | undefined = Number(urlParams['survey_critter_id']); + const surveyCritterId: number | undefined = Number(urlParams['critter_id']); const captureId: string | undefined = String(urlParams['capture_id']); const { locationChangeInterceptor } = useUnsavedChangesDialog(); @@ -164,7 +164,9 @@ export const EditCapturePage = () => { } // Refresh page - animalPageContext.critterDataLoader.refresh(critterbaseCritterId); + if (surveyCritterId) { + animalPageContext.critterDataLoader.refresh(projectId, surveyId, surveyCritterId); + } history.push(`/admin/projects/${projectId}/surveys/${surveyId}/animals/details`, SKIP_CONFIRMATION_DIALOG); } catch (error) { diff --git a/app/src/features/surveys/animals/profile/captures/capture-form/edit/utils.ts b/app/src/features/surveys/animals/profile/captures/capture-form/edit/utils.ts index 57ed035d9f..99fd7f27f3 100644 --- a/app/src/features/surveys/animals/profile/captures/capture-form/edit/utils.ts +++ b/app/src/features/surveys/animals/profile/captures/capture-form/edit/utils.ts @@ -101,7 +101,7 @@ export const formatCritterDetailsForBulkUpdate = ( !markings.some((incomingMarking) => incomingMarking.marking_id === existingmarkingsOnCapture.marking_id) ) // The remaining markings are the ones to delete from the critter for the current capture - .map((item) => ({ ...item, critter_id: critter.critter_id, _delete: true })); + .map((item) => ({ ...item, critter_id: critter.critterbase_critter_id, _delete: true })); // Find markings for create const markingsForCreate = markings @@ -110,7 +110,7 @@ export const formatCritterDetailsForBulkUpdate = ( .map((marking) => ({ ...marking, marking_id: marking.marking_id, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, capture_id: captureId })); @@ -121,7 +121,7 @@ export const formatCritterDetailsForBulkUpdate = ( .map((marking) => ({ ...marking, marking_id: marking.marking_id, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, capture_id: captureId })); @@ -129,7 +129,7 @@ export const formatCritterDetailsForBulkUpdate = ( const qualitativeMeasurementsForCreate = measurements .filter(isQualitativeMeasurementCreate) .map((measurement: IQualitativeMeasurementCreate) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, capture_id: captureId, taxon_measurement_id: measurement.taxon_measurement_id, qualitative_option_id: measurement.qualitative_option_id, @@ -141,7 +141,7 @@ export const formatCritterDetailsForBulkUpdate = ( const quantitativeMeasurementsForCreate = measurements .filter(isQuantitativeMeasurementCreate) .map((measurement: IQuantitativeMeasurementCreate) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, capture_id: captureId, taxon_measurement_id: measurement.taxon_measurement_id, value: measurement.value, @@ -153,7 +153,7 @@ export const formatCritterDetailsForBulkUpdate = ( const qualitativeMeasurementsForUpdate = measurements .filter(isQualitativeMeasurementUpdate) .map((measurement: IQualitativeMeasurementUpdate) => ({ - // critter_id: critter.critter_id, + // critter_id: critter.critterbase_critter_id, capture_id: captureId, measurement_qualitative_id: measurement.measurement_qualitative_id, taxon_measurement_id: measurement.taxon_measurement_id, @@ -166,7 +166,7 @@ export const formatCritterDetailsForBulkUpdate = ( const quantitativeMeasurementsForUpdate = measurements .filter(isQuantitativeMeasurementUpdate) .map((measurement: IQuantitativeMeasurementUpdate) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, measurement_quantitative_id: measurement.measurement_quantitative_id, capture_id: captureId, taxon_measurement_id: measurement.taxon_measurement_id, diff --git a/app/src/features/surveys/animals/profile/captures/components/AnimalCaptureCardContainer.tsx b/app/src/features/surveys/animals/profile/captures/components/AnimalCaptureCardContainer.tsx index 5843757a69..1d679c018b 100644 --- a/app/src/features/surveys/animals/profile/captures/components/AnimalCaptureCardContainer.tsx +++ b/app/src/features/surveys/animals/profile/captures/components/AnimalCaptureCardContainer.tsx @@ -27,7 +27,7 @@ import { AnimalCaptureCardDetailsContainer } from './capture-card-details/Animal interface IAnimalCaptureCardContainer { captures: ICaptureWithSupplementaryData[]; selectedAnimal: ISurveyCritter; - handleDelete: (selectedCapture: string, critterbase_critter_id: string) => Promise; + handleDelete: (selectedCapture: string, critter_id: number) => Promise; } /** * Returns accordion cards for displaying animal capture details on the animal profile page @@ -77,7 +77,7 @@ export const AnimalCaptureCardContainer = (props: IAnimalCaptureCardContainer) = } }}> + to={`/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.critterbase_critter_id}/capture/${selectedCapture}/edit`}> @@ -111,7 +111,7 @@ export const AnimalCaptureCardContainer = (props: IAnimalCaptureCardContainer) = open={Boolean(captureForDelete)} onYes={() => { setCaptureForDelete(false); - handleDelete(selectedCapture, selectedAnimal.critterbase_critter_id); + handleDelete(selectedCapture, selectedAnimal.critter_id); }} onClose={() => setCaptureForDelete(false)} onNo={() => setCaptureForDelete(false)} diff --git a/app/src/features/surveys/animals/profile/captures/components/AnimalCapturesMap.tsx b/app/src/features/surveys/animals/profile/captures/components/AnimalCapturesMap.tsx index 602774f9fc..df194fc722 100644 --- a/app/src/features/surveys/animals/profile/captures/components/AnimalCapturesMap.tsx +++ b/app/src/features/surveys/animals/profile/captures/components/AnimalCapturesMap.tsx @@ -20,7 +20,7 @@ export const AnimalCapturesMap = (props: IAnimalCapturesMapProps) => { const { captures, isLoading } = props; // Only include captures with valid locations - const captureMapFeatures: Feature[] = []; + const captureMapFeatures = []; for (const capture of captures) { if ( @@ -28,7 +28,8 @@ export const AnimalCapturesMap = (props: IAnimalCapturesMapProps) => { isDefined(capture.capture_location.latitude) && isDefined(capture.capture_location.longitude) ) { - const feature: Feature = { + const feature = { + id: capture.capture_id, type: 'Feature', geometry: { type: 'Point', @@ -45,15 +46,16 @@ export const AnimalCapturesMap = (props: IAnimalCapturesMapProps) => { popupRecordTitle: 'Capture Location', features: [ { - key: `${feature.geometry}-${index}`, - geoJSON: feature + id: feature.id, + key: `capture-location-${feature.geometry}-${index}`, + geoJSON: feature as Feature } ] })); return ( - + ); }; diff --git a/app/src/features/surveys/animals/profile/details/components/AnimalProfileHeader.tsx b/app/src/features/surveys/animals/profile/details/components/AnimalProfileHeader.tsx index 4bc257ae98..91b87833b3 100644 --- a/app/src/features/surveys/animals/profile/details/components/AnimalProfileHeader.tsx +++ b/app/src/features/surveys/animals/profile/details/components/AnimalProfileHeader.tsx @@ -71,15 +71,15 @@ export const AnimalProfileHeader = (props: IAnimalProfileHeaderProps) => { Unique ID:  - {critter.critter_id} + {critter.critterbase_critter_id} { - if (!critter.critter_id) { + if (!critter.critterbase_critter_id) { return; } - copyToClipboard(critter.critter_id, () => + copyToClipboard(critter.critterbase_critter_id, () => setMessageSnackbar('Unique ID copied to clipboard', dialogContext) ).catch((error) => { console.error('Could not copy text: ', error); diff --git a/app/src/features/surveys/animals/profile/mortality/AnimalMortalityContainer.tsx b/app/src/features/surveys/animals/profile/mortality/AnimalMortalityContainer.tsx index 8a84c19faf..ac70ae4e8d 100644 --- a/app/src/features/surveys/animals/profile/mortality/AnimalMortalityContainer.tsx +++ b/app/src/features/surveys/animals/profile/mortality/AnimalMortalityContainer.tsx @@ -66,7 +66,7 @@ const AnimalMortalityContainer = () => { } })) || []; - const handleDelete = async (selectedMortality: string, critterbase_critter_id: string) => { + const handleDelete = async (selectedMortality: string, critterId: number) => { // Delete markings and measurements associated with the mortality to avoid foreign key constraint error await critterbaseApi.critters.bulkUpdate({ markings: data?.markings @@ -96,7 +96,9 @@ const AnimalMortalityContainer = () => { await critterbaseApi.mortality.deleteMortality(selectedMortality); // Refresh mortality container - animalPageContext.critterDataLoader.refresh(critterbase_critter_id); + if (critterId) { + animalPageContext.critterDataLoader.refresh(projectId, surveyId, critterId); + } }; return ( @@ -105,7 +107,7 @@ const AnimalMortalityContainer = () => { mortalityCount={mortality.length} onAddAnimalMortality={() => { history.push( - `/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.survey_critter_id}/mortality/create` + `/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.critter_id}/mortality/create` ); }} /> diff --git a/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityCardContainer.tsx b/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityCardContainer.tsx index d011db6e25..a5a8d1e6ad 100644 --- a/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityCardContainer.tsx +++ b/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityCardContainer.tsx @@ -26,7 +26,7 @@ import { getFormattedDate } from 'utils/Utils'; interface IAnimalMortalityCardContainer { mortality: IMortalityWithSupplementaryData[]; selectedAnimal: ISurveyCritter; - handleDelete: (selectedMortality: string, critterbase_critter_id: string) => Promise; + handleDelete: (selectedMortality: string, critterId: number) => Promise; } /** * Returns accordion cards for displaying animal mortality details on the animal profile page @@ -76,7 +76,7 @@ export const AnimalMortalityCardContainer = (props: IAnimalMortalityCardContaine } }}> + to={`/admin/projects/${projectId}/surveys/${surveyId}/animals/${selectedAnimal.critterbase_critter_id}/mortality/${selectedMortality}/edit`}> @@ -108,7 +108,7 @@ export const AnimalMortalityCardContainer = (props: IAnimalMortalityCardContaine open={Boolean(mortalityForDelete)} onYes={() => { setMortalityForDelete(false); - handleDelete(selectedMortality, selectedAnimal.critterbase_critter_id); + handleDelete(selectedMortality, selectedAnimal.critter_id); }} onClose={() => setMortalityForDelete(false)} onNo={() => setMortalityForDelete(false)} diff --git a/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityMap.tsx b/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityMap.tsx index 04deba620f..902279e06c 100644 --- a/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityMap.tsx +++ b/app/src/features/surveys/animals/profile/mortality/components/AnimalMortalityMap.tsx @@ -22,28 +22,30 @@ export const AnimalMortalityMap = (props: IAnimalMortalityMapProps) => { const mortalityMapFeatures = mortality .filter((mortality) => isDefined(mortality.location?.latitude) && isDefined(mortality.location?.longitude)) .map((mortality) => ({ + id: mortality.mortality_id, type: 'Feature', geometry: { type: 'Point', coordinates: [mortality.location?.longitude, mortality.location?.latitude] }, properties: { mortalityId: mortality.mortality_id, date: mortality.mortality_timestamp } - })) as Feature[]; + })); const staticLayers: IStaticLayer[] = mortalityMapFeatures.map((feature, index) => ({ layerName: 'Mortality', popupRecordTitle: 'Capture Location', features: [ { - key: `${feature.geometry}-${index}`, - geoJSON: feature + id: feature.id, + key: `mortality-location-${feature.geometry}-${index}`, + geoJSON: feature as Feature } ] })); return ( - + ); }; diff --git a/app/src/features/surveys/animals/profile/mortality/mortality-form/components/location/MortalityLocationMapControl.tsx b/app/src/features/surveys/animals/profile/mortality/mortality-form/components/location/MortalityLocationMapControl.tsx index c62570a36d..cc8e56b281 100644 --- a/app/src/features/surveys/animals/profile/mortality/mortality-form/components/location/MortalityLocationMapControl.tsx +++ b/app/src/features/surveys/animals/profile/mortality/mortality-form/components/location/MortalityLocationMapControl.tsx @@ -29,6 +29,7 @@ import { useEffect, useMemo, useRef, useState } from 'react'; import { FeatureGroup, LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; import { calculateUpdatedMapBounds } from 'utils/mapBoundaryUploadHelpers'; import { getCoordinatesFromGeoJson, isGeoJsonPointFeature, isValidCoordinates } from 'utils/spatial-utils'; +import { v4 as uuid } from 'uuid'; export interface IMortalityLocationMapControlProps { name: string; @@ -274,7 +275,15 @@ export const MortalityLocationMapControl = diff --git a/app/src/features/surveys/animals/profile/mortality/mortality-form/create/CreateMortalityPage.tsx b/app/src/features/surveys/animals/profile/mortality/mortality-form/create/CreateMortalityPage.tsx index 1891e96882..c854ac04f4 100644 --- a/app/src/features/surveys/animals/profile/mortality/mortality-form/create/CreateMortalityPage.tsx +++ b/app/src/features/surveys/animals/profile/mortality/mortality-form/create/CreateMortalityPage.tsx @@ -62,7 +62,7 @@ export const CreateMortalityPage = () => { const animalPageContext = useAnimalPageContext(); const urlParams: Record = useParams(); - const surveyCritterId: number | undefined = Number(urlParams['survey_critter_id']); + const surveyCritterId: number | undefined = Number(urlParams['critter_id']); const { locationChangeInterceptor } = useUnsavedChangesDialog(); @@ -182,7 +182,7 @@ export const CreateMortalityPage = () => { } // Refresh page - animalPageContext.critterDataLoader.refresh(critterbaseCritterId); + animalPageContext.critterDataLoader.refresh(projectId, surveyId, surveyCritterId); history.push(`/admin/projects/${projectId}/surveys/${surveyId}/animals/details`, SKIP_CONFIRMATION_DIALOG); } catch (error) { diff --git a/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/EditMortalityPage.tsx b/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/EditMortalityPage.tsx index bc4b6e567d..737235ba72 100644 --- a/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/EditMortalityPage.tsx +++ b/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/EditMortalityPage.tsx @@ -41,7 +41,7 @@ export const EditMortalityPage = () => { const urlParams: Record = useParams(); - const surveyCritterId: number | undefined = Number(urlParams['survey_critter_id']); + const surveyCritterId: number | undefined = Number(urlParams['critter_id']); const mortalityId: string | undefined = String(urlParams['mortality_id']); const { locationChangeInterceptor } = useUnsavedChangesDialog(); @@ -171,7 +171,7 @@ export const EditMortalityPage = () => { } // Refresh page - animalPageContext.critterDataLoader.refresh(critterbaseCritterId); + if (surveyCritterId) animalPageContext.critterDataLoader.refresh(projectId, surveyId, surveyCritterId); history.push(`/admin/projects/${projectId}/surveys/${surveyId}/animals/details`, SKIP_CONFIRMATION_DIALOG); } catch (error) { diff --git a/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/utils.ts b/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/utils.ts index ab16e4174d..2c43dcbc7e 100644 --- a/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/utils.ts +++ b/app/src/features/surveys/animals/profile/mortality/mortality-form/edit/utils.ts @@ -105,7 +105,7 @@ export const formatCritterDetailsForBulkUpdate = ( !markings.some((incomingMarking) => incomingMarking.marking_id === existingmarkingsOnMortality.marking_id) ) // The remaining markings are the ones to delete from the critter for the current mortality - .map((item) => ({ ...item, critter_id: critter.critter_id, _delete: true })); + .map((item) => ({ ...item, critter_id: critter.critterbase_critter_id, _delete: true })); // Find markings for create const markingsForCreate = markings @@ -114,7 +114,7 @@ export const formatCritterDetailsForBulkUpdate = ( .map((marking) => ({ ...marking, marking_id: marking.marking_id, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId })); @@ -125,13 +125,13 @@ export const formatCritterDetailsForBulkUpdate = ( .map((marking) => ({ ...marking, marking_id: marking.marking_id, - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId })); // Find qualitative measurements for create const qualitativeMeasurementsForCreate = measurements.filter(isQualitativeMeasurementCreate).map((measurement) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId, taxon_measurement_id: measurement.taxon_measurement_id, qualitative_option_id: measurement.qualitative_option_id, @@ -141,7 +141,7 @@ export const formatCritterDetailsForBulkUpdate = ( // Find quantitative measurements for create const quantitativeMeasurementsForCreate = measurements.filter(isQuantitativeMeasurementCreate).map((measurement) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId, taxon_measurement_id: measurement.taxon_measurement_id, value: measurement.value, @@ -151,7 +151,7 @@ export const formatCritterDetailsForBulkUpdate = ( // Find qualitative measurements for update const qualitativeMeasurementsForUpdate = measurements.filter(isQualitativeMeasurementUpdate).map((measurement) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId, measurement_qualitative_id: measurement.measurement_qualitative_id, taxon_measurement_id: measurement.taxon_measurement_id, @@ -162,7 +162,7 @@ export const formatCritterDetailsForBulkUpdate = ( // Find quantitative measurements for update const quantitativeMeasurementsForUpdate = measurements.filter(isQuantitativeMeasurementUpdate).map((measurement) => ({ - critter_id: critter.critter_id, + critter_id: critter.critterbase_critter_id, mortality_id: mortalityId, measurement_quantitative_id: measurement.measurement_quantitative_id, taxon_measurement_id: measurement.taxon_measurement_id, diff --git a/app/src/features/surveys/components/SurveyProgressChip.tsx b/app/src/features/surveys/components/SurveyProgressChip.tsx index f39a5dea6b..d68e0e940a 100644 --- a/app/src/features/surveys/components/SurveyProgressChip.tsx +++ b/app/src/features/surveys/components/SurveyProgressChip.tsx @@ -2,6 +2,7 @@ import { ChipProps } from '@mui/material'; import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { getSurveyProgressColour, SurveyProgressKeys } from 'constants/colours'; import { useCodesContext } from 'hooks/useContext'; +import { useEffect } from 'react'; import { getCodesName } from 'utils/Utils'; interface ISurveyProgressChipProps extends ChipProps { @@ -17,6 +18,10 @@ interface ISurveyProgressChipProps extends ChipProps { export const SurveyProgressChip = (props: ISurveyProgressChipProps) => { const codesContext = useCodesContext(); + useEffect(() => { + codesContext.codesDataLoader.load(); + }, [codesContext.codesDataLoader]); + const codeName = getCodesName(codesContext.codesDataLoader.data, 'survey_progress', props.progress_id) ?? ''; return ( diff --git a/app/src/features/surveys/components/agreements/ProprietaryDataForm.tsx b/app/src/features/surveys/components/agreements/ProprietaryDataForm.tsx index 933fe8af56..72ec4ad53f 100644 --- a/app/src/features/surveys/components/agreements/ProprietaryDataForm.tsx +++ b/app/src/features/surveys/components/agreements/ProprietaryDataForm.tsx @@ -1,6 +1,5 @@ import Alert from '@mui/material/Alert'; import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; import FormControl from '@mui/material/FormControl'; import FormControlLabel from '@mui/material/FormControlLabel'; import FormHelperText from '@mui/material/FormHelperText'; @@ -17,25 +16,6 @@ import React, { useState } from 'react'; import { StringBoolean } from 'types/misc'; import yup from 'utils/YupSchema'; -const useStyles = () => { - return { - alignCenter: { - display: 'flex', - alignItems: 'center' - }, - learnMoreBtn: { - textDecoration: 'underline', - lineHeight: 'auto', - '&:hover': { - textDecoration: 'underline' - } - }, - dialogText: { - maxWidth: '72ch' - } - }; -}; - export interface IProprietaryDataForm { proprietor: { survey_data_proprietary: StringBoolean; @@ -95,7 +75,6 @@ export interface IProprietaryDataFormProps { */ const ProprietaryDataForm: React.FC = (props) => { const [openDialog, setOpenDialog] = useState(false); - const classes = useStyles(); const { values, touched, errors, handleChange, setFieldValue, setFieldTouched, setFieldError } = useFormikContext(); @@ -122,16 +101,6 @@ const ProprietaryDataForm: React.FC = (props) => { error={ touched.proprietor?.survey_data_proprietary && Boolean(errors.proprietor?.survey_data_proprietary) }> - - Is the data captured in this survey proprietary? - - = (props) => { } handleChange(event); }}> - } label="No" /> - } label="Yes" /> + } label="No" /> + } label="Yes" /> {errors.proprietor?.survey_data_proprietary} diff --git a/app/src/features/surveys/components/funding/SurveyFundingSourceForm.tsx b/app/src/features/surveys/components/funding/SurveyFundingSourceForm.tsx index 7909568607..a05fbd82df 100644 --- a/app/src/features/surveys/components/funding/SurveyFundingSourceForm.tsx +++ b/app/src/features/surveys/components/funding/SurveyFundingSourceForm.tsx @@ -5,15 +5,21 @@ import Button from '@mui/material/Button'; import Card from '@mui/material/Card'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; +import FormControlLabel from '@mui/material/FormControlLabel'; import IconButton from '@mui/material/IconButton'; +import Radio from '@mui/material/Radio'; +import RadioGroup from '@mui/material/RadioGroup'; import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; +import AlertBar from 'components/alert/AlertBar'; import AutocompleteField from 'components/fields/AutocompleteField'; import DollarAmountField from 'components/fields/DollarAmountField'; import { FieldArray, FieldArrayRenderProps, useFormikContext } from 'formik'; import { useBiohubApi } from 'hooks/useBioHubApi'; import useDataLoader from 'hooks/useDataLoader'; import { IEditSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import get from 'lodash-es/get'; +import { useEffect } from 'react'; import { TransitionGroup } from 'react-transition-group'; import yup from 'utils/YupSchema'; @@ -21,15 +27,16 @@ export interface ISurveyFundingSource { funding_source_id: number; amount: number; revision_count: number; - survey_funding_source_id?: number; + survey_funding_source_id?: number | null; survey_id: number; funding_source_name?: string; - start_date?: string; - end_date?: string; - description?: string; + start_date?: string | null; + end_date?: string | null; + description?: string | null; } export interface ISurveyFundingSourceForm { + funding_used: boolean | null; funding_sources: ISurveyFundingSource[]; } @@ -42,10 +49,15 @@ const SurveyFundingSourceInitialValues: ISurveyFundingSource = { }; export const SurveyFundingSourceFormInitialValues: ISurveyFundingSourceForm = { + funding_used: null, funding_sources: [] }; export const SurveyFundingSourceFormYupSchema = yup.object().shape({ + funding_used: yup + .boolean() + .nullable() + .required('You must indicate whether a funding source requires this survey to be submitted'), funding_sources: yup.array( yup.object().shape({ funding_source_id: yup @@ -82,7 +94,16 @@ export const SurveyFundingSourceFormYupSchema = yup.object().shape({ */ const SurveyFundingSourceForm = () => { const formikProps = useFormikContext(); - const { values, handleChange, handleSubmit, errors } = formikProps; + const { values, handleChange, handleSubmit, errors, setFieldValue, submitCount, setFieldError } = formikProps; + + // Determine value of funding_used based on whether funding_sources exist + useEffect(() => { + if (values.funding_sources.length > 0) { + setFieldValue('funding_used', values.funding_used); + } else if (!values.funding_sources.length) { + setFieldValue('funding_used', values.funding_used); + } + }, [setFieldValue, values.funding_sources, values.funding_used]); const biohubApi = useBiohubApi(); const fundingSourcesDataLoader = useDataLoader(() => biohubApi.funding.getAllFundingSources()); @@ -90,12 +111,52 @@ const SurveyFundingSourceForm = () => { const fundingSources = fundingSourcesDataLoader.data ?? []; + // Determine the radio button value + const getFundingUsedValue = () => { + if (values.funding_used === true) { + return 'true'; + } + if (values.funding_used === false) { + return 'false'; + } + return null; + }; + return ( ( + {get(errors, 'funding_used') && submitCount > 0 && ( + + )} + { + const value = event.target.value === 'true' ? true : false; + setFieldValue('funding_used', value); + if (value) { + arrayHelpers.push(SurveyFundingSourceInitialValues); + } else { + setFieldValue('funding_sources', []); + } + setFieldError('funding_used', undefined); + }}> + } label="Yes" /> + } label="No" /> + + { gap={2} sx={{ width: '100%', + mt: 1, p: 2, backgroundColor: grey[100] }}> @@ -162,19 +224,21 @@ const SurveyFundingSourceForm = () => { {errors.funding_sources} )} - + {values.funding_used && ( + + )} )} /> diff --git a/app/src/features/surveys/components/general-information/GeneralInformationForm.tsx b/app/src/features/surveys/components/general-information/GeneralInformationForm.tsx index 0dedfb5b46..5156d7680a 100644 --- a/app/src/features/surveys/components/general-information/GeneralInformationForm.tsx +++ b/app/src/features/surveys/components/general-information/GeneralInformationForm.tsx @@ -1,18 +1,11 @@ -import Box from '@mui/material/Box'; import Grid from '@mui/material/Grid'; -import Typography from '@mui/material/Typography'; +import AutocompleteField from 'components/fields/AutocompleteField'; import CustomTextField from 'components/fields/CustomTextField'; -import { IMultiAutocompleteFieldOption } from 'components/fields/MultiAutocompleteField'; -import MultiAutocompleteFieldVariableSize from 'components/fields/MultiAutocompleteFieldVariableSize'; -import SelectWithSubtextField, { ISelectWithSubtextFieldOption } from 'components/fields/SelectWithSubtext'; +import { ISelectWithSubtextFieldOption } from 'components/fields/SelectWithSubtext'; import StartEndDateFields from 'components/fields/StartEndDateFields'; -import AncillarySpeciesComponent from 'components/species/AncillarySpeciesComponent'; -import FocalSpeciesComponent from 'components/species/FocalSpeciesComponent'; -import { useFormikContext } from 'formik'; -import { ITaxonomy } from 'interfaces/useTaxonomyApi.interface'; import React from 'react'; import yup from 'utils/YupSchema'; -import SurveyPermitForm, { SurveyPermitFormYupSchema } from '../../SurveyPermitForm'; +import { SurveyPermitFormYupSchema } from '../permit/SurveyPermitForm'; export const AddPermitFormInitialValues = { permits: [ @@ -37,14 +30,10 @@ export interface IGeneralInformationForm { survey_name: string; start_date: string; end_date: string; - progress_id: number | null; + progress_id: number; survey_types: number[]; revision_count: number; }; - species: { - focal_species: ITaxonomy[]; - ancillary_species: ITaxonomy[]; - }; permit: { permits: { permit_id?: number; @@ -59,14 +48,10 @@ export const GeneralInformationInitialValues: IGeneralInformationForm = { survey_name: '', start_date: '', end_date: '', - progress_id: null, + progress_id: null as unknown as number, survey_types: [], revision_count: 0 }, - species: { - focal_species: [], - ancillary_species: [] - }, permit: { permits: [] } @@ -80,26 +65,21 @@ export const GeneralInformationYupSchema = () => { survey_name: yup.string().required('Survey Name is Required'), start_date: yup.string().isValidDateString().required('Start Date is Required'), end_date: yup.string().nullable().isValidDateString(), - survey_types: yup - .array(yup.number()) - .min(1, 'One or more Types are required') - .required('One or more Types are required'), progress_id: yup .number() .min(1, 'Survey Progress is Required') .required('Survey Progress is Required') - .nullable() - }), - species: yup.object().shape({ - focal_species: yup.array().min(1, 'You must specify a focal species').required('Required'), - ancillary_species: yup.array().isUniqueFocalAncillarySpecies('Focal and Ancillary species must be unique') + .nullable(), + survey_types: yup + .array(yup.number()) + .min(1, 'One or more data types are required') + .required('One or more data types are required') }) }) .concat(SurveyPermitFormYupSchema); }; export interface IGeneralInformationFormProps { - type: IMultiAutocompleteFieldOption[]; progress: ISelectWithSubtextFieldOption[]; } @@ -109,72 +89,36 @@ export interface IGeneralInformationFormProps { * @return {*} */ const GeneralInformationForm: React.FC = (props) => { - const formikProps = useFormikContext(); - return ( - <> - - - - - - - - - - - - - + + + - - - - Species - - - - - - - - - - - - - - Permits - - - - - - + + + + + + + ); }; diff --git a/app/src/features/surveys/components/locations/SurveyAreaMapControl.tsx b/app/src/features/surveys/components/locations/SurveyAreaMapControl.tsx index a5ce02fc17..b7ce0bb06a 100644 --- a/app/src/features/surveys/components/locations/SurveyAreaMapControl.tsx +++ b/app/src/features/surveys/components/locations/SurveyAreaMapControl.tsx @@ -211,7 +211,11 @@ export const SurveyAreaMapControl = (props: ISurveyAreMapControlProps) => { // Map geojson features into layer objects for leaflet return { layerName: location.name, - features: location.geojson.map((geo) => ({ geoJSON: geo, key: location.uuid ?? v4() })) + features: location.geojson.map((geo) => ({ + id: location.uuid ?? v4(), + key: `study-area-${location.uuid ?? v4()}`, + geoJSON: geo + })) }; })} /> diff --git a/app/src/features/surveys/components/methodology/PurposeAndMethodologyForm.tsx b/app/src/features/surveys/components/methodology/PurposeAndMethodologyForm.tsx index d322138e0f..17119f47d5 100644 --- a/app/src/features/surveys/components/methodology/PurposeAndMethodologyForm.tsx +++ b/app/src/features/surveys/components/methodology/PurposeAndMethodologyForm.tsx @@ -1,6 +1,5 @@ import Box from '@mui/material/Box'; import Grid from '@mui/material/Grid'; -import Typography from '@mui/material/Typography'; import CustomTextField from 'components/fields/CustomTextField'; import MultiAutocompleteField from 'components/fields/MultiAutocompleteField'; import MultiAutocompleteFieldVariableSize, { @@ -14,7 +13,6 @@ export interface IPurposeAndMethodologyForm { purpose_and_methodology: { intended_outcome_ids: number[]; additional_details: string; - vantage_code_ids: number[]; revision_count: number; }; } @@ -23,7 +21,6 @@ export const PurposeAndMethodologyInitialValues: IPurposeAndMethodologyForm = { purpose_and_methodology: { intended_outcome_ids: [], additional_details: '', - vantage_code_ids: [], revision_count: 0 } }; @@ -31,14 +28,13 @@ export const PurposeAndMethodologyInitialValues: IPurposeAndMethodologyForm = { export const PurposeAndMethodologyYupSchema = yup.object().shape({ purpose_and_methodology: yup.object().shape({ additional_details: yup.string(), - intended_outcome_ids: yup.array().min(1, 'One or more Ecological Variables are Required').required('Required'), - vantage_code_ids: yup.array().min(1, 'One or more Vantage Codes are Required').required('Required') + intended_outcome_ids: yup.array().min(1, 'One or more Ecological Variables are Required').required('Required') }) }); export interface IPurposeAndMethodologyFormProps { intended_outcomes: ISelectWithSubtextFieldOption[]; - vantage_codes: IMultiAutocompleteFieldOption[]; + type: IMultiAutocompleteFieldOption[]; } /** @@ -50,14 +46,19 @@ const PurposeAndMethodologyForm: React.FC = (pr return ( - - Purpose of Survey - + + + @@ -65,23 +66,8 @@ const PurposeAndMethodologyForm: React.FC = (pr - - - - - - Survey Methodology - - - - diff --git a/app/src/features/surveys/components/participants/SurveyUserForm.tsx b/app/src/features/surveys/components/participants/SurveyUserForm.tsx index c553276f8a..dc02dcd567 100644 --- a/app/src/features/surveys/components/participants/SurveyUserForm.tsx +++ b/app/src/features/surveys/components/participants/SurveyUserForm.tsx @@ -114,23 +114,12 @@ const SurveyUserForm = (props: ISurveyUserFormProps) => { return ( - - Add Participants - - Add particpants to this survey and assign each a role. - - {errors?.['participants'] && values.participants.length > 0 && ( )} - + { borderTop: '1px solid' + grey[300] } }} - key={renderOption.system_user_id} - {...renderProps}> + {...renderProps} + key={renderOption.system_user_id}> { it('deletes existing permits when delete icon is clicked', async () => { const existingFormValues: ISurveyPermitForm = { + permit_used: true, permit: { permits: [ { diff --git a/app/src/features/surveys/SurveyPermitForm.tsx b/app/src/features/surveys/components/permit/SurveyPermitForm.tsx similarity index 56% rename from app/src/features/surveys/SurveyPermitForm.tsx rename to app/src/features/surveys/components/permit/SurveyPermitForm.tsx index fbc90d84a5..b7a5e1a085 100644 --- a/app/src/features/surveys/SurveyPermitForm.tsx +++ b/app/src/features/surveys/components/permit/SurveyPermitForm.tsx @@ -6,68 +6,86 @@ import Card from '@mui/material/Card'; import Collapse from '@mui/material/Collapse'; import grey from '@mui/material/colors/grey'; import FormControl from '@mui/material/FormControl'; +import FormControlLabel from '@mui/material/FormControlLabel'; import FormHelperText from '@mui/material/FormHelperText'; import IconButton from '@mui/material/IconButton'; import InputLabel from '@mui/material/InputLabel'; import MenuItem from '@mui/material/MenuItem'; +import Radio from '@mui/material/Radio'; +import RadioGroup from '@mui/material/RadioGroup'; import Select from '@mui/material/Select'; import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; +import AlertBar from 'components/alert/AlertBar'; import CustomTextField from 'components/fields/CustomTextField'; import { FieldArray, FieldArrayRenderProps, useFormikContext } from 'formik'; -import React from 'react'; +import { get } from 'lodash-es'; +import React, { useEffect } from 'react'; import { TransitionGroup } from 'react-transition-group'; import yup from 'utils/YupSchema'; -export interface ISurveyPermitFormArrayItem { - permit_id: number; +export interface ISurveyPermit { + permit_id?: number; permit_number: string; permit_type: string; } export interface ISurveyPermitForm { + permit_used: boolean | null; permit: { - permits: ISurveyPermitFormArrayItem[]; + permits: ISurveyPermit[]; }; } -export const SurveyPermitFormArrayItemInitialValues: ISurveyPermitFormArrayItem = { +export const SurveyPermitFormArrayItemInitialValues: ISurveyPermit = { permit_id: null as unknown as number, permit_number: '', permit_type: '' }; export const SurveyPermitFormInitialValues: ISurveyPermitForm = { + permit_used: null, permit: { permits: [] } }; export const SurveyPermitFormYupSchema = yup.object().shape({ + permit_used: yup.boolean().nullable().required('You must indicate whether a permit was used'), permit: yup.object().shape({ - permits: yup.array().of( - yup.object().shape({ - permit_id: yup.number().nullable(true), - permit_number: yup - .string() - .max(100, 'Cannot exceed 100 characters') - .required('Permit Number is Required') - .test('is-unique-permit-number', 'Permit numbers must be unique', function (permitNumber) { - const formValues = this.options.context; - - if (!formValues?.permit?.permits?.length) { - return true; - } - - return ( - formValues.permit.permits.filter( - (permit: ISurveyPermitFormArrayItem) => permit.permit_number === permitNumber - ).length <= 1 - ); - }), - permit_type: yup.string().required('Permit Type is Required') + permits: yup + .array() + .of( + yup.object().shape({ + permit_id: yup.number().nullable(true), + permit_number: yup + .string() + .max(100, 'Cannot exceed 100 characters') + .required('Permit Number is Required') + .test('is-unique-permit-number', 'Permit numbers must be unique', function (permitNumber) { + const formValues = this.options.context; + + if (!formValues?.permit?.permits?.length) { + return true; + } + + return ( + formValues.permit.permits.filter((permit: ISurveyPermit) => permit.permit_number === permitNumber) + .length <= 1 + ); + }), + permit_type: yup.string().required('Permit Type is Required') + }) + ) + .test('is-permit-used', 'You must add at least one permit', function (permits) { + const formValues = this.options.context; + + if (!formValues?.permit_used) { + return true; + } + + return !!permits?.length; }) - ) }) }); @@ -77,37 +95,70 @@ export const SurveyPermitFormYupSchema = yup.object().shape({ * @return {*} */ const SurveyPermitForm: React.FC = () => { - const { values, handleChange, getFieldMeta, errors } = useFormikContext(); + const { values, handleChange, getFieldMeta, errors, setFieldValue, submitCount } = + useFormikContext(); + + useEffect(() => { + setFieldValue('permit_used', values.permit_used); + }, [setFieldValue, values.permit_used]); + + const getPermitUsedValue = () => { + if (values.permit_used === true) { + return 'true'; + } + if (values.permit_used === false) { + return 'false'; + } + return null; + }; return ( ( - 0 && ( + + )} + { + const permitsUsed = event.target.value === 'true' ? true : false; + setFieldValue('permit_used', permitsUsed); + if (permitsUsed) { + setFieldValue('permit.permits', [SurveyPermitFormArrayItemInitialValues]); + } else if (!permitsUsed) { + setFieldValue('permit.permits', []); } }}> - {values.permit.permits?.map((permit: ISurveyPermitFormArrayItem, index) => { + } label="Yes" /> + } label="No" /> + + + + {values.permit.permits.map((permit: ISurveyPermit, index) => { const permitNumberMeta = getFieldMeta(`permit.permits.[${index}].permit_number`); const permitTypeMeta = getFieldMeta(`permit.permits.[${index}].permit_type`); return ( - + { {errors.permit.permits} )} - - + {values.permit_used && ( + + )} )} /> diff --git a/app/src/features/surveys/components/sampling-strategy/SamplingStrategyForm.tsx b/app/src/features/surveys/components/sampling-strategy/SamplingStrategyForm.tsx index d278a50c1e..d60bab9f44 100644 --- a/app/src/features/surveys/components/sampling-strategy/SamplingStrategyForm.tsx +++ b/app/src/features/surveys/components/sampling-strategy/SamplingStrategyForm.tsx @@ -11,10 +11,7 @@ const SamplingStrategyForm = () => { return ( <> - - Site Selection Strategies - - + Add Stratum @@ -35,7 +32,7 @@ const SamplingStrategyForm = () => { sx={{ mb: 0 }}> - Add Blocks (Optional) + Add Blocks (optional) { /> { )} - {values.site_selection.stratums.map((stratum: IGetSurveyStratum, index: number) => { + {values.site_selection.stratums.map((stratum, index: number) => { const key = `${stratum.name}-${index}`; return ( diff --git a/app/src/features/surveys/components/species/SpeciesForm.tsx b/app/src/features/surveys/components/species/SpeciesForm.tsx new file mode 100644 index 0000000000..a4fab7b867 --- /dev/null +++ b/app/src/features/surveys/components/species/SpeciesForm.tsx @@ -0,0 +1,87 @@ +import Box from '@mui/material/Box'; +import Grid from '@mui/material/Grid'; +import { FocalSpeciesForm } from 'features/surveys/components/species/components/FocalSpeciesForm'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import yup from 'utils/YupSchema'; + +export type IEcologicalUnit = { + critterbase_collection_category_id: string | null; + critterbase_collection_unit_id: string | null; +}; + +export const EcologicalUnitInitialValues: IEcologicalUnit = { + critterbase_collection_category_id: null, + critterbase_collection_unit_id: null +}; + +export interface ITaxonomyWithEcologicalUnits extends IPartialTaxonomy { + ecological_units: IEcologicalUnit[]; +} + +export interface ISpeciesForm { + species: { + focal_species: ITaxonomyWithEcologicalUnits[]; + }; +} + +export const SpeciesInitialValues: ISpeciesForm = { + species: { + focal_species: [] + } +}; + +export const SpeciesYupSchema = yup.object().shape({ + species: yup.object().shape({ + focal_species: yup + .array() + .of( + yup.object().shape({ + ecological_units: yup.array().of( + yup.object().shape({ + critterbase_collection_category_id: yup.string().nullable().required('Ecological unit is required'), + critterbase_collection_unit_id: yup.string().nullable().required('Ecological unit is required') + }) + ) + }) + ) + .min(1, 'You must specify a focal species') + .required('Required') + .test('is-unique-ecological-unit', 'Ecological units must be unique', function () { + const focalSpecies = (this.options.context?.species.focal_species ?? []) as ITaxonomyWithEcologicalUnits[]; + + const seenCollectionUnitIts = new Set(); + + for (const focalSpeciesItem of focalSpecies) { + for (const ecologicalUnit of focalSpeciesItem.ecological_units) { + if (seenCollectionUnitIts.has(ecologicalUnit.critterbase_collection_category_id)) { + // Duplicate ecological collection category id found, return false + return false; + } + seenCollectionUnitIts.add(ecologicalUnit.critterbase_collection_category_id); + } + } + + // Valid, return true + return true; + }) + }) +}); + +/** + * Create survey - species information fields + * + * @return {*} + */ +const SpeciesForm = () => { + return ( + + + + + + + + ); +}; + +export default SpeciesForm; diff --git a/app/src/features/surveys/components/species/components/FocalSpeciesAlert.tsx b/app/src/features/surveys/components/species/components/FocalSpeciesAlert.tsx new file mode 100644 index 0000000000..13fd339187 --- /dev/null +++ b/app/src/features/surveys/components/species/components/FocalSpeciesAlert.tsx @@ -0,0 +1,25 @@ +import AlertBar from 'components/alert/AlertBar'; +import { useFormikContext } from 'formik'; +import { ICreateSurveyRequest, IEditSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import get from 'lodash-es/get'; + +/** + * Renders an alert if formik has an error for the 'species.focal_species' field. + * + * @return {*} + */ +export const FocalSpeciesAlert = () => { + const { errors } = useFormikContext(); + + const errorText = get(errors, 'species.focal_species'); + + if (!errorText) { + return null; + } + + if (typeof errorText !== 'string') { + return null; + } + + return ; +}; diff --git a/app/src/features/surveys/components/species/components/FocalSpeciesEcologicalUnitsForm.tsx b/app/src/features/surveys/components/species/components/FocalSpeciesEcologicalUnitsForm.tsx new file mode 100644 index 0000000000..d877370212 --- /dev/null +++ b/app/src/features/surveys/components/species/components/FocalSpeciesEcologicalUnitsForm.tsx @@ -0,0 +1,94 @@ +import { mdiPlus } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import Stack from '@mui/material/Stack'; +import { EcologicalUnitsSelect } from 'components/species/ecological-units/EcologicalUnitsSelect'; +import { initialEcologicalUnitValues } from 'features/surveys/animals/animal-form/components/ecological-units/EcologicalUnitsForm'; +import { FieldArray, FieldArrayRenderProps, useFormikContext } from 'formik'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { ICreateSurveyRequest, IEditSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import { useEffect } from 'react'; +import { isDefined } from 'utils/Utils'; +import { v4 } from 'uuid'; + +export interface ISelectedSpeciesProps { + /** + * The species to display. + * + * @type {IPartialTaxonomy} + * @memberof ISelectedSpeciesProps + */ + species: IPartialTaxonomy; + /** + * The index of the component in the list. + * + * @type {number} + * @memberof ISelectedSpeciesProps + */ + index: number; +} + +/** + * Renders form controls for selecting ecological units for a focal species. + * + * @param {ISelectedSpeciesProps} props + * @return {*} + */ +export const FocalSpeciesEcologicalUnitsForm = (props: ISelectedSpeciesProps) => { + const { index, species } = props; + + const { values } = useFormikContext(); + + const critterbaseApi = useCritterbaseApi(); + + const ecologicalUnitDataLoader = useDataLoader((tsn: number) => critterbaseApi.xref.getTsnCollectionCategories(tsn)); + + useEffect(() => { + ecologicalUnitDataLoader.load(species.tsn); + }, [ecologicalUnitDataLoader, species.tsn]); + + const ecologicalUnitsForSpecies = ecologicalUnitDataLoader.data ?? []; + + const selectedUnits = + values.species.focal_species.filter((item) => item.tsn === species.tsn).flatMap((item) => item.ecological_units) ?? + []; + + return ( + ( + + {selectedUnits.map((ecological_unit, ecologicalUnitIndex) => ( + unit.critterbase_collection_category_id) + .filter(isDefined)} + ecologicalUnits={ecologicalUnitsForSpecies} + arrayHelpers={arrayHelpers} + index={ecologicalUnitIndex} + /> + ))} + + + + + )} + /> + ); +}; diff --git a/app/src/features/surveys/components/species/components/FocalSpeciesForm.tsx b/app/src/features/surveys/components/species/components/FocalSpeciesForm.tsx new file mode 100644 index 0000000000..7b0368a847 --- /dev/null +++ b/app/src/features/surveys/components/species/components/FocalSpeciesForm.tsx @@ -0,0 +1,69 @@ +import Collapse from '@mui/material/Collapse'; +import { grey } from '@mui/material/colors'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import SpeciesAutocompleteField from 'components/species/components/SpeciesAutocompleteField'; +import SpeciesSelectedCard from 'components/species/components/SpeciesSelectedCard'; +import { FocalSpeciesAlert } from 'features/surveys/components/species/components/FocalSpeciesAlert'; +import { FocalSpeciesEcologicalUnitsForm } from 'features/surveys/components/species/components/FocalSpeciesEcologicalUnitsForm'; +import { ITaxonomyWithEcologicalUnits } from 'features/surveys/components/species/SpeciesForm'; +import { FieldArray, useFormikContext } from 'formik'; +import { ICreateSurveyRequest, IEditSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import get from 'lodash-es/get'; +import { TransitionGroup } from 'react-transition-group'; + +/** + * Returns a form control for selecting focal species and ecological units for each focal species. + * + * @return {*} + */ +export const FocalSpeciesForm = () => { + const { values } = useFormikContext(); + + const selectedSpecies: ITaxonomyWithEcologicalUnits[] = get(values, 'species.focal_species') ?? []; + + return ( + { + return ( + + + + { + if (values.species.focal_species.some((focalSpecies) => focalSpecies.tsn === species.tsn)) { + // Species was already added, do not add again + return; + } + + arrayHelpers.push({ ...species, ecological_units: [] }); + }} + clearOnSelect={true} + /> + + + {selectedSpecies.map((species, index) => ( + + + { + arrayHelpers.remove(index); + }} + /> + + + + ))} + + + ); + }} + /> + ); +}; diff --git a/app/src/features/surveys/edit/EditSurveyForm.tsx b/app/src/features/surveys/edit/EditSurveyForm.tsx index 0335e9eec6..c228734833 100644 --- a/app/src/features/surveys/edit/EditSurveyForm.tsx +++ b/app/src/features/surveys/edit/EditSurveyForm.tsx @@ -1,4 +1,5 @@ import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; import Divider from '@mui/material/Divider'; import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; @@ -6,16 +7,18 @@ import FormikErrorSnackbar from 'components/alert/FormikErrorSnackbar'; import HorizontalSplitFormComponent from 'components/fields/HorizontalSplitFormComponent'; import { CodesContext } from 'contexts/codesContext'; import { ProjectContext } from 'contexts/projectContext'; +import SurveyPermitForm, { ISurveyPermitForm } from 'features/surveys/components/permit/SurveyPermitForm'; import SamplingStrategyForm from 'features/surveys/components/sampling-strategy/SamplingStrategyForm'; import SurveyPartnershipsForm, { SurveyPartnershipsFormYupSchema } from 'features/surveys/view/components/SurveyPartnershipsForm'; import { Formik, FormikProps } from 'formik'; -import { ICreateSurveyRequest, IEditSurveyRequest, SurveyUpdateObject } from 'interfaces/useSurveyApi.interface'; -import React, { useContext } from 'react'; +import { ICreateSurveyRequest, IUpdateSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import React, { useContext, useEffect } from 'react'; import AgreementsForm, { AgreementsYupSchema } from '../components/agreements/AgreementsForm'; import ProprietaryDataForm, { ProprietaryDataYupSchema } from '../components/agreements/ProprietaryDataForm'; import SurveyFundingSourceForm, { + ISurveyFundingSourceForm, SurveyFundingSourceFormYupSchema } from '../components/funding/SurveyFundingSourceForm'; import GeneralInformationForm, { @@ -27,11 +30,16 @@ import PurposeAndMethodologyForm, { } from '../components/methodology/PurposeAndMethodologyForm'; import SurveyUserForm, { SurveyUserJobYupSchema } from '../components/participants/SurveyUserForm'; import { SurveySiteSelectionYupSchema } from '../components/sampling-strategy/SurveySiteSelectionForm'; - -export interface IEditSurveyForm { - initialSurveyData: SurveyUpdateObject | ICreateSurveyRequest; - handleSubmit: (formikData: IEditSurveyRequest) => void; - formikRef: React.RefObject>; +import SpeciesForm, { SpeciesYupSchema } from '../components/species/SpeciesForm'; + +export interface IEditSurveyForm< + T extends + | (IUpdateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) + | (ICreateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) +> { + initialSurveyData: T; + handleSubmit: (formikData: T) => void; + formikRef: React.RefObject>; } /** @@ -39,15 +47,25 @@ export interface IEditSurveyForm { * * @return {*} */ -const EditSurveyForm = (props: IEditSurveyForm) => { +const EditSurveyForm = < + T extends + | (IUpdateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) + | (ICreateSurveyRequest & ISurveyPermitForm & ISurveyFundingSourceForm) +>( + props: IEditSurveyForm +) => { const projectContext = useContext(ProjectContext); const projectData = projectContext.projectDataLoader.data?.projectData; const codesContext = useContext(CodesContext); const codes = codesContext.codesDataLoader.data; + useEffect(() => { + codesContext.codesDataLoader.load(); + }, [codesContext.codesDataLoader]); + if (!projectData || !codes) { - return <>; + return ; } const surveyEditYupSchemas = GeneralInformationYupSchema() @@ -58,12 +76,13 @@ const EditSurveyForm = (props: IEditSurveyForm) => { .concat(SurveyUserJobYupSchema) .concat(SurveyLocationYupSchema) .concat(SurveySiteSelectionYupSchema) - .concat(SurveyPartnershipsFormYupSchema); + .concat(SurveyPartnershipsFormYupSchema) + .concat(SpeciesYupSchema); return ( - innerRef={props.formikRef} - initialValues={props.initialSurveyData as IEditSurveyRequest} + initialValues={props.initialSurveyData} validationSchema={surveyEditYupSchemas} validateOnBlur={false} validateOnChange={false} @@ -72,13 +91,9 @@ const EditSurveyForm = (props: IEditSurveyForm) => { { - return { value: item.id, label: item.name }; - }) || [] - } progress={ codes?.survey_progress?.map((item) => { return { value: item.id, label: item.name, subText: item.description }; @@ -89,8 +104,43 @@ const EditSurveyForm = (props: IEditSurveyForm) => { + + + + + + + + Were any permits used in this survey? + + + } + /> + + + + + Do any funding agencies require this survey to be submitted? + + + } + /> + + + { return { value: item.id, label: item.name, subText: item.description }; }) || [] } - vantage_codes={ - codes.vantage_codes.map((item) => { + type={ + codes?.type?.map((item) => { return { value: item.id, label: item.name }; }) || [] } @@ -110,34 +160,23 @@ const EditSurveyForm = (props: IEditSurveyForm) => { } /> - - Add Funding Sources - - - - Additional Partnerships - - - - } + title="Partnerships" + summary="Enter any partners involved in the survey" + component={} /> } /> @@ -145,41 +184,39 @@ const EditSurveyForm = (props: IEditSurveyForm) => { - Define Survey Study Area - - - Import, draw or select a feature from an existing layer to define the study areas for this survey. - - - - - } + summary="Import, draw or select a feature from an existing layer to define the study areas for this survey" + component={} /> { - return { value: item.id, label: item.name, is_first_nation: item.is_first_nation }; - }) || [] - } - first_nations={ - codes.first_nations?.map((item) => { - return { value: item.id, label: item.name }; - }) || [] - } - /> + + Is any data in this survey proprietary? + { + return { value: item.id, label: item.name, is_first_nation: item.is_first_nation }; + }) || [] + } + first_nations={ + codes.first_nations?.map((item) => { + return { value: item.id, label: item.name }; + }) || [] + } + /> + }> - }> + }> diff --git a/app/src/features/surveys/edit/EditSurveyPage.tsx b/app/src/features/surveys/edit/EditSurveyPage.tsx index c0a7563eaa..96e384c016 100644 --- a/app/src/features/surveys/edit/EditSurveyPage.tsx +++ b/app/src/features/surveys/edit/EditSurveyPage.tsx @@ -59,15 +59,15 @@ const EditSurveyPage = () => { const surveyContext = useContext(SurveyContext); - const editSurveyDataLoader = useDataLoader((projectId: number, surveyId: number) => + const getSurveyForUpdateDataLoader = useDataLoader((projectId: number, surveyId: number) => biohubApi.survey.getSurveyForUpdate(projectId, surveyId) ); if (surveyId) { - editSurveyDataLoader.load(projectContext.projectId, surveyId); + getSurveyForUpdateDataLoader.load(projectContext.projectId, surveyId); } - const surveyData = editSurveyDataLoader.data?.surveyData; + const surveyData = getSurveyForUpdateDataLoader.data?.surveyData; const handleCancel = () => { history.push('details'); @@ -97,6 +97,7 @@ const EditSurveyPage = () => { setIsSaving(true); try { + // Remove the permit_used and funding_used properties const response = await biohubApi.survey.updateSurvey(projectContext.projectId, surveyId, { blocks: values.blocks, funding_sources: values.funding_sources, @@ -109,9 +110,10 @@ const EditSurveyPage = () => { })), participants: values.participants, partnerships: values.partnerships, - permit: values.permit, + permit: { + permits: values.permit.permits + }, proprietor: values.proprietor, - purpose_and_methodology: values.purpose_and_methodology, site_selection: { stratums: values.site_selection.stratums.map((stratum) => ({ survey_stratum_id: stratum.survey_stratum_id, @@ -121,7 +123,9 @@ const EditSurveyPage = () => { strategies: values.site_selection.strategies }, species: values.species, - survey_details: values.survey_details + survey_details: values.survey_details, + purpose_and_methodology: values.purpose_and_methodology, + agreements: values.agreements }); if (!response?.id) { @@ -194,7 +198,27 @@ const EditSurveyPage = () => { - + { it('renders correctly with an empty list of surveys', async () => { const mockCodesContext: ICodesContext = { codesDataLoader: { - data: codes + data: codes, + load: () => {} } as DataLoader }; const mockProjectContext: IProjectContext = { projectDataLoader: { data: getProjectForViewResponse } as DataLoader, - surveysListDataLoader: { data: [], refresh: jest.fn() } as unknown as DataLoader, + surveysListDataLoader: { data: [], isLoading: false, isReady: true, refresh: jest.fn() } as unknown as DataLoader< + any, + any, + any + >, artifactDataLoader: { data: null } as DataLoader, projectId: 1 }; @@ -62,7 +67,7 @@ describe('SurveysListPage', () => { const authState = getMockAuthState({ base: SystemAdminAuthState }); - const { getByText } = render( + const { getByTestId } = render( @@ -77,16 +82,15 @@ describe('SurveysListPage', () => { ); await waitFor(() => { - expect(getByText(/^Surveys/)).toBeInTheDocument(); - expect(getByText('Create Survey')).toBeInTheDocument(); - expect(getByText('No surveys found')).toBeInTheDocument(); + expect(getByTestId('survey-list-no-data-overlay')).toBeInTheDocument(); }); }); it('renders correctly with a populated list of surveys', async () => { const mockCodesContext: ICodesContext = { codesDataLoader: { - data: codes + data: codes, + load: () => {} } as DataLoader }; @@ -103,11 +107,12 @@ describe('SurveysListPage', () => { projectDataLoader: { data: getProjectForViewResponse } as DataLoader, - surveysListDataLoader: { data: getSurveyForListResponse, refresh: jest.fn() } as unknown as DataLoader< - any, - any, - any - >, + surveysListDataLoader: { + data: getSurveyForListResponse, + isLoading: false, + isReady: true, + refresh: jest.fn() + } as unknown as DataLoader, artifactDataLoader: { data: null } as DataLoader, projectId: 1 }; diff --git a/app/src/features/surveys/list/SurveysListPage.tsx b/app/src/features/surveys/list/SurveysListPage.tsx index fe3cc79810..55474b8ba4 100644 --- a/app/src/features/surveys/list/SurveysListPage.tsx +++ b/app/src/features/surveys/list/SurveysListPage.tsx @@ -1,13 +1,17 @@ -import { mdiPlus } from '@mdi/js'; +import { mdiArrowTopRight, mdiPlus } from '@mdi/js'; import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; +import { grey } from '@mui/material/colors'; import Divider from '@mui/material/Divider'; import Link from '@mui/material/Link'; import Toolbar from '@mui/material/Toolbar'; import Typography from '@mui/material/Typography'; import { GridColDef, GridPaginationModel, GridSortModel } from '@mui/x-data-grid'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { ProjectRoleGuard } from 'components/security/Guards'; import { DATE_FORMAT } from 'constants/dateTimeFormats'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; @@ -53,7 +57,25 @@ const SurveysListPage = () => { // eslint-disable-next-line react-hooks/exhaustive-deps }, [sortModel, paginationModel]); + const surveys = projectContext.surveysListDataLoader.data?.surveys ?? []; + const columns: GridColDef[] = [ + { + field: 'survey_id', + headerName: 'ID', + width: 70, + minWidth: 70, + renderHeader: () => ( + + ID + + ), + renderCell: (params) => ( + + {params.row.survey_id} + + ) + }, { field: 'name', headerName: 'Name', @@ -131,30 +153,47 @@ const SurveysListPage = () => { - + + + - row.survey_id} - pageSizeOptions={[...pageSizeOptions]} - paginationMode="server" - sortingMode="server" - sortModel={sortModel} - paginationModel={paginationModel} - onPaginationModelChange={setPaginationModel} - onSortModelChange={setSortModel} - rowSelection={false} - checkboxSelection={false} - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - sortingOrder={['asc', 'desc']} - /> + } + isLoadingFallbackDelay={100} + hasNoData={!surveys.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.survey_id} + pageSizeOptions={[...pageSizeOptions]} + paginationMode="server" + sortingMode="server" + sortModel={sortModel} + paginationModel={paginationModel} + onPaginationModelChange={setPaginationModel} + onSortModelChange={setSortModel} + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + disableColumnSelector + disableColumnFilter + disableColumnMenu + sortingOrder={['asc', 'desc']} + /> + ); diff --git a/app/src/features/surveys/observations/observations-table/ObservationsTable.tsx b/app/src/features/surveys/observations/observations-table/ObservationsTable.tsx index e523621720..7c3afd2cbe 100644 --- a/app/src/features/surveys/observations/observations-table/ObservationsTable.tsx +++ b/app/src/features/surveys/observations/observations-table/ObservationsTable.tsx @@ -26,152 +26,150 @@ const ObservationsTable = (props: ISpeciesObservationTableProps) => { const observationsTableContext = useObservationsTableContext(); return ( - <> - observationsTableContext.onRowEditStart(params.id)} - onRowEditStop={(_params, event) => { - event.defaultMuiPrevented = true; - }} - // Row selection - checkboxSelection - disableRowSelectionOnClick - rowSelectionModel={observationsTableContext.rowSelectionModel} - onRowSelectionModelChange={observationsTableContext.onRowSelectionModelChange} - // Styling - localeText={{ - noRowsLabel: 'No Records' - }} - rowHeight={56} - getRowHeight={() => 'auto'} - getRowClassName={(params) => (has(observationsTableContext.validationModel, params.row.id) ? 'error' : '')} - // Loading - loading={observationsTableContext.isLoading} - slots={{ - loadingOverlay: SkeletonTable - }} - // Styles - sx={{ - border: 'none', - borderRadius: 0, - '&:after': { - content: '" "', - position: 'absolute', - top: 0, - right: 0, - width: 100, - height: 55 - }, - '& .pinnedColumn': { - position: 'sticky', - right: 0, - top: 0, - borderLeft: '1px solid' + grey[300] - }, - '& .MuiDataGrid-columnHeaders': { - position: 'relative', - background: grey[50] - }, - '& .MuiDataGrid-columnHeader:focus-within': { - outline: 'none', - background: grey[200] - }, - '& .MuiDataGrid-columnHeaderTitle': { - fontWeight: 700, - textTransform: 'uppercase', - color: 'text.secondary' + observationsTableContext.onRowEditStart(params.id)} + onRowEditStop={(_params, event) => { + event.defaultMuiPrevented = true; + }} + // Row selection + checkboxSelection + disableRowSelectionOnClick + rowSelectionModel={observationsTableContext.rowSelectionModel} + onRowSelectionModelChange={observationsTableContext.onRowSelectionModelChange} + // Styling + localeText={{ + noRowsLabel: 'No Records' + }} + rowHeight={56} + getRowHeight={() => 'auto'} + getRowClassName={(params) => (has(observationsTableContext.validationModel, params.row.id) ? 'error' : '')} + // Loading + loading={observationsTableContext.isLoading} + slots={{ + loadingOverlay: SkeletonTable + }} + // Styles + sx={{ + border: 'none', + borderRadius: 0, + '&:after': { + content: '" "', + position: 'absolute', + top: 0, + right: 0, + width: 100, + height: 55 + }, + '& .pinnedColumn': { + position: 'sticky', + right: 0, + top: 0, + borderLeft: '1px solid' + grey[300] + }, + '& .MuiDataGrid-columnHeaders': { + position: 'relative', + background: grey[50] + }, + '& .MuiDataGrid-columnHeader:focus-within': { + outline: 'none', + background: grey[200] + }, + '& .MuiDataGrid-columnHeaderTitle': { + fontWeight: 700, + textTransform: 'uppercase', + color: 'text.secondary' + }, + '& .MuiDataGrid-cell': { + py: 0.75, + background: '#fff', + '&.MuiDataGrid-cell--editing:focus-within': { + outline: 'none' }, + '&.MuiDataGrid-cell--editing': { + p: 0.5, + backgroundColor: cyan[100] + } + }, + '& .MuiDataGrid-row--editing': { + boxShadow: 'none', + backgroundColor: cyan[50], '& .MuiDataGrid-cell': { - py: 0.75, - background: '#fff', - '&.MuiDataGrid-cell--editing:focus-within': { - outline: 'none' - }, - '&.MuiDataGrid-cell--editing': { - p: 0.5, - backgroundColor: cyan[100] - } + backgroundColor: cyan[50] }, - '& .MuiDataGrid-row--editing': { - boxShadow: 'none', - backgroundColor: cyan[50], - '& .MuiDataGrid-cell': { - backgroundColor: cyan[50] - }, - '&.error': { - '& .MuiDataGrid-cell, .MuiDataGrid-cell--editing': { - backgroundColor: 'rgb(251, 237, 238)' - } - } - }, - '& .MuiDataGrid-editInputCell': { - border: '1px solid #ccc', - '&:hover': { - borderColor: 'primary.main' - }, - '&.Mui-focused': { - borderColor: 'primary.main', - outlineWidth: '2px', - outlineStyle: 'solid', - outlineColor: 'primary.main', - outlineOffset: '-2px' - } - }, - '& .MuiInputBase-root': { - height: '40px', - borderRadius: '4px', - background: '#fff', - fontSize: '0.875rem', - '&.MuiDataGrid-editInputCell': { - padding: 0 - } - }, - '& .MuiOutlinedInput-root': { - borderRadius: '4px', - background: '#fff', - border: 'none', - '&:hover': { - borderColor: 'primary.main' - }, - '&:hover > fieldset': { - border: '1px solid primary.main' + '&.error': { + '& .MuiDataGrid-cell, .MuiDataGrid-cell--editing': { + backgroundColor: 'rgb(251, 237, 238)' } + } + }, + '& .MuiDataGrid-editInputCell': { + border: '1px solid #ccc', + '&:hover': { + borderColor: 'primary.main' }, - '& .MuiOutlinedInput-notchedOutline': { - border: '1px solid ' + grey[300], - '&.Mui-focused': { - borderColor: 'primary.main' - } + '&.Mui-focused': { + borderColor: 'primary.main', + outlineWidth: '2px', + outlineStyle: 'solid', + outlineColor: 'primary.main', + outlineOffset: '-2px' + } + }, + '& .MuiInputBase-root': { + height: '40px', + borderRadius: '4px', + background: '#fff', + fontSize: '0.875rem', + '&.MuiDataGrid-editInputCell': { + padding: 0 + } + }, + '& .MuiOutlinedInput-root': { + borderRadius: '4px', + background: '#fff', + border: 'none', + '&:hover': { + borderColor: 'primary.main' }, - '& .MuiDataGrid-virtualScrollerContent, .MuiDataGrid-overlay': { - background: grey[100] + '&:hover > fieldset': { + border: '1px solid primary.main' + } + }, + '& .MuiOutlinedInput-notchedOutline': { + border: '1px solid ' + grey[300], + '&.Mui-focused': { + borderColor: 'primary.main' } - }} - /> - + }, + '& .MuiDataGrid-virtualScrollerContent, .MuiDataGrid-overlay': { + background: grey[100] + } + }} + /> ); }; diff --git a/app/src/features/surveys/observations/observations-table/ObservationsTableContainer.tsx b/app/src/features/surveys/observations/observations-table/ObservationsTableContainer.tsx index c7ac13bbde..24e300a0b7 100644 --- a/app/src/features/surveys/observations/observations-table/ObservationsTableContainer.tsx +++ b/app/src/features/surveys/observations/observations-table/ObservationsTableContainer.tsx @@ -39,7 +39,7 @@ import { IGetSampleMethodDetails, IGetSamplePeriodRecord } from 'interfaces/useSamplingSiteApi.interface'; -import { useContext } from 'react'; +import { useContext, useMemo } from 'react'; import { getCodesName } from 'utils/Utils'; import { ConfigureColumnsButton } from './configure-columns/ConfigureColumnsButton'; import ExportHeadersButton from './export-button/ExportHeadersButton'; @@ -57,12 +57,19 @@ const ObservationsTableContainer = () => { const observationsTableContext = useObservationsTableContext(); // Collect sample sites - const surveySampleSites: IGetSampleLocationDetails[] = surveyContext.sampleSiteDataLoader.data?.sampleSites ?? []; - const sampleSiteOptions: ISampleSiteOption[] = - surveySampleSites.map((site) => ({ - survey_sample_site_id: site.survey_sample_site_id, - sample_site_name: site.name - })) ?? []; + const surveySampleSites: IGetSampleLocationDetails[] = useMemo( + () => surveyContext.sampleSiteDataLoader.data?.sampleSites ?? [], + [surveyContext.sampleSiteDataLoader.data?.sampleSites] + ); + + const sampleSiteOptions: ISampleSiteOption[] = useMemo( + () => + surveySampleSites.map((site) => ({ + survey_sample_site_id: site.survey_sample_site_id, + sample_site_name: site.name + })) ?? [], + [surveySampleSites] + ); // Collect sample methods const surveySampleMethods: IGetSampleMethodDetails[] = surveySampleSites @@ -91,22 +98,55 @@ const ObservationsTableContainer = () => { })); // The column definitions of the columns to render in the observations table - const columns: GridColDef[] = [ - // Add standard observation columns to the table - TaxonomyColDef({ hasError: observationsTableContext.hasError }), - SampleSiteColDef({ sampleSiteOptions, hasError: observationsTableContext.hasError }), - SampleMethodColDef({ sampleMethodOptions, hasError: observationsTableContext.hasError }), - SamplePeriodColDef({ samplePeriodOptions, hasError: observationsTableContext.hasError }), - ObservationCountColDef({ sampleMethodOptions, hasError: observationsTableContext.hasError }), - GenericDateColDef({ field: 'observation_date', headerName: 'Date', hasError: observationsTableContext.hasError }), - GenericTimeColDef({ field: 'observation_time', headerName: 'Time', hasError: observationsTableContext.hasError }), - GenericLatitudeColDef({ field: 'latitude', headerName: 'Lat', hasError: observationsTableContext.hasError }), - GenericLongitudeColDef({ field: 'longitude', headerName: 'Long', hasError: observationsTableContext.hasError }), - // Add measurement columns to the table - ...getMeasurementColumnDefinitions(observationsTableContext.measurementColumns, observationsTableContext.hasError), - // Add environment columns to the table - ...getEnvironmentColumnDefinitions(observationsTableContext.environmentColumns, observationsTableContext.hasError) - ]; + const columns: GridColDef[] = useMemo( + () => [ + // Add standard observation columns to the table + TaxonomyColDef({ hasError: observationsTableContext.hasError }), + SampleSiteColDef({ sampleSiteOptions, hasError: observationsTableContext.hasError }), + SampleMethodColDef({ sampleMethodOptions, hasError: observationsTableContext.hasError }), + SamplePeriodColDef({ samplePeriodOptions, hasError: observationsTableContext.hasError }), + ObservationCountColDef({ sampleMethodOptions, hasError: observationsTableContext.hasError }), + GenericDateColDef({ + field: 'observation_date', + headerName: 'Date', + description: 'The date when the observation was made', + hasError: observationsTableContext.hasError + }), + GenericTimeColDef({ + field: 'observation_time', + headerName: 'Time', + description: 'The time when the observation was made', + hasError: observationsTableContext.hasError + }), + GenericLatitudeColDef({ + field: 'latitude', + headerName: 'Latitude', + description: 'The latitude where the observation was made', + hasError: observationsTableContext.hasError + }), + GenericLongitudeColDef({ + field: 'longitude', + headerName: 'Longitude', + description: 'The longitude where the observation was made', + hasError: observationsTableContext.hasError + }), + // Add measurement columns to the table + ...getMeasurementColumnDefinitions( + observationsTableContext.measurementColumns, + observationsTableContext.hasError + ), + // Add environment columns to the table + ...getEnvironmentColumnDefinitions(observationsTableContext.environmentColumns, observationsTableContext.hasError) + ], + [ + observationsTableContext.environmentColumns, + observationsTableContext.hasError, + observationsTableContext.measurementColumns, + sampleMethodOptions, + samplePeriodOptions, + sampleSiteOptions + ] + ); return ( diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsDialog.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsDialog.tsx index 55a02aab10..4d942a67bb 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsDialog.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsDialog.tsx @@ -125,7 +125,7 @@ export const ConfigureColumnsDialog = (props: IConfigureColumnsDialogProps) => { return ( { measurements. - + { /> - - Close + + Save & Close diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsPage.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsPage.tsx index 2d5f97e20c..3dd4626823 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsPage.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/ConfigureColumnsPage.tsx @@ -127,7 +127,7 @@ export const ConfigureColumnsPage = (props: IConfigureColumnsPageProps) => { const [activeView, setActiveView] = useState(ConfigureColumnsViewEnum.GENERAL); return ( - + { startIcon={} disabled={disabled} value={ConfigureColumnsViewEnum.MEASUREMENTS}> - Measurements + Species Attributes { - + {activeView === ConfigureColumnsViewEnum.GENERAL && ( + - Configure Environment Columns + Add Environmental Variables onAddEnvironmentColumns(environmentColumn)} /> - - {hasEnvironmentColumns ? ( - <> - - Selected environments - - - {environmentColumns.qualitative_environments.map((environment) => ( - - - - - onRemoveEnvironmentColumns({ - qualitative_environments: [environment.environment_qualitative_id], - quantitative_environments: [] - }) - } - data-testid="configure-environment-qualitative-column-remove-button"> - - - + {hasEnvironmentColumns ? ( + <> + + Selected environments + + + {environmentColumns.qualitative_environments.map((environment) => ( + + + {environment.options.map((option) => ( + + ))} + + } + /> + + + onRemoveEnvironmentColumns({ + qualitative_environments: [environment.environment_qualitative_id], + quantitative_environments: [] + }) + } + data-testid="configure-environment-qualitative-column-remove-button"> + + - ))} - {environmentColumns.quantitative_environments.map((environment) => ( - - - - - onRemoveEnvironmentColumns({ - qualitative_environments: [], - quantitative_environments: [environment.environment_quantitative_id] - }) - } - data-testid="configure-environment-quantitative-column-remove-button"> - - - + + ))} + {environmentColumns.quantitative_environments.map((environment) => ( + + : undefined + } + /> + + + onRemoveEnvironmentColumns({ + qualitative_environments: [], + quantitative_environments: [environment.environment_quantitative_id] + }) + } + data-testid="configure-environment-quantitative-column-remove-button"> + + - ))} - - - ) : ( - - No environmental variables selected - - )} - - + + ))} + + + ) : ( + + )} + ); }; diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/general/ConfigureGeneralColumns.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/general/ConfigureGeneralColumns.tsx index 3ca4654a46..39a1e4b84f 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/general/ConfigureGeneralColumns.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/general/ConfigureGeneralColumns.tsx @@ -97,18 +97,10 @@ export const ConfigureGeneralColumns = (props: IConfigureGeneralColumnsProps) => } = props; return ( - - - Select Columns to Show - - + // display="flex" and flexDirection="column" is necessary for the scrollbars to be correctly positioned + + + Select Columns to Show checked={hiddenFields.length === 0} onClick={() => onToggleShowHideAll()} disabled={disabled} + sx={{ m: 0, p: 0 }} /> } label={ - + Show/Hide all } @@ -130,12 +128,14 @@ export const ConfigureGeneralColumns = (props: IConfigureGeneralColumnsProps) => component={Stack} gap={0.5} sx={{ + my: 2, p: 0.5, - maxHeight: { sm: 300, md: 500 }, + maxHeight: '100%', overflowY: 'auto' }} disablePadding> {hideableColumns.map((column) => { + const isSelected = !hiddenFields.includes(column.field); return ( dense onClick={() => onToggleColumnVisibility(column.field)} disabled={disabled} - sx={{ background: grey[50], borderRadius: '5px' }}> + sx={{ + background: isSelected ? grey[50] : '#fff', + borderRadius: '5px', + alignItems: 'flex-start', + '& .MuiListItemText-root': { my: 0.25 } + }}> - + - {column.headerName} + + {column.headerName} + + {column.description} + + ); diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/ConfigureMeasurementColumns.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/ConfigureMeasurementColumns.tsx index f36b2763e5..2b8e1b6dbb 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/ConfigureMeasurementColumns.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/ConfigureMeasurementColumns.tsx @@ -1,8 +1,19 @@ -import { mdiTrashCanOutline } from '@mdi/js'; +import { mdiArrowTopRight, mdiTrashCanOutline } from '@mdi/js'; import Icon from '@mdi/react'; -import { Box, IconButton, Stack, Typography } from '@mui/material'; -import MeasurementStandardCard from 'features/standards/view/components/MeasurementStandardCard'; +import Box from '@mui/material/Box'; +import Checkbox from '@mui/material/Checkbox'; +import { blueGrey, grey } from '@mui/material/colors'; +import FormControlLabel from '@mui/material/FormControlLabel'; +import FormGroup from '@mui/material/FormGroup'; +import IconButton from '@mui/material/IconButton'; +import List from '@mui/material/List'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { AccordionStandardCard } from 'features/standards/view/components/AccordionStandardCard'; import { CBMeasurementType } from 'interfaces/useCritterApi.interface'; +import { useState } from 'react'; import { MeasurementsSearch } from './search/MeasurementsSearch'; export interface IConfigureMeasurementColumnsProps { @@ -33,54 +44,98 @@ export interface IConfigureMeasurementColumnsProps { * @param {IConfigureMeasurementColumnsProps} props * @return {*} */ + export const ConfigureMeasurementColumns = (props: IConfigureMeasurementColumnsProps) => { const { measurementColumns, onAddMeasurementColumns, onRemoveMeasurementColumns } = props; + const [isFocalSpeciesMeasurementsOnly, setIsFocalSpeciesMeasurementsOnly] = useState(true); + return ( - <> + - Configure Measurement Columns + Add Species Attributes onAddMeasurementColumns([measurementColumn])} + focalOrObservedSpeciesOnly={isFocalSpeciesMeasurementsOnly} /> - - {measurementColumns.length ? ( - <> - - Selected measurements - - - {measurementColumns.map((measurement) => ( - - - - onRemoveMeasurementColumns([measurement.taxon_measurement_id])} - data-testid="configure-measurement-column-remove-button"> - - - - - ))} - - - ) : ( - - No measurements selected - - )} - - + + setIsFocalSpeciesMeasurementsOnly((prev) => !prev)} + /> + } + /> + + {measurementColumns.length ? ( + + {measurementColumns.map((measurement) => ( + + + {measurement.options.map((option) => ( + + ))} + + ) : undefined + } + ornament={ + 'unit' in measurement && measurement.unit ? ( + + ) : undefined + } + /> + + onRemoveMeasurementColumns([measurement.taxon_measurement_id])} + data-testid="configure-measurement-column-remove-button"> + + + + + ))} + + ) : ( + + )} + ); }; diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearch.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearch.tsx index 00540e15a4..d8c2d8762d 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearch.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearch.tsx @@ -1,4 +1,8 @@ +import green from '@mui/material/colors/green'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { MeasurementsSearchAutocomplete } from 'features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearchAutocomplete'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useObservationsContext, useSurveyContext } from 'hooks/useContext'; import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; import useDataLoader from 'hooks/useDataLoader'; import { CBMeasurementType } from 'interfaces/useCritterApi.interface'; @@ -17,6 +21,12 @@ export interface IMeasurementsSearchProps { * @memberof IMeasurementsSearchProps */ onAddMeasurementColumn: (measurementColumn: CBMeasurementType) => void; + /** + * Whether to only show measurements that focal or observed species can have + * + * @memberof IMeasurementsSearchProps + */ + focalOrObservedSpeciesOnly?: boolean; } /** @@ -25,20 +35,59 @@ export interface IMeasurementsSearchProps { * @param {IMeasurementsSearchProps} props * @return {*} */ -export const MeasurementsSearch = (props: IMeasurementsSearchProps) => { - const { selectedMeasurements, onAddMeasurementColumn } = props; +import React, { useEffect } from 'react'; + +export const MeasurementsSearch: React.FC = (props) => { + const { selectedMeasurements, onAddMeasurementColumn, focalOrObservedSpeciesOnly } = props; const critterbaseApi = useCritterbaseApi(); + const surveyContext = useSurveyContext(); + const observationsContext = useObservationsContext(); + const biohubApi = useBiohubApi(); + + const measurementsDataLoader = useDataLoader((searchTerm: string, tsns?: number[]) => + critterbaseApi.xref.getMeasurementTypeDefinitionsBySearchTerm(searchTerm, tsns) + ); + + const hierarchyDataLoader = useDataLoader((tsns: number[]) => biohubApi.taxonomy.getTaxonHierarchyByTSNs(tsns)); + + useEffect(() => { + if (!observationsContext.observedSpeciesDataLoader.data) { + observationsContext.observedSpeciesDataLoader.load(); + } + }, [observationsContext.observedSpeciesDataLoader]); + + const focalOrObservedSpecies: number[] = [ + ...(surveyContext.surveyDataLoader.data?.surveyData.species.focal_species.map((species) => species.tsn) ?? []), + ...(observationsContext.observedSpeciesDataLoader.data?.map((species) => species.tsn) ?? []) + ]; + + useEffect(() => { + if (focalOrObservedSpecies.length) { + hierarchyDataLoader.load(focalOrObservedSpecies); + } + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [hierarchyDataLoader]); + + const getOptions = async (inputValue: string): Promise => { + const response = focalOrObservedSpeciesOnly + ? await measurementsDataLoader.refresh(inputValue, focalOrObservedSpecies) + : await measurementsDataLoader.refresh(inputValue); + + return response ? [...response.qualitative, ...response.quantitative] : []; + }; - const measurementsDataLoader = useDataLoader(critterbaseApi.xref.getMeasurementTypeDefinitionsBySearchTerm); + const focalOrObservedSpeciesTsns = [ + ...focalOrObservedSpecies, + ...(hierarchyDataLoader.data?.flatMap((taxon) => taxon.hierarchy) ?? []) + ]; return ( { - const response = await measurementsDataLoader.refresh(inputValue); - return (response && [...response.qualitative, ...response.quantitative]) || []; - }} + ornament={} + applicableTsns={focalOrObservedSpeciesTsns} + getOptions={getOptions} onAddMeasurementColumn={onAddMeasurementColumn} /> ); diff --git a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearchAutocomplete.tsx b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearchAutocomplete.tsx index a531d1d57a..0d72aa8b43 100644 --- a/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearchAutocomplete.tsx +++ b/app/src/features/surveys/observations/observations-table/configure-columns/components/measurements/search/MeasurementsSearchAutocomplete.tsx @@ -2,10 +2,13 @@ import { mdiMagnify } from '@mdi/js'; import Icon from '@mdi/react'; import Autocomplete from '@mui/material/Autocomplete'; import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; import ListItem from '@mui/material/ListItem'; import Stack from '@mui/material/Stack'; import TextField from '@mui/material/TextField'; import Typography from '@mui/material/Typography'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { useTaxonomyContext } from 'hooks/useContext'; import { CBMeasurementType } from 'interfaces/useCritterApi.interface'; import { debounce } from 'lodash-es'; import { useMemo, useState } from 'react'; @@ -39,6 +42,20 @@ export interface IMeasurementsSearchAutocompleteProps { * @memberof IMeasurementsSearchAutocompleteProps */ speciesTsn?: number[]; + /** + * Measurements applied to any of these TSNs will have the ornament applied to them in the options list + * + * @type {number[]} + * @memberof IMeasurementsSearchAutocompleteProps + */ + applicableTsns?: number[]; + /** + * Ornament to display on the option card, typically indicating whether focal species can have the measurement + * + * @type {JSX.Element} + * @memberof IMeasurementSearchAutocompleteProps + */ + ornament?: JSX.Element; } /** @@ -48,10 +65,11 @@ export interface IMeasurementsSearchAutocompleteProps { * @return {*} */ export const MeasurementsSearchAutocomplete = (props: IMeasurementsSearchAutocompleteProps) => { - const { selectedOptions, getOptions, onAddMeasurementColumn } = props; + const { selectedOptions, getOptions, onAddMeasurementColumn, ornament, applicableTsns } = props; const [inputValue, setInputValue] = useState(''); const [options, setOptions] = useState([]); + const [isLoading, setIsLoading] = useState(false); const handleSearch = useMemo( () => @@ -62,14 +80,17 @@ export const MeasurementsSearchAutocomplete = (props: IMeasurementsSearchAutocom [getOptions] ); + const taxonomyContext = useTaxonomyContext(); + return ( option.measurement_name} @@ -103,8 +124,10 @@ export const MeasurementsSearchAutocomplete = (props: IMeasurementsSearchAutocom } setInputValue(value); + setIsLoading(true); handleSearch(value, (newOptions) => { setOptions(() => newOptions); + setIsLoading(false); }); }} value={null} // The selected value is not displayed in the input field or tracked by this component @@ -116,53 +139,49 @@ export const MeasurementsSearchAutocomplete = (props: IMeasurementsSearchAutocom } }} renderOption={(renderProps, renderOption) => { + const isApplicable = renderOption.itis_tsn && applicableTsns?.includes(renderOption.itis_tsn); + return ( - - - - {renderOption.itis_tsn} - - {/* - {renderOption.commonNames ? ( - <> - {renderOption.commonNames}  - - ({renderOption.scientificName}) - - - ) : ( - {renderOption.scientificName} - )} - */} - - - - {renderOption.measurement_name} - - + + - {renderOption.measurement_desc} - + name={ + renderOption.itis_tsn + ? taxonomyContext.getCachedSpeciesTaxonomyById(renderOption.itis_tsn)?.scientificName ?? '' + : '' + } + /> + {isApplicable && ornament} + + {renderOption.measurement_name} + + + {renderOption.measurement_desc} + ); @@ -180,6 +199,12 @@ export const MeasurementsSearchAutocomplete = (props: IMeasurementsSearchAutocom + ), + endAdornment: ( + <> + {inputValue && isLoading ? : null} + {params.InputProps.endAdornment} + ) }} data-testid="measurements-autocomplete-input" diff --git a/app/src/features/surveys/observations/observations-table/grid-column-definitions/GridColumnDefinitions.tsx b/app/src/features/surveys/observations/observations-table/grid-column-definitions/GridColumnDefinitions.tsx index 06e7e9315c..fe13e339a2 100644 --- a/app/src/features/surveys/observations/observations-table/grid-column-definitions/GridColumnDefinitions.tsx +++ b/app/src/features/surveys/observations/observations-table/grid-column-definitions/GridColumnDefinitions.tsx @@ -40,6 +40,7 @@ export const TaxonomyColDef = (props: { return { field: 'itis_tsn', headerName: 'Species', + description: 'The observed species, or if the species is unknown, a higher taxon', editable: true, hideable: true, flex: 1, @@ -67,6 +68,7 @@ export const SampleSiteColDef = (props: { return { field: 'survey_sample_site_id', + description: 'A sampling site where the observation was made', headerName: 'Site', editable: true, hideable: true, @@ -111,6 +113,7 @@ export const SampleMethodColDef = (props: { return { field: 'survey_sample_method_id', headerName: 'Method', + description: 'A method with which the observation was made', editable: true, hideable: true, flex: 1, @@ -158,6 +161,7 @@ export const SamplePeriodColDef = (props: { return { field: 'survey_sample_period_id', headerName: 'Period', + description: 'A sampling period in which the observation was made', editable: true, hideable: true, flex: 0, @@ -211,6 +215,7 @@ export const ObservationCountColDef = (props: { return { field: 'count', headerName: 'Count', + description: 'The number of individuals observed', editable: true, hideable: true, type: 'number', @@ -271,6 +276,7 @@ export const ObservationQuantitativeMeasurementColDef = (props: { return { field: measurement.taxon_measurement_id, headerName: measurement.measurement_name, + description: measurement.measurement_desc ?? '', editable: true, hideable: true, sortable: false, @@ -326,6 +332,7 @@ export const ObservationQualitativeMeasurementColDef = (props: { return { field: measurement.taxon_measurement_id, headerName: measurement.measurement_name, + description: measurement.measurement_desc ?? '', editable: true, hideable: true, sortable: false, @@ -355,6 +362,7 @@ export const ObservationQuantitativeEnvironmentColDef = (props: { return { field: String(environment.environment_quantitative_id), headerName: environment.name, + description: environment.description ?? '', editable: true, hideable: true, sortable: false, @@ -409,6 +417,7 @@ export const ObservationQualitativeEnvironmentColDef = (props: { return { field: String(environment.environment_qualitative_id), headerName: environment.name, + description: environment.description ?? '', editable: true, hideable: true, sortable: false, diff --git a/app/src/features/surveys/observations/observations-table/observation-row-validation/ObservationRowValidationUtils.ts b/app/src/features/surveys/observations/observations-table/observation-row-validation/ObservationRowValidationUtils.ts index 949b4d779a..814986e8df 100644 --- a/app/src/features/surveys/observations/observations-table/observation-row-validation/ObservationRowValidationUtils.ts +++ b/app/src/features/surveys/observations/observations-table/observation-row-validation/ObservationRowValidationUtils.ts @@ -34,7 +34,7 @@ export const validateObservationTableRowMeasurements = async ( return []; } - const taxonMeasurements = await getTsnMeasurementTypeDefinitionMap(Number(row.itis_tsn)); + const taxonMeasurements = await getTsnMeasurementTypeDefinitionMap(row.itis_tsn); if (!taxonMeasurements) { // This taxon has no valid measurements, return an error diff --git a/app/src/features/surveys/observations/sampling-sites/SamplingSiteListContainer.tsx b/app/src/features/surveys/observations/sampling-sites/SamplingSiteListContainer.tsx index 6212c09039..48a0ba96d3 100644 --- a/app/src/features/surveys/observations/sampling-sites/SamplingSiteListContainer.tsx +++ b/app/src/features/surveys/observations/sampling-sites/SamplingSiteListContainer.tsx @@ -19,7 +19,7 @@ import Typography from '@mui/material/Typography'; import { SkeletonList } from 'components/loading/SkeletonLoaders'; import { SamplingSiteListSite } from 'features/surveys/observations/sampling-sites/components/SamplingSiteListSite'; import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCodesContext, useDialogContext, useObservationsPageContext, useSurveyContext } from 'hooks/useContext'; +import { useDialogContext, useObservationsPageContext, useSurveyContext } from 'hooks/useContext'; import { useEffect, useState } from 'react'; import { Link as RouterLink } from 'react-router-dom'; @@ -30,15 +30,10 @@ import { Link as RouterLink } from 'react-router-dom'; */ export const SamplingSiteListContainer = () => { const surveyContext = useSurveyContext(); - const codesContext = useCodesContext(); const dialogContext = useDialogContext(); const observationsPageContext = useObservationsPageContext(); const biohubApi = useBiohubApi(); - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - useEffect(() => { surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); // eslint-disable-next-line react-hooks/exhaustive-deps @@ -295,7 +290,7 @@ export const SamplingSiteListContainer = () => { - {surveyContext.sampleSiteDataLoader.isLoading || codesContext.codesDataLoader.isLoading ? ( + {surveyContext.sampleSiteDataLoader.isLoading ? ( ) : ( diff --git a/app/src/features/surveys/observations/sampling-sites/components/SamplingSiteListMethod.tsx b/app/src/features/surveys/observations/sampling-sites/components/SamplingSiteListMethod.tsx index aed4ad87ba..39be47b8e5 100644 --- a/app/src/features/surveys/observations/sampling-sites/components/SamplingSiteListMethod.tsx +++ b/app/src/features/surveys/observations/sampling-sites/components/SamplingSiteListMethod.tsx @@ -3,9 +3,8 @@ import List from '@mui/material/List'; import ListItem from '@mui/material/ListItem'; import ListItemText from '@mui/material/ListItemText'; import { SamplingSiteListPeriod } from 'features/surveys/observations/sampling-sites/components/SamplingSiteListPeriod'; -import { useCodesContext, useObservationsContext, useObservationsPageContext } from 'hooks/useContext'; +import { useObservationsContext, useObservationsPageContext } from 'hooks/useContext'; import { IGetSampleMethodDetails } from 'interfaces/useSamplingSiteApi.interface'; -import { useEffect } from 'react'; export interface ISamplingSiteListMethodProps { sampleMethod: IGetSampleMethodDetails; @@ -20,14 +19,9 @@ export interface ISamplingSiteListMethodProps { export const SamplingSiteListMethod = (props: ISamplingSiteListMethodProps) => { const { sampleMethod } = props; - const codesContext = useCodesContext(); const observationsPageContext = useObservationsPageContext(); const observationsContext = useObservationsContext(); - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - return ( { const staticLayers: IStaticLayer[] = [ { layerName: 'Sample Sites', - layerColors: { color: blue[500], fillColor: blue[500] }, + layerOptions: { color: blue[500], fillColor: blue[500] }, features: [ { - key: sampleSite.survey_sample_site_id, + id: sampleSite.survey_sample_site_id, + key: `sampling-site-${sampleSite.survey_sample_site_id}`, geoJSON: sampleSite.geojson } ] @@ -161,7 +162,7 @@ export const SamplingSiteListSite = (props: ISamplingSiteListSiteProps) => { })} - + diff --git a/app/src/features/surveys/sampling-information/SamplingRouter.tsx b/app/src/features/surveys/sampling-information/SamplingRouter.tsx index 0917b2df2c..dd35c9af94 100644 --- a/app/src/features/surveys/sampling-information/SamplingRouter.tsx +++ b/app/src/features/surveys/sampling-information/SamplingRouter.tsx @@ -4,8 +4,8 @@ import { DialogContextProvider } from 'contexts/dialogContext'; import { SamplingSiteManagePage } from 'features/surveys/sampling-information/manage/SamplingSiteManagePage'; import { CreateSamplingSitePage } from 'features/surveys/sampling-information/sites/create/CreateSamplingSitePage'; import { EditSamplingSitePage } from 'features/surveys/sampling-information/sites/edit/EditSamplingSitePage'; -import { CreateTechniquePage } from 'features/surveys/sampling-information/techniques/form/create/CreateTechniquePage'; -import { EditTechniquePage } from 'features/surveys/sampling-information/techniques/form/edit/EditTechniquePage'; +import { CreateTechniquePage } from 'features/surveys/sampling-information/techniques/create/CreateTechniquePage'; +import { EditTechniquePage } from 'features/surveys/sampling-information/techniques/edit/EditTechniquePage'; import { Switch } from 'react-router'; import RouteWithTitle from 'utils/RouteWithTitle'; import { getTitle } from 'utils/Utils'; diff --git a/app/src/features/surveys/sampling-information/manage/SamplingSiteManagePage.tsx b/app/src/features/surveys/sampling-information/manage/SamplingSiteManagePage.tsx index f38c90653e..7830445b02 100644 --- a/app/src/features/surveys/sampling-information/manage/SamplingSiteManagePage.tsx +++ b/app/src/features/surveys/sampling-information/manage/SamplingSiteManagePage.tsx @@ -2,9 +2,9 @@ import Container from '@mui/material/Container'; import Paper from '@mui/material/Paper'; import Stack from '@mui/material/Stack'; import { SamplingSiteManageHeader } from 'features/surveys/sampling-information/manage/SamplingSiteManageHeader'; -import { SamplingSiteManageSiteList } from 'features/surveys/sampling-information/sites/manage/SamplingSiteManageSiteList'; import { SamplingTechniqueContainer } from 'features/surveys/sampling-information/techniques/SamplingTechniqueContainer'; import { useProjectContext, useSurveyContext } from 'hooks/useContext'; +import SamplingSiteContainer from '../sites/SamplingSiteContainer'; /** * Page for managing sampling information (sampling techniques and sites). @@ -29,7 +29,7 @@ export const SamplingSiteManagePage = () => { - + diff --git a/app/src/features/surveys/sampling-information/methods/components/SamplingMethodForm.tsx b/app/src/features/surveys/sampling-information/methods/components/SamplingMethodForm.tsx index 365e6b5a8f..2a9f7b03f2 100644 --- a/app/src/features/surveys/sampling-information/methods/components/SamplingMethodForm.tsx +++ b/app/src/features/surveys/sampling-information/methods/components/SamplingMethodForm.tsx @@ -3,7 +3,6 @@ import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; import AutocompleteField, { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; import CustomTextField from 'components/fields/CustomTextField'; -import SelectWithSubtextField from 'components/fields/SelectWithSubtext'; import { CodesContext } from 'contexts/codesContext'; import { useFormikContext } from 'formik'; import { useSurveyContext } from 'hooks/useContext'; @@ -87,7 +86,7 @@ export const SamplingMethodForm = () => { Details - - {dayjs(item.start_date).format(DATE_FORMAT.MediumDateFormat)} –  - {dayjs(item.end_date).format(DATE_FORMAT.MediumDateFormat)} - + + + {dayjs(item.start_date).format(DATE_FORMAT.MediumDateFormat)}  + + {item.start_time} + + + – + + {dayjs(item.end_date).format(DATE_FORMAT.MediumDateFormat)}  + + {item.end_time} + + + } action={ } /> - - {/* */} - ))} diff --git a/app/src/features/surveys/sampling-information/periods/table/SamplingPeriodTable.tsx b/app/src/features/surveys/sampling-information/periods/table/SamplingPeriodTable.tsx new file mode 100644 index 0000000000..ea9bcec0f8 --- /dev/null +++ b/app/src/features/surveys/sampling-information/periods/table/SamplingPeriodTable.tsx @@ -0,0 +1,106 @@ +import Typography from '@mui/material/Typography'; +import { GridColDef } from '@mui/x-data-grid'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { useCodesContext } from 'hooks/useContext'; +import { getCodesName } from 'utils/Utils'; + +export interface ISamplingSitePeriodRowData { + id: number; + sample_site: string; + sample_method: string; + method_response_metric_id: number; + start_date: string; + end_date: string; + start_time: string | null; + end_time: string | null; +} + +interface ISamplingPeriodTableProps { + periods: ISamplingSitePeriodRowData[]; +} + +/** + * Renders a table of sampling periods. + * + * @param props {} + * @returns {*} + */ +export const SamplingPeriodTable = (props: ISamplingPeriodTableProps) => { + const { periods } = props; + + const codesContext = useCodesContext(); + + const columns: GridColDef[] = [ + { + field: 'sample_site', + headerName: 'Site', + flex: 1 + }, + { + field: 'sample_method', + headerName: 'Technique', + flex: 1 + }, + { + field: 'method_response_metric_id', + headerName: 'Response Metric', + flex: 1, + renderCell: (params) => ( + <> + {getCodesName( + codesContext.codesDataLoader.data, + 'method_response_metrics', + params.row.method_response_metric_id + )} + + ) + }, + { + field: 'start_date', + headerName: 'Start date', + flex: 1, + renderCell: (params) => ( + {dayjs(params.row.start_date).format(DATE_FORMAT.MediumDateFormat)} + ) + }, + { + field: 'start_time', + headerName: 'Start time', + flex: 1 + }, + { + field: 'end_date', + headerName: 'End date', + flex: 1, + renderCell: (params) => ( + {dayjs(params.row.end_date).format(DATE_FORMAT.MediumDateFormat)} + ) + }, + { + field: 'end_time', + headerName: 'End time', + flex: 1 + } + ]; + + return ( + 'auto'} + disableColumnMenu + rows={periods} + getRowId={(row: ISamplingSitePeriodRowData) => row.id} + columns={columns} + checkboxSelection={false} + disableRowSelectionOnClick + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 10 } + } + }} + pageSizeOptions={[10, 25, 50]} + /> + ); +}; diff --git a/app/src/features/surveys/sampling-information/sites/SamplingSiteContainer.tsx b/app/src/features/surveys/sampling-information/sites/SamplingSiteContainer.tsx new file mode 100644 index 0000000000..ffa68724c9 --- /dev/null +++ b/app/src/features/surveys/sampling-information/sites/SamplingSiteContainer.tsx @@ -0,0 +1,265 @@ +import { mdiArrowTopRight, mdiDotsVertical, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import Divider from '@mui/material/Divider'; +import IconButton from '@mui/material/IconButton'; +import ListItemIcon from '@mui/material/ListItemIcon'; +import ListItemText from '@mui/material/ListItemText'; +import Menu from '@mui/material/Menu'; +import MenuItem from '@mui/material/MenuItem'; +import Paper from '@mui/material/Paper'; +import Toolbar from '@mui/material/Toolbar'; +import Typography from '@mui/material/Typography'; +import { GridRowSelectionModel } from '@mui/x-data-grid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonMap, SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { + ISamplingSitePeriodRowData, + SamplingPeriodTable +} from 'features/surveys/sampling-information/periods/table/SamplingPeriodTable'; +import { SamplingSiteMapContainer } from 'features/surveys/sampling-information/sites/map/SamplingSiteMapContainer'; +import { SamplingSiteTable } from 'features/surveys/sampling-information/sites/table/SamplingSiteTable'; +import { + SamplingSiteManageTableView, + SamplingSiteTabs +} from 'features/surveys/sampling-information/sites/table/SamplingSiteTabs'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useSurveyContext } from 'hooks/useContext'; +import { useEffect, useMemo, useState } from 'react'; +import { Link as RouterLink } from 'react-router-dom'; + +/** + * Component for managing sampling sites, methods, and periods. + * Returns a map and data grids displaying sampling information. + * + * @returns {*} + */ +const SamplingSiteContainer = () => { + const surveyContext = useSurveyContext(); + const dialogContext = useDialogContext(); + const biohubApi = useBiohubApi(); + + // State for bulk actions + const [headerAnchorEl, setHeaderAnchorEl] = useState(null); + const [siteSelection, setSiteSelection] = useState([]); + + // Controls whether sites, methods, or periods are shown + const [activeView, setActiveView] = useState(SamplingSiteManageTableView.SITES); + + const sampleSites = useMemo( + () => surveyContext.sampleSiteDataLoader.data?.sampleSites ?? [], + [surveyContext.sampleSiteDataLoader.data?.sampleSites] + ); + const sampleSiteCount = surveyContext.sampleSiteDataLoader.data?.pagination.total ?? 0; + + const samplePeriods: ISamplingSitePeriodRowData[] = useMemo(() => { + const data: ISamplingSitePeriodRowData[] = []; + + for (const site of sampleSites) { + for (const method of site.sample_methods) { + for (const period of method.sample_periods) { + data.push({ + id: period.survey_sample_period_id, + sample_site: site.name, + sample_method: method.technique.name, + method_response_metric_id: method.method_response_metric_id, + start_date: period.start_date, + end_date: period.end_date, + start_time: period.start_time, + end_time: period.end_time + }); + } + } + } + + return data; + }, [sampleSites]); + + useEffect(() => { + surveyContext.sampleSiteDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + }, [surveyContext.sampleSiteDataLoader, surveyContext.projectId, surveyContext.surveyId]); + + // Handler for bulk delete operation + const handleBulkDelete = async () => { + try { + await biohubApi.samplingSite.deleteSampleSites( + surveyContext.projectId, + surveyContext.surveyId, + siteSelection.map((site) => Number(site)) // Convert GridRowId to number[] + ); + dialogContext.setYesNoDialog({ open: false }); // Close confirmation dialog + setSiteSelection([]); // Clear selection + surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); // Refresh data + } catch (error) { + dialogContext.setYesNoDialog({ open: false }); // Close confirmation dialog on error + setSiteSelection([]); // Clear selection + // Show snackbar with error message + dialogContext.setSnackbar({ + snackbarMessage: ( + <> + + Error Deleting Items + + + {String(error)} + + + ), + open: true + }); + } + }; + + // Handler for clicking on header menu (bulk actions) + const handleHeaderMenuClick = (event: React.MouseEvent) => { + setHeaderAnchorEl(event.currentTarget); + }; + + // Handler for confirming bulk delete operation + const handlePromptConfirmBulkDelete = () => { + setHeaderAnchorEl(null); // Close header menu + dialogContext.setYesNoDialog({ + dialogTitle: 'Delete Sampling Sites?', + dialogContent: ( + + Are you sure you want to delete the selected sampling sites? + + ), + yesButtonLabel: 'Delete Sampling Sites', + noButtonLabel: 'Cancel', + yesButtonProps: { color: 'error' }, + onClose: () => dialogContext.setYesNoDialog({ open: false }), + onNo: () => dialogContext.setYesNoDialog({ open: false }), + open: true, + onYes: handleBulkDelete + }); + }; + + // Counts for the toggle button labels + const viewCounts = { + [SamplingSiteManageTableView.SITES]: sampleSiteCount, + [SamplingSiteManageTableView.PERIODS]: samplePeriods.length + }; + + return ( + <> + {/* Bulk action menu */} + setHeaderAnchorEl(null)} + anchorEl={headerAnchorEl} + anchorOrigin={{ vertical: 'top', horizontal: 'right' }} + transformOrigin={{ vertical: 'top', horizontal: 'right' }}> + + + + + Delete + + + + + + + Sampling Sites ‌ + + ({sampleSiteCount}) + + + + + + + + + + + + + + + + } + isLoadingFallbackDelay={100}> + + + {/* Toggle buttons for changing between sites, methods, and periods */} + + + + + {/* Data tables */} + + {activeView === SamplingSiteManageTableView.SITES && ( + } + isLoadingFallbackDelay={100} + hasNoData={!viewCounts[SamplingSiteManageTableView.SITES]} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + + )} + + {activeView === SamplingSiteManageTableView.PERIODS && ( + } + isLoadingFallbackDelay={100} + hasNoData={!viewCounts[SamplingSiteManageTableView.PERIODS]} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + + )} + + + + + + ); +}; + +export default SamplingSiteContainer; diff --git a/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteEditMapControl.tsx b/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteEditMapControl.tsx index 2273cbe10d..9a5614b6ed 100644 --- a/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteEditMapControl.tsx +++ b/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteEditMapControl.tsx @@ -107,7 +107,11 @@ const SamplingSiteEditMapControl = (props: ISamplingSiteEditMapControlProps) => const staticLayers: IStaticLayer[] = [ { layerName: 'Sampling Sites', - features: samplingSiteGeoJsonFeatures.map((feature: Feature, index) => ({ geoJSON: feature, key: index })) + features: samplingSiteGeoJsonFeatures.map((feature: Feature, index) => ({ + id: feature.id || index, + key: `sampling-site-${feature.id || index}`, + geoJSON: feature + })) } ]; diff --git a/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteMapControl.tsx b/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteMapControl.tsx index 2422f0fd58..9085af7c82 100644 --- a/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteMapControl.tsx +++ b/app/src/features/surveys/sampling-information/sites/components/map/SamplingSiteMapControl.tsx @@ -216,8 +216,12 @@ const SamplingSiteMapControl = (props: ISamplingSiteMapControlProps) => { { layerName: 'Sampling Sites', features: samplingSiteGeoJsonFeatures - .filter((item) => item?.id) // Filter for only drawn features - .map((feature, index) => ({ geoJSON: feature, key: index })) + .filter((feature) => feature?.id) // Filter for only drawn features + .map((feature, index) => ({ + id: feature.id || index, + key: `sampling-site-${feature.id || index}`, + geoJSON: feature + })) } ]} /> diff --git a/app/src/features/surveys/sampling-information/sites/components/site-groupings/SamplingStratumForm.tsx b/app/src/features/surveys/sampling-information/sites/components/site-groupings/SamplingStratumForm.tsx index 967fc74b0d..459d5433e4 100644 --- a/app/src/features/surveys/sampling-information/sites/components/site-groupings/SamplingStratumForm.tsx +++ b/app/src/features/surveys/sampling-information/sites/components/site-groupings/SamplingStratumForm.tsx @@ -13,7 +13,7 @@ import { SurveyContext } from 'contexts/surveyContext'; import { BlockStratumCard } from 'features/surveys/sampling-information/sites/components/site-groupings/BlockStratumCard'; import { useFormikContext } from 'formik'; import { IGetSampleLocationDetails, IGetSampleStratumDetails } from 'interfaces/useSamplingSiteApi.interface'; -import { IGetSurveyStratum } from 'interfaces/useSurveyApi.interface'; +import { IGetSurveyStratum, IPostSurveyStratum } from 'interfaces/useSurveyApi.interface'; import { useContext, useState } from 'react'; import { TransitionGroup } from 'react-transition-group'; @@ -30,7 +30,7 @@ export const SamplingStratumForm = () => { const [searchText, setSearchText] = useState(''); - const handleAddStratum = (stratum: IGetSurveyStratum) => { + const handleAddStratum = (stratum: IPostSurveyStratum | IGetSurveyStratum) => { setFieldValue(`stratums[${values.stratums.length}]`, stratum); }; const handleRemoveItem = (stratum: IGetSurveyStratum | IGetSampleStratumDetails) => { @@ -59,7 +59,7 @@ export const SamplingStratumForm = () => { noOptionsText="No records found" options={options} filterOptions={(options, state) => { - const searchFilter = createFilterOptions({ ignoreCase: true }); + const searchFilter = createFilterOptions({ ignoreCase: true }); const unselectedOptions = options.filter((option) => values.stratums.every((existing) => existing.survey_stratum_id !== option.survey_stratum_id) ); diff --git a/app/src/features/surveys/sampling-information/sites/create/CreateSamplingSitePage.tsx b/app/src/features/surveys/sampling-information/sites/create/CreateSamplingSitePage.tsx index 8fe0550e6e..454dcf5be8 100644 --- a/app/src/features/surveys/sampling-information/sites/create/CreateSamplingSitePage.tsx +++ b/app/src/features/surveys/sampling-information/sites/create/CreateSamplingSitePage.tsx @@ -124,7 +124,7 @@ export const CreateSamplingSitePage = () => { validateOnBlur={true} validateOnChange={false} onSubmit={handleSubmit}> - + ) => void; - isChecked?: boolean; - handleCheckboxChange?: (sampleSiteId: number) => void; -} - -export const SamplingSiteCard = (props: ISamplingSiteCardProps) => { - const { sampleSite, handleMenuClick, handleCheckboxChange, isChecked } = props; - - return ( - - - {handleCheckboxChange && ( - - { - event.stopPropagation(); - handleCheckboxChange(sampleSite.survey_sample_site_id); - }} - inputProps={{ 'aria-label': 'controlled' }} - /> - - )} - - {sampleSite.name} - - - - {sampleSite.description} - - - } - detailsContent={ - - {sampleSite.description} - {sampleSite.name} - - } - onMenuClick={handleMenuClick} - /> - ); -}; diff --git a/app/src/features/surveys/sampling-information/sites/manage/SamplingSiteManageSiteList.tsx b/app/src/features/surveys/sampling-information/sites/manage/SamplingSiteManageSiteList.tsx deleted file mode 100644 index 2766f741fb..0000000000 --- a/app/src/features/surveys/sampling-information/sites/manage/SamplingSiteManageSiteList.tsx +++ /dev/null @@ -1,367 +0,0 @@ -import { mdiDotsVertical, mdiPencilOutline, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Checkbox from '@mui/material/Checkbox'; -import grey from '@mui/material/colors/grey'; -import Divider from '@mui/material/Divider'; -import FormControlLabel from '@mui/material/FormControlLabel'; -import FormGroup from '@mui/material/FormGroup'; -import IconButton from '@mui/material/IconButton'; -import ListItemIcon from '@mui/material/ListItemIcon'; -import ListItemText from '@mui/material/ListItemText'; -import Menu, { MenuProps } from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; -import Paper from '@mui/material/Paper'; -import Stack from '@mui/material/Stack'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import { LoadingGuard } from 'components/loading/LoadingGuard'; -import { SkeletonMap, SkeletonTable } from 'components/loading/SkeletonLoaders'; -import { SamplingSiteCard } from 'features/surveys/sampling-information/sites/manage/SamplingSiteCard'; -import { SamplingSiteMapContainer } from 'features/surveys/sampling-information/sites/manage/SamplingSiteMapContainer'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCodesContext, useDialogContext, useSurveyContext } from 'hooks/useContext'; -import { useEffect, useState } from 'react'; -import { Link as RouterLink } from 'react-router-dom'; - -/** - * Renders a list of sampling sites. - * - * @return {*} - */ -export const SamplingSiteManageSiteList = () => { - const surveyContext = useSurveyContext(); - const codesContext = useCodesContext(); - const dialogContext = useDialogContext(); - const biohubApi = useBiohubApi(); - - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - - useEffect(() => { - surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, []); - - const [sampleSiteAnchorEl, setSampleSiteAnchorEl] = useState(null); - const [headerAnchorEl, setHeaderAnchorEl] = useState(null); - const [selectedSampleSiteId, setSelectedSampleSiteId] = useState(); - const [checkboxSelectedIds, setCheckboxSelectedIds] = useState([]); - - const sampleSites = surveyContext.sampleSiteDataLoader.data?.sampleSites ?? []; - - // eslint-disable-next-line @typescript-eslint/no-unused-vars - const handleSampleSiteMenuClick = ( - event: React.MouseEvent, - sample_site_id: number - ) => { - setSampleSiteAnchorEl(event.currentTarget); - setSelectedSampleSiteId(sample_site_id); - }; - - const handleHeaderMenuClick = (event: React.MouseEvent) => { - setHeaderAnchorEl(event.currentTarget); - }; - - /** - * Handle the delete sampling site API call. - * - */ - const handleDeleteSampleSite = async () => { - await biohubApi.samplingSite - .deleteSampleSite(surveyContext.projectId, surveyContext.surveyId, Number(selectedSampleSiteId)) - .then(() => { - dialogContext.setYesNoDialog({ open: false }); - setSampleSiteAnchorEl(null); - surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - }) - .catch((error: any) => { - dialogContext.setYesNoDialog({ open: false }); - setSampleSiteAnchorEl(null); - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error Deleting Sampling Site - - - {String(error)} - - - ), - open: true - }); - }); - }; - - /** - * Display the delete sampling site dialog. - * - */ - const deleteSampleSiteDialog = () => { - dialogContext.setYesNoDialog({ - dialogTitle: 'Delete Sampling Site?', - dialogContent: ( - - Are you sure you want to delete this sampling site? - - ), - yesButtonLabel: 'Delete Sampling Site', - noButtonLabel: 'Cancel', - yesButtonProps: { color: 'error' }, - onClose: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - onNo: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - open: true, - onYes: () => { - handleDeleteSampleSite(); - } - }); - }; - - const handleBulkDeleteSampleSites = async () => { - await biohubApi.samplingSite - .deleteSampleSites(surveyContext.projectId, surveyContext.surveyId, checkboxSelectedIds) - .then(() => { - dialogContext.setYesNoDialog({ open: false }); - setCheckboxSelectedIds([]); - setHeaderAnchorEl(null); - surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - }) - .catch((error: any) => { - dialogContext.setYesNoDialog({ open: false }); - setCheckboxSelectedIds([]); - setHeaderAnchorEl(null); - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error Deleting Sampling Sites - - - {String(error)} - - - ), - open: true - }); - }); - }; - - const handlePromptConfirmBulkDelete = () => { - dialogContext.setYesNoDialog({ - dialogTitle: 'Delete Sampling Sites?', - dialogContent: ( - - Are you sure you want to delete the selected sampling sites? - - ), - yesButtonLabel: 'Delete Sampling Sites', - noButtonLabel: 'Cancel', - yesButtonProps: { color: 'error' }, - onClose: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - onNo: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - open: true, - onYes: () => { - handleBulkDeleteSampleSites(); - } - }); - }; - - const handleCheckboxChange = (sampleSiteId: number) => { - setCheckboxSelectedIds((prev) => { - if (prev.includes(sampleSiteId)) { - return prev.filter((item) => item !== sampleSiteId); - } else { - return [...prev, sampleSiteId]; - } - }); - }; - - const samplingSiteCount = sampleSites.length ?? 0; - - return ( - <> - setSampleSiteAnchorEl(null)} - anchorEl={sampleSiteAnchorEl} - anchorOrigin={{ - vertical: 'top', - horizontal: 'right' - }} - transformOrigin={{ - vertical: 'top', - horizontal: 'right' - }}> - - - - - - Edit Details - - - - - - - Delete - - - - setHeaderAnchorEl(null)} - anchorEl={headerAnchorEl} - anchorOrigin={{ - vertical: 'top', - horizontal: 'right' - }} - transformOrigin={{ - vertical: 'top', - horizontal: 'right' - }}> - - - - - Delete - - - - - - - Sites ‌ - - ({samplingSiteCount}) - - - - - - - - - - - - - - } - delay={200}> - - - - - - Select All - - } - control={ - 0 && checkboxSelectedIds.length === samplingSiteCount} - indeterminate={ - checkboxSelectedIds.length >= 1 && checkboxSelectedIds.length < samplingSiteCount - } - onClick={() => { - if (checkboxSelectedIds.length === samplingSiteCount) { - setCheckboxSelectedIds([]); - return; - } - - const sampleSiteIds = sampleSites.map((sampleSite) => sampleSite.survey_sample_site_id); - setCheckboxSelectedIds(sampleSiteIds); - }} - inputProps={{ 'aria-label': 'controlled' }} - /> - } - /> - - - - - {surveyContext.sampleSiteDataLoader.data?.sampleSites.map((sampleSite) => { - return ( - { - setSampleSiteAnchorEl(event.currentTarget); - setSelectedSampleSiteId(sampleSite.survey_sample_site_id); - }} - key={sampleSite.survey_sample_site_id} - /> - ); - })} - - - - - - - ); -}; diff --git a/app/src/features/surveys/sampling-information/sites/manage/SamplingSiteMapContainer.tsx b/app/src/features/surveys/sampling-information/sites/map/SamplingSiteMapContainer.tsx similarity index 75% rename from app/src/features/surveys/sampling-information/sites/manage/SamplingSiteMapContainer.tsx rename to app/src/features/surveys/sampling-information/sites/map/SamplingSiteMapContainer.tsx index 3efe5e4094..c9154faa58 100644 --- a/app/src/features/surveys/sampling-information/sites/manage/SamplingSiteMapContainer.tsx +++ b/app/src/features/surveys/sampling-information/sites/map/SamplingSiteMapContainer.tsx @@ -11,10 +11,11 @@ interface ISamplingSitesMapContainerProps { export const SamplingSiteMapContainer = (props: ISamplingSitesMapContainerProps) => { const staticLayers: IStaticLayer[] = props.samplingSites.map((sampleSite) => ({ layerName: 'Sample Sites', - layerColors: { color: blue[500], fillColor: blue[500] }, + layerOptions: { color: blue[500], fillColor: blue[500] }, features: [ { - key: sampleSite.survey_sample_site_id, + id: sampleSite.survey_sample_site_id, + key: `sample-site-${sampleSite.survey_sample_site_id}`, geoJSON: sampleSite.geojson } ] @@ -22,7 +23,7 @@ export const SamplingSiteMapContainer = (props: ISamplingSitesMapContainerProps) return ( - + ); }; diff --git a/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTable.tsx b/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTable.tsx new file mode 100644 index 0000000000..8d446333a9 --- /dev/null +++ b/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTable.tsx @@ -0,0 +1,256 @@ +import { mdiDotsVertical, mdiPencilOutline, mdiTrashCanOutline } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import { blueGrey } from '@mui/material/colors'; +import IconButton from '@mui/material/IconButton'; +import ListItemIcon from '@mui/material/ListItemIcon'; +import ListItemText from '@mui/material/ListItemText'; +import Menu, { MenuProps } from '@mui/material/Menu'; +import MenuItem from '@mui/material/MenuItem'; +import Typography from '@mui/material/Typography'; +import { GridColDef, GridRowSelectionModel } from '@mui/x-data-grid'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { Feature } from 'geojson'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useSurveyContext } from 'hooks/useContext'; +import { IGetSampleLocationDetails } from 'interfaces/useSamplingSiteApi.interface'; +import { useState } from 'react'; +import { Link as RouterLink } from 'react-router-dom'; +import { getSamplingSiteSpatialType } from 'utils/spatial-utils'; + +export interface ISamplingSiteRowData { + id: number; + name: string; + description: string; + geojson: Feature; + blocks: string[]; + stratums: string[]; +} + +interface ISamplingSiteTableProps { + sites: IGetSampleLocationDetails[]; + bulkActionSites: GridRowSelectionModel; + setBulkActionSites: (selection: GridRowSelectionModel) => void; +} + +/** + * Returns a table of sampling sites with edit actions + * + * @param props {} + * @returns {*} + */ +export const SamplingSiteTable = (props: ISamplingSiteTableProps) => { + const { sites, bulkActionSites, setBulkActionSites } = props; + + const biohubApi = useBiohubApi(); + const surveyContext = useSurveyContext(); + const dialogContext = useDialogContext(); + + const [actionMenuSite, setActionMenuSite] = useState(); + const [actionMenuAnchorEl, setActionMenuAnchorEl] = useState(null); + + const handleCloseActionMenu = () => { + setActionMenuAnchorEl(null); + }; + + const handleDeleteSamplingSite = async () => { + await biohubApi.samplingSite + .deleteSampleSite(surveyContext.projectId, surveyContext.surveyId, Number(actionMenuSite)) + .then(() => { + dialogContext.setYesNoDialog({ open: false }); + setActionMenuAnchorEl(null); + surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); + }) + .catch((error: any) => { + dialogContext.setYesNoDialog({ open: false }); + setActionMenuAnchorEl(null); + dialogContext.setSnackbar({ + snackbarMessage: ( + <> + + Error Deleting SamplingSite + + + {String(error)} + + + ), + open: true + }); + }); + }; + + /** + * Display the delete samplingSite dialog. + * + */ + const deleteSamplingSiteDialog = () => { + dialogContext.setYesNoDialog({ + dialogTitle: 'Delete sampling site?', + dialogText: 'Are you sure you want to permanently delete this sampling site?', + yesButtonLabel: 'Delete Site', + noButtonLabel: 'Cancel', + yesButtonProps: { color: 'error' }, + onClose: () => { + dialogContext.setYesNoDialog({ open: false }); + }, + onNo: () => { + dialogContext.setYesNoDialog({ open: false }); + }, + open: true, + onYes: () => { + handleDeleteSamplingSite(); + } + }); + }; + + const rows: ISamplingSiteRowData[] = sites.map((site) => ({ + id: site.survey_sample_site_id, + name: site.name, + description: site.description || '', + geojson: site.geojson, + blocks: site.blocks.map((block) => block.name), + stratums: site.stratums.map((stratum) => stratum.name) + })); + + const columns: GridColDef[] = [ + { + field: 'name', + headerName: 'Name', + flex: 1 + }, + { + field: 'geometry_type', + headerName: 'Geometry', + flex: 1, + renderCell: (params) => ( + + + + ) + }, + { + field: 'description', + headerName: 'Description', + flex: 1 + }, + + { + field: 'blocks', + headerName: 'Blocks', + flex: 1, + renderCell: (params) => ( + + {params.row.blocks.map((block) => ( + + + + ))} + + ) + }, + { + field: 'stratums', + headerName: 'Strata', + flex: 1, + renderCell: (params) => ( + + {params.row.stratums.map((stratum) => ( + + + + ))} + + ) + }, + { + field: 'actions', + type: 'actions', + sortable: false, + width: 10, + align: 'right', + renderCell: (params) => { + return ( + + { + setActionMenuSite(params.row.id); + setActionMenuAnchorEl(event.currentTarget); + }}> + + + + ); + } + } + ]; + + return ( + <> + {/* ROW ACTION MENU */} + + + + + + + Edit Details + + + { + handleCloseActionMenu(); + deleteSamplingSiteDialog(); + }}> + + + + Delete + + + + {/* DATA TABLE */} + 'auto'} + disableColumnMenu + rows={rows} + getRowId={(row: ISamplingSiteRowData) => row.id} + columns={columns} + rowSelectionModel={bulkActionSites} + onRowSelectionModelChange={setBulkActionSites} + checkboxSelection + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 10 } + } + }} + pageSizeOptions={[10, 25, 50]} + /> + + ); +}; diff --git a/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTabs.tsx b/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTabs.tsx new file mode 100644 index 0000000000..f7060fb206 --- /dev/null +++ b/app/src/features/surveys/sampling-information/sites/table/SamplingSiteTabs.tsx @@ -0,0 +1,76 @@ +import { mdiCalendarRange, mdiMapMarker } from '@mdi/js'; +import { Icon } from '@mdi/react'; +import Button from '@mui/material/Button'; +import ToggleButton from '@mui/material/ToggleButton'; +import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; +import Toolbar from '@mui/material/Toolbar'; +import { SetStateAction } from 'react'; + +export enum SamplingSiteManageTableView { + SITES = 'SITES', + PERIODS = 'PERIODS' +} + +interface ISamplingSiteManageTableView { + value: SamplingSiteManageTableView; + icon: React.ReactNode; +} + +export type ISamplingSiteCount = Record; + +interface ISamplingSiteTabsProps { + activeView: SamplingSiteManageTableView; + setActiveView: React.Dispatch>; + viewCounts: Record; +} + +/** + * Renders tab controls for the sampling site table, which allow the user to switch between viewing sites and periods. + * + * @param {ISamplingSiteTabsProps} props + * @return {*} + */ +export const SamplingSiteTabs = (props: ISamplingSiteTabsProps) => { + const { activeView, setActiveView, viewCounts } = props; + + const views: ISamplingSiteManageTableView[] = [ + { value: SamplingSiteManageTableView.SITES, icon: }, + { value: SamplingSiteManageTableView.PERIODS, icon: } + ]; + + const activeViewCount = viewCounts[activeView]; + + const updateDatasetView = (_: React.MouseEvent, view: SamplingSiteManageTableView) => { + if (view) { + setActiveView(view); + } + }; + + return ( + + + {views.map((view) => ( + + {view.value} ({activeViewCount}) + + ))} + + + ); +}; diff --git a/app/src/features/surveys/sampling-information/techniques/SamplingTechniqueContainer.tsx b/app/src/features/surveys/sampling-information/techniques/SamplingTechniqueContainer.tsx index a34f1facfb..fe860d44ad 100644 --- a/app/src/features/surveys/sampling-information/techniques/SamplingTechniqueContainer.tsx +++ b/app/src/features/surveys/sampling-information/techniques/SamplingTechniqueContainer.tsx @@ -1,5 +1,6 @@ import { mdiDotsVertical, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; import Divider from '@mui/material/Divider'; import IconButton from '@mui/material/IconButton'; @@ -18,7 +19,7 @@ import { useBiohubApi } from 'hooks/useBioHubApi'; import { useDialogContext, useSurveyContext } from 'hooks/useContext'; import { useEffect, useState } from 'react'; import { Link as RouterLink } from 'react-router-dom'; -import { SamplingTechniqueCardContainer } from './components/SamplingTechniqueCardContainer'; +import { SamplingTechniqueTable } from './table/SamplingTechniqueTable'; /** * Renders a list of techniques. @@ -124,7 +125,7 @@ export const SamplingTechniqueContainer = () => { sx={{ flex: '0 0 auto', pr: 3, - pl: 2 + pl: 3 }}> Techniques ‌ @@ -157,13 +158,15 @@ export const SamplingTechniqueContainer = () => { } - delay={200}> - + isLoadingFallback={} + isLoadingFallbackDelay={100}> + + + ); diff --git a/app/src/features/surveys/sampling-information/techniques/components/NoTechniquesOverlay.tsx b/app/src/features/surveys/sampling-information/techniques/components/NoTechniquesOverlay.tsx deleted file mode 100644 index c47fde60b3..0000000000 --- a/app/src/features/surveys/sampling-information/techniques/components/NoTechniquesOverlay.tsx +++ /dev/null @@ -1,28 +0,0 @@ -import { mdiArrowTopRight } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import grey from '@mui/material/colors/grey'; -import Typography from '@mui/material/Typography'; - -export const NoTechniquesOverlay = () => { - return ( - - - - Add a technique  - - - - Techniques describe how you collected data. You can apply your techniques to sampling sites, during which - you'll also create sampling periods that describe when a technique was conducted. - - - - ); -}; diff --git a/app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCard.tsx b/app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCard.tsx deleted file mode 100644 index 9a382b6ec1..0000000000 --- a/app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCard.tsx +++ /dev/null @@ -1,72 +0,0 @@ -import Box from '@mui/material/Box'; -import { blue } from '@mui/material/colors'; -import Stack from '@mui/material/Stack'; -import Typography from '@mui/material/Typography'; -import { AccordionCard } from 'components/accordion/AccordionCard'; -import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; -import { IGetTechniqueResponse } from 'interfaces/useTechniqueApi.interface'; - -interface ISamplingTechniqueCardProps { - technique: IGetTechniqueResponse; - method_lookup_name: string; - handleMenuClick?: (event: React.MouseEvent) => void; -} - -const SamplingTechniqueCard = (props: ISamplingTechniqueCardProps) => { - const { technique, method_lookup_name, handleMenuClick } = props; - - const attributes = [...technique.attributes.qualitative_attributes, ...technique.attributes.qualitative_attributes]; - - return ( - - - {technique.name} - - - - {technique.description} - - - } - detailsContent={ - - - - - Release time - - - - - {technique.description && ( - - - Technique comment - - - {technique.description} - - - )} - - {attributes.map((attribute) => ( - {attribute.method_technique_attribute_qualitative_id} - ))} - - } - onMenuClick={handleMenuClick} - /> - ); -}; - -export default SamplingTechniqueCard; diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/TechniqueForm.tsx b/app/src/features/surveys/sampling-information/techniques/components/TechniqueForm.tsx similarity index 93% rename from app/src/features/surveys/sampling-information/techniques/form/components/TechniqueForm.tsx rename to app/src/features/surveys/sampling-information/techniques/components/TechniqueForm.tsx index cbe5eb6e2f..df999b5a4d 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/components/TechniqueForm.tsx +++ b/app/src/features/surveys/sampling-information/techniques/components/TechniqueForm.tsx @@ -1,11 +1,11 @@ import Divider from '@mui/material/Divider'; import Stack from '@mui/material/Stack'; import HorizontalSplitFormComponent from 'components/fields/HorizontalSplitFormComponent'; -import { TechniqueAttributesForm } from 'features/surveys/sampling-information/techniques/form/components/attributes/TechniqueAttributesForm'; +import { TechniqueAttributesForm } from 'features/surveys/sampling-information/techniques/components/attributes/TechniqueAttributesForm'; import { CreateTechniqueFormValues, UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; import { useFormikContext } from 'formik'; import { useBiohubApi } from 'hooks/useBioHubApi'; import useDataLoader from 'hooks/useDataLoader'; diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer.tsx b/app/src/features/surveys/sampling-information/techniques/components/TechniqueFormContainer.tsx similarity index 98% rename from app/src/features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer.tsx rename to app/src/features/surveys/sampling-information/techniques/components/TechniqueFormContainer.tsx index eecf6dd6a7..95a8f4a046 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer.tsx +++ b/app/src/features/surveys/sampling-information/techniques/components/TechniqueFormContainer.tsx @@ -1,6 +1,6 @@ import Stack from '@mui/material/Stack'; import FormikErrorSnackbar from 'components/alert/FormikErrorSnackbar'; -import { TechniqueForm } from 'features/surveys/sampling-information/techniques/form/components/TechniqueForm'; +import { TechniqueForm } from 'features/surveys/sampling-information/techniques/components/TechniqueForm'; import { Formik, FormikProps } from 'formik'; import { ICreateTechniqueRequest, IGetTechniqueResponse } from 'interfaces/useTechniqueApi.interface'; import { isDefined } from 'utils/Utils'; diff --git a/app/src/features/surveys/sampling-information/techniques/components/attractants/TechniqueAttractantsForm.tsx b/app/src/features/surveys/sampling-information/techniques/components/attractants/TechniqueAttractantsForm.tsx new file mode 100644 index 0000000000..d7160c0e8b --- /dev/null +++ b/app/src/features/surveys/sampling-information/techniques/components/attractants/TechniqueAttractantsForm.tsx @@ -0,0 +1,114 @@ +import { mdiClose } from '@mdi/js'; +import { Icon } from '@mdi/react'; +import Box from '@mui/material/Box'; +import Collapse from '@mui/material/Collapse'; +import grey from '@mui/material/colors/grey'; +import Grid from '@mui/material/Grid'; +import IconButton from '@mui/material/IconButton'; +import Paper from '@mui/material/Paper'; +import Typography from '@mui/material/Typography'; +import AutocompleteField from 'components/fields/AutocompleteField'; +import { + CreateTechniqueFormValues, + UpdateTechniqueFormValues +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; + +import { useFormikContext } from 'formik'; +import { useCodesContext } from 'hooks/useContext'; +import { useEffect } from 'react'; +import { TransitionGroup } from 'react-transition-group'; + +/** + * Technique attractants form. + * + * @template FormValues + * @return {*} + */ +export const TechniqueAttractantsForm = < + FormValues extends CreateTechniqueFormValues | UpdateTechniqueFormValues +>() => { + const codesContext = useCodesContext(); + + const { values, setFieldValue } = useFormikContext(); + + useEffect(() => { + codesContext.codesDataLoader.load(); + }, [codesContext.codesDataLoader]); + + const attractants = codesContext.codesDataLoader.data?.attractants ?? []; + + return ( + + + Attractants (optional) + ({ + value: option.id, + label: option.name, + description: option.description + })) + .filter( + (option) => !values.attractants.some((attractant) => attractant.attractant_lookup_id === option.value) + ) ?? [] + } + onChange={(_, value) => { + if (value?.value) { + setFieldValue('attractants', [...values.attractants, { attractant_lookup_id: value.value }]); + } + }} + /> + + + + {values.attractants.map((attractant, index) => { + const lookup = attractants.find((option) => option.id === attractant.attractant_lookup_id); + return ( + + + + {lookup?.name} + + {lookup?.description} + + + + { + setFieldValue( + 'attractants', + values.attractants.length > 1 ? values.attractants.filter((id) => id !== attractant) : [] + ); + }}> + + + + + + ); + })} + + + + ); +}; diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/TechniqueAttributesForm.tsx b/app/src/features/surveys/sampling-information/techniques/components/attributes/TechniqueAttributesForm.tsx similarity index 97% rename from app/src/features/surveys/sampling-information/techniques/form/components/attributes/TechniqueAttributesForm.tsx rename to app/src/features/surveys/sampling-information/techniques/components/attributes/TechniqueAttributesForm.tsx index db8c22f651..52f12b6ebe 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/TechniqueAttributesForm.tsx +++ b/app/src/features/surveys/sampling-information/techniques/components/attributes/TechniqueAttributesForm.tsx @@ -7,7 +7,7 @@ import { CreateTechniqueFormValues, TechniqueAttributeFormValues, UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; import { FieldArray, FieldArrayRenderProps, useFormikContext } from 'formik'; import { ITechniqueAttributeQualitative, ITechniqueAttributeQuantitative } from 'interfaces/useReferenceApi.interface'; import { TransitionGroup } from 'react-transition-group'; diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeForm.tsx b/app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeForm.tsx similarity index 92% rename from app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeForm.tsx rename to app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeForm.tsx index f45bd05ee8..a794356a34 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeForm.tsx +++ b/app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeForm.tsx @@ -6,17 +6,17 @@ import grey from '@mui/material/colors/grey'; import IconButton from '@mui/material/IconButton'; import Stack from '@mui/material/Stack'; import AutocompleteField from 'components/fields/AutocompleteField'; -import { TechniqueAttributeValueControl } from 'features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeValueControl'; +import { TechniqueAttributeValueControl } from 'features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeValueControl'; import { formatAttributesForAutoComplete, getAttributeId, getAttributeType, getRemainingAttributes -} from 'features/surveys/sampling-information/techniques/form/components/attributes/components/utils'; +} from 'features/surveys/sampling-information/techniques/components/attributes/components/utils'; import { CreateTechniqueFormValues, UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; import { FieldArrayRenderProps, useFormikContext } from 'formik'; import { ITechniqueAttributeQualitative, ITechniqueAttributeQuantitative } from 'interfaces/useReferenceApi.interface'; import { useMemo } from 'react'; @@ -111,7 +111,6 @@ export const TechniqueAttributeForm = diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeValueControl.tsx b/app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeValueControl.tsx similarity index 88% rename from app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeValueControl.tsx rename to app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeValueControl.tsx index 70ea10f4f8..6d5830fd8a 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/components/attributes/components/TechniqueAttributeValueControl.tsx +++ b/app/src/features/surveys/sampling-information/techniques/components/attributes/components/TechniqueAttributeValueControl.tsx @@ -3,13 +3,12 @@ import CustomTextField from 'components/fields/CustomTextField'; import { CreateTechniqueFormValues, UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; -import { FieldArrayRenderProps, useFormikContext } from 'formik'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; +import { useFormikContext } from 'formik'; import { ITechniqueAttributeQualitative, ITechniqueAttributeQuantitative } from 'interfaces/useReferenceApi.interface'; interface ITechniqueAttributeValueControlProps { selectedAttributeTypeDefinition?: ITechniqueAttributeQuantitative | ITechniqueAttributeQualitative; - arrayHelpers: FieldArrayRenderProps; index: number; } @@ -76,7 +75,7 @@ export const TechniqueAttributeValueControl = < return ( - - - - - - ({ - value: option.value as number, - label: option.label, - description: option.subText - }))} - onChange={(_, value) => { - if (value?.value) { - setFieldValue('method_lookup_id', value.value); - } - }} - /> - - - - + + + - + + ({ + value: option.value as number, + label: option.label, + description: option.subText + }))} + onChange={(_, value) => { + if (value?.value) { + setFieldValue('method_lookup_id', value.value); + } + }} + /> + + + + + ); }; diff --git a/app/src/features/surveys/sampling-information/techniques/form/create/CreateTechniquePage.tsx b/app/src/features/surveys/sampling-information/techniques/create/CreateTechniquePage.tsx similarity index 98% rename from app/src/features/surveys/sampling-information/techniques/form/create/CreateTechniquePage.tsx rename to app/src/features/surveys/sampling-information/techniques/create/CreateTechniquePage.tsx index 414390df00..c44f9db7d0 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/create/CreateTechniquePage.tsx +++ b/app/src/features/surveys/sampling-information/techniques/create/CreateTechniquePage.tsx @@ -11,7 +11,7 @@ import PageHeader from 'components/layout/PageHeader'; import { CreateTechniqueI18N } from 'constants/i18n'; import TechniqueFormContainer, { CreateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; import { FormikProps } from 'formik'; import { APIError } from 'hooks/api/useAxios'; import { useBiohubApi } from 'hooks/useBioHubApi'; diff --git a/app/src/features/surveys/sampling-information/techniques/form/edit/EditTechniquePage.tsx b/app/src/features/surveys/sampling-information/techniques/edit/EditTechniquePage.tsx similarity index 98% rename from app/src/features/surveys/sampling-information/techniques/form/edit/EditTechniquePage.tsx rename to app/src/features/surveys/sampling-information/techniques/edit/EditTechniquePage.tsx index 45c742c015..4ed1ce7ba9 100644 --- a/app/src/features/surveys/sampling-information/techniques/form/edit/EditTechniquePage.tsx +++ b/app/src/features/surveys/sampling-information/techniques/edit/EditTechniquePage.tsx @@ -11,7 +11,7 @@ import PageHeader from 'components/layout/PageHeader'; import { EditTechniqueI18N } from 'constants/i18n'; import TechniqueFormContainer, { UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; +} from 'features/surveys/sampling-information/techniques/components/TechniqueFormContainer'; import { FormikProps } from 'formik'; import { APIError } from 'hooks/api/useAxios'; import { useBiohubApi } from 'hooks/useBioHubApi'; diff --git a/app/src/features/surveys/sampling-information/techniques/form/components/attractants/TechniqueAttractantsForm.tsx b/app/src/features/surveys/sampling-information/techniques/form/components/attractants/TechniqueAttractantsForm.tsx deleted file mode 100644 index 847fab3806..0000000000 --- a/app/src/features/surveys/sampling-information/techniques/form/components/attractants/TechniqueAttractantsForm.tsx +++ /dev/null @@ -1,116 +0,0 @@ -import { mdiClose } from '@mdi/js'; -import { Icon } from '@mdi/react'; -import Box from '@mui/material/Box'; -import Collapse from '@mui/material/Collapse'; -import grey from '@mui/material/colors/grey'; -import Grid from '@mui/material/Grid'; -import IconButton from '@mui/material/IconButton'; -import Paper from '@mui/material/Paper'; -import Typography from '@mui/material/Typography'; -import AutocompleteField from 'components/fields/AutocompleteField'; -import { - CreateTechniqueFormValues, - UpdateTechniqueFormValues -} from 'features/surveys/sampling-information/techniques/form/components/TechniqueFormContainer'; - -import { useFormikContext } from 'formik'; -import { useCodesContext } from 'hooks/useContext'; -import { useEffect } from 'react'; -import { TransitionGroup } from 'react-transition-group'; - -/** - * Technique attractants form. - * - * @template FormValues - * @return {*} - */ -export const TechniqueAttractantsForm = < - FormValues extends CreateTechniqueFormValues | UpdateTechniqueFormValues ->() => { - const codesContext = useCodesContext(); - - const { values, setFieldValue } = useFormikContext(); - - useEffect(() => { - codesContext.codesDataLoader.load(); - }, [codesContext.codesDataLoader]); - - const attractants = codesContext.codesDataLoader.data?.attractants ?? []; - - return ( - <> - - - Attractants (optional) - ({ - value: option.id, - label: option.name, - description: option.description - })) - .filter( - (option) => !values.attractants.some((attractant) => attractant.attractant_lookup_id === option.value) - ) ?? [] - } - onChange={(_, value) => { - if (value?.value) { - setFieldValue('attractants', [...values.attractants, { attractant_lookup_id: value.value }]); - } - }} - /> - - - - {values.attractants.map((attractant, index) => { - const lookup = attractants.find((option) => option.id === attractant.attractant_lookup_id); - return ( - - - - {lookup?.name} - - {lookup?.description} - - - - { - setFieldValue( - 'attractants', - values.attractants.length > 1 ? values.attractants.filter((id) => id !== attractant) : [] - ); - }}> - - - - - - ); - })} - - - - - ); -}; diff --git a/app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCardContainer.tsx b/app/src/features/surveys/sampling-information/techniques/table/SamplingTechniqueTable.tsx similarity index 74% rename from app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCardContainer.tsx rename to app/src/features/surveys/sampling-information/techniques/table/SamplingTechniqueTable.tsx index eda2fc5012..6374ad0796 100644 --- a/app/src/features/surveys/sampling-information/techniques/components/SamplingTechniqueCardContainer.tsx +++ b/app/src/features/surveys/sampling-information/techniques/table/SamplingTechniqueTable.tsx @@ -9,26 +9,29 @@ import Menu, { MenuProps } from '@mui/material/Menu'; import MenuItem from '@mui/material/MenuItem'; import Typography from '@mui/material/Typography'; import { GridRowSelectionModel } from '@mui/x-data-grid'; -import { GridOverlay } from '@mui/x-data-grid/components/containers/GridOverlay'; import { GridColDef } from '@mui/x-data-grid/models/colDef/gridColDef'; import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { DeleteTechniqueI18N } from 'constants/i18n'; import { useBiohubApi } from 'hooks/useBioHubApi'; import { useCodesContext, useDialogContext, useSurveyContext } from 'hooks/useContext'; -import { IGetTechniqueResponse } from 'interfaces/useTechniqueApi.interface'; -import { useState } from 'react'; +import { IGetTechniqueResponse, TechniqueAttractant } from 'interfaces/useTechniqueApi.interface'; +import { useEffect, useState } from 'react'; import { Link as RouterLink } from 'react-router-dom'; import { getCodesName } from 'utils/Utils'; -interface ITechniqueRowData { +export interface ITechniqueRowData { id: number; - method_lookup: string; + method_lookup_id: number; name: string; description: string | null; + attractants: TechniqueAttractant[]; + distance_threshold: number | null; } -interface ISamplingTechniqueCardContainer { +interface ISamplingTechniqueTable { techniques: IGetTechniqueResponse[]; bulkActionTechniques: GridRowSelectionModel; setBulkActionTechniques: (selection: GridRowSelectionModel) => void; @@ -39,7 +42,7 @@ interface ISamplingTechniqueCardContainer { * * @returns */ -export const SamplingTechniqueCardContainer = (props: ISamplingTechniqueCardContainer) => { +export const SamplingTechniqueTable = (props: ISamplingTechniqueTable) => { const { techniques, bulkActionTechniques, setBulkActionTechniques } = props; // Individual row action menu @@ -51,6 +54,10 @@ export const SamplingTechniqueCardContainer = (prop const codesContext = useCodesContext(); const biohubApi = useBiohubApi(); + useEffect(() => { + codesContext.codesDataLoader.load(); + }, [codesContext.codesDataLoader]); + /** * Handle the delete technique API call. * @@ -109,10 +116,11 @@ export const SamplingTechniqueCardContainer = (prop const rows: ITechniqueRowData[] = techniques.map((technique) => ({ id: technique.method_technique_id, - method_lookup: - getCodesName(codesContext.codesDataLoader.data, 'sample_methods', technique.method_lookup_id) ?? '', + method_lookup_id: technique.method_lookup_id, name: technique.name, - description: technique.description + description: technique.description, + attractants: technique.attractants, + distance_threshold: technique.distance_threshold })) || []; const columns: GridColDef[] = [ @@ -123,7 +131,10 @@ export const SamplingTechniqueCardContainer = (prop headerName: 'Method', renderCell: (params) => ( - + ) }, @@ -152,11 +163,36 @@ export const SamplingTechniqueCardContainer = (prop ); } }, + { + field: 'attractants', + flex: 0.5, + headerName: 'Attractants', + renderCell: (params) => ( + + {params.row.attractants.map((attractant) => ( + + + + ))} + + ) + }, + { + field: 'distance_threshold', + headerName: 'Distance threshold', + flex: 0.3, + renderCell: (params) => (params.row.distance_threshold ? <>{params.row.distance_threshold} m : <>) + }, { field: 'actions', type: 'actions', sortable: false, - flex: 1, + flex: 0.3, align: 'right', renderCell: (params) => { return ( @@ -224,10 +260,18 @@ export const SamplingTechniqueCardContainer = (prop - + + } + hasNoDataFallbackDelay={100}> 'auto'} rows={rows} columns={columns} disableRowSelectionOnClick @@ -235,41 +279,14 @@ export const SamplingTechniqueCardContainer = (prop checkboxSelection rowSelectionModel={bulkActionTechniques} onRowSelectionModelChange={setBulkActionTechniques} - noRowsOverlay={ - - - - Start by adding sampling information  - - - - Add techniques, then apply your techniques to sampling sites - - - - } - sx={{ - '& .MuiDataGrid-virtualScroller': { - height: rows.length === 0 ? '250px' : 'unset', - overflowY: 'auto !important', - overflowX: 'hidden' - }, - '& .MuiDataGrid-overlay': { - height: '250px', - display: 'flex', - justifyContent: 'center', - alignItems: 'center' - }, - '& .MuiDataGrid-columnHeaderDraggableContainer': { - minWidth: '50px' - }, - // '& .MuiDataGrid-cell--textLeft': { justifyContent: 'flex-end' } - '& .MuiDataGrid-cell--textLeft:last-child': { - // justifyContent: 'flex-end !important' + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 10 } } }} + pageSizeOptions={[10, 25, 50]} /> - + ); }; diff --git a/app/src/features/surveys/telemetry/ManualTelemetryList.tsx b/app/src/features/surveys/telemetry/ManualTelemetryList.tsx deleted file mode 100644 index 6ffb733aca..0000000000 --- a/app/src/features/surveys/telemetry/ManualTelemetryList.tsx +++ /dev/null @@ -1,601 +0,0 @@ -import { mdiPencilOutline, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import { LoadingButton } from '@mui/lab'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import grey from '@mui/material/colors/grey'; -import Dialog from '@mui/material/Dialog'; -import DialogActions from '@mui/material/DialogActions'; -import DialogContent from '@mui/material/DialogContent'; -import DialogTitle from '@mui/material/DialogTitle'; -import Divider from '@mui/material/Divider'; -import FormControl from '@mui/material/FormControl'; -import FormHelperText from '@mui/material/FormHelperText'; -import InputLabel from '@mui/material/InputLabel'; -import ListItemIcon from '@mui/material/ListItemIcon'; -import Menu, { MenuProps } from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; -import Paper from '@mui/material/Paper'; -import Select from '@mui/material/Select'; -import Stack from '@mui/material/Stack'; -import useTheme from '@mui/material/styles/useTheme'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import useMediaQuery from '@mui/material/useMediaQuery'; -import { useOnMount } from '@mui/x-data-grid/internals'; -import { SkeletonListStack } from 'components/loading/SkeletonLoaders'; -import { AttachmentType } from 'constants/attachments'; -import { DialogContext } from 'contexts/dialogContext'; -import { SurveyContext } from 'contexts/surveyContext'; -import { TelemetryDataContext } from 'contexts/telemetryDataContext'; -import { default as dayjs } from 'dayjs'; -import { Formik } from 'formik'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useTelemetryApi } from 'hooks/useTelemetryApi'; -import { ISimpleCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; -import { isEqual as _deepEquals } from 'lodash'; -import { get } from 'lodash-es'; -import { useContext, useMemo, useState } from 'react'; -import { datesSameNullable } from 'utils/Utils'; -import yup from 'utils/YupSchema'; -import { InferType } from 'yup'; -import { ANIMAL_FORM_MODE } from '../view/survey-animals/animal'; -import { AnimalTelemetryDeviceSchema, Device, IAnimalDeployment } from '../view/survey-animals/telemetry-device/device'; -import TelemetryDeviceForm from '../view/survey-animals/telemetry-device/TelemetryDeviceForm'; -import ManualTelemetryCard from './ManualTelemetryCard'; - -export const AnimalDeploymentSchema = AnimalTelemetryDeviceSchema.shape({ - survey_critter_id: yup.number().required('An animal selection is required'), // add survey critter id to form - critter_id: yup.string(), - attachmentFile: yup.mixed(), - attachmentType: yup.mixed().oneOf(Object.values(AttachmentType)) -}); -export type AnimalDeployment = InferType; - -export interface ICritterDeployment { - critter: ISimpleCritterWithInternalId; - deployment: IAnimalDeployment; -} - -const ManualTelemetryList = () => { - const theme = useTheme(); - const fullScreen = useMediaQuery(theme.breakpoints.down('sm')); - const surveyContext = useContext(SurveyContext); - const telemetryContext = useContext(TelemetryDataContext); - const dialogContext = useContext(DialogContext); - const biohubApi = useBiohubApi(); - const telemetryApi = useTelemetryApi(); - - const defaultFormValues = { - survey_critter_id: '' as unknown as number, // form needs '' to display the no value text - deployments: [ - { - deployment_id: '', - attachment_start: '', - attachment_end: undefined - } - ], - device_id: '' as unknown as number, // form needs '' to display the no value text - device_make: '', - device_model: '', - frequency: undefined, - frequency_unit: undefined, - attachmentType: undefined, - attachmentFile: undefined, - critter_id: '' - }; - - const [anchorEl, setAnchorEl] = useState(null); - - const [showDialog, setShowDialog] = useState(false); - const [isLoading, setIsLoading] = useState(false); - const [formMode, setFormMode] = useState(ANIMAL_FORM_MODE.ADD); - const [critterId, setCritterId] = useState(''); - const [deviceId, setDeviceId] = useState(0); - const [formData, setFormData] = useState(defaultFormValues); - - useOnMount(() => { - surveyContext.deploymentDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - surveyContext.critterDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - }); - - const deployments = surveyContext.deploymentDataLoader.data; - const critters = surveyContext.critterDataLoader.data; - - const critterDeployments: ICritterDeployment[] = useMemo(() => { - const data: ICritterDeployment[] = []; - // combine all critter and deployments into a flat list - surveyContext.deploymentDataLoader.data?.forEach((deployment) => { - const critter = surveyContext.critterDataLoader.data?.find( - (critter) => critter.critter_id === deployment.critter_id - ); - if (critter) { - data.push({ critter, deployment }); - } - }); - return data; - }, [surveyContext.critterDataLoader.data, surveyContext.deploymentDataLoader.data]); - - const handleMenuOpen = async (event: React.MouseEvent, device_id: number) => { - setAnchorEl(event.currentTarget); - setDeviceId(device_id); - - const critterDeployment = critterDeployments.find((item) => item.deployment.device_id === device_id); - - // need to map deployment back into object for initial values - if (critterDeployment) { - const deviceDetails = await telemetryApi.devices.getDeviceDetails( - device_id, - critterDeployment.deployment.device_make - ); - const editData: AnimalDeployment = { - survey_critter_id: Number(critterDeployment.critter?.survey_critter_id), - deployments: [ - { - deployment_id: critterDeployment.deployment.deployment_id, - attachment_start: dayjs(critterDeployment.deployment.attachment_start).format('YYYY-MM-DD'), - attachment_end: critterDeployment.deployment.attachment_end - ? dayjs(critterDeployment.deployment.attachment_end).format('YYYY-MM-DD') - : null - } - ], - device_id: critterDeployment.deployment.device_id, - device_make: deviceDetails.device?.device_make ? String(deviceDetails.device?.device_make) : '', - device_model: deviceDetails.device?.device_model ? String(deviceDetails.device?.device_model) : '', - frequency: deviceDetails.device?.frequency ? Number(deviceDetails.device?.frequency) : undefined, - frequency_unit: deviceDetails.device?.frequency_unit ? String(deviceDetails.device?.frequency_unit) : '', - attachmentType: undefined, - attachmentFile: undefined, - critter_id: critterDeployment.deployment.critter_id - }; - setCritterId(critterDeployment.critter?.survey_critter_id); - setFormData(editData); - } - }; - - const handleSubmit = async (data: AnimalDeployment) => { - if (formMode === ANIMAL_FORM_MODE.ADD) { - // ADD NEW DEPLOYMENT - await handleAddDeployment(data); - } else { - // EDIT EXISTING DEPLOYMENT - await handleEditDeployment(data); - } - // UPLOAD/ REPLACE ANY FILES FOUND - if (data.attachmentFile && data.attachmentType) { - await handleUploadFile(data.attachmentFile, data.attachmentType); - } - }; - - const handleDeleteDeployment = async () => { - try { - const deployment = deployments?.find((item) => item.device_id === deviceId); - if (!deployment) { - throw new Error('Invalid Deployment Data'); - } - const critter = critters?.find((item) => item.critter_id === deployment?.critter_id); - if (!critter) { - throw new Error('Invalid Critter Data'); - } - - const found = telemetryContext.telemetryDataLoader.data?.find( - (item) => item.deployment_id === deployment.deployment_id - ); - if (!found) { - await biohubApi.survey.removeDeployment( - surveyContext.projectId, - surveyContext.surveyId, - critter.survey_critter_id, - deployment.deployment_id - ); - dialogContext.setYesNoDialog({ open: false }); - surveyContext.deploymentDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - } else { - dialogContext.setYesNoDialog({ open: false }); - // Deployment is used in telemetry, do not delete until it is scrubbed - throw new Error('Deployment is used in telemetry'); - } - } catch (e) { - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error Deleting Deployment - - - {String(e)} - - - ), - open: true - }); - } - }; - - const deleteDeploymentDialog = () => { - dialogContext.setYesNoDialog({ - dialogTitle: 'Delete Deployment?', - dialogContent: ( - - Are you sure you want to delete this deployment? - - ), - yesButtonLabel: 'Delete Deployment', - noButtonLabel: 'Cancel', - yesButtonProps: { color: 'error' }, - onClose: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - onNo: () => { - dialogContext.setYesNoDialog({ open: false }); - }, - open: true, - onYes: () => { - handleDeleteDeployment(); - } - }); - }; - - const handleAddDeployment = async (data: AnimalDeployment) => { - try { - const critter = critters?.find((a) => a.survey_critter_id === data.survey_critter_id); - - if (!critter) { - throw new Error('Invalid critter data'); - } - - await biohubApi.survey.addDeployment( - surveyContext.projectId, - surveyContext.surveyId, - Number(data.survey_critter_id), - //Being explicit here for simplicity. - { - critter_id: critter.critter_id, - device_id: Number(data.device_id), - device_make: data.device_make ?? undefined, - frequency: data.frequency ?? undefined, - frequency_unit: data.frequency_unit ?? undefined, - device_model: data.device_model ?? undefined, - attachment_start: data.deployments?.[0].attachment_start, - attachment_end: data.deployments?.[0].attachment_end ?? undefined - } - ); - surveyContext.deploymentDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); - // success snack bar - dialogContext.setSnackbar({ - snackbarMessage: ( - - Deployment Added - - ), - open: true - }); - } catch (error) { - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error adding Deployment - - - {String(error)} - - - ), - open: true - }); - } - }; - - const handleEditDeployment = async (data: AnimalDeployment) => { - try { - await updateDeployments(data); - await updateDevice(data); - dialogContext.setSnackbar({ - snackbarMessage: ( - - Deployment Updated - - ), - open: true - }); - } catch (error) { - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error Deleting Sampling Site - - - {String(error)} - - - ), - open: true - }); - } - }; - - const updateDeployments = async (data: AnimalDeployment) => { - for (const deployment of data.deployments ?? []) { - const existingDeployment = deployments?.find((item) => item.deployment_id === deployment.deployment_id); - if ( - !datesSameNullable(deployment?.attachment_start, existingDeployment?.attachment_start) || - !datesSameNullable(deployment?.attachment_end, existingDeployment?.attachment_end) - ) { - try { - await biohubApi.survey.updateDeployment( - surveyContext.projectId, - surveyContext.surveyId, - data.survey_critter_id, - deployment - ); - } catch (error) { - throw new Error(`Failed to update deployment ${deployment.deployment_id}`); - } - } - } - }; - - const updateDevice = async (data: AnimalDeployment) => { - const existingDevice = critterDeployments.find((item) => item.deployment.device_id === data.device_id); - const device = new Device({ ...data, collar_id: existingDevice?.deployment.collar_id }); - try { - if (existingDevice && !_deepEquals(new Device(existingDevice.deployment), device)) { - await telemetryApi.devices.upsertCollar(device); - } - } catch (error) { - throw new Error(`Failed to update collar ${device.collar_id}`); - } - }; - - const handleUploadFile = async (file?: File, attachmentType?: AttachmentType) => { - try { - if (file && attachmentType === AttachmentType.KEYX) { - await biohubApi.survey.uploadSurveyKeyx(surveyContext.projectId, surveyContext.surveyId, file); - } else if (file && attachmentType === AttachmentType.OTHER) { - await biohubApi.survey.uploadSurveyAttachments(surveyContext.projectId, surveyContext.surveyId, file); - } - } catch (error) { - dialogContext.setSnackbar({ - snackbarMessage: ( - <> - - Error Uploading File - - - {`Failed to upload attachment ${file?.name}`} - - - ), - open: true - }); - } - }; - - return ( - <> - { - setAnchorEl(null); - setCritterId(''); - setDeviceId(0); - }} - anchorEl={anchorEl} - anchorOrigin={{ - vertical: 'top', - horizontal: 'right' - }} - transformOrigin={{ - vertical: 'top', - horizontal: 'right' - }}> - { - setFormMode(ANIMAL_FORM_MODE.EDIT); - setShowDialog(true); - setAnchorEl(null); - }}> - - - - Edit Details - - { - setAnchorEl(null); - deleteDeploymentDialog(); - }}> - - - - Delete - - - { - setIsLoading(true); - await handleSubmit(values); - setIsLoading(false); - setShowDialog(false); - actions.resetForm(); - setCritterId(''); - }}> - {(formikProps) => { - return ( - <> - - Critter Deployments - - <> - - Critter - - - - {get(formikProps.errors, 'survey_critter_id')} - - - - - - - - { - formikProps.submitForm(); - }}> - Save - - - - - - - - - Deployments ‌ - - ({Number(critterDeployments?.length ?? 0).toLocaleString()}) - - - - - - - - {surveyContext.deploymentDataLoader.isLoading ? ( - - ) : ( - <> - {!critterDeployments.length && ( - - No Deployments - - )} - {critterDeployments?.map((item) => ( - { - handleMenuOpen(event, id); - }} - /> - ))} - - )} - - - - - ); - }} - - - ); -}; - -export default ManualTelemetryList; diff --git a/app/src/features/surveys/telemetry/ManualTelemetryPage.tsx b/app/src/features/surveys/telemetry/ManualTelemetryPage.tsx deleted file mode 100644 index cdbc745ac3..0000000000 --- a/app/src/features/surveys/telemetry/ManualTelemetryPage.tsx +++ /dev/null @@ -1,59 +0,0 @@ -import Box from '@mui/material/Box'; -import CircularProgress from '@mui/material/CircularProgress'; -import Stack from '@mui/material/Stack'; -import { ProjectContext } from 'contexts/projectContext'; -import { SurveyContext } from 'contexts/surveyContext'; -import { TelemetryDataContextProvider } from 'contexts/telemetryDataContext'; -import { TelemetryTableContextProvider } from 'contexts/telemetryTableContext'; -import { useContext, useMemo } from 'react'; -import ManualTelemetryHeader from './ManualTelemetryHeader'; -import ManualTelemetryList from './ManualTelemetryList'; -import ManualTelemetryTableContainer from './telemetry-table/ManualTelemetryTableContainer'; - -const ManualTelemetryPage = () => { - const surveyContext = useContext(SurveyContext); - const projectContext = useContext(ProjectContext); - - const deploymentIds = useMemo(() => { - return surveyContext.deploymentDataLoader.data?.map((item) => item.deployment_id); - }, [surveyContext.deploymentDataLoader.data]); - - if (!surveyContext.surveyDataLoader.data || !projectContext.projectDataLoader.data) { - return ; - } - - return ( - - - - - {/* Telematry List */} - - - - {/* Telemetry Component */} - - - - - - - - - ); -}; - -export default ManualTelemetryPage; diff --git a/app/src/features/surveys/telemetry/ManualTelemetrySection.tsx b/app/src/features/surveys/telemetry/ManualTelemetrySection.tsx deleted file mode 100644 index 38a1548bc8..0000000000 --- a/app/src/features/surveys/telemetry/ManualTelemetrySection.tsx +++ /dev/null @@ -1,33 +0,0 @@ -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Divider from '@mui/material/Divider'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import { Link as RouterLink } from 'react-router-dom'; -import NoSurveySectionData from '../components/NoSurveySectionData'; - -const ManualTelemetrySection = () => { - return ( - - - - Telemetry - - - - - - - - - ); -}; - -export default ManualTelemetrySection; diff --git a/app/src/features/surveys/telemetry/ManualTelemetryCard.tsx b/app/src/features/surveys/telemetry/TelemetryCard.tsx similarity index 94% rename from app/src/features/surveys/telemetry/ManualTelemetryCard.tsx rename to app/src/features/surveys/telemetry/TelemetryCard.tsx index b77f6b3e85..2f3755329b 100644 --- a/app/src/features/surveys/telemetry/ManualTelemetryCard.tsx +++ b/app/src/features/surveys/telemetry/TelemetryCard.tsx @@ -8,7 +8,7 @@ import grey from '@mui/material/colors/grey'; import IconButton from '@mui/material/IconButton'; import Typography from '@mui/material/Typography'; import { default as dayjs } from 'dayjs'; -export interface ManualTelemetryCardProps { +export interface TelemetryCardProps { device_id: number; device_make: string; name: string; // should be animal alias @@ -18,7 +18,7 @@ export interface ManualTelemetryCardProps { onMenu: (e: React.MouseEvent, id: number) => void; } -const ManualTelemetryCard = (props: ManualTelemetryCardProps) => { +export const TelemetryCard = (props: TelemetryCardProps) => { return ( { ); }; - -export default ManualTelemetryCard; diff --git a/app/src/features/surveys/telemetry/ManualTelemetryHeader.tsx b/app/src/features/surveys/telemetry/TelemetryHeader.tsx similarity index 86% rename from app/src/features/surveys/telemetry/ManualTelemetryHeader.tsx rename to app/src/features/surveys/telemetry/TelemetryHeader.tsx index f8fa0dd22a..85fb278961 100644 --- a/app/src/features/surveys/telemetry/ManualTelemetryHeader.tsx +++ b/app/src/features/surveys/telemetry/TelemetryHeader.tsx @@ -4,14 +4,14 @@ import Typography from '@mui/material/Typography'; import PageHeader from 'components/layout/PageHeader'; import { Link as RouterLink } from 'react-router-dom'; -export interface ManualTelemetryHeaderProps { +export interface TelemetryHeaderProps { project_id: number; project_name: string; survey_id: number; survey_name: string; } -const ManualTelemetryHeader: React.FC = (props) => { +export const TelemetryHeader = (props: TelemetryHeaderProps) => { const { project_id, project_name, survey_id, survey_name } = props; return ( = (props) => { /> ); }; - -export default ManualTelemetryHeader; diff --git a/app/src/features/surveys/telemetry/TelemetryPage.tsx b/app/src/features/surveys/telemetry/TelemetryPage.tsx new file mode 100644 index 0000000000..51e0123188 --- /dev/null +++ b/app/src/features/surveys/telemetry/TelemetryPage.tsx @@ -0,0 +1,57 @@ +import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; +import Stack from '@mui/material/Stack'; +import { TelemetryTableContextProvider } from 'contexts/telemetryTableContext'; +import { SurveyDeploymentList } from 'features/surveys/telemetry/list/SurveyDeploymentList'; +import { TelemetryTableContainer } from 'features/surveys/telemetry/table/TelemetryTableContainer'; +import { TelemetryHeader } from 'features/surveys/telemetry/TelemetryHeader'; +import { useProjectContext, useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import { useEffect } from 'react'; + +export const TelemetryPage = () => { + const projectContext = useProjectContext(); + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const deploymentsDataLoader = telemetryDataContext.deploymentsDataLoader; + + useEffect(() => { + deploymentsDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + }, [deploymentsDataLoader, surveyContext.projectId, surveyContext.surveyId]); + + if (!surveyContext.surveyDataLoader.data || !projectContext.projectDataLoader.data) { + return ; + } + + return ( + + + + {/* Telematry List */} + + + + {/* Telemetry Component */} + + deployment.bctw_deployment_id) ?? []}> + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/TelemetryRouter.tsx b/app/src/features/surveys/telemetry/TelemetryRouter.tsx new file mode 100644 index 0000000000..999be6ba09 --- /dev/null +++ b/app/src/features/surveys/telemetry/TelemetryRouter.tsx @@ -0,0 +1,65 @@ +import { ProjectRoleRouteGuard } from 'components/security/RouteGuards'; +import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; +import { DialogContextProvider } from 'contexts/dialogContext'; +import { CreateDeploymentPage } from 'features/surveys/telemetry/deployments/create/CreateDeploymentPage'; +import { EditDeploymentPage } from 'features/surveys/telemetry/deployments/edit/EditDeploymentPage'; +import { TelemetryPage } from 'features/surveys/telemetry/TelemetryPage'; +import { Redirect, Switch } from 'react-router'; +import RouteWithTitle from 'utils/RouteWithTitle'; +import { getTitle } from 'utils/Utils'; + +/** + * Router for all `/admin/projects/:id/surveys/:survey_id/telemetry/*` pages. + * + * @return {*} + */ +export const TelemetryRouter = () => { + return ( + + + + + + + + + + + + + + + + + + + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/components/form/DeploymentForm.tsx b/app/src/features/surveys/telemetry/deployments/components/form/DeploymentForm.tsx new file mode 100644 index 0000000000..87b947112b --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/components/form/DeploymentForm.tsx @@ -0,0 +1,142 @@ +import LoadingButton from '@mui/lab/LoadingButton/LoadingButton'; +import Button from '@mui/material/Button'; +import Container from '@mui/material/Container'; +import Divider from '@mui/material/Divider'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import HorizontalSplitFormComponent from 'components/fields/HorizontalSplitFormComponent'; +import { + DeploymentDetailsForm, + DeploymentDetailsFormInitialValues, + DeploymentDetailsFormYupSchema +} from 'features/surveys/telemetry/deployments/components/form/deployment-details/DeploymentDetailsForm'; +import { + DeploymentDeviceDetailsForm, + DeploymentDeviceDetailsFormInitialValues, + DeploymentDeviceDetailsFormYupSchema +} from 'features/surveys/telemetry/deployments/components/form/device-details/DeploymentDeviceDetailsForm'; +import { + DeploymentTimelineForm, + DeploymentTimelineFormInitialValues, + DeploymentTimelineFormYupSchema +} from 'features/surveys/telemetry/deployments/components/form/timeline/DeploymentTimelineForm'; +import { useFormikContext } from 'formik'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useEffect } from 'react'; +import { useHistory } from 'react-router'; + +export const DeploymentFormInitialValues = { + ...DeploymentDetailsFormInitialValues, + ...DeploymentTimelineFormInitialValues, + ...DeploymentDeviceDetailsFormInitialValues +}; + +export const DeploymentFormYupSchema = DeploymentDetailsFormYupSchema.concat(DeploymentTimelineFormYupSchema).concat( + DeploymentDeviceDetailsFormYupSchema +); + +interface IDeploymentFormProps { + isSubmitting: boolean; + isEdit?: boolean; +} + +/** + * Deployment form component. + * + * @param {IDeploymentFormProps} props + * @return {*} + */ +export const DeploymentForm = (props: IDeploymentFormProps) => { + const { isSubmitting, isEdit } = props; + + const { submitForm, values } = useFormikContext(); + + const surveyContext = useSurveyContext(); + + const biohubApi = useBiohubApi(); + + const history = useHistory(); + + const critterDataLoader = useDataLoader((critterId: number) => + biohubApi.survey.getCritterById(surveyContext.projectId, surveyContext.surveyId, critterId) + ); + + const frequencyUnitDataLoader = useDataLoader(() => biohubApi.telemetry.getCodeValues('frequency_unit')); + const deviceMakesDataLoader = useDataLoader(() => biohubApi.telemetry.getCodeValues('device_make')); + + // Fetch frequency unit and device make code values from BCTW on component mount + useEffect(() => { + frequencyUnitDataLoader.load(); + deviceMakesDataLoader.load(); + }, [deviceMakesDataLoader, frequencyUnitDataLoader]); + + // Fetch critter data when critter_id changes (ie. when the user selects a critter) + useEffect(() => { + if (values.critter_id) { + critterDataLoader.refresh(values.critter_id); + } + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [values.critter_id]); + + return ( + + + + + ({ label: data.code, value: data.id })) ?? []} + isEdit={isEdit} + /> + + + + + + + + + + + + ({ label: data.code, value: data.id })) ?? []} + /> + + + + + + { + submitForm(); + }}> + Save and Exit + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/components/form/DeploymentFormHeader.tsx b/app/src/features/surveys/telemetry/deployments/components/form/DeploymentFormHeader.tsx new file mode 100644 index 0000000000..b575cefc52 --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/components/form/DeploymentFormHeader.tsx @@ -0,0 +1,106 @@ +import { LoadingButton } from '@mui/lab'; +import Breadcrumbs from '@mui/material/Breadcrumbs'; +import Button from '@mui/material/Button'; +import { grey } from '@mui/material/colors'; +import Container from '@mui/material/Container'; +import Link from '@mui/material/Link'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import { useFormikContext } from 'formik'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useHistory } from 'react-router'; +import { Link as RouterLink } from 'react-router-dom'; + +export interface IDeploymentFormHeaderProps { + project_id: number; + project_name: string; + survey_id: number; + survey_name: string; + is_submitting: boolean; + title: string; + breadcrumb: string; +} + +/** + * Renders the header of the create and edit deployment pages. + * + * @param {IDeploymentFormHeaderProps} props + * @return {*} + */ +export const DeploymentFormHeader = (props: IDeploymentFormHeaderProps) => { + const history = useHistory(); + const formikProps = useFormikContext(); + + const { project_id, survey_id, survey_name, project_name, is_submitting, title, breadcrumb } = props; + + return ( + <> + + + + + {project_name} + + + {survey_name} + + + Manage Telemetry + + + {breadcrumb} + + + + + {title} + + + { + formikProps.submitForm(); + }}> + Save and Exit + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/components/form/deployment-details/DeploymentDetailsForm.tsx b/app/src/features/surveys/telemetry/deployments/components/form/deployment-details/DeploymentDetailsForm.tsx new file mode 100644 index 0000000000..6f5c1ee0ba --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/components/form/deployment-details/DeploymentDetailsForm.tsx @@ -0,0 +1,137 @@ +import Grid from '@mui/material/Grid'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import { AnimalAutocompleteField } from 'components/fields/AnimalAutocompleteField'; +import AutocompleteField, { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; +import CustomTextField from 'components/fields/CustomTextField'; +import { useFormikContext } from 'formik'; +import { useSurveyContext } from 'hooks/useContext'; +import { ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { Link as RouterLink } from 'react-router-dom'; +import { isDefined } from 'utils/Utils'; +import yup from 'utils/YupSchema'; + +export const DeploymentDetailsFormInitialValues: yup.InferType = { + device_id: null as unknown as string, + critter_id: null as unknown as number, + frequency: null, + frequency_unit: null +}; + +export const DeploymentDetailsFormYupSchema = yup.object({ + device_id: yup.string().nullable().required('You must enter the device ID. This is typically the serial number'), + critter_id: yup.number().nullable().required('You must select the animal that the device is associated to'), + frequency: yup.lazy(() => + yup + .number() + .nullable() + .when('frequency_unit', { + is: (frequency_unit: number) => isDefined(frequency_unit), // when frequency_unit is defined + then: yup.number().nullable().required('Frequency is required') + }) + ), + frequency_unit: yup.lazy(() => + yup + .number() + .nullable() + .when('frequency', { + is: (frequency: number) => isDefined(frequency), // when frequency is defined + then: yup.number().nullable().required('Frequency unit is required') + }) + ) +}); + +interface IDeploymentDetailsFormProps { + surveyAnimals: ICritterSimpleResponse[]; + frequencyUnits: IAutocompleteFieldOption[]; + isEdit?: boolean; +} + +/** + * Deployment form - deployment details section. + * + * @param {IDeploymentDetailsFormProps} props + * @return {*} + */ +export const DeploymentDetailsForm = (props: IDeploymentDetailsFormProps) => { + const { surveyAnimals, frequencyUnits, isEdit } = props; + + const { setFieldValue, values } = useFormikContext(); + + const surveyContext = useSurveyContext(); + + return ( + <> + + + + You must  + + add the animal + +  to your Survey before associating it to a telemetry device. Add animals via the  + + Manage Animals + +  page. + + + + + animal.critter_id === values.critter_id)} + required + clearOnSelect + onSelect={(animal: ICritterSimpleResponse) => { + if (animal) { + setFieldValue('critter_id', animal.critter_id); + } + }} + /> + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/components/form/device-details/DeploymentDeviceDetailsForm.tsx b/app/src/features/surveys/telemetry/deployments/components/form/device-details/DeploymentDeviceDetailsForm.tsx new file mode 100644 index 0000000000..5e74ea44c4 --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/components/form/device-details/DeploymentDeviceDetailsForm.tsx @@ -0,0 +1,41 @@ +import Grid from '@mui/material/Grid'; +import AutocompleteField, { IAutocompleteFieldOption } from 'components/fields/AutocompleteField'; +import CustomTextField from 'components/fields/CustomTextField'; +import yup from 'utils/YupSchema'; + +export const DeploymentDeviceDetailsFormInitialValues: yup.InferType = { + device_make: null as unknown as number, + device_model: null +}; + +export const DeploymentDeviceDetailsFormYupSchema = yup.object({ + device_make: yup.number().nullable().required('You must enter the device make'), + device_model: yup.string().nullable() +}); + +interface IDeploymentDeviceDetailsFormProps { + deviceMakes: IAutocompleteFieldOption[]; +} + +/** + * Deployment form - device details section. + * + * @param {IDeploymentDeviceDetailsFormProps} props + * @return {*} + */ +export const DeploymentDeviceDetailsForm = (props: IDeploymentDeviceDetailsFormProps) => { + const { deviceMakes } = props; + + return ( + <> + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/components/form/timeline/DeploymentTimelineForm.tsx b/app/src/features/surveys/telemetry/deployments/components/form/timeline/DeploymentTimelineForm.tsx new file mode 100644 index 0000000000..df3b446537 --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/components/form/timeline/DeploymentTimelineForm.tsx @@ -0,0 +1,277 @@ +import Box from '@mui/material/Box'; +import Collapse from '@mui/material/Collapse'; +import FormControlLabel from '@mui/material/FormControlLabel'; +import Grid from '@mui/material/Grid'; +import Radio from '@mui/material/Radio'; +import RadioGroup from '@mui/material/RadioGroup'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import AutocompleteField from 'components/fields/AutocompleteField'; +import { DateField } from 'components/fields/DateField'; +import { TimeField } from 'components/fields/TimeField'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { useFormikContext } from 'formik'; +import { useSurveyContext } from 'hooks/useContext'; +import { ICaptureResponse, IMortalityResponse } from 'interfaces/useCritterApi.interface'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useMemo, useState } from 'react'; +import { Link as RouterLink } from 'react-router-dom'; +import { TransitionGroup } from 'react-transition-group'; +import yup from 'utils/YupSchema'; + +// Types to know how the deployment ended, determining which form components to display +type DeploymentEndType = 'capture' | 'mortality' | 'fell_off'; + +export const DeploymentTimelineFormInitialValues: yup.InferType = { + critterbase_start_capture_id: null as unknown as string, + critterbase_end_mortality_id: null, + critterbase_end_capture_id: null, + attachment_end_date: null, + attachment_end_time: null +}; + +export const DeploymentTimelineFormYupSchema = yup.object({ + critterbase_start_capture_id: yup.string().nullable().required('You must select the initial capture event'), + critterbase_end_mortality_id: yup.string().uuid().nullable(), + critterbase_end_capture_id: yup.string().uuid().nullable(), + attachment_end_date: yup.lazy(() => + yup + .string() + .nullable() + .when('attachment_end_time', { + is: (attachment_end_time: string | null) => attachment_end_time !== null, + then: yup.string().nullable().required('End Date is required'), + otherwise: yup.string().nullable() + }) + ), + attachment_end_time: yup.lazy(() => + yup + .string() + .nullable() + .when('attachment_end_date', { + is: (attachment_end_date: string | null) => attachment_end_date !== null, + then: yup.string().nullable().required('End time is required'), + otherwise: yup.string().nullable() + }) + ) +}); + +interface IDeploymentTimelineFormProps { + captures: ICaptureResponse[]; + mortalities: IMortalityResponse[]; +} + +/** + * Deployment form - deployment timeline section. + * + * @param {IDeploymentTimelineFormProps} props + * @return {*} + */ +export const DeploymentTimelineForm = (props: IDeploymentTimelineFormProps) => { + const { captures, mortalities } = props; + + const formikProps = useFormikContext(); + + const { values, setFieldValue } = formikProps; + + // Determine the initial deployment end type based on the form values + const initialDeploymentEndType = useMemo(() => { + if (values.critterbase_end_mortality_id) { + return 'mortality'; + } else if (values.critterbase_end_capture_id) { + return 'capture'; + } else if (values.attachment_end_date) { + return 'fell_off'; + } else { + return null; + } + }, [values]); + + const [deploymentEndType, setDeploymentEndType] = useState(initialDeploymentEndType); + + const surveyContext = useSurveyContext(); + + return ( + + + + Start of deployment + + + You must  + {values.critter_id ? ( + + add the capture + + ) : ( + 'add the capture' + )} +  during which the device was deployed before adding the deployment. + + ({ + value: capture.capture_id, + label: dayjs(capture.capture_date).format(DATE_FORMAT.LongDateTimeFormat) + }))} + required + /> + + + + + End of deployment (optional) + + + Select how the deployment ended. If due to a mortality, you must  + {values.critter_id ? ( + + report the mortality + + ) : ( + 'report the mortality' + )} +  before removing the device. + + + + } + label="Fell off" + onChange={() => { + setDeploymentEndType('fell_off'); + setFieldValue('critterbase_end_capture_id', null); + setFieldValue('critterbase_end_mortality_id', null); + }} + onClick={() => { + if (deploymentEndType === 'fell_off') { + // if the user clicks on the selected radio button, unselect it + setDeploymentEndType(null); + setFieldValue('attachment_end_date', null); + setFieldValue('attachment_end_time', null); + setFieldValue('critterbase_end_capture_id', null); + setFieldValue('critterbase_end_mortality_id', null); + } + }} + /> + } + label="Capture" + onChange={() => { + setDeploymentEndType('capture'); + setFieldValue('attachment_end_date', null); + setFieldValue('attachment_end_time', null); + setFieldValue('critterbase_end_mortality_id', null); + }} + onClick={() => { + if (deploymentEndType === 'capture') { + // if the user clicks on the selected radio button, unselect it + setDeploymentEndType(null); + setFieldValue('attachment_end_date', null); + setFieldValue('attachment_end_time', null); + setFieldValue('critterbase_end_capture_id', null); + setFieldValue('critterbase_end_mortality_id', null); + } + }} + /> + } + disabled={!mortalities.length} + label="Mortality" + onChange={() => { + setDeploymentEndType('mortality'); + setFieldValue('attachment_end_date', null); + setFieldValue('attachment_end_time', null); + setFieldValue('critterbase_end_capture_id', null); + }} + onClick={() => { + if (deploymentEndType === 'mortality') { + // if the user clicks on the selected radio button, unselect it + setDeploymentEndType(null); + setFieldValue('attachment_end_date', null); + setFieldValue('attachment_end_time', null); + setFieldValue('critterbase_end_capture_id', null); + setFieldValue('critterbase_end_mortality_id', null); + } + }} + /> + + + + + + {deploymentEndType === 'capture' && ( + { + if (option?.value) { + setFieldValue('critterbase_end_capture_id', option.value); + } + }} + options={captures.map((capture) => ({ + value: capture.capture_id, + label: dayjs(capture.capture_date).format(DATE_FORMAT.LongDateTimeFormat) + }))} + sx={{ width: '100%' }} + /> + )} + {deploymentEndType === 'fell_off' && ( + + + + + )} + {deploymentEndType === 'mortality' && ( + + ({ + value: mortality.mortality_id, + label: dayjs(mortality.mortality_timestamp).format(DATE_FORMAT.LongDateTimeFormat) + }))} + sx={{ width: '100%' }} + /> + + )} + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/create/CreateDeploymentPage.tsx b/app/src/features/surveys/telemetry/deployments/create/CreateDeploymentPage.tsx new file mode 100644 index 0000000000..319d87c619 --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/create/CreateDeploymentPage.tsx @@ -0,0 +1,122 @@ +import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; +import FormikErrorSnackbar from 'components/alert/FormikErrorSnackbar'; +import { CreateAnimalDeploymentI18N } from 'constants/i18n'; +import { + DeploymentForm, + DeploymentFormInitialValues, + DeploymentFormYupSchema +} from 'features/surveys/telemetry/deployments/components/form/DeploymentForm'; +import { DeploymentFormHeader } from 'features/surveys/telemetry/deployments/components/form/DeploymentFormHeader'; +import { Formik, FormikProps } from 'formik'; +import { APIError } from 'hooks/api/useAxios'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useProjectContext, useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import { SKIP_CONFIRMATION_DIALOG, useUnsavedChangesDialog } from 'hooks/useUnsavedChangesDialog'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useRef, useState } from 'react'; +import { Prompt, useHistory } from 'react-router'; + +/** + * Renders the Create Deployment page. + * + * @return {*} + */ +export const CreateDeploymentPage = () => { + const history = useHistory(); + + const biohubApi = useBiohubApi(); + + const dialogContext = useDialogContext(); + const projectContext = useProjectContext(); + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const formikRef = useRef>(null); + const [isSubmitting, setIsSubmitting] = useState(false); + + const { locationChangeInterceptor } = useUnsavedChangesDialog(); + + const critters = surveyContext.critterDataLoader.data ?? []; + + if (!surveyContext.surveyDataLoader.data || !projectContext.projectDataLoader.data) { + return ; + } + + const handleSubmit = async (values: ICreateAnimalDeployment) => { + setIsSubmitting(true); + + try { + const critter_id = Number(critters?.find((animal) => animal.critter_id === values.critter_id)?.critter_id); + + if (!critter_id) { + throw new Error('Invalid critter data'); + } + + await biohubApi.survey.createDeployment(surveyContext.projectId, surveyContext.surveyId, critter_id, { + device_id: Number(values.device_id), + device_make: values.device_make, + frequency: values.frequency, + frequency_unit: values.frequency_unit, + device_model: values.device_model, + critterbase_start_capture_id: values.critterbase_start_capture_id, + critterbase_end_capture_id: values.critterbase_end_capture_id, + critterbase_end_mortality_id: values.critterbase_end_mortality_id, + attachment_end_date: values.attachment_end_date, + attachment_end_time: values.attachment_end_time + }); + + telemetryDataContext.deploymentsDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); + + // create complete, navigate back to telemetry page + history.push( + `/admin/projects/${surveyContext.projectId}/surveys/${surveyContext.surveyId}/telemetry`, + SKIP_CONFIRMATION_DIALOG + ); + } catch (error) { + dialogContext.setErrorDialog({ + dialogTitle: CreateAnimalDeploymentI18N.createErrorTitle, + dialogText: CreateAnimalDeploymentI18N.createErrorText, + dialogError: (error as APIError).message, + dialogErrorDetails: (error as APIError)?.errors, + onClose: () => { + dialogContext.setErrorDialog({ open: false }); + }, + onOk: () => { + dialogContext.setErrorDialog({ open: false }); + }, + open: true + }); + setIsSubmitting(false); + } + }; + + return ( + <> + + + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/deployments/edit/EditDeploymentPage.tsx b/app/src/features/surveys/telemetry/deployments/edit/EditDeploymentPage.tsx new file mode 100644 index 0000000000..aceb5e4c7f --- /dev/null +++ b/app/src/features/surveys/telemetry/deployments/edit/EditDeploymentPage.tsx @@ -0,0 +1,148 @@ +import Box from '@mui/material/Box'; +import CircularProgress from '@mui/material/CircularProgress'; +import FormikErrorSnackbar from 'components/alert/FormikErrorSnackbar'; +import { EditAnimalDeploymentI18N } from 'constants/i18n'; +import { + DeploymentForm, + DeploymentFormYupSchema +} from 'features/surveys/telemetry/deployments/components/form/DeploymentForm'; +import { DeploymentFormHeader } from 'features/surveys/telemetry/deployments/components/form/DeploymentFormHeader'; +import { Formik, FormikProps } from 'formik'; +import { APIError } from 'hooks/api/useAxios'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useProjectContext, useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { SKIP_CONFIRMATION_DIALOG, useUnsavedChangesDialog } from 'hooks/useUnsavedChangesDialog'; +import { ICreateAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useEffect, useRef, useState } from 'react'; +import { Prompt, useHistory, useParams } from 'react-router'; + +/** + * Renders the Edit Deployment page. + * + * @return {*} + */ +export const EditDeploymentPage = () => { + const history = useHistory(); + + const biohubApi = useBiohubApi(); + + const dialogContext = useDialogContext(); + const projectContext = useProjectContext(); + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const formikRef = useRef>(null); + const [isSubmitting, setIsSubmitting] = useState(false); + + const { locationChangeInterceptor } = useUnsavedChangesDialog(); + + const urlParams: Record = useParams(); + const deploymentId: number | undefined = Number(urlParams['deployment_id']); + + const critters = surveyContext.critterDataLoader.data ?? []; + + const deploymentDataLoader = useDataLoader(biohubApi.survey.getDeploymentById); + const deployment = deploymentDataLoader.data; + + useEffect(() => { + deploymentDataLoader.load(surveyContext.projectId, surveyContext.surveyId, deploymentId); + }, [deploymentDataLoader, deploymentId, surveyContext.projectId, surveyContext.surveyId]); + + if (!surveyContext.surveyDataLoader.data || !projectContext.projectDataLoader.data || !deployment) { + return ; + } + + const deploymentFormInitialValues = { + critter_id: deployment.critter_id, + device_id: String(deployment.device_id), + frequency: deployment.frequency, + frequency_unit: deployment.frequency_unit, + device_model: deployment.device_model, + device_make: deployment.device_make, + critterbase_start_capture_id: deployment.critterbase_start_capture_id, + critterbase_end_capture_id: deployment.critterbase_end_capture_id, + critterbase_end_mortality_id: deployment.critterbase_end_mortality_id, + attachment_end_date: deployment.attachment_end_date, + attachment_end_time: deployment.attachment_end_time + }; + + const handleSubmit = async (values: ICreateAnimalDeployment) => { + setIsSubmitting(true); + + try { + const critter_id = Number(critters?.find((animal) => animal.critter_id === values.critter_id)?.critter_id); + + if (!critter_id) { + throw new Error('Invalid critter data'); + } + + await biohubApi.survey.updateDeployment(surveyContext.projectId, surveyContext.surveyId, deploymentId, { + critter_id: values.critter_id, + device_id: Number(values.device_id), + device_make: values.device_make, + frequency: values.frequency, + frequency_unit: values.frequency_unit, + device_model: values.device_model, + critterbase_start_capture_id: values.critterbase_start_capture_id, + critterbase_end_capture_id: values.critterbase_end_capture_id, + critterbase_end_mortality_id: values.critterbase_end_mortality_id, + attachment_end_date: values.attachment_end_date, + attachment_end_time: values.attachment_end_time + }); + + telemetryDataContext.deploymentsDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); + + // edit complete, navigate back to telemetry page + history.push( + `/admin/projects/${surveyContext.projectId}/surveys/${surveyContext.surveyId}/telemetry`, + SKIP_CONFIRMATION_DIALOG + ); + } catch (error) { + dialogContext.setErrorDialog({ + dialogTitle: EditAnimalDeploymentI18N.createErrorTitle, + dialogText: EditAnimalDeploymentI18N.createErrorText, + dialogError: (error as APIError).message, + dialogErrorDetails: (error as APIError)?.errors, + onClose: () => { + dialogContext.setErrorDialog({ open: false }); + }, + onOk: () => { + dialogContext.setErrorDialog({ open: false }); + }, + open: true + }); + + setIsSubmitting(false); + } + }; + + return ( + <> + + + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysButton.tsx b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysButton.tsx new file mode 100644 index 0000000000..556fa99888 --- /dev/null +++ b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysButton.tsx @@ -0,0 +1,36 @@ +import { mdiKeyWireless } from '@mdi/js'; +import Icon from '@mdi/react'; +import IconButton from '@mui/material/IconButton'; +import { TelemetryDeviceKeysDialog } from 'features/surveys/telemetry/device-keys/TelemetryDeviceKeysDialog'; +import { useState } from 'react'; + +export interface ITelemetryDeviceKeysButtonProps { + /** + * Controls the disabled state of the button. + * + * @type {boolean} + * @memberof ITelemetryDeviceKeysButtonProps + */ + disabled?: boolean; +} + +export const TelemetryDeviceKeysButton = (props: ITelemetryDeviceKeysButtonProps) => { + const { disabled } = props; + + const [open, setOpen] = useState(false); + + return ( + <> + { + setOpen(false); + }} + /> + + setOpen(true)} disabled={disabled} aria-label="Manage telemetry device keys"> + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysDialog.tsx b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysDialog.tsx new file mode 100644 index 0000000000..ab379def70 --- /dev/null +++ b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysDialog.tsx @@ -0,0 +1,146 @@ +import LoadingButton from '@mui/lab/LoadingButton'; +import Box from '@mui/material/Box'; +import Dialog from '@mui/material/Dialog'; +import DialogActions from '@mui/material/DialogActions'; +import DialogContent from '@mui/material/DialogContent'; +import DialogTitle from '@mui/material/DialogTitle'; +import useTheme from '@mui/material/styles/useTheme'; +import Typography from '@mui/material/Typography'; +import useMediaQuery from '@mui/material/useMediaQuery'; +import { AxiosProgressEvent, CancelTokenSource } from 'axios'; +import FileUpload from 'components/file-upload/FileUpload'; +import { AttachmentTypeFileExtensions } from 'constants/attachments'; +import { TelemetryDeviceKeysList } from 'features/surveys/telemetry/device-keys/TelemetryDeviceKeysList'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import useIsMounted from 'hooks/useIsMounted'; +import { useEffect } from 'react'; + +export interface ITelemetryDeviceKeysDialogProps { + /** + * Set to `true` to open the dialog, `false` to close the dialog. + */ + open: boolean; + /** + * Callback fired when the dialog is closed. + */ + onClose?: () => void; +} + +/** + * A dialog for managing telemetry device keys. + * + * @param {ITelemetryDeviceKeysDialogProps} props + * @return {*} + */ +export const TelemetryDeviceKeysDialog = (props: ITelemetryDeviceKeysDialogProps) => { + const { open, onClose } = props; + + const theme = useTheme(); + const fullScreen = useMediaQuery(theme.breakpoints.down('sm')); + + const surveyContext = useSurveyContext(); + const biohubApi = useBiohubApi(); + + const isMounted = useIsMounted(); + + const uploadHandler = async ( + file: File, + cancelToken: CancelTokenSource, + handleFileUploadProgress: (progressEvent: AxiosProgressEvent) => void + ) => { + return biohubApi.telemetry + .uploadTelemetryDeviceCredentialFile( + surveyContext.projectId, + surveyContext.surveyId, + file, + cancelToken, + handleFileUploadProgress + ) + .then(() => { + if (!isMounted()) { + return; + } + + telemetryDeviceKeyFileDataLoader.refresh(); + }) + .catch((error) => { + if (!isMounted()) { + return; + } + + throw error; + }) + .finally(() => { + if (!isMounted()) { + return; + } + }); + }; + + const acceptedFileExtensions = Array.from( + new Set([...AttachmentTypeFileExtensions.KEYX, ...AttachmentTypeFileExtensions.CFG]) + ); + + const telemetryDeviceKeyFileDataLoader = useDataLoader(() => + biohubApi.telemetry.getTelemetryDeviceKeyFiles(surveyContext.projectId, surveyContext.surveyId) + ); + + useEffect(() => { + if (!open) { + // If the dialog is not open, do not load the data + return; + } + + telemetryDeviceKeyFileDataLoader.load(); + }, [open, telemetryDeviceKeyFileDataLoader]); + + if (!open) { + return <>; + } + + return ( + + + Manage Device Keys + + + + Device keys allow telemetry data from Vectronic to be automatically loaded into your Survey. + + Vectronic device keys are .keyx files. + Lotek device keys are .cfg files. + + Telemetry data from other manufacturers must be imported manually. + + + + + + + + + + Close + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysList.tsx b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysList.tsx new file mode 100644 index 0000000000..4acb190112 --- /dev/null +++ b/app/src/features/surveys/telemetry/device-keys/TelemetryDeviceKeysList.tsx @@ -0,0 +1,156 @@ +import { mdiArrowTopRight } from '@mdi/js'; +import Box from '@mui/material/Box'; +import { grey } from '@mui/material/colors'; +import Link from '@mui/material/Link'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import { GridColDef } from '@mui/x-data-grid'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonList } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import { TelemetryDeviceKeyFileI18N } from 'constants/i18n'; +import { APIError } from 'hooks/api/useAxios'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useSurveyContext } from 'hooks/useContext'; +import { TelemetryDeviceKeyFile } from 'interfaces/useTelemetryApi.interface'; +import { getFormattedDate } from 'utils/Utils'; + +export interface ITelemetryDeviceKeysListProps { + isLoading?: boolean; + telementryCredentialAttachments: TelemetryDeviceKeyFile[]; +} + +export const TelemetryDeviceKeysList = (props: ITelemetryDeviceKeysListProps) => { + const { isLoading, telementryCredentialAttachments } = props; + + const dialogContext = useDialogContext(); + const surveyContext = useSurveyContext(); + + const biohubApi = useBiohubApi(); + + const handleDownload = async (attachment: TelemetryDeviceKeyFile) => { + try { + const response = await biohubApi.survey.getSurveyAttachmentSignedURL( + surveyContext.projectId, + surveyContext.surveyId, + attachment.survey_telemetry_credential_attachment_id, + attachment.file_type + ); + + if (!response) { + return; + } + + window.open(response); + } catch (error) { + const apiError = error as APIError; + // Show error dialog + dialogContext.setErrorDialog({ + open: true, + dialogTitle: TelemetryDeviceKeyFileI18N.downloadErrorTitle, + dialogText: TelemetryDeviceKeyFileI18N.downloadErrorText, + dialogErrorDetails: apiError.errors, + onOk: () => dialogContext.setErrorDialog({ open: false }), + onClose: () => dialogContext.setErrorDialog({ open: false }) + }); + } + }; + + const rows = telementryCredentialAttachments; + + // Define the columns for the DataGrid + const columns: GridColDef[] = [ + { + field: 'survey_telemetry_credential_attachment_id', + headerName: 'ID', + width: 70, + minWidth: 70, + renderHeader: () => ( + + ID + + ), + renderCell: (params) => ( + + {params.row.survey_telemetry_credential_attachment_id} + + ) + }, + { + field: 'file_name', + headerName: 'Name', + flex: 1, + disableColumnMenu: true, + renderCell: (params) => { + return ( + + handleDownload(params.row)} tabIndex={0}> + {params.value} + + + ); + } + }, + { + field: 'last_modified', + headerName: 'Last Modified', + flex: 1, + disableColumnMenu: true, + renderHeader: () => ( + + Last Modified + + ), + renderCell: (params) => ( + + {getFormattedDate(DATE_FORMAT.ShortMediumDateTimeFormat, params.row.update_date ?? params.row.create_date)} + + ) + } + ]; + + return ( + } + isLoadingFallbackDelay={100} + hasNoData={false} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + row.survey_telemetry_credential_attachment_id} + columns={columns} + pageSizeOptions={[5]} + rowSelection={false} + checkboxSelection={false} + hideFooter + disableRowSelectionOnClick + disableColumnSelector + disableColumnFilter + disableColumnMenu + sortingOrder={['asc', 'desc']} + data-testid="funding-source-table" + /> + + + ); +}; diff --git a/app/src/features/surveys/telemetry/list/SurveyDeploymentList.tsx b/app/src/features/surveys/telemetry/list/SurveyDeploymentList.tsx new file mode 100644 index 0000000000..74478d3932 --- /dev/null +++ b/app/src/features/surveys/telemetry/list/SurveyDeploymentList.tsx @@ -0,0 +1,335 @@ +import { mdiDotsVertical, mdiPencilOutline, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import Checkbox from '@mui/material/Checkbox'; +import grey from '@mui/material/colors/grey'; +import Divider from '@mui/material/Divider'; +import FormControlLabel from '@mui/material/FormControlLabel'; +import FormGroup from '@mui/material/FormGroup'; +import IconButton from '@mui/material/IconButton'; +import ListItemIcon from '@mui/material/ListItemIcon'; +import Menu, { MenuProps } from '@mui/material/Menu'; +import MenuItem from '@mui/material/MenuItem'; +import Paper from '@mui/material/Paper'; +import Stack from '@mui/material/Stack'; +import Toolbar from '@mui/material/Toolbar'; +import Typography from '@mui/material/Typography'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonList } from 'components/loading/SkeletonLoaders'; +import { TelemetryDeviceKeysButton } from 'features/surveys/telemetry/device-keys/TelemetryDeviceKeysButton'; +import { SurveyDeploymentListItem } from 'features/surveys/telemetry/list/SurveyDeploymentListItem'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useDialogContext, useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { useEffect, useState } from 'react'; +import { Link as RouterLink } from 'react-router-dom'; + +/** + * Renders a list of all deployments in the survey + * + * @returns {*} + */ +export const SurveyDeploymentList = () => { + const dialogContext = useDialogContext(); + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const biohubApi = useBiohubApi(); + + const [anchorEl, setAnchorEl] = useState(null); + + const [checkboxSelectedIds, setCheckboxSelectedIds] = useState([]); + const [selectedDeploymentId, setSelectedDeploymentId] = useState(); + + const frequencyUnitDataLoader = useDataLoader(() => biohubApi.telemetry.getCodeValues('frequency_unit')); + const deviceMakesDataLoader = useDataLoader(() => biohubApi.telemetry.getCodeValues('device_make')); + + const deploymentsDataLoader = telemetryDataContext.deploymentsDataLoader; + const deployments = deploymentsDataLoader.data ?? []; + const deploymentCount = deployments?.length ?? 0; + + useEffect(() => { + frequencyUnitDataLoader.load(); + deviceMakesDataLoader.load(); + deploymentsDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + }, [ + deploymentsDataLoader, + deviceMakesDataLoader, + frequencyUnitDataLoader, + surveyContext.projectId, + surveyContext.surveyId + ]); + + /** + * Callback for when a deployment action menu is clicked. + * + * @param {React.MouseEvent} event + * @param {number} deploymentId + */ + const handledDeploymentMenuClick = (event: React.MouseEvent, deploymentId: number) => { + setAnchorEl(event.currentTarget); + setSelectedDeploymentId(deploymentId); + }; + + /** + * Callback for when a checkbox is toggled. + * + * @param {number} deploymentId + */ + const handleCheckboxChange = (deploymentId: number) => { + setCheckboxSelectedIds((prev) => { + if (prev.includes(deploymentId)) { + return prev.filter((item) => item !== deploymentId); + } else { + return [...prev, deploymentId]; + } + }); + }; + + /** + * Callback for when the delete deployment action is confirmed. + */ + const handleDeleteDeployment = async () => { + await biohubApi.survey + .deleteDeployment(surveyContext.projectId, surveyContext.surveyId, Number(selectedDeploymentId)) + .then(() => { + dialogContext.setYesNoDialog({ open: false }); + setAnchorEl(null); + deploymentsDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId); + }) + .catch((error: any) => { + dialogContext.setYesNoDialog({ open: false }); + setAnchorEl(null); + dialogContext.setSnackbar({ + snackbarMessage: ( + <> + + Error Deleting Deployment + + + {String(error)} + + + ), + open: true + }); + }); + }; + + /** + * Display the delete deployment confirmation dialog. + */ + const renderDeleteDeploymentDialog = () => { + dialogContext.setYesNoDialog({ + dialogTitle: 'Delete Deployment?', + dialogContent: ( + + Are you sure you want to delete this deployment? All telemetry data from the deployment will also be + permanently deleted. + + ), + yesButtonLabel: 'Delete Deployment', + noButtonLabel: 'Cancel', + yesButtonProps: { color: 'error' }, + onClose: () => { + dialogContext.setYesNoDialog({ open: false }); + }, + onNo: () => { + dialogContext.setYesNoDialog({ open: false }); + }, + open: true, + onYes: () => { + handleDeleteDeployment(); + } + }); + }; + + return ( + <> + { + setAnchorEl(null); + }} + anchorEl={anchorEl} + anchorOrigin={{ + vertical: 'top', + horizontal: 'right' + }} + transformOrigin={{ + vertical: 'top', + horizontal: 'right' + }}> + setAnchorEl(null)}> + + + + Edit Details + + { + renderDeleteDeploymentDialog(); + setAnchorEl(null); + }}> + + + + Delete + + + + + + + Deployments ‌ + + ({deploymentCount}) + + + + + + + + + + + + + + + } + isLoadingFallbackDelay={100} + hasNoData={!deploymentCount} + hasNoDataFallback={ + + No Deployments + + } + hasNoDataFallbackDelay={100}> + + + + + Select All + + } + control={ + 0 && checkboxSelectedIds.length === deploymentCount} + indeterminate={ + checkboxSelectedIds.length >= 1 && checkboxSelectedIds.length < deploymentCount + } + onClick={() => { + if (checkboxSelectedIds.length === deploymentCount) { + setCheckboxSelectedIds([]); + return; + } + + const deploymentIds = deployments.map((deployment) => deployment.deployment_id); + setCheckboxSelectedIds(deploymentIds); + }} + inputProps={{ 'aria-label': 'controlled' }} + /> + } + /> + + + + + {deployments.map((deployment) => { + const animal = surveyContext.critterDataLoader.data?.find( + (animal) => animal.critterbase_critter_id === deployment.critterbase_critter_id + ); + + if (!animal) { + return null; + } + + // Replace the deployment frequency_unit IDs with their human readable codes + const hydratedDeployment = { + ...deployment, + frequency_unit: + frequencyUnitDataLoader.data?.find( + (frequencyUnitOption) => frequencyUnitOption.id === deployment.frequency_unit + )?.code ?? null + }; + + return ( + + ); + })} + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/list/SurveyDeploymentListItem.tsx b/app/src/features/surveys/telemetry/list/SurveyDeploymentListItem.tsx new file mode 100644 index 0000000000..fe139225e9 --- /dev/null +++ b/app/src/features/surveys/telemetry/list/SurveyDeploymentListItem.tsx @@ -0,0 +1,154 @@ +import { mdiChevronDown, mdiDotsVertical } from '@mdi/js'; +import Icon from '@mdi/react'; +import Accordion from '@mui/material/Accordion'; +import AccordionDetails from '@mui/material/AccordionDetails'; +import AccordionSummary from '@mui/material/AccordionSummary'; +import Box from '@mui/material/Box'; +import Checkbox from '@mui/material/Checkbox'; +import green from '@mui/material/colors/green'; +import grey from '@mui/material/colors/grey'; +import IconButton from '@mui/material/IconButton'; +import List from '@mui/material/List'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; +import { PulsatingDot } from 'components/misc/PulsatingDot'; +import dayjs from 'dayjs'; +import { SurveyDeploymentListItemDetails } from 'features/surveys/telemetry/list/SurveyDeploymentListItemDetails'; +import { ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; +import { IAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; + +export interface ISurveyDeploymentListItemProps { + animal: ICritterSimpleResponse; + deployment: Omit & { frequency_unit: string | null }; + isChecked: boolean; + handleDeploymentMenuClick: (event: React.MouseEvent, deploymentId: number) => void; + handleCheckboxChange: (deploymentId: number) => void; +} + +/** + * Renders a list item for a single deployment record. + * + * @param {ISurveyDeploymentListItemProps} props + * @return {*} + */ +export const SurveyDeploymentListItem = (props: ISurveyDeploymentListItemProps) => { + const { animal, deployment, isChecked, handleDeploymentMenuClick, handleCheckboxChange } = props; + + const isDeploymentOver = + deployment.critterbase_end_mortality_id || + deployment.critterbase_end_capture_id || + dayjs(`${deployment.attachment_end_date} ${deployment.attachment_end_time}`).isBefore(dayjs()); + + return ( + + + } + aria-controls="panel1bh-content" + sx={{ + flex: '1 1 auto', + py: 0, + pr: 7, + pl: 0, + height: 75, + overflow: 'hidden', + '& .MuiAccordionSummary-content': { + flex: '1 1 auto', + py: 0, + pl: 0, + overflow: 'hidden', + whiteSpace: 'nowrap' + } + }}> + + { + event.stopPropagation(); + handleCheckboxChange(deployment.deployment_id); + }} + inputProps={{ 'aria-label': 'controlled' }} + /> + + + + {deployment.device_id} + + + {deployment.frequency} {deployment.frequency_unit} + + + + {animal.animal_id} + + + + + + {!isDeploymentOver && ( + + + + )} + + ) => + handleDeploymentMenuClick(event, deployment.deployment_id) + } + aria-label="deployment-settings"> + + + + + + + + + + ); +}; diff --git a/app/src/features/surveys/telemetry/list/SurveyDeploymentListItemDetails.tsx b/app/src/features/surveys/telemetry/list/SurveyDeploymentListItemDetails.tsx new file mode 100644 index 0000000000..7c1d130914 --- /dev/null +++ b/app/src/features/surveys/telemetry/list/SurveyDeploymentListItemDetails.tsx @@ -0,0 +1,92 @@ +import { mdiArrowRightThin } from '@mdi/js'; +import { Icon } from '@mdi/react'; +import Box from '@mui/material/Box'; +import grey from '@mui/material/colors/grey'; +import Skeleton from '@mui/material/Skeleton'; +import Typography from '@mui/material/Typography'; +import { DATE_FORMAT, TIME_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { IAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; +import { useEffect } from 'react'; + +interface ISurveyDeploymentListItemDetailsProps { + deployment: Omit & { frequency_unit: string | null }; +} + +/** + * Renders information about a single telemetry deployment such as start and end dates + * + * @param props {ISurveyDeploymentListItemDetailsProps} + * @returns + */ +export const SurveyDeploymentListItemDetails = (props: ISurveyDeploymentListItemDetailsProps) => { + const { deployment } = props; + const critterbaseApi = useCritterbaseApi(); + + // TODO: Make these API calls in the parent as once call, then pass data as props + const startCaptureDataLoader = useDataLoader((captureId: string) => critterbaseApi.capture.getCapture(captureId)); + const endCaptureDataLoader = useDataLoader((captureId: string) => critterbaseApi.capture.getCapture(captureId)); + const endMortalityDataLoader = useDataLoader((mortalityId: string) => + critterbaseApi.mortality.getMortality(mortalityId) + ); + + useEffect(() => { + startCaptureDataLoader.load(deployment.critterbase_start_capture_id); + if (deployment.critterbase_end_capture_id) { + endCaptureDataLoader.load(deployment.critterbase_end_capture_id); + } + if (deployment.critterbase_end_mortality_id) { + endMortalityDataLoader.load(deployment.critterbase_end_mortality_id); + } + }, [startCaptureDataLoader, endCaptureDataLoader, endMortalityDataLoader, deployment]); + + const endCapture = endCaptureDataLoader.data; + const endMortality = endMortalityDataLoader.data; + + const endDate = endCapture?.capture_date || endMortality?.mortality_timestamp || deployment.attachment_end_date; + + const endDateFormatted = endDate ? dayjs(endDate).format(DATE_FORMAT.MediumDateFormat) : null; + + if (!startCaptureDataLoader.data) { + return ; + } + + const startDate = dayjs(startCaptureDataLoader.data.capture_date).format(DATE_FORMAT.MediumDateFormat); + const startTime = startCaptureDataLoader.data.capture_time; + + const endTime = + endCapture?.capture_time || + (endMortality?.mortality_timestamp && + dayjs(endMortality?.mortality_timestamp).format(TIME_FORMAT.LongTimeFormat24Hour)) || + deployment.attachment_end_time; + + return ( + + + + {startDate} + + + {startTime} + + + {endDateFormatted && ( + <> + + + + + + {endDateFormatted} + + + {endTime} + + + + )} + + ); +}; diff --git a/app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTable.tsx b/app/src/features/surveys/telemetry/table/TelemetryTable.tsx similarity index 67% rename from app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTable.tsx rename to app/src/features/surveys/telemetry/table/TelemetryTable.tsx index 3340509d4f..b01def63f0 100644 --- a/app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTable.tsx +++ b/app/src/features/surveys/telemetry/table/TelemetryTable.tsx @@ -1,18 +1,23 @@ import { cyan, grey } from '@mui/material/colors'; -import { DataGrid, GridColDef, GridRowParams } from '@mui/x-data-grid'; +import { DataGrid, GridColDef } from '@mui/x-data-grid'; import { - GenericActionsColDef, GenericDateColDef, GenericLatitudeColDef, GenericLongitudeColDef, GenericTimeColDef } from 'components/data-grid/GenericGridColumnDefinitions'; import { SkeletonTable } from 'components/loading/SkeletonLoaders'; -import { SurveyContext } from 'contexts/surveyContext'; import { IManualTelemetryTableRow } from 'contexts/telemetryTableContext'; -import { useTelemetryTableContext } from 'hooks/useContext'; -import { useCallback, useContext } from 'react'; -import { DeploymentColDef, TelemetryTypeColDef } from './utils/GridColumnDefinitions'; +import { + DeploymentColDef, + DeviceColDef, + TelemetryTypeColDef +} from 'features/surveys/telemetry/table/utils/GridColumnDefinitions'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext, useTelemetryDataContext, useTelemetryTableContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { IAnimalDeploymentWithCritter } from 'interfaces/useSurveyApi.interface'; +import { useEffect, useMemo } from 'react'; const MANUAL_TELEMETRY_TYPE = 'MANUAL'; @@ -20,28 +25,56 @@ interface IManualTelemetryTableProps { isLoading: boolean; } -const ManualTelemetryTable = (props: IManualTelemetryTableProps) => { +export const TelemetryTable = (props: IManualTelemetryTableProps) => { + const biohubApi = useBiohubApi(); + + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); const telemetryTableContext = useTelemetryTableContext(); - const surveyContext = useContext(SurveyContext); - const { critterDeployments } = surveyContext; + const deploymentDataLoader = telemetryDataContext.deploymentsDataLoader; + const critterDataLoader = useDataLoader(biohubApi.survey.getSurveyCritters); - // Disable the delete action when record is 'Manual' telemetry or saving - const actionsDisabled = useCallback( - (params: GridRowParams) => { - return telemetryTableContext.isSaving || params.row.telemetry_type !== MANUAL_TELEMETRY_TYPE; - }, - [telemetryTableContext.isSaving] - ); + useEffect(() => { + deploymentDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + critterDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + }, [critterDataLoader, deploymentDataLoader, surveyContext.projectId, surveyContext.surveyId]); + + /** + * Merges critters with associated deployments + * + * @returns {ICritterDeployment[]} Critter deployments + */ + const critterDeployments: IAnimalDeploymentWithCritter[] = useMemo(() => { + const critterDeployments: IAnimalDeploymentWithCritter[] = []; + const critters = critterDataLoader.data ?? []; + const deployments = deploymentDataLoader.data ?? []; + + if (!critters.length || !deployments.length) { + return []; + } + + const critterMap = new Map(critters.map((critter) => [critter.critterbase_critter_id, critter])); + + deployments.forEach((deployment) => { + const critter = critterMap.get(String(deployment.critterbase_critter_id)); + if (critter) { + critterDeployments.push({ critter, deployment }); + } + }); + + return critterDeployments; + }, [critterDataLoader.data, deploymentDataLoader.data]); const columns: GridColDef[] = [ DeploymentColDef({ critterDeployments, hasError: telemetryTableContext.hasError }), - TelemetryTypeColDef(), + // TODO: Show animal nickname as a column + DeviceColDef({ critterDeployments }), GenericDateColDef({ field: 'date', headerName: 'Date', hasError: telemetryTableContext.hasError }), GenericTimeColDef({ field: 'time', headerName: 'Time', hasError: telemetryTableContext.hasError }), GenericLatitudeColDef({ field: 'latitude', headerName: 'Latitude', hasError: telemetryTableContext.hasError }), GenericLongitudeColDef({ field: 'longitude', headerName: 'Longitude', hasError: telemetryTableContext.hasError }), - GenericActionsColDef({ disabled: actionsDisabled, onDelete: telemetryTableContext.deleteRecords }) + TelemetryTypeColDef() ]; return ( @@ -76,6 +109,12 @@ const ManualTelemetryTable = (props: IManualTelemetryTableProps) => { noRowsLabel: 'No Records' }} getRowHeight={() => 'auto'} + initialState={{ + pagination: { + paginationModel: { page: 0, pageSize: 25 } + } + }} + pageSizeOptions={[25, 50, 100]} slots={{ loadingOverlay: SkeletonTable }} @@ -164,5 +203,3 @@ const ManualTelemetryTable = (props: IManualTelemetryTableProps) => { /> ); }; - -export default ManualTelemetryTable; diff --git a/app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTableContainer.tsx b/app/src/features/surveys/telemetry/table/TelemetryTableContainer.tsx similarity index 96% rename from app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTableContainer.tsx rename to app/src/features/surveys/telemetry/table/TelemetryTableContainer.tsx index 6487d76000..1115fbf82e 100644 --- a/app/src/features/surveys/telemetry/telemetry-table/ManualTelemetryTableContainer.tsx +++ b/app/src/features/surveys/telemetry/table/TelemetryTableContainer.tsx @@ -22,14 +22,14 @@ import { UploadFileStatus } from 'components/file-upload/FileUploadItem'; import { TelemetryTableI18N } from 'constants/i18n'; import { DialogContext, ISnackbarProps } from 'contexts/dialogContext'; import { SurveyContext } from 'contexts/surveyContext'; +import { TelemetryTable } from 'features/surveys/telemetry/table/TelemetryTable'; +import { useBiohubApi } from 'hooks/useBioHubApi'; import { useTelemetryTableContext } from 'hooks/useContext'; -import { useTelemetryApi } from 'hooks/useTelemetryApi'; import { useContext, useDeferredValue, useState } from 'react'; import { pluralize as p } from 'utils/Utils'; -import ManualTelemetryTable from './ManualTelemetryTable'; -const ManualTelemetryTableContainer = () => { - const telemetryApi = useTelemetryApi(); +export const TelemetryTableContainer = () => { + const biohubApi = useBiohubApi(); const dialogContext = useContext(DialogContext); const telemetryTableContext = useTelemetryTableContext(); @@ -58,10 +58,10 @@ const ManualTelemetryTableContainer = () => { }; const handleFileImport = async (file: File) => { - telemetryApi.uploadCsvForImport(surveyContext.projectId, surveyContext.surveyId, file).then((response) => { + biohubApi.telemetry.uploadCsvForImport(surveyContext.projectId, surveyContext.surveyId, file).then((response) => { setShowImportDialog(false); setProcessingRecords(true); - telemetryApi + biohubApi.telemetry .processTelemetryCsvSubmission(response.submission_id) .then(() => { showSnackBar({ @@ -276,12 +276,10 @@ const ManualTelemetryTableContainer = () => { - + ); }; - -export default ManualTelemetryTableContainer; diff --git a/app/src/features/surveys/telemetry/telemetry-table/utils/GridColumnDefinitions.tsx b/app/src/features/surveys/telemetry/table/utils/GridColumnDefinitions.tsx similarity index 69% rename from app/src/features/surveys/telemetry/telemetry-table/utils/GridColumnDefinitions.tsx rename to app/src/features/surveys/telemetry/table/utils/GridColumnDefinitions.tsx index 288ed17557..a18885cc98 100644 --- a/app/src/features/surveys/telemetry/telemetry-table/utils/GridColumnDefinitions.tsx +++ b/app/src/features/surveys/telemetry/table/utils/GridColumnDefinitions.tsx @@ -1,9 +1,10 @@ +import { Typography } from '@mui/material'; import { GridCellParams, GridColDef } from '@mui/x-data-grid'; import AutocompleteDataGridEditCell from 'components/data-grid/autocomplete/AutocompleteDataGridEditCell'; import AutocompleteDataGridViewCell from 'components/data-grid/autocomplete/AutocompleteDataGridViewCell'; import { IManualTelemetryTableRow } from 'contexts/telemetryTableContext'; +import { IAnimalDeploymentWithCritter } from 'interfaces/useSurveyApi.interface'; import { capitalize } from 'lodash-es'; -import { ICritterDeployment } from '../../ManualTelemetryList'; export const TelemetryTypeColDef = (): GridColDef => { return { @@ -21,7 +22,7 @@ export const TelemetryTypeColDef = (): GridColDef => { }; export const DeploymentColDef = (props: { - critterDeployments: ICritterDeployment[]; + critterDeployments: IAnimalDeploymentWithCritter[]; hasError: (params: GridCellParams) => boolean; }): GridColDef => { return { @@ -42,7 +43,7 @@ export const DeploymentColDef = (props: { options={props.critterDeployments.map((item) => { return { label: `${item.critter.animal_id}: ${item.deployment.device_id}`, - value: item.deployment.deployment_id + value: item.deployment.bctw_deployment_id }; })} error={error} @@ -57,7 +58,7 @@ export const DeploymentColDef = (props: { dataGridProps={params} options={props.critterDeployments.map((item) => ({ label: `${item.critter.animal_id}: ${item.deployment.device_id}`, - value: item.deployment.deployment_id + value: item.deployment.bctw_deployment_id }))} error={error} /> @@ -65,3 +66,26 @@ export const DeploymentColDef = (props: { } }; }; + +export const DeviceColDef = (props: { + critterDeployments: IAnimalDeploymentWithCritter[]; +}): GridColDef => { + return { + field: 'device_id', + headerName: 'Device', + hideable: true, + minWidth: 120, + disableColumnMenu: true, + headerAlign: 'left', + align: 'left', + renderCell: (params) => ( + + { + props.critterDeployments.find( + (deployment) => deployment.deployment.bctw_deployment_id === params.row.deployment_id + )?.deployment.device_id + } + + ) + }; +}; diff --git a/app/src/features/surveys/view/SurveyAnimals.test.tsx b/app/src/features/surveys/view/SurveyAnimals.test.tsx deleted file mode 100644 index b72538159e..0000000000 --- a/app/src/features/surveys/view/SurveyAnimals.test.tsx +++ /dev/null @@ -1,145 +0,0 @@ -import { AuthStateContext } from 'contexts/authStateContext'; -import { IProjectAuthStateContext, ProjectAuthStateContext } from 'contexts/projectAuthStateContext'; -import { IProjectContext, ProjectContext } from 'contexts/projectContext'; -import { ISurveyContext, SurveyContext } from 'contexts/surveyContext'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { DataLoader } from 'hooks/useDataLoader'; -import { useTelemetryApi } from 'hooks/useTelemetryApi'; -import { BrowserRouter } from 'react-router-dom'; -import { getMockAuthState, SystemAdminAuthState } from 'test-helpers/auth-helpers'; -import { cleanup, fireEvent, render, waitFor } from 'test-helpers/test-utils'; -import SurveyAnimals from './SurveyAnimals'; - -jest.mock('../../../hooks/useBioHubApi'); -jest.mock('../../../hooks/useTelemetryApi'); -const mockBiohubApi = useBiohubApi as jest.Mock; -const mockTelemetryApi = useTelemetryApi as jest.Mock; - -const mockUseBiohub = { - survey: { - getSurveyCritters: jest.fn(), - getDeploymentsInSurvey: jest.fn(), - createCritterAndAddToSurvey: jest.fn(), - addDeployment: jest.fn() - } -}; - -const mockUseTelemetry = { - devices: { - getDeviceDetails: jest.fn() - } -}; - -describe('SurveyAnimals', () => { - const mockSurveyContext: ISurveyContext = { - artifactDataLoader: { - data: null, - load: jest.fn() - } as unknown as DataLoader, - surveyId: 1, - projectId: 1, - surveyDataLoader: { - data: { surveyData: { survey_details: { survey_name: 'name' } } }, - load: jest.fn() - } as unknown as DataLoader - } as unknown as ISurveyContext; - - const mockProjectAuthStateContext: IProjectAuthStateContext = { - getProjectParticipant: () => null, - hasProjectRole: () => true, - hasProjectPermission: () => true, - hasSystemRole: () => true, - getProjectId: () => 1, - hasLoadedParticipantInfo: true - }; - - const mockProjectContext: IProjectContext = { - artifactDataLoader: { - data: null, - load: jest.fn() - } as unknown as DataLoader, - projectId: 1, - projectDataLoader: { - data: { projectData: { project: { project_name: 'name' } } }, - load: jest.fn() - } as unknown as DataLoader - } as unknown as IProjectContext; - - const authState = getMockAuthState({ base: SystemAdminAuthState }); - - beforeEach(() => { - mockBiohubApi.mockImplementation(() => mockUseBiohub); - mockUseBiohub.survey.getDeploymentsInSurvey.mockClear(); - mockUseBiohub.survey.getSurveyCritters.mockClear(); - mockUseBiohub.survey.createCritterAndAddToSurvey.mockClear(); - mockUseBiohub.survey.addDeployment.mockClear(); - - mockTelemetryApi.mockImplementation(() => mockUseTelemetry); - mockUseTelemetry.devices.getDeviceDetails.mockClear(); - }); - - afterEach(() => { - cleanup(); - }); - - it('renders correctly with no animals', async () => { - const { getByText } = render( - - - - - - - - - - - - ); - - await waitFor(() => { - expect(getByText('No Animals')).toBeInTheDocument(); - }); - }); - - it('renders correctly with animals', async () => { - mockUseBiohub.survey.getSurveyCritters.mockResolvedValueOnce([ - { - critter_id: 'critter_uuid', - survey_critter_id: 1, - animal_id: 'animal_alias', - taxon: 'a', - created_at: 'a', - wlh_id: '123-45' - } - ]); - - mockUseBiohub.survey.getDeploymentsInSurvey.mockResolvedValue([{ critter_id: 'critter_uuid', device_id: 123 }]); - mockUseBiohub.survey.createCritterAndAddToSurvey.mockResolvedValue({}); - mockUseTelemetry.devices.getDeviceDetails.mockResolvedValue({ device: undefined, deployments: [] }); - const { getByText, getByTestId } = render( - - - - - - - - - - - - ); - - await waitFor(() => { - expect(getByText('123-45')).toBeInTheDocument(); - expect(getByTestId('survey-animal-table')).toBeInTheDocument(); - fireEvent.click(getByTestId('animal actions')); - fireEvent.click(getByTestId('animal-table-row-edit-critter')); - }); - await waitFor(() => { - expect(getByText('Manage Animals')).toBeInTheDocument(); - expect(getByText('animal_alias')).toBeInTheDocument(); - }); - }); -}); diff --git a/app/src/features/surveys/view/SurveyAnimals.tsx b/app/src/features/surveys/view/SurveyAnimals.tsx deleted file mode 100644 index fe7e168078..0000000000 --- a/app/src/features/surveys/view/SurveyAnimals.tsx +++ /dev/null @@ -1,184 +0,0 @@ -import { mdiCog } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Divider from '@mui/material/Divider'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import ComponentDialog from 'components/dialog/ComponentDialog'; -import YesNoDialog from 'components/dialog/YesNoDialog'; -import { ProjectRoleGuard } from 'components/security/Guards'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; -import { DialogContext } from 'contexts/dialogContext'; -import { SurveyContext } from 'contexts/surveyContext'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import useDataLoader from 'hooks/useDataLoader'; -import React, { useContext, useEffect, useMemo, useState } from 'react'; -import { Link as RouterLink, useHistory } from 'react-router-dom'; -import NoSurveySectionData from '../components/NoSurveySectionData'; -import { SurveyAnimalsTable } from './survey-animals/SurveyAnimalsTable'; -import TelemetryMap from './survey-animals/telemetry-device/TelemetryMap'; - -const SurveyAnimals: React.FC = () => { - const biohubApi = useBiohubApi(); - const dialogContext = useContext(DialogContext); - const surveyContext = useContext(SurveyContext); - const history = useHistory(); - - const [openRemoveCritterDialog, setOpenRemoveCritterDialog] = useState(false); - const [openViewTelemetryDialog, setOpenViewTelemetryDialog] = useState(false); - const [selectedCritterId, setSelectedCritterId] = useState(null); - - const { projectId, surveyId } = surveyContext; - const { - refresh: refreshCritters, - load: loadCritters, - data: critterData - } = useDataLoader(() => biohubApi.survey.getSurveyCritters(projectId, surveyId)); - - const { load: loadDeployments, data: deploymentData } = useDataLoader(() => - biohubApi.survey.getDeploymentsInSurvey(projectId, surveyId) - ); - - if (!critterData) { - loadCritters(); - } - - const currentCritterbaseCritterId = useMemo( - () => critterData?.find((a) => a.survey_critter_id === selectedCritterId)?.critter_id, - [critterData, selectedCritterId] - ); - - if (!deploymentData) { - loadDeployments(); - } - - const { - refresh: refreshTelemetry, - data: telemetryData, - isLoading: telemetryLoading - } = useDataLoader(() => - biohubApi.survey.getCritterTelemetry( - projectId, - surveyId, - selectedCritterId ?? 0, - '1970-01-01', - new Date().toISOString() - ) - ); - - useEffect(() => { - if (currentCritterbaseCritterId) { - refreshTelemetry(); - } - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [currentCritterbaseCritterId]); - - const setPopup = (message: string) => { - dialogContext.setSnackbar({ - open: true, - snackbarMessage: ( - - {message} - - ) - }); - }; - - const handleRemoveCritter = async () => { - try { - if (!selectedCritterId) { - setPopup('Failed to remove critter from survey.'); - return; - } - await biohubApi.survey.removeCrittersFromSurvey(projectId, surveyId, [selectedCritterId]); - } catch (e) { - setPopup('Failed to remove critter from survey.'); - } - setOpenRemoveCritterDialog(false); - refreshCritters(); - }; - - return ( - - setOpenRemoveCritterDialog(false)} - onNo={() => setOpenRemoveCritterDialog(false)} - onYes={handleRemoveCritter} - /> - - - Animals - - - - - - - - {critterData?.length ? ( - { - setOpenRemoveCritterDialog(true); - }} - onEditCritter={() => { - history.push(`animals/${selectedCritterId}/edit`); - }} - onMapOpen={() => { - setOpenViewTelemetryDialog(true); - }} - /> - ) : ( - - )} - - setOpenViewTelemetryDialog(false)}> - {telemetryData?.points.features.length ? ( - a.critter_id === currentCritterbaseCritterId)} - /> - ) : ( - - {telemetryLoading - ? 'Loading telemetry...' - : "No telemetry has been collected for this animal's deployments."} - - )} - - - ); -}; -export default SurveyAnimals; diff --git a/app/src/features/surveys/view/SurveyAttachments.test.tsx b/app/src/features/surveys/view/SurveyAttachments.test.tsx index 5c796e4f7c..aa6f6bcc91 100644 --- a/app/src/features/surveys/view/SurveyAttachments.test.tsx +++ b/app/src/features/surveys/view/SurveyAttachments.test.tsx @@ -120,7 +120,9 @@ describe('SurveyAttachments', () => { const mockSurveyContext: ISurveyContext = { artifactDataLoader: { data: null, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, surveyId: 1, projectId: 1, @@ -152,7 +154,7 @@ describe('SurveyAttachments', () => { } as unknown as DataLoader } as unknown as IProjectContext; - const { getByText } = render( + const { getByTestId } = render( @@ -168,7 +170,7 @@ describe('SurveyAttachments', () => { ); await waitFor(() => { - expect(getByText('No documents found')).toBeInTheDocument(); + expect(getByTestId('survey-attachments-list-no-data-overlay')).toBeInTheDocument(); }); }); @@ -185,7 +187,9 @@ describe('SurveyAttachments', () => { } ] }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, surveyId: 1, projectId: 1, @@ -263,13 +267,17 @@ describe('SurveyAttachments', () => { } ] }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, surveyId: 1, projectId: 1, surveyDataLoader: { data: { surveyData: { survey_details: { survey_name: 'name' } } }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader } as unknown as ISurveyContext; @@ -356,13 +364,17 @@ describe('SurveyAttachments', () => { } ] }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, surveyId: 1, projectId: 1, surveyDataLoader: { data: { surveyData: { survey_details: { survey_name: 'name' } } }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader } as unknown as ISurveyContext; @@ -448,13 +460,17 @@ describe('SurveyAttachments', () => { } ] }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader, surveyId: 1, projectId: 1, surveyDataLoader: { data: { surveyData: { survey_details: { survey_name: 'name' } } }, - load: jest.fn() + load: jest.fn(), + isLoading: false, + isReady: true } as unknown as DataLoader } as unknown as ISurveyContext; diff --git a/app/src/features/surveys/view/SurveyAttachments.tsx b/app/src/features/surveys/view/SurveyAttachments.tsx index bcef262b37..36e9b2c8c8 100644 --- a/app/src/features/surveys/view/SurveyAttachments.tsx +++ b/app/src/features/surveys/view/SurveyAttachments.tsx @@ -1,4 +1,4 @@ -import { mdiAttachment, mdiFilePdfBox, mdiFolderKeyOutline, mdiTrayArrowUp } from '@mdi/js'; +import { mdiAttachment, mdiFilePdfBox, mdiTrayArrowUp } from '@mdi/js'; import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; @@ -11,11 +11,11 @@ import { H2MenuToolbar } from 'components/toolbar/ActionToolbars'; import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; import { SurveyContext } from 'contexts/surveyContext'; import { useBiohubApi } from 'hooks/useBioHubApi'; -import React, { useContext, useState } from 'react'; +import { useContext, useState } from 'react'; import { AttachmentType } from '../../../constants/attachments'; import SurveyAttachmentsList from './SurveyAttachmentsList'; -const SurveyAttachments: React.FC = () => { +const SurveyAttachments = () => { const biohubApi = useBiohubApi(); const surveyContext = useContext(SurveyContext); @@ -23,20 +23,15 @@ const SurveyAttachments: React.FC = () => { const { projectId, surveyId } = surveyContext; const [openUploadAttachments, setOpenUploadAttachments] = useState(false); - const [attachmentType, setAttachmentType] = useState< - AttachmentType.REPORT | AttachmentType.OTHER | AttachmentType.KEYX - >(AttachmentType.OTHER); + const [attachmentType, setAttachmentType] = useState( + AttachmentType.OTHER + ); const handleUploadReportClick = () => { setAttachmentType(AttachmentType.REPORT); setOpenUploadAttachments(true); }; - const handleUploadKeyxClick = () => { - setAttachmentType(AttachmentType.KEYX); - setOpenUploadAttachments(true); - }; - const handleUploadAttachmentClick = () => { setAttachmentType(AttachmentType.OTHER); setOpenUploadAttachments(true); @@ -44,9 +39,7 @@ const SurveyAttachments: React.FC = () => { const getUploadHandler = (): IUploadHandler => { return (file, cancelToken, handleFileUploadProgress) => { - return attachmentType === AttachmentType.KEYX - ? biohubApi.survey.uploadSurveyKeyx(projectId, surveyId, file, cancelToken, handleFileUploadProgress) - : biohubApi.survey.uploadSurveyAttachments(projectId, surveyId, file, cancelToken, handleFileUploadProgress); + return biohubApi.survey.uploadSurveyAttachments(projectId, surveyId, file, cancelToken, handleFileUploadProgress); }; }; @@ -64,8 +57,6 @@ const SurveyAttachments: React.FC = () => { switch (attachmentType) { case AttachmentType.REPORT: return 'Upload Report'; - case AttachmentType.KEYX: - return 'Upload KeyX'; case AttachmentType.OTHER: return 'Upload Attachments'; default: @@ -99,11 +90,6 @@ const SurveyAttachments: React.FC = () => { menuIcon: , menuOnClick: handleUploadReportClick }, - { - menuLabel: 'Upload KeyX Files', - menuIcon: , - menuOnClick: handleUploadKeyxClick - }, { menuLabel: 'Upload Attachments', menuIcon: , diff --git a/app/src/features/surveys/view/SurveyAttachmentsList.tsx b/app/src/features/surveys/view/SurveyAttachmentsList.tsx index b4fdde67ee..939d6ec04a 100644 --- a/app/src/features/surveys/view/SurveyAttachmentsList.tsx +++ b/app/src/features/surveys/view/SurveyAttachmentsList.tsx @@ -1,5 +1,9 @@ +import { mdiArrowTopRight } from '@mdi/js'; import AttachmentsList from 'components/attachments/list/AttachmentsList'; import SurveyReportAttachmentDialog from 'components/dialog/attachments/survey/SurveyReportAttachmentDialog'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { AttachmentsI18N } from 'constants/i18n'; import { DialogContext } from 'contexts/dialogContext'; import { SurveyContext } from 'contexts/surveyContext'; @@ -96,6 +100,11 @@ const SurveyAttachmentsList: React.FC = () => { }); }; + const attachments = [ + ...(surveyContext.artifactDataLoader.data?.attachmentsList || []), + ...(surveyContext.artifactDataLoader.data?.reportAttachmentsList || []) + ]; + return ( <> { open={viewReportDetailsDialogOpen} onClose={() => setViewReportDetailsDialogOpen(false)} /> - - attachments={[ - ...(surveyContext.artifactDataLoader.data?.attachmentsList || []), - ...(surveyContext.artifactDataLoader.data?.reportAttachmentsList || []) - ]} - handleDownload={handleDownload} - handleDelete={handleDelete} - handleViewDetails={handleViewDetails} - emptyStateText="No documents found" - /> + } + isLoadingFallbackDelay={100} + hasNoData={!attachments.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + attachments={attachments} + handleDownload={handleDownload} + handleDelete={handleDelete} + handleViewDetails={handleViewDetails} + emptyStateText="No documents found" + /> + ); }; diff --git a/app/src/features/surveys/view/SurveyDetails.test.tsx b/app/src/features/surveys/view/SurveyDetails.test.tsx index 51999f09c1..7c6044d245 100644 --- a/app/src/features/surveys/view/SurveyDetails.test.tsx +++ b/app/src/features/surveys/view/SurveyDetails.test.tsx @@ -53,7 +53,6 @@ describe('SurveyDetails', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; it('renders correctly', async () => { @@ -63,13 +62,11 @@ describe('SurveyDetails', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, techniqueDataLoader: mockTechniqueDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + critterDataLoader: mockCritterDataLoader }}> diff --git a/app/src/features/surveys/view/SurveyHeader.test.tsx b/app/src/features/surveys/view/SurveyHeader.test.tsx index 0bcb3a8342..a1c685afab 100644 --- a/app/src/features/surveys/view/SurveyHeader.test.tsx +++ b/app/src/features/surveys/view/SurveyHeader.test.tsx @@ -1,4 +1,5 @@ import { AuthStateContext, IAuthState } from 'contexts/authStateContext'; +import { CodesContext, ICodesContext } from 'contexts/codesContext'; import { ConfigContext, IConfig } from 'contexts/configContext'; import { DialogContextProvider } from 'contexts/dialogContext'; import { IProjectAuthStateContext, ProjectAuthStateContext } from 'contexts/projectAuthStateContext'; @@ -12,6 +13,7 @@ import { IGetProjectForViewResponse } from 'interfaces/useProjectApi.interface'; import { IGetSurveyForViewResponse } from 'interfaces/useSurveyApi.interface'; import { Router } from 'react-router'; import { getMockAuthState, SystemAdminAuthState, SystemUserAuthState } from 'test-helpers/auth-helpers'; +import { codes } from 'test-helpers/code-helpers'; import { getProjectForViewResponse } from 'test-helpers/project-helpers'; import { getSurveyForViewResponse } from 'test-helpers/survey-helpers'; import { cleanup, fireEvent, render, waitFor } from 'test-helpers/test-utils'; @@ -28,6 +30,13 @@ const mockUseApi = { } }; +const mockCodesContext: ICodesContext = { + codesDataLoader: { + data: codes, + load: () => {} + } as DataLoader +}; + const mockSurveyContext: ISurveyContext = { surveyDataLoader: { data: getSurveyForViewResponse @@ -41,13 +50,9 @@ const mockSurveyContext: ISurveyContext = { critterDataLoader: { data: null } as DataLoader, - deploymentDataLoader: { - data: null - } as DataLoader, techniqueDataLoader: { data: [] } as DataLoader, - critterDeployments: [], surveyId: 1, projectId: 1 }; @@ -104,11 +109,13 @@ describe('SurveyHeader', () => { - - - - - + + + + + + + diff --git a/app/src/features/surveys/view/SurveyMap.tsx b/app/src/features/surveys/view/SurveyMap.tsx index 624e8ee0b9..586501c5ea 100644 --- a/app/src/features/surveys/view/SurveyMap.tsx +++ b/app/src/features/surveys/view/SurveyMap.tsx @@ -11,77 +11,23 @@ import { useMemo } from 'react'; import { LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; import { calculateUpdatedMapBounds } from 'utils/mapBoundaryUploadHelpers'; -export interface ISurveyMapPointMetadata { - label: string; - value: string; -} - -export interface ISurveyMapSupplementaryLayer { - /** - * The name of the layer - */ - layerName: string; - /** - * The colour of the layer - */ - layerColors?: { - color: string; - fillColor: string; - opacity?: number; - }; - /** - * The array of map points - */ - mapPoints: ISurveyMapPoint[]; - /** - * The title of the feature type displayed in the popup - */ - popupRecordTitle: string; -} - -export interface ISurveyMapPoint { - /** - * Unique key for the point - */ - key: string; - /** - * The geometric feature to display - */ - feature: Feature; - - /** - * Callback to fetch metadata, which is fired when the geometry's popup - * is opened - */ - onLoadMetadata: () => Promise; - /** - * Optional link that renders a button to view/manage/edit the data - * that the geometry belongs to - */ - link?: string; -} - interface ISurveyMapProps { staticLayers: IStaticLayer[]; - supplementaryLayers: ISurveyMapSupplementaryLayer[]; isLoading: boolean; } const SurveyMap = (props: ISurveyMapProps) => { const bounds: LatLngBoundsExpression | undefined = useMemo(() => { - const allMapFeatures: Feature[] = [ - ...props.supplementaryLayers.flatMap((supplementaryLayer) => - supplementaryLayer.mapPoints.map((mapPoint) => mapPoint.feature) - ), - ...props.staticLayers.flatMap((staticLayer) => staticLayer.features.map((feature) => feature.geoJSON)) - ]; + const allMapFeatures: Feature[] = props.staticLayers.flatMap((staticLayer) => + staticLayer.features.map((feature) => feature.geoJSON) + ); if (allMapFeatures.length > 0) { return calculateUpdatedMapBounds(allMapFeatures); } else { return calculateUpdatedMapBounds([ALL_OF_BC_BOUNDARY]); } - }, [props.supplementaryLayers, props.staticLayers]); + }, [props.staticLayers]); return ( <> diff --git a/app/src/features/surveys/view/SurveyMapPopup.tsx b/app/src/features/surveys/view/SurveyMapPopup.tsx index 7fdb8a8caa..7dbf8ad007 100644 --- a/app/src/features/surveys/view/SurveyMapPopup.tsx +++ b/app/src/features/surveys/view/SurveyMapPopup.tsx @@ -2,44 +2,49 @@ import Box from '@mui/material/Box'; import Skeleton from '@mui/material/Skeleton'; import Stack from '@mui/material/Stack'; import Typography from '@mui/material/Typography'; -import { ISurveyMapPointMetadata } from './SurveyMap'; -interface ISurveyMapPopupProps { +export interface ISurveyMapPopupProps { isLoading: boolean; title: string; - metadata: ISurveyMapPointMetadata[]; + metadata: { + label: string; + value: string | number; + }[]; } /** * Returns a popup component for displaying information about a leaflet map layer upon being clicked * - * @param props {ISurveyMapPopupProps} - * @returns + * @param {ISurveyMapPopupProps} props + * @return {*} */ -const SurveyMapPopup = (props: ISurveyMapPopupProps) => { +export const SurveyMapPopup = (props: ISurveyMapPopupProps) => { + const { isLoading, title, metadata } = props; + return ( - {props.isLoading ? ( - + {isLoading ? ( + - + - + - + @@ -57,17 +62,17 @@ const SurveyMapPopup = (props: ISurveyMapPopupProps) => { textOverflow: 'ellipsis', textTransform: 'uppercase' }}> - {props.title} + {title} - {props.metadata.map((metadata) => ( + {metadata.map((metadata) => ( - + {metadata.label}: @@ -81,5 +86,3 @@ const SurveyMapPopup = (props: ISurveyMapPopupProps) => { ); }; - -export default SurveyMapPopup; diff --git a/app/src/features/surveys/view/SurveyMapTooltip.tsx b/app/src/features/surveys/view/SurveyMapTooltip.tsx index d672a8d57d..654392e14a 100644 --- a/app/src/features/surveys/view/SurveyMapTooltip.tsx +++ b/app/src/features/surveys/view/SurveyMapTooltip.tsx @@ -1,20 +1,23 @@ import Typography from '@mui/material/Typography'; +import { Tooltip } from 'react-leaflet'; interface ISurveyMapTooltipProps { - label: string; + title: string; } /** * Returns a popup component for displaying information about a leaflet map layer upon hover * - * @param props {ISurveyMapPopupProps} - * @returns + * @param {ISurveyMapTooltipProps} props + * @return {*} */ const SurveyMapTooltip = (props: ISurveyMapTooltipProps) => { return ( - - {props.label} - + + + {props.title} + + ); }; diff --git a/app/src/features/surveys/view/SurveyPage.tsx b/app/src/features/surveys/view/SurveyPage.tsx index 26502c5ccd..a1e7c05aac 100644 --- a/app/src/features/surveys/view/SurveyPage.tsx +++ b/app/src/features/surveys/view/SurveyPage.tsx @@ -8,9 +8,8 @@ import { TaxonomyContextProvider } from 'contexts/taxonomyContext'; import SurveyDetails from 'features/surveys/view/SurveyDetails'; import React, { useContext, useEffect } from 'react'; import { SurveySamplingContainer } from './components/sampling-data/SurveySamplingContainer'; -import SurveySpatialData from './components/spatial-data/SurveySpatialData'; import SurveyStudyArea from './components/SurveyStudyArea'; -import SurveyAnimals from './SurveyAnimals'; +import { SurveySpatialContainer } from './survey-spatial/SurveySpatialContainer'; import SurveyAttachments from './SurveyAttachments'; import SurveyHeader from './SurveyHeader'; @@ -40,12 +39,10 @@ const SurveyPage: React.FC = () => { - - - - - + + + diff --git a/app/src/features/surveys/view/components/Partnerships.tsx b/app/src/features/surveys/view/components/Partnerships.tsx index 1bae504921..3040371202 100644 --- a/app/src/features/surveys/view/components/Partnerships.tsx +++ b/app/src/features/surveys/view/components/Partnerships.tsx @@ -29,25 +29,60 @@ const Partnerships = () => { Indigenous Partnerships - {surveyData.partnerships.indigenous_partnerships?.map((indigenousPartnership: number) => { - return ( - - {codes.first_nations?.find((item: any) => item.id === indigenousPartnership)?.name} - - ); - })} + + {surveyData.partnerships.indigenous_partnerships?.map((indigenousPartnership: number) => { + return ( + + {codes.first_nations?.find((item: any) => item.id === indigenousPartnership)?.name} + + ); + })} + + {!hasIndigenousPartnerships && None} Other Partnerships - {surveyData.partnerships.stakeholder_partnerships?.map((stakeholderPartnership: string) => { - return ( - - {stakeholderPartnership} - - ); - })} + + {surveyData.partnerships.stakeholder_partnerships?.map((stakeholderPartnership: string) => { + return ( + + {stakeholderPartnership} + + ); + })} + {!hasStakeholderPartnerships && None} diff --git a/app/src/features/surveys/view/components/SamplingMethods.tsx b/app/src/features/surveys/view/components/SamplingMethods.tsx index 1350db1bd0..a2ee8a2e0f 100644 --- a/app/src/features/surveys/view/components/SamplingMethods.tsx +++ b/app/src/features/surveys/view/components/SamplingMethods.tsx @@ -5,7 +5,7 @@ import ListItemText from '@mui/material/ListItemText'; import Typography from '@mui/material/Typography'; import { CodesContext } from 'contexts/codesContext'; import { SurveyContext } from 'contexts/surveyContext'; -import { IGetSurveyBlock, IGetSurveyStratum } from 'interfaces/useSurveyApi.interface'; +import { IGetSurveyBlock } from 'interfaces/useSurveyApi.interface'; import { useContext } from 'react'; /** @@ -53,7 +53,7 @@ const SamplingMethods = () => { Stratums - {site_selection.stratums?.map((stratum: IGetSurveyStratum) => { + {site_selection.stratums?.map((stratum) => { return ( { ))} ) : ( - - No funding sources found + + + No funding sources found + )} diff --git a/app/src/features/surveys/view/components/SurveyGeneralInformation.test.tsx b/app/src/features/surveys/view/components/SurveyGeneralInformation.test.tsx index 91b33810fb..1bb03a26b5 100644 --- a/app/src/features/surveys/view/components/SurveyGeneralInformation.test.tsx +++ b/app/src/features/surveys/view/components/SurveyGeneralInformation.test.tsx @@ -25,7 +25,6 @@ describe('SurveyGeneralInformation', () => { const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const { getByTestId } = render( @@ -37,9 +36,7 @@ describe('SurveyGeneralInformation', () => { artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, techniqueDataLoader: mockTechniqueDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, - critterDeployments: [] + critterDataLoader: mockCritterDataLoader }}> @@ -66,7 +63,6 @@ describe('SurveyGeneralInformation', () => { const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const { getByTestId } = render( @@ -78,9 +74,7 @@ describe('SurveyGeneralInformation', () => { artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, critterDataLoader: mockCritterDataLoader, - techniqueDataLoader: mockTechniqueDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, - critterDeployments: [] + techniqueDataLoader: mockTechniqueDataLoader }}> @@ -95,9 +89,7 @@ describe('SurveyGeneralInformation', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; - const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const { container } = render( @@ -109,9 +101,7 @@ describe('SurveyGeneralInformation', () => { artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, techniqueDataLoader: mockTechniqueDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, - critterDeployments: [] + critterDataLoader: mockCritterDataLoader }}> diff --git a/app/src/features/surveys/view/components/SurveyGeneralInformation.tsx b/app/src/features/surveys/view/components/SurveyGeneralInformation.tsx index 36066eecaf..057c79ecfb 100644 --- a/app/src/features/surveys/view/components/SurveyGeneralInformation.tsx +++ b/app/src/features/surveys/view/components/SurveyGeneralInformation.tsx @@ -73,51 +73,26 @@ const SurveyGeneralInformation = () => { display: 'inline-block', mr: 1.25, '&::after': { - content: `','`, + content: "';'", position: 'absolute', top: 0 }, '&:last-child::after': { display: 'none' } - }}> - {[...focalSpecies.commonNames, `(${focalSpecies.scientificName})`].filter(Boolean).join(' ')} + }} + data-testid="focal_species"> + + {focalSpecies.commonNames.join(',')} + {' '} + + ({focalSpecies.scientificName}) + ); })} - - - Secondary Species - - {species.ancillary_species?.map((ancillarySpecies: ITaxonomy) => { - return ( - - {[...ancillarySpecies.commonNames, `(${ancillarySpecies.scientificName})`].filter(Boolean).join(' ')} - - ); - })} - {species.ancillary_species?.length <= 0 && ( - No secondary species of interest - )} - - ); }; diff --git a/app/src/features/surveys/view/components/SurveyProprietaryData.test.tsx b/app/src/features/surveys/view/components/SurveyProprietaryData.test.tsx index c9f7f79040..ef52862732 100644 --- a/app/src/features/surveys/view/components/SurveyProprietaryData.test.tsx +++ b/app/src/features/surveys/view/components/SurveyProprietaryData.test.tsx @@ -15,7 +15,6 @@ describe('SurveyProprietaryData', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { getByTestId } = render( @@ -23,13 +22,11 @@ describe('SurveyProprietaryData', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, techniqueDataLoader: mockTechniqueDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + critterDataLoader: mockCritterDataLoader }}> @@ -47,7 +44,6 @@ describe('SurveyProprietaryData', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { getByTestId } = render( @@ -55,13 +51,11 @@ describe('SurveyProprietaryData', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, techniqueDataLoader: mockTechniqueDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + critterDataLoader: mockCritterDataLoader }}> @@ -77,7 +71,6 @@ describe('SurveyProprietaryData', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { container } = render( @@ -85,12 +78,10 @@ describe('SurveyProprietaryData', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, techniqueDataLoader: mockTechniqueDataLoader }}> diff --git a/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.test.tsx b/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.test.tsx index a45560e2c3..3390775e55 100644 --- a/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.test.tsx +++ b/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.test.tsx @@ -23,22 +23,19 @@ describe('SurveyPurposeAndMethodologyData', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; - const { getByTestId, getAllByTestId } = render( + const { getByTestId } = render( @@ -46,10 +43,6 @@ describe('SurveyPurposeAndMethodologyData', () => { ); expect(getByTestId('intended_outcome_codes').textContent).toEqual('Intended Outcome 1'); - expect(getAllByTestId('survey_vantage_code').map((item) => item.textContent)).toEqual([ - 'Vantage Code 1', - 'Vantage Code 2' - ]); expect(getByTestId('survey_additional_details').textContent).toEqual('details'); }); @@ -75,21 +68,18 @@ describe('SurveyPurposeAndMethodologyData', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; - const { getByTestId, getAllByTestId, queryByTestId } = render( + const { getByTestId, queryByTestId } = render( @@ -98,10 +88,6 @@ describe('SurveyPurposeAndMethodologyData', () => { ); expect(getByTestId('intended_outcome_codes').textContent).toEqual('Intended Outcome 1'); - expect(getAllByTestId('survey_vantage_code').map((item) => item.textContent)).toEqual([ - 'Vantage Code 1', - 'Vantage Code 2' - ]); expect(queryByTestId('survey_additional_details')).toBeNull(); }); }); diff --git a/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.tsx b/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.tsx index a4169fd42b..2e276cb1f3 100644 --- a/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.tsx +++ b/app/src/features/surveys/view/components/SurveyPurposeAndMethodologyData.tsx @@ -26,29 +26,31 @@ const SurveyPurposeAndMethodologyData = () => { Ecological Variables - {surveyData.purpose_and_methodology.intended_outcome_ids?.map((outcomeId: number) => { - return ( - - {codes?.intended_outcomes?.find((item: any) => item.id === outcomeId)?.name} - - ); - })} + + {surveyData.purpose_and_methodology.intended_outcome_ids?.map((intended_outcome_id: number) => { + return ( + + {codes?.intended_outcomes?.find((item: any) => item.id === intended_outcome_id)?.name} + + ); + })} + {surveyData.purpose_and_methodology.additional_details && ( <> @@ -60,33 +62,6 @@ const SurveyPurposeAndMethodologyData = () => { )} - - - Vantage Code(s) - {surveyData.purpose_and_methodology.vantage_code_ids?.map((vc_id: number) => { - return ( - - {codes?.vantage_codes?.find((item: any) => item.id === vc_id)?.name} - - ); - })} - ); }; diff --git a/app/src/features/surveys/view/components/SurveyStudyArea.test.tsx b/app/src/features/surveys/view/components/SurveyStudyArea.test.tsx index 0817cb6a2b..47e7ca53e1 100644 --- a/app/src/features/surveys/view/components/SurveyStudyArea.test.tsx +++ b/app/src/features/surveys/view/components/SurveyStudyArea.test.tsx @@ -44,7 +44,6 @@ describe.skip('SurveyStudyArea', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { container } = render( @@ -52,13 +51,11 @@ describe.skip('SurveyStudyArea', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, techniqueDataLoader: mockTechniqueDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + critterDataLoader: mockCritterDataLoader }}> @@ -83,7 +80,6 @@ describe.skip('SurveyStudyArea', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { container, queryByTestId } = render( @@ -91,13 +87,11 @@ describe.skip('SurveyStudyArea', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, techniqueDataLoader: mockTechniqueDataLoader, - critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + critterDataLoader: mockCritterDataLoader }}> @@ -114,7 +108,6 @@ describe.skip('SurveyStudyArea', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const { container, getByTestId } = render( @@ -122,12 +115,10 @@ describe.skip('SurveyStudyArea', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, techniqueDataLoader: mockTechniqueDataLoader }}> @@ -149,7 +140,6 @@ describe.skip('SurveyStudyArea', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; const mockProjectAuthStateContext: IProjectAuthStateContext = { @@ -167,12 +157,10 @@ describe.skip('SurveyStudyArea', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, critterDataLoader: mockCritterDataLoader, - deploymentDataLoader: mockDeploymentDataLoader, techniqueDataLoader: mockTechniqueDataLoader }}> @@ -244,7 +232,6 @@ describe.skip('SurveyStudyArea', () => { const mockArtifactDataLoader = { data: null } as DataLoader; const mockSampleSiteDataLoader = { data: null } as DataLoader; const mockCritterDataLoader = { data: [] } as DataLoader; - const mockDeploymentDataLoader = { data: [] } as DataLoader; const mockTechniqueDataLoader = { data: [] } as DataLoader; mockUseApi.survey.getSurveyForView.mockResolvedValue({ @@ -280,13 +267,11 @@ describe.skip('SurveyStudyArea', () => { value={{ projectId: 1, surveyId: 1, - critterDeployments: [], surveyDataLoader: mockSurveyDataLoader, artifactDataLoader: mockArtifactDataLoader, sampleSiteDataLoader: mockSampleSiteDataLoader, critterDataLoader: mockCritterDataLoader, - techniqueDataLoader: mockTechniqueDataLoader, - deploymentDataLoader: mockDeploymentDataLoader + techniqueDataLoader: mockTechniqueDataLoader }}> diff --git a/app/src/features/surveys/view/components/analytics/SurveyObservationAnalytics.tsx b/app/src/features/surveys/view/components/analytics/SurveyObservationAnalytics.tsx new file mode 100644 index 0000000000..a12191b6b1 --- /dev/null +++ b/app/src/features/surveys/view/components/analytics/SurveyObservationAnalytics.tsx @@ -0,0 +1,194 @@ +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import Checkbox from '@mui/material/Checkbox'; +import grey from '@mui/material/colors/grey'; +import Divider from '@mui/material/Divider'; +import Stack from '@mui/material/Stack'; +import ToggleButton from '@mui/material/ToggleButton'; +import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; +import Typography from '@mui/material/Typography'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { ObservationAnalyticsDataTableContainer } from 'features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import startCase from 'lodash-es/startCase'; +import { useEffect, useState } from 'react'; +import { ObservationAnalyticsNoDataOverlay } from './components/ObservationAnalyticsNoDataOverlay'; +type GroupByColumnType = 'column' | 'quantitative_measurement' | 'qualitative_measurement'; + +export type IGroupByOption = { + label: string; + field: string; + type: GroupByColumnType; +}; + +const initialGroupByColumnOptions: IGroupByOption[] = [ + { label: 'Sampling Site', field: 'survey_sample_site_id', type: 'column' } +]; + +const allGroupByColumnOptions: IGroupByOption[] = [ + ...initialGroupByColumnOptions, + { label: 'Sampling Method', field: 'survey_sample_method_id', type: 'column' }, + { label: 'Sampling Period', field: 'survey_sample_period_id', type: 'column' }, + { label: 'Species', field: 'itis_tsn', type: 'column' }, + { label: 'Date', field: 'observation_date', type: 'column' } +]; + +export const SurveyObservationAnalytics = () => { + const biohubApi = useBiohubApi(); + + const { surveyId, projectId } = useSurveyContext(); + + const [groupByColumns, setGroupByColumns] = useState(initialGroupByColumnOptions); + const [groupByQualitativeMeasurements, setGroupByQualitativeMeasurements] = useState([]); + const [groupByQuantitativeMeasurements, setGroupByQuantitativeMeasurements] = useState([]); + + const measurementDefinitionsDataLoader = useDataLoader(() => + biohubApi.observation.getObservationMeasurementDefinitions(projectId, surveyId) + ); + + useEffect(() => { + measurementDefinitionsDataLoader.load(); + }, [measurementDefinitionsDataLoader]); + + const groupByOptions: IGroupByOption[] = [ + ...allGroupByColumnOptions, + ...(measurementDefinitionsDataLoader.data?.qualitative_measurements.map((measurement) => ({ + label: startCase(measurement.measurement_name), + field: measurement.taxon_measurement_id, + type: 'qualitative_measurement' as GroupByColumnType + })) ?? []), + ...(measurementDefinitionsDataLoader.data?.quantitative_measurements.map((measurement) => ({ + label: startCase(measurement.measurement_name), + field: measurement.taxon_measurement_id, + type: 'quantitative_measurement' as GroupByColumnType + })) ?? []) + ]; + + const handleToggleChange = (_: React.MouseEvent, value: IGroupByOption[]) => { + if (!value[0]?.type) return; + + // Update group by arrays + if (value[0].type === 'column') { + updateGroupBy(value[0], setGroupByColumns); + } + if (value[0].type === 'qualitative_measurement') { + updateGroupBy(value[0], setGroupByQualitativeMeasurements); + } + if (value[0].type === 'quantitative_measurement') { + updateGroupBy(value[0], setGroupByQuantitativeMeasurements); + } + }; + + const updateGroupBy = (value: IGroupByOption, setGroupBy: React.Dispatch>) => + setGroupBy((groupBy) => + groupBy.some((item) => item.field === value.field) + ? groupBy.filter((item) => item.field !== value.field) + : [...groupBy, value] + ); + + const allGroupByColumns = [...groupByColumns, ...groupByQualitativeMeasurements, ...groupByQuantitativeMeasurements]; + + return ( + + + + + } + isLoadingFallbackDelay={100}> + + {/* Group by header */} + + + GROUP BY + + + + + {/* Render toggle buttons for each group by option */} + {groupByOptions.map((option) => ( + item.field === option.field) || + groupByQualitativeMeasurements.some((item) => item.field === option.field) || + groupByQuantitativeMeasurements.some((item) => item.field === option.field) + }> + + item.field === option.field) || + groupByQualitativeMeasurements.some((item) => item.field === option.field) || + groupByQuantitativeMeasurements.some((item) => item.field === option.field) + } + /> + {option.label} + + + ))} + + + + + + + {/* Overlay for when no group by columns are selected */} + {allGroupByColumns.length === 0 && !measurementDefinitionsDataLoader.isLoading && ( + + )} + + {/* Data grid displaying fetched data */} + {measurementDefinitionsDataLoader.data && allGroupByColumns.length > 0 && ( + + )} + + + ); +}; diff --git a/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTable.tsx b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTable.tsx new file mode 100644 index 0000000000..2fed674685 --- /dev/null +++ b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTable.tsx @@ -0,0 +1,68 @@ +import { GridColDef, GridColumnVisibilityModel } from '@mui/x-data-grid'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { IObservationAnalyticsRow } from 'features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer'; + +const rowHeight = 50; + +interface IObservationAnalyticsDataTableProps { + isLoading: boolean; + columns: GridColDef[]; + rows: IObservationAnalyticsRow[]; + columnVisibilityModel: GridColumnVisibilityModel; +} + +/** + * Observation Analytics Data Table. + * + * @param {IObservationAnalyticsDataTableProps} props + * @return {*} + */ +export const ObservationAnalyticsDataTable = (props: IObservationAnalyticsDataTableProps) => { + const { isLoading, columns, rows, columnVisibilityModel } = props; + + return ( + + ); +}; diff --git a/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer.tsx b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer.tsx new file mode 100644 index 0000000000..b5e09248f1 --- /dev/null +++ b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer.tsx @@ -0,0 +1,154 @@ +import { GridColumnVisibilityModel } from '@mui/x-data-grid'; +import { ObservationAnalyticsDataTable } from 'features/surveys/view/components/analytics/components/ObservationAnalyticsDataTable'; +import { IGroupByOption } from 'features/surveys/view/components/analytics/SurveyObservationAnalytics'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext, useTaxonomyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { IObservationCountByGroup } from 'interfaces/useAnalyticsApi.interface'; +import { useEffect, useMemo } from 'react'; +import { + getBasicGroupByColDefs, + getDateColDef, + getIndividualCountColDef, + getIndividualPercentageColDef, + getRowCountColDef, + getSamplingMethodColDef, + getSamplingPeriodColDef, + getSamplingSiteColDef, + getSpeciesColDef +} from './ObservationsAnalyticsGridColumnDefinitions'; + +export type IObservationAnalyticsRow = Omit< + IObservationCountByGroup, + 'quantitative_measurements' | 'qualitative_measurements' +> & { + [key: string]: string | number | null; +}; + +// Base columns that are always displayed, and not part of the group by columns +const BaseColumns = ['row_count', 'individual_count', 'individual_percentage']; + +interface IObservationAnalyticsDataTableContainerProps { + groupByColumns: IGroupByOption[]; + groupByQuantitativeMeasurements: IGroupByOption[]; + groupByQualitativeMeasurements: IGroupByOption[]; +} + +/** + * Observation Analytics Data Table Container. + * Fetches and parses the observation analytics data and passes it to the ObservationAnalyticsDataTable component. + * + * @param {IObservationAnalyticsDataTableContainerProps} props + * @return {*} + */ +export const ObservationAnalyticsDataTableContainer = (props: IObservationAnalyticsDataTableContainerProps) => { + const { groupByColumns, groupByQuantitativeMeasurements, groupByQualitativeMeasurements } = props; + + const biohubApi = useBiohubApi(); + const surveyContext = useSurveyContext(); + const taxonomyContext = useTaxonomyContext(); + + const analyticsDataLoader = useDataLoader( + ( + surveyId: number, + groupByColumns: IGroupByOption[], + groupByQuantitativeMeasurements: IGroupByOption[], + groupByQualitativeMeasurements: IGroupByOption[] + ) => + biohubApi.analytics.getObservationCountByGroup( + [surveyId], + groupByColumns.map((item) => item.field), + groupByQuantitativeMeasurements.map((item) => item.field), + groupByQualitativeMeasurements.map((item) => item.field) + ) + ); + + useEffect( + () => { + analyticsDataLoader.refresh( + surveyContext.surveyId, + groupByColumns, + groupByQuantitativeMeasurements, + groupByQualitativeMeasurements + ); + }, + // eslint-disable-next-line + [groupByColumns, groupByQualitativeMeasurements, groupByQuantitativeMeasurements, surveyContext.surveyId] + ); + + const rows = useMemo( + () => + analyticsDataLoader?.data?.map((row) => { + const { quantitative_measurements, qualitative_measurements, ...nonMeasurementRows } = row; + + const newRow: IObservationAnalyticsRow = nonMeasurementRows; + + qualitative_measurements.forEach((measurement) => { + newRow[measurement.taxon_measurement_id] = measurement.option.option_label; + }); + + quantitative_measurements.forEach((measurement) => { + newRow[measurement.taxon_measurement_id] = measurement.value; + }); + + return newRow; + }) ?? [], + [analyticsDataLoader?.data] + ); + + const sampleSites = useMemo( + () => surveyContext.sampleSiteDataLoader.data?.sampleSites ?? [], + [surveyContext.sampleSiteDataLoader.data?.sampleSites] + ); + + const allGroupByColumns = useMemo( + () => [...groupByColumns, ...groupByQualitativeMeasurements, ...groupByQuantitativeMeasurements], + [groupByColumns, groupByQualitativeMeasurements, groupByQuantitativeMeasurements] + ); + + const columns = useMemo( + () => [ + getRowCountColDef(), + getIndividualCountColDef(), + getIndividualPercentageColDef(), + getSamplingSiteColDef(sampleSites), + getSamplingMethodColDef(sampleSites), + getSamplingPeriodColDef(sampleSites), + getSpeciesColDef(taxonomyContext.getCachedSpeciesTaxonomyById), + getDateColDef(), + ...getBasicGroupByColDefs([...groupByQualitativeMeasurements, ...groupByQuantitativeMeasurements]) + ], + // eslint-disable-next-line + [rows, allGroupByColumns] + ); + + const columnVisibilityModel = useMemo(() => { + const _columnVisibilityModel: GridColumnVisibilityModel = {}; + + for (const column of columns) { + // Set all columns to visible by default + _columnVisibilityModel[column.field] = true; + + if (BaseColumns.includes(column.field)) { + // Don't hide base columns + continue; + } + + if (!allGroupByColumns.some((item) => item.field === column.field)) { + // Set columns that are not part of the group by columns (not selected in the UI) to hidden + _columnVisibilityModel[column.field] = false; + } + } + + return _columnVisibilityModel; + }, [allGroupByColumns, columns]); + + return ( + + ); +}; diff --git a/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsNoDataOverlay.tsx b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsNoDataOverlay.tsx new file mode 100644 index 0000000000..f56d03e844 --- /dev/null +++ b/app/src/features/surveys/view/components/analytics/components/ObservationAnalyticsNoDataOverlay.tsx @@ -0,0 +1,49 @@ +import Box from '@mui/material/Box'; +import grey from '@mui/material/colors/grey'; +import Stack from '@mui/material/Stack'; +import Typography from '@mui/material/Typography'; + +/** + * Returns an overlay with instructions on how to use the analytics feature. + * + * @return {*} + */ +export const ObservationAnalyticsNoDataOverlay = () => { + return ( + + + Calculate sex ratios, demographics, and more + + + Choose fields to analyze + + + The group by options depend on which fields apply to your observations. To add options, such as life stage + and sex, add fields to your observations by configuring your observations table. + + + + + How the calculations work  + + + The number observations and individuals will be calculated for each group. For example, if you group by life + stage, the number of individuals belonging to each life stage category will be calculated. If you group by + multiple fields, such as life stage and sex, the number of individuals belonging to each life stage and sex + combination will be calculated. + + + + + ); +}; diff --git a/app/src/features/surveys/view/components/analytics/components/ObservationsAnalyticsGridColumnDefinitions.tsx b/app/src/features/surveys/view/components/analytics/components/ObservationsAnalyticsGridColumnDefinitions.tsx new file mode 100644 index 0000000000..b24ef04e98 --- /dev/null +++ b/app/src/features/surveys/view/components/analytics/components/ObservationsAnalyticsGridColumnDefinitions.tsx @@ -0,0 +1,221 @@ +import grey from '@mui/material/colors/grey'; +import Typography from '@mui/material/Typography'; +import { GridColDef } from '@mui/x-data-grid'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { IObservationAnalyticsRow } from 'features/surveys/view/components/analytics/components/ObservationAnalyticsDataTableContainer'; +import { IGroupByOption } from 'features/surveys/view/components/analytics/SurveyObservationAnalytics'; +import { IGetSampleLocationDetails } from 'interfaces/useSamplingSiteApi.interface'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import isEqual from 'lodash-es/isEqual'; + +/** + * Get the column definition for the row count. + * + * @return {*} {GridColDef} + */ +export const getRowCountColDef = (): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'row_count', + headerName: 'Number of observations', + type: 'number', + flex: 1, + minWidth: 180 +}); + +/** + * Get the column definition for the individual count. + * + * @return {*} {GridColDef} + */ +export const getIndividualCountColDef = (): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'individual_count', + headerName: 'Number of individuals', + type: 'number', + flex: 1, + minWidth: 180 +}); + +/** + * Get the column definition for the individual percentage. + * + * @return {*} {GridColDef} + */ +export const getIndividualPercentageColDef = (): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'individual_percentage', + headerName: 'Percentage of individuals', + type: 'number', + flex: 1, + minWidth: 180, + renderCell: (params) => ( + + {params.row.individual_percentage}  + + % + + + ) +}); + +/** + * Get the column definition for the species. + * + * @param {((id: number) => IPartialTaxonomy | null)} getFunction + * @return {*} {GridColDef} + */ +export const getSpeciesColDef = ( + getFunction: (id: number) => IPartialTaxonomy | null +): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'itis_tsn', + headerName: 'Species', + minWidth: 180, + renderCell: (params) => { + if (!params.row.itis_tsn) { + return null; + } + + const species = getFunction(params.row.itis_tsn); + + return ; + } +}); + +/** + * Get the column definition for the sampling site. + * + * @param {IGetSampleLocationDetails[]} sampleSites + * @return {*} {GridColDef} + */ +export const getSamplingSiteColDef = ( + sampleSites: IGetSampleLocationDetails[] +): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'survey_sample_site_id', + headerName: 'Site', + minWidth: 180, + renderCell: (params) => { + if (!params.row.survey_sample_site_id) { + return null; + } + + const site = sampleSites.find((site) => isEqual(params.row.survey_sample_site_id, site.survey_sample_site_id)); + + if (!site) { + return null; + } + + return {site.name}; + } +}); + +/** + * Get the column definition for the sampling method. + * + * @param {IGetSampleLocationDetails[]} sampleSites + * @return {*} {GridColDef} + */ +export const getSamplingMethodColDef = ( + sampleSites: IGetSampleLocationDetails[] +): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'survey_sample_method_id', + headerName: 'Method', + minWidth: 180, + renderCell: (params) => { + if (!params.row.survey_sample_method_id) { + return null; + } + + const method = sampleSites + .flatMap((site) => site.sample_methods) + .find((method) => isEqual(params.row.survey_sample_method_id, method.survey_sample_method_id)); + + if (!method) { + return null; + } + + return {method.technique.name}; + } +}); + +/** + * Get the column definition for the sampling period. + * + * @param {IGetSampleLocationDetails[]} sampleSites + * @return {*} {GridColDef} + */ +export const getSamplingPeriodColDef = ( + sampleSites: IGetSampleLocationDetails[] +): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'survey_sample_period_id', + headerName: 'Period', + minWidth: 220, + renderCell: (params) => { + if (!params.row.survey_sample_period_id) { + return null; + } + + const period = sampleSites + .flatMap((site) => site.sample_methods) + .flatMap((method) => method.sample_periods) + .find((period) => isEqual(params.row.survey_sample_period_id, period.survey_sample_period_id)); + + if (!period) { + return null; + } + + return ( + + {dayjs(period.start_date).format(DATE_FORMAT.ShortMediumDateFormat)}– + {dayjs(period.end_date).format(DATE_FORMAT.ShortMediumDateFormat)} + + ); + } +}); + +/** + * Get the column definition for the date. + * + * @return {*} {GridColDef} + */ +export const getDateColDef = (): GridColDef => ({ + headerAlign: 'left', + align: 'left', + field: 'observation_date', + headerName: 'Date', + minWidth: 180, + renderCell: (params) => + params.row.observation_date ? ( + {dayjs(params.row.observation_date).format(DATE_FORMAT.MediumDateFormat)} + ) : null +}); + +/** + * Get basic group by column definitions for the provided group by options. + * + * @param {IGroupByOption[]} groupByOptions + * @return {*} {GridColDef[]} + */ +export const getBasicGroupByColDefs = (groupByOptions: IGroupByOption[]): GridColDef[] => { + if (!groupByOptions.length) { + return []; + } + + return groupByOptions.map((item) => ({ + field: item.field, + headerName: item.label, + minWidth: 180 + })); +}; diff --git a/app/src/features/surveys/view/components/data-container/SurveyObservationTabularDataContainer.tsx b/app/src/features/surveys/view/components/data-container/SurveyObservationTabularDataContainer.tsx new file mode 100644 index 0000000000..3fc75572f8 --- /dev/null +++ b/app/src/features/surveys/view/components/data-container/SurveyObservationTabularDataContainer.tsx @@ -0,0 +1,81 @@ +import { mdiChartBar, mdiTallyMark5 } from '@mdi/js'; +import Icon from '@mdi/react'; +import Box from '@mui/material/Box'; +import Button from '@mui/material/Button'; +import ToggleButton from '@mui/material/ToggleButton'; +import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; +import { useState } from 'react'; +import { SurveySpatialObservationTable } from '../../survey-spatial/components/observation/SurveySpatialObservationTable'; +import { SurveyObservationAnalytics } from '../analytics/SurveyObservationAnalytics'; + +export enum SurveyObservationTabularDataContainerViewEnum { + COUNTS = 'COUNTS', + ANALYTICS = 'ANALYTICS' +} + +interface ISurveyObservationTabularDataContainerProps { + isLoading: boolean; +} + +const SurveyObservationTabularDataContainer = (props: ISurveyObservationTabularDataContainerProps) => { + const { isLoading } = props; + + const [activeDataView, setActiveDataView] = useState( + SurveyObservationTabularDataContainerViewEnum.COUNTS + ); + + const views = [ + { label: 'Counts', value: SurveyObservationTabularDataContainerViewEnum.COUNTS, icon: mdiTallyMark5 }, + { label: 'Analytics', value: SurveyObservationTabularDataContainerViewEnum.ANALYTICS, icon: mdiChartBar } + ]; + + return ( + <> + + { + if (!view) { + // An active view must be selected at all times + return; + } + + setActiveDataView(view); + }} + exclusive + sx={{ + display: 'flex', + gap: 1, + '& Button': { + py: 0.25, + px: 1.5, + border: 'none', + borderRadius: '4px !important', + fontSize: '0.875rem', + fontWeight: 700, + letterSpacing: '0.02rem' + } + }}> + {views.map((view) => ( + } + value={view.value}> + {view.label} + + ))} + + + + {activeDataView === SurveyObservationTabularDataContainerViewEnum.COUNTS && ( + + )} + {activeDataView === SurveyObservationTabularDataContainerViewEnum.ANALYTICS && } + + + ); +}; + +export default SurveyObservationTabularDataContainer; diff --git a/app/src/features/surveys/view/components/sampling-data/SurveySamplingContainer.tsx b/app/src/features/surveys/view/components/sampling-data/SurveySamplingContainer.tsx index 5e890b6aaf..7d37ea1279 100644 --- a/app/src/features/surveys/view/components/sampling-data/SurveySamplingContainer.tsx +++ b/app/src/features/surveys/view/components/sampling-data/SurveySamplingContainer.tsx @@ -1,24 +1,21 @@ import Box from '@mui/material/Box'; import Divider from '@mui/material/Divider'; -import Paper from '@mui/material/Paper'; import { SurveySamplingTabs } from 'features/surveys/view/components/sampling-data/components/SurveySamplingTabs'; import { SurveySamplingHeader } from './components/SurveySamplingHeader'; export const SurveySamplingContainer = () => { return ( - - - + + - + - - - + + ); }; diff --git a/app/src/features/surveys/view/components/sampling-data/components/SurveySamplingTabs.tsx b/app/src/features/surveys/view/components/sampling-data/components/SurveySamplingTabs.tsx index 320a95eeb0..fb71f4ccf4 100644 --- a/app/src/features/surveys/view/components/sampling-data/components/SurveySamplingTabs.tsx +++ b/app/src/features/surveys/view/components/sampling-data/components/SurveySamplingTabs.tsx @@ -1,4 +1,4 @@ -import { mdiAutoFix, mdiMapMarker } from '@mdi/js'; +import { mdiArrowTopRight, mdiAutoFix, mdiCalendarRange, mdiMapMarker } from '@mdi/js'; import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; @@ -7,14 +7,26 @@ import ToggleButton from '@mui/material/ToggleButton'; import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; import { LoadingGuard } from 'components/loading/LoadingGuard'; import { SkeletonTable } from 'components/loading/SkeletonLoaders'; -import { SurveySitesTable } from 'features/surveys/view/components/sampling-data/components/SurveySitesTable'; -import { SurveyTechniquesTable } from 'features/surveys/view/components/sampling-data/components/SurveyTechniquesTable'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { + ISamplingSitePeriodRowData, + SamplingPeriodTable +} from 'features/surveys/sampling-information/periods/table/SamplingPeriodTable'; +import { + ISurveySitesRowData, + SurveySitesTable +} from 'features/surveys/view/components/sampling-data/components/SurveySitesTable'; +import { + ISurveyTechniqueRowData, + SurveyTechniquesTable +} from 'features/surveys/view/components/sampling-data/components/SurveyTechniquesTable'; import { useSurveyContext } from 'hooks/useContext'; -import { useEffect, useState } from 'react'; +import { useEffect, useMemo, useState } from 'react'; export enum SurveySamplingView { TECHNIQUES = 'TECHNIQUES', - SITES = 'SITES' + SITES = 'SITES', + PERIODS = 'PERIODS' } export const SurveySamplingTabs = () => { @@ -49,6 +61,56 @@ export const SurveySamplingTabs = () => { surveyContext.surveyId ]); + const techniques: ISurveyTechniqueRowData[] = + surveyContext.techniqueDataLoader.data?.techniques.map((technique) => ({ + id: technique.method_technique_id, + name: technique.name, + method_lookup_id: technique.method_lookup_id, + description: technique.description, + attractants: technique.attractants, + distance_threshold: technique.distance_threshold + })) ?? []; + + const sampleSites: ISurveySitesRowData[] = useMemo( + () => + surveyContext.sampleSiteDataLoader.data?.sampleSites.map((site) => ({ + id: site.survey_sample_site_id, + name: site.name, + description: site.description, + geojson: site.geojson, + blocks: site.blocks.map((block) => block.name), + stratums: site.stratums.map((stratum) => stratum.name) + })) ?? [], + [surveyContext.sampleSiteDataLoader.data?.sampleSites] + ); + + const samplePeriods: ISamplingSitePeriodRowData[] = useMemo(() => { + const data: ISamplingSitePeriodRowData[] = []; + + for (const site of surveyContext.sampleSiteDataLoader.data?.sampleSites ?? []) { + for (const method of site.sample_methods) { + for (const period of method.sample_periods) { + data.push({ + id: period.survey_sample_period_id, + sample_site: site.name, + sample_method: method.technique.name, + method_response_metric_id: method.method_response_metric_id, + start_date: period.start_date, + end_date: period.end_date, + start_time: period.start_time, + end_time: period.end_time + }); + } + } + } + + return data; + }, [surveyContext.sampleSiteDataLoader.data?.sampleSites]); + + const techniquesCount = surveyContext.techniqueDataLoader.data?.count; + const sampleSitesCount = surveyContext.sampleSiteDataLoader.data?.sampleSites.length; + const samplePeriodsCount = samplePeriods.length; + return ( <> @@ -82,7 +144,7 @@ export const SurveySamplingTabs = () => { color="primary" startIcon={} value={SurveySamplingView.TECHNIQUES}> - {`Techniques (${surveyContext.techniqueDataLoader.data?.count ?? 0})`} + {`${SurveySamplingView.TECHNIQUES} (${techniquesCount ?? 0})`} { color="primary" startIcon={} value={SurveySamplingView.SITES}> - {`Sites (${surveyContext.sampleSiteDataLoader.data?.sampleSites.length ?? 0})`} + {`${SurveySamplingView.SITES} (${sampleSitesCount ?? 0})`} + + } + value={SurveySamplingView.PERIODS}> + {`${SurveySamplingView.PERIODS} (${samplePeriodsCount ?? 0})`} - - - {activeView === SurveySamplingView.TECHNIQUES && ( - - } - delay={200}> - - - - )} - - {activeView === SurveySamplingView.SITES && ( - - } - delay={200}> - - - - )} - + + {activeView === SurveySamplingView.TECHNIQUES && ( + <> + } + isLoadingFallbackDelay={100} + hasNoData={!techniquesCount} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + + + )} + + {activeView === SurveySamplingView.SITES && ( + <> + } + isLoadingFallbackDelay={100} + hasNoData={!sampleSitesCount} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + + + )} + + {activeView === SurveySamplingView.PERIODS && ( + <> + } + isLoadingFallbackDelay={100} + hasNoData={!samplePeriodsCount} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + + + + )} ); diff --git a/app/src/features/surveys/view/components/sampling-data/components/SurveySitesTable.tsx b/app/src/features/surveys/view/components/sampling-data/components/SurveySitesTable.tsx index 3fd7f9022e..521efccde4 100644 --- a/app/src/features/surveys/view/components/sampling-data/components/SurveySitesTable.tsx +++ b/app/src/features/surveys/view/components/sampling-data/components/SurveySitesTable.tsx @@ -1,56 +1,79 @@ -import { mdiArrowTopRight } from '@mdi/js'; -import Icon from '@mdi/react'; import Box from '@mui/material/Box'; -import Typography from '@mui/material/Typography'; -import { GridColDef, GridOverlay } from '@mui/x-data-grid'; +import blueGrey from '@mui/material/colors/blueGrey'; +import { GridColDef } from '@mui/x-data-grid'; +import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; -import { IGetSampleSiteResponse } from 'interfaces/useSamplingSiteApi.interface'; -import { IGetTechniqueResponse } from 'interfaces/useTechniqueApi.interface'; +import { ISamplingSiteRowData } from 'features/surveys/sampling-information/sites/table/SamplingSiteTable'; +import { Feature } from 'geojson'; +import { getSamplingSiteSpatialType } from 'utils/spatial-utils'; + +export interface ISurveySitesRowData { + id: number; + name: string; + description: string; + geojson: Feature; + blocks: string[]; + stratums: string[]; +} export interface ISurveySitesTableProps { - sites?: IGetSampleSiteResponse; + sites: ISurveySitesRowData[]; } export const SurveySitesTable = (props: ISurveySitesTableProps) => { const { sites } = props; - const rows = - sites?.sampleSites.map((site) => ({ - id: site.survey_sample_site_id, - name: site.name, - description: site.description - })) || []; - - const columns: GridColDef[] = [ + const columns: GridColDef[] = [ { field: 'name', headerName: 'Name', - flex: 0.3 + flex: 1 + }, + { + field: 'geometry_type', + headerName: 'Geometry', + flex: 1, + renderCell: (params) => ( + + + + ) }, { field: 'description', headerName: 'Description', + flex: 1 + }, + { + field: 'blocks', + headerName: 'Blocks', + flex: 1, + renderCell: (params) => ( + + {params.row.blocks.map((block) => ( + + + + ))} + + ) + }, + { + field: 'stratums', + headerName: 'Strata', flex: 1, - renderCell: (params) => { - return ( - - - {params.row.description} - - - ); - } + renderCell: (params) => ( + + {params.row.stratums.map((stratum) => ( + + + + ))} + + ) } ]; @@ -60,36 +83,16 @@ export const SurveySitesTable = (props: ISurveySitesTableProps) => { rowSelection={false} autoHeight getRowHeight={() => 'auto'} - rows={rows} + rows={sites} getRowId={(row) => row.id} columns={columns} disableRowSelectionOnClick - noRowsOverlay={ - - - - Start by adding sampling information  - - - - Add Techniques, then apply your techniques to Sites - - - - } - sx={{ - '& .MuiDataGrid-virtualScroller': { - height: rows.length === 0 ? '250px' : 'unset', - overflowY: 'auto !important', - overflowX: 'hidden' - }, - '& .MuiDataGrid-overlay': { - height: '250px', - display: 'flex', - justifyContent: 'center', - alignItems: 'center' + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 10 } } }} + pageSizeOptions={[10, 25, 50]} /> ); }; diff --git a/app/src/features/surveys/view/components/sampling-data/components/SurveyTechniquesTable.tsx b/app/src/features/surveys/view/components/sampling-data/components/SurveyTechniquesTable.tsx index 144be73dd8..3aa338f693 100644 --- a/app/src/features/surveys/view/components/sampling-data/components/SurveyTechniquesTable.tsx +++ b/app/src/features/surveys/view/components/sampling-data/components/SurveyTechniquesTable.tsx @@ -1,17 +1,25 @@ -import { mdiArrowTopRight } from '@mdi/js'; -import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import blueGrey from '@mui/material/colors/blueGrey'; import Typography from '@mui/material/Typography'; -import { GridColDef, GridOverlay } from '@mui/x-data-grid'; +import { GridColDef } from '@mui/x-data-grid'; import ColouredRectangleChip from 'components/chips/ColouredRectangleChip'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { ITechniqueRowData } from 'features/surveys/sampling-information/techniques/table/SamplingTechniqueTable'; import { useCodesContext } from 'hooks/useContext'; -import { IGetTechniqueResponse, IGetTechniquesResponse } from 'interfaces/useTechniqueApi.interface'; +import { TechniqueAttractant } from 'interfaces/useTechniqueApi.interface'; import { getCodesName } from 'utils/Utils'; +export interface ISurveyTechniqueRowData { + id: number; + method_lookup_id: number; + name: string; + description: string | null; + attractants: TechniqueAttractant[]; + distance_threshold: number | null; +} + export interface ISurveyTechniquesTableProps { - techniques?: IGetTechniquesResponse; + techniques: ISurveyTechniqueRowData[]; } export const SurveyTechniquesTable = (props: ISurveyTechniquesTableProps) => { @@ -19,23 +27,15 @@ export const SurveyTechniquesTable = (props: ISurveyTechniquesTableProps) => { const codesContext = useCodesContext(); - const rows = - techniques?.techniques.map((technique) => ({ - id: technique.method_technique_id, - name: getCodesName(codesContext.codesDataLoader.data, 'sample_methods', technique.method_lookup_id) ?? '', - method_lookup_id: technique.method_lookup_id, - description: technique.description - })) || []; - - const columns: GridColDef[] = [ + const columns: GridColDef[] = [ { field: 'name', headerName: 'Name', - flex: 0.3 + flex: 1 }, { field: 'method_lookup_id', - flex: 0.3, + flex: 1, headerName: 'Method', renderCell: (params) => ( { ); } + }, + { + field: 'attractants', + flex: 1, + headerName: 'Attractants', + renderCell: (params) => ( + + {params.row.attractants.map((attractant) => ( + + + + ))} + + ) + }, + { + field: 'distance_threshold', + headerName: 'Distance threshold', + flex: 1, + renderCell: (params) => (params.row.distance_threshold ? <>{params.row.distance_threshold} m : <>) } ]; @@ -77,36 +102,16 @@ export const SurveyTechniquesTable = (props: ISurveyTechniquesTableProps) => { rowSelection={false} autoHeight getRowHeight={() => 'auto'} - rows={rows} + rows={techniques} getRowId={(row) => row.id} columns={columns} disableRowSelectionOnClick - noRowsOverlay={ - - - - Start by adding sampling information  - - - - Add Techniques, then apply your techniques to Sites - - - - } - sx={{ - '& .MuiDataGrid-virtualScroller': { - height: rows.length === 0 ? '250px' : 'unset', - overflowY: 'auto !important', - overflowX: 'hidden' - }, - '& .MuiDataGrid-overlay': { - height: '250px', - display: 'flex', - justifyContent: 'center', - alignItems: 'center' + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 10 } } }} + pageSizeOptions={[10, 25, 50]} /> ); }; diff --git a/app/src/features/surveys/view/components/spatial-data/SurveySpatialData.tsx b/app/src/features/surveys/view/components/spatial-data/SurveySpatialData.tsx deleted file mode 100644 index f4722d6ada..0000000000 --- a/app/src/features/surveys/view/components/spatial-data/SurveySpatialData.tsx +++ /dev/null @@ -1,384 +0,0 @@ -import { mdiBroadcast, mdiEye } from '@mdi/js'; -import Box from '@mui/material/Box'; -import Paper from '@mui/material/Paper'; -import { IStaticLayer, IStaticLayerFeature } from 'components/map/components/StaticLayers'; -import { DATE_FORMAT } from 'constants/dateTimeFormats'; -import { SURVEY_MAP_LAYER_COLOURS } from 'constants/spatial'; -import { CodesContext } from 'contexts/codesContext'; -import { SurveyContext } from 'contexts/surveyContext'; -import { TelemetryDataContext } from 'contexts/telemetryDataContext'; -import dayjs from 'dayjs'; -import { Position } from 'geojson'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useObservationsContext, useTaxonomyContext } from 'hooks/useContext'; -import useDataLoader from 'hooks/useDataLoader'; -import { ITelemetry } from 'hooks/useTelemetryApi'; -import { ISimpleCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; -import { useContext, useEffect, useMemo, useState } from 'react'; -import { getCodesName, getFormattedDate } from 'utils/Utils'; -import { IAnimalDeployment } from '../../survey-animals/telemetry-device/device'; -import SurveyMap, { ISurveyMapPoint, ISurveyMapPointMetadata, ISurveyMapSupplementaryLayer } from '../../SurveyMap'; -import SurveyMapPopup from '../../SurveyMapPopup'; -import SurveyMapTooltip from '../../SurveyMapTooltip'; -import SurveySpatialObservationDataTable from './SurveySpatialObservationDataTable'; -import SurveySpatialTelemetryDataTable from './SurveySpatialTelemetryDataTable'; -import SurveySpatialToolbar, { SurveySpatialDatasetViewEnum } from './SurveySpatialToolbar'; - -const SurveySpatialData = () => { - const [activeView, setActiveView] = useState(SurveySpatialDatasetViewEnum.OBSERVATIONS); - - const observationsContext = useObservationsContext(); - const telemetryContext = useContext(TelemetryDataContext); - const taxonomyContext = useTaxonomyContext(); - const surveyContext = useContext(SurveyContext); - const codesContext = useContext(CodesContext); - const { projectId, surveyId } = useContext(SurveyContext); - - const biohubApi = useBiohubApi(); - - const [mapPointMetadata, setMapPointMetadata] = useState>({}); - - // Fetch observations spatial data - const observationsGeometryDataLoader = useDataLoader(() => - biohubApi.observation.getObservationsGeometry(projectId, surveyId) - ); - observationsGeometryDataLoader.load(); - - // Fetch study area data - const studyAreaLocations = useMemo( - () => surveyContext.surveyDataLoader.data?.surveyData.locations ?? [], - [surveyContext.surveyDataLoader.data] - ); - - const sampleSites = useMemo( - () => surveyContext.sampleSiteDataLoader.data?.sampleSites ?? [], - [surveyContext.sampleSiteDataLoader.data] - ); - - useEffect(() => { - if (surveyContext.deploymentDataLoader.data) { - const deploymentIds = surveyContext.deploymentDataLoader.data.map((item) => item.deployment_id); - telemetryContext.telemetryDataLoader.refresh(deploymentIds); - } - // Should not re-run this effect on `telemetryContext.telemetryDataLoader.refresh` changes - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [surveyContext.deploymentDataLoader.data]); - - // Fetch/cache all taxonomic data for the observations - useEffect(() => { - const cacheTaxonomicData = async () => { - if (observationsContext.observationsDataLoader.data) { - // fetch all unique itis_tsn's from observations to find taxonomic names - const taxonomicIds = [ - ...new Set(observationsContext.observationsDataLoader.data.surveyObservations.map((item) => item.itis_tsn)) - ].filter((tsn): tsn is number => tsn !== null); - await taxonomyContext.cacheSpeciesTaxonomyByIds(taxonomicIds); - } - }; - - cacheTaxonomicData(); - // Should not re-run this effect on `taxonomyContext` changes - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [observationsContext.observationsDataLoader.data]); - - /** - * Because Telemetry data is client-side paginated, we can collect all spatial points from - * traversing the array of telemetry data. - */ - const telemetryPoints: ISurveyMapPoint[] = useMemo(() => { - const deployments: IAnimalDeployment[] = surveyContext.deploymentDataLoader.data ?? []; - const critters: ISimpleCritterWithInternalId[] = surveyContext.critterDataLoader.data ?? []; - const telemetry: ITelemetry[] = telemetryContext.telemetryDataLoader.data ?? []; - - return ( - telemetry - .filter((telemetry) => telemetry.latitude !== undefined && telemetry.longitude !== undefined) - - // Combine all critter and deployments data into a flat list - .reduce( - ( - acc: { deployment: IAnimalDeployment; critter: ISimpleCritterWithInternalId; telemetry: ITelemetry }[], - telemetry: ITelemetry - ) => { - const deployment = deployments.find( - (animalDeployment) => animalDeployment.deployment_id === telemetry.deployment_id - ); - const critter = critters.find((detailedCritter) => detailedCritter.critter_id === deployment?.critter_id); - if (critter && deployment) { - acc.push({ deployment, critter, telemetry }); - } - - return acc; - }, - [] - ) - .map(({ telemetry, deployment, critter }) => { - return { - feature: { - type: 'Feature', - properties: {}, - geometry: { - type: 'Point', - coordinates: [telemetry.longitude, telemetry.latitude] as Position - } - }, - key: `telemetry-${telemetry.id}`, - onLoadMetadata: async (): Promise => { - return Promise.resolve([ - { label: 'Device ID', value: String(deployment.device_id) }, - { label: 'Alias', value: critter.animal_id ?? '' }, - { - label: 'Location', - value: [telemetry.latitude, telemetry.longitude] - .filter((coord): coord is number => coord !== null) - .map((coord) => coord.toFixed(6)) - .join(', ') - }, - { label: 'Date', value: dayjs(telemetry.acquisition_date).toISOString() } - ]); - } - }; - }) - ); - }, [ - surveyContext.critterDataLoader.data, - surveyContext.deploymentDataLoader.data, - telemetryContext.telemetryDataLoader.data - ]); - - /** - * Because Observations data is server-side paginated, we must collect all spatial points from - * a dedicated endpoint. - */ - const observationPoints: ISurveyMapPoint[] = useMemo(() => { - return (observationsGeometryDataLoader.data?.surveyObservationsGeometry ?? []).map((observation) => { - const point: ISurveyMapPoint = { - feature: { - type: 'Feature', - properties: {}, - geometry: observation.geometry - }, - key: `observation-${observation.survey_observation_id}`, - onLoadMetadata: async (): Promise => { - const response = await biohubApi.observation.getObservationRecord( - projectId, - surveyId, - observation.survey_observation_id - ); - - return [ - { label: 'Taxon ID', value: String(response.itis_tsn) }, - { label: 'Count', value: String(response.count) }, - { - label: 'Coords', - value: [response.latitude, response.longitude] - .filter((coord): coord is number => coord !== null) - .map((coord) => coord.toFixed(6)) - .join(', ') - }, - { - label: 'Date', - value: getFormattedDate( - response.observation_time ? DATE_FORMAT.ShortMediumDateTimeFormat : DATE_FORMAT.ShortMediumDateFormat, - `${response.observation_date} ${response.observation_time}` - ) - } - ]; - } - }; - - return point; - }); - }, [biohubApi.observation, observationsGeometryDataLoader.data?.surveyObservationsGeometry, projectId, surveyId]); - - let isLoading = false; - if (activeView === SurveySpatialDatasetViewEnum.OBSERVATIONS) { - isLoading = - codesContext.codesDataLoader.isLoading ?? - surveyContext.sampleSiteDataLoader.isLoading ?? - observationsContext.observationsDataLoader.isLoading; - } - - if (activeView === SurveySpatialDatasetViewEnum.TELEMETRY) { - isLoading = - codesContext.codesDataLoader.isLoading ?? - surveyContext.deploymentDataLoader.isLoading ?? - surveyContext.critterDataLoader.isLoading; - } - - const supplementaryLayers: ISurveyMapSupplementaryLayer[] = useMemo(() => { - switch (activeView) { - case SurveySpatialDatasetViewEnum.OBSERVATIONS: - return [ - { - layerName: 'Observations', - layerColors: { - fillColor: SURVEY_MAP_LAYER_COLOURS.OBSERVATIONS_COLOUR, - color: SURVEY_MAP_LAYER_COLOURS.OBSERVATIONS_COLOUR - }, - popupRecordTitle: 'Observation Record', - mapPoints: observationPoints - } - ]; - case SurveySpatialDatasetViewEnum.TELEMETRY: - return [ - { - layerName: 'Telemetry', - layerColors: { - fillColor: SURVEY_MAP_LAYER_COLOURS.TELEMETRY_COLOUR, - color: SURVEY_MAP_LAYER_COLOURS.TELEMETRY_COLOUR, - opacity: 0.5 - }, - popupRecordTitle: 'Telemetry Record', - mapPoints: telemetryPoints - } - ]; - case SurveySpatialDatasetViewEnum.MARKED_ANIMALS: - default: - return []; - } - }, [activeView, observationPoints, telemetryPoints]); - - const staticLayers: IStaticLayer[] = [ - { - layerName: 'Study Areas', - layerColors: { - color: SURVEY_MAP_LAYER_COLOURS.STUDY_AREA_COLOUR, - fillColor: SURVEY_MAP_LAYER_COLOURS.STUDY_AREA_COLOUR - }, - features: studyAreaLocations.flatMap((location) => { - return location.geojson.map((feature, index) => { - return { - key: `${location.survey_location_id}-${index}`, - geoJSON: feature, - popup: ( - - ), - tooltip: - }; - }); - }) - }, - { - layerName: 'Sample Sites', - layerColors: { - color: SURVEY_MAP_LAYER_COLOURS.SAMPLING_SITE_COLOUR, - fillColor: SURVEY_MAP_LAYER_COLOURS.SAMPLING_SITE_COLOUR - }, - features: sampleSites.map((sampleSite, index) => { - return { - key: `${sampleSite.survey_sample_site_id}-${index}`, - geoJSON: sampleSite.geojson, - popup: ( - - getCodesName( - codesContext.codesDataLoader.data, - 'sample_methods', - method.technique.method_technique_id - ) ?? '' - ) - .filter(Boolean) - .join(', ') - } - ]} - /> - ), - tooltip: - }; - }) - }, - ...supplementaryLayers.map((supplementaryLayer) => { - return { - layerName: supplementaryLayer.layerName, - layerColors: { - fillColor: supplementaryLayer.layerColors?.fillColor ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, - color: supplementaryLayer.layerColors?.color ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, - fillOpacity: supplementaryLayer.layerColors?.opacity ?? 1 - }, - features: supplementaryLayer.mapPoints.map((mapPoint: ISurveyMapPoint): IStaticLayerFeature => { - const isLoading = !mapPointMetadata[mapPoint.key]; - - return { - key: mapPoint.key, - geoJSON: mapPoint.feature, - GeoJSONProps: { - onEachFeature: (_, layer) => { - layer.on({ - popupopen: () => { - if (mapPointMetadata[mapPoint.key]) { - return; - } - mapPoint.onLoadMetadata().then((metadata) => { - setMapPointMetadata((prev) => ({ ...prev, [mapPoint.key]: metadata })); - }); - } - }); - } - }, - popup: ( - - ), - tooltip: - }; - }) - }; - }) - ]; - - return ( - - - - - - - - - {activeView === SurveySpatialDatasetViewEnum.OBSERVATIONS && ( - - )} - - {activeView === SurveySpatialDatasetViewEnum.TELEMETRY && ( - - )} - - - ); -}; - -export default SurveySpatialData; diff --git a/app/src/features/surveys/view/components/spatial-data/SurveySpatialTelemetryDataTable.tsx b/app/src/features/surveys/view/components/spatial-data/SurveySpatialTelemetryDataTable.tsx deleted file mode 100644 index 845dd6eded..0000000000 --- a/app/src/features/surveys/view/components/spatial-data/SurveySpatialTelemetryDataTable.tsx +++ /dev/null @@ -1,132 +0,0 @@ -import grey from '@mui/material/colors/grey'; -import Skeleton from '@mui/material/Skeleton'; -import Stack from '@mui/material/Stack'; -import { GridColDef } from '@mui/x-data-grid'; -import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; -import { SurveyContext } from 'contexts/surveyContext'; -import dayjs from 'dayjs'; -import { useContext, useMemo } from 'react'; - -// Set height so we the skeleton loader will match table rows -const rowHeight = 52; - -interface ITelemetryData { - id: number; - critter_id: string | null; - device_id: number; - start: string; - end: string; -} - -interface ISurveySpatialTelemetryDataTableProps { - isLoading: boolean; -} - -// Skeleton Loader template -const SkeletonRow = () => ( - - - - - - - - - - - -); - -const SurveySpatialTelemetryDataTable = (props: ISurveySpatialTelemetryDataTableProps) => { - const surveyContext = useContext(SurveyContext); - - const tableRows = useMemo(() => { - return surveyContext.critterDeployments.map((item) => ({ - // critters in this table may use multiple devices accross multiple timespans - id: `${item.critter.survey_critter_id}-${item.deployment.device_id}-${item.deployment.attachment_start}`, - alias: item.critter.animal_id, - device_id: item.deployment.device_id, - start: dayjs(item.deployment.attachment_start).format('YYYY-MM-DD'), - end: item.deployment.attachment_end ? dayjs(item.deployment.attachment_end).format('YYYY-MM-DD') : 'Still Active' - })); - }, [surveyContext.critterDeployments]); - - const columns: GridColDef[] = [ - { - field: 'alias', - headerName: 'Alias', - flex: 1 - }, - { - field: 'device_id', - headerName: 'Device ID', - flex: 1 - }, - { - field: 'start', - headerName: 'Start', - flex: 1 - }, - { - field: 'end', - headerName: 'End', - flex: 1 - } - ]; - - return ( - <> - {props.isLoading ? ( - - - - - - ) : ( - row.id} - columns={columns} - initialState={{ - pagination: { - paginationModel: { page: 1, pageSize: 5 } - } - }} - pageSizeOptions={[5]} - rowSelection={false} - checkboxSelection={false} - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - disableVirtualization - sortingOrder={['asc', 'desc']} - data-testid="survey-spatial-telemetry-data-table" - /> - )} - - ); -}; - -export default SurveySpatialTelemetryDataTable; diff --git a/app/src/features/surveys/view/survey-animals/AnimalList.tsx b/app/src/features/surveys/view/survey-animals/AnimalList.tsx deleted file mode 100644 index 5d66936179..0000000000 --- a/app/src/features/surveys/view/survey-animals/AnimalList.tsx +++ /dev/null @@ -1,242 +0,0 @@ -import { - mdiChevronDown, - mdiFamilyTree, - mdiFormatListGroup, - mdiInformationOutline, - mdiPlus, - mdiRuler, - mdiSkullOutline, - mdiSpiderWeb, - mdiTagOutline -} from '@mdi/js'; -import Icon from '@mdi/react'; -import Accordion from '@mui/material/Accordion'; -import AccordionDetails from '@mui/material/AccordionDetails'; -import AccordionSummary from '@mui/material/AccordionSummary'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import grey from '@mui/material/colors/grey'; -import Divider from '@mui/material/Divider'; -import List from '@mui/material/List'; -import ListItemButton from '@mui/material/ListItemButton'; -import ListItemIcon from '@mui/material/ListItemIcon'; -import ListItemText from '@mui/material/ListItemText'; -import Paper from '@mui/material/Paper'; -import Skeleton from '@mui/material/Skeleton'; -import Stack from '@mui/material/Stack'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import { useQuery } from 'hooks/useQuery'; -import { ICritterDetailedResponse } from 'interfaces/useCritterApi.interface'; -import { ISimpleCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; -import { useHistory } from 'react-router-dom'; -import { ANIMAL_SECTION } from './animal'; - -interface IAnimalListProps { - isLoading?: boolean; - surveyCritters?: ISimpleCritterWithInternalId[]; - selectedSection: ANIMAL_SECTION; - onSelectSection: (section: ANIMAL_SECTION) => void; - refreshCritter: (critter_id: string) => Promise; - onAddButton: () => void; -} - -const ListPlaceholder = (props: { displaySkeleton: boolean }) => - props.displaySkeleton ? ( - - - - - ) : ( - - No Animals - - ); - -const AnimalList = (props: IAnimalListProps) => { - const { isLoading, selectedSection, onSelectSection, refreshCritter, surveyCritters, onAddButton } = props; - - const history = useHistory(); - const { critter_id } = useQuery(); - - const survey_critter_id = Number(critter_id); - - const getSectionIcon = (section: ANIMAL_SECTION) => { - switch (section) { - case ANIMAL_SECTION.GENERAL: - return mdiInformationOutline; - case ANIMAL_SECTION.COLLECTION_UNITS: - return mdiFormatListGroup; - case ANIMAL_SECTION.MARKINGS: - return mdiTagOutline; - case ANIMAL_SECTION.MEASUREMENTS: - return mdiRuler; - case ANIMAL_SECTION.CAPTURES: - return mdiSpiderWeb; - case ANIMAL_SECTION.MORTALITY: - return mdiSkullOutline; - case ANIMAL_SECTION.FAMILY: - return mdiFamilyTree; - default: - return mdiInformationOutline; - } - }; - - const handleCritterSelect = async (critter: ISimpleCritterWithInternalId) => { - if (critter.survey_critter_id === Number(survey_critter_id)) { - history.replace(history.location.pathname); - } else { - refreshCritter(critter.critter_id); - history.push(`?critter_id=${critter.survey_critter_id}`); - } - onSelectSection(ANIMAL_SECTION.GENERAL); - }; - - return ( - - - - Animals - - - - - - - {!surveyCritters?.length ? ( - - ) : ( - surveyCritters.map((critter) => ( - - - } - onClick={() => handleCritterSelect(critter)} - aria-controls="panel1bh-content" - sx={{ - flex: '1 1 auto', - gap: '16px', - height: '70px', - px: 2, - overflow: 'hidden', - '& .MuiAccordionSummary-content': { - flex: '1 1 auto', - overflow: 'hidden', - whiteSpace: 'nowrap' - } - }}> - - - {critter.animal_id} - - - {critter.itis_scientific_name} | {critter.sex} - - - - - - - {(Object.values(ANIMAL_SECTION) as ANIMAL_SECTION[]).map((section) => ( - { - onSelectSection(section); - }}> - - - - {section} - - ))} - - - - )) - )} - - - - ); -}; - -export default AnimalList; diff --git a/app/src/features/surveys/view/survey-animals/AnimalSection.test.tsx b/app/src/features/surveys/view/survey-animals/AnimalSection.test.tsx deleted file mode 100644 index f3ac7781ec..0000000000 --- a/app/src/features/surveys/view/survey-animals/AnimalSection.test.tsx +++ /dev/null @@ -1,150 +0,0 @@ -import { render } from '@testing-library/react'; -import { AuthStateContext } from 'contexts/authStateContext'; -import { ConfigContext, IConfig } from 'contexts/configContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { IDetailedCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; -import { AuthProvider, AuthProviderProps } from 'react-oidc-context'; -import { getMockAuthState, SystemAdminAuthState } from 'test-helpers/auth-helpers'; -import { cleanup, waitFor } from 'test-helpers/test-utils'; -import { ANIMAL_SECTION } from './animal'; -import { AnimalSection } from './AnimalSection'; -jest.mock('../../../../hooks/useCritterbaseApi'); -const mockCritterbaseApi = useCritterbaseApi as jest.Mock; - -const mockRefreshCritter = jest.fn(); - -const authState = getMockAuthState({ base: SystemAdminAuthState }); - -const authConfig: AuthProviderProps = { - authority: 'authority', - client_id: 'client', - redirect_uri: 'redirect' -}; - -const animalSection = (section: ANIMAL_SECTION, critter?: IDetailedCritterWithInternalId) => ( - - - - - - - -); - -describe('AnimalSection', () => { - beforeEach(() => { - mockCritterbaseApi.mockImplementation(() => ({ - family: { - getAllFamilies: jest.fn() - } - })); - }); - afterEach(() => { - cleanup(); - }); - it('should mount with empty state with no critter', async () => { - const screen = render(animalSection(ANIMAL_SECTION.GENERAL)); - await waitFor(() => { - const header = screen.getByRole('heading', { name: /no animal selected/i }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the general section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.GENERAL, { - critter_id: 'blah', - survey_critter_id: 1 - } as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.GENERAL }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the collection units section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.COLLECTION_UNITS, { - critter_id: 'blah', - survey_critter_id: 1, - collection_units: [] - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.COLLECTION_UNITS }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the markings section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.MARKINGS, { - critter_id: 'blah', - survey_critter_id: 1, - markings: [] - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.MARKINGS }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the measurements section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.MEASUREMENTS, { - critter_id: 'blah', - survey_critter_id: 1, - measurements: { qualitative: [], quantitative: [] } - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.MEASUREMENTS }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the captures section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.CAPTURES, { - critter_id: 'blah', - survey_critter_id: 1, - captures: [] - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.CAPTURES }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the mortality section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.MORTALITY, { - critter_id: 'blah', - survey_critter_id: 1, - mortality: [] - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.MORTALITY }); - expect(header).toBeInTheDocument(); - }); - }); - - it('should render the family section', async () => { - const screen = render( - animalSection(ANIMAL_SECTION.FAMILY, { - critter_id: 'blah', - survey_critter_id: 1, - family_parent: [], - family_child: [] - } as unknown as IDetailedCritterWithInternalId) - ); - await waitFor(() => { - const header = screen.getByRole('heading', { name: ANIMAL_SECTION.FAMILY }); - expect(header).toBeInTheDocument(); - }); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/AnimalSection.tsx b/app/src/features/surveys/view/survey-animals/AnimalSection.tsx deleted file mode 100644 index 7e1e00c39b..0000000000 --- a/app/src/features/surveys/view/survey-animals/AnimalSection.tsx +++ /dev/null @@ -1,410 +0,0 @@ -import { mdiPlus } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Collapse from '@mui/material/Collapse'; -import grey from '@mui/material/colors/grey'; -import Typography from '@mui/material/Typography'; -import { SurveyAnimalsI18N } from 'constants/i18n'; -import dayjs from 'dayjs'; -import utc from 'dayjs/plugin/utc'; -import { EditDeleteStubCard } from 'features/surveys/components/EditDeleteStubCard'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICritterDetailedResponse, IFamilyChildResponse } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; -import { TransitionGroup } from 'react-transition-group'; -import { AnimalRelationship, ANIMAL_FORM_MODE, ANIMAL_SECTION } from './animal'; -import { AnimalSectionWrapper } from './AnimalSectionWrapper'; -import CaptureAnimalForm from './form-sections/CaptureAnimalForm'; -import CollectionUnitAnimalForm from './form-sections/CollectionUnitAnimalForm'; -import { FamilyAnimalForm } from './form-sections/FamilyAnimalForm'; -import GeneralAnimalForm from './form-sections/GeneralAnimalForm'; -import { MarkingAnimalForm } from './form-sections/MarkingAnimalForm'; -import MeasurementAnimalForm from './form-sections/MeasurementAnimalForm'; -import MortalityAnimalForm from './form-sections/MortalityAnimalForm'; -import GeneralAnimalSummary from './GeneralAnimalSummary'; - -dayjs.extend(utc); - -type SubHeaderData = Record; -type DeleteFn = (...args: any[]) => Promise; - -interface IAnimalSectionProps { - /** - * Detailed Critter from Critterbase. - * In most cases the Critter will be defined with the exception of adding new. - */ - critter?: ICritterDetailedResponse; - /** - * Callback to refresh the detailed Critter. - * Children with the transition component are dependent on the Critter updating to trigger the transitions. - */ - refreshCritter: (critter_id: string) => Promise; - /** - * The selected section. - * - * example: 'Captures' | 'Markings'. - */ - section: ANIMAL_SECTION; -} - -/** - * This component acts as a switch for the animal form sections. - * - * Goal was to make the form sections share common props and also make it flexible - * handling the different requirements / needs of the individual sections. - * - * @param {IAnimalSectionProps} props - * @returns {*} - */ -export const AnimalSection = (props: IAnimalSectionProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [formObject, setFormObject] = useState(undefined); - const [openForm, setOpenForm] = useState(false); - - const formatDate = (dt: Date) => dayjs(dt).utc().format('MMMM D, YYYY'); - - const handleOpenAddForm = () => { - setFormObject(undefined); - setOpenForm(true); - }; - - const handleOpenEditForm = (editObject: any) => { - setFormObject(editObject); - setOpenForm(true); - }; - - const refreshDetailedCritter = async () => { - if (props.critter) { - return props.refreshCritter(props.critter.critter_id); - } - }; - - const handleCloseForm = () => { - setFormObject(undefined); - setOpenForm(false); - refreshDetailedCritter(); - }; - - const handleDelete = async (name: string, deleteService: T, ...args: Parameters) => { - const closeConfirmDialog = () => dialog.setYesNoDialog({ open: false }); - - dialog.setYesNoDialog({ - dialogTitle: `Delete ${name[0].toUpperCase() + name.slice(1)}`, - dialogText: 'Are you sure you want to delete this record?', - open: true, - onYes: () => { - const handleConfirmDelete = async () => { - closeConfirmDialog(); - try { - await deleteService(...args); - await refreshDetailedCritter(); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully deleted ${name}` }); - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Failed to delete ${name}` }); - } - }; - handleConfirmDelete(); - }, - onNo: () => closeConfirmDialog(), - onClose: () => closeConfirmDialog() - }); - }; - - /** - * Formats the data card sub header to a unified format. - * - * example: 'marking: ear tag | colour: blue' - * - * @param {SubHeaderData} subHeaderData - Key value pairs. - * @returns {string} Formatted sub-header. - */ - const formatSubHeader = (subHeaderData: SubHeaderData) => { - const formatArr: string[] = []; - const entries = Object.entries(subHeaderData); - entries.forEach(([key, value]) => { - if (value == null || value === '') { - return; - } - formatArr.push(`${key}: ${value}`); - }); - return formatArr.join(' | '); - }; - - const getAddButton = (label: string) => ( - - ); - - /** - * If the critter is not defined, render the empty state. - * - */ - if (!props.critter) { - return ( - - - - No Animal Selected - - - - ); - } - - /** - * Shared animal form props. - * - */ - const SECTION_FORM_PROPS = { - formMode: formObject ? ANIMAL_FORM_MODE.EDIT : ANIMAL_FORM_MODE.ADD, - formObject: formObject, - critter: props.critter, - open: openForm, - handleClose: handleCloseForm - } as const; - - /** - * Switch statements for the different form sections. - * - */ - if (props.section === ANIMAL_SECTION.GENERAL) { - return ( - } - infoText={SurveyAnimalsI18N.animalGeneralHelp} - section={props.section} - critter={props.critter}> - handleOpenEditForm(props.critter)} /> - - ); - } - - if (props.section === ANIMAL_SECTION.COLLECTION_UNITS) { - return ( - } - addBtn={getAddButton(SurveyAnimalsI18N.animalCollectionUnitAddBtn)} - infoText={SurveyAnimalsI18N.animalCollectionUnitHelp} - section={props.section} - critter={props.critter}> - - {props.critter.collection_units.map((unit) => ( - - handleOpenEditForm(unit)} - onClickDelete={async () => { - handleDelete( - 'ecological unit', - critterbaseApi.collectionUnit.deleteCritterCollectionUnit, - unit.critter_collection_unit_id - ); - }} - /> - - ))} - - - ); - } - - if (props.section === ANIMAL_SECTION.MARKINGS) { - return ( - } - addBtn={getAddButton(SurveyAnimalsI18N.animalMarkingAddBtn)} - infoText={SurveyAnimalsI18N.animalMarkingHelp} - section={props.section} - critter={props.critter}> - - {props.critter.markings.map((marking) => ( - - handleOpenEditForm(marking)} - onClickDelete={async () => { - handleDelete('marking', critterbaseApi.marking.deleteMarking, marking.marking_id); - }} - /> - - ))} - - - ); - } - - if (props.section === ANIMAL_SECTION.MEASUREMENTS) { - return ( - } - infoText={SurveyAnimalsI18N.animalMeasurementHelp} - addBtn={getAddButton(SurveyAnimalsI18N.animalMeasurementAddBtn)} - section={props.section} - critter={props.critter}> - - {props.critter.measurements.quantitative.map((measurement) => ( - - handleOpenEditForm(measurement)} - onClickDelete={async () => { - handleDelete( - 'measurement', - critterbaseApi.measurement.deleteQuantitativeMeasurement, - measurement.measurement_quantitative_id - ); - }} - /> - - ))} - {props.critter.measurements.qualitative.map((measurement) => ( - - handleOpenEditForm(measurement)} - onClickDelete={async () => { - handleDelete( - 'measurement', - critterbaseApi.measurement.deleteQualitativeMeasurement, - measurement.measurement_qualitative_id - ); - }} - /> - - ))} - - - ); - } - - if (props.section === ANIMAL_SECTION.MORTALITY) { - return ( - } - infoText={SurveyAnimalsI18N.animalMortalityHelp} - addBtn={ - props.critter.mortality.length === 0 ? getAddButton(SurveyAnimalsI18N.animalMortalityAddBtn) : undefined - } - section={props.section} - critter={props.critter}> - - {props.critter.mortality.map((mortality) => ( - - handleOpenEditForm(mortality)} - onClickDelete={async () => { - handleDelete('mortality', critterbaseApi.mortality.deleteMortality, mortality.mortality_id); - }} - /> - - ))} - - - ); - } - - if (props.section === ANIMAL_SECTION.FAMILY) { - return ( - } - infoText={SurveyAnimalsI18N.animalFamilyHelp} - addBtn={getAddButton(SurveyAnimalsI18N.animalFamilyAddBtn)} - section={props.section} - critter={props.critter}> - - {[...props.critter.family_child, ...props.critter.family_parent].map((family) => { - const isChild = (family as IFamilyChildResponse)?.child_critter_id; - return ( - - handleOpenEditForm({ ...family, critter_id: props.critter?.critter_id })} - onClickDelete={async () => { - handleDelete('family relationship', critterbaseApi.family.deleteRelationship, { - relationship: isChild ? AnimalRelationship.CHILD : AnimalRelationship.PARENT, - family_id: family.family_id, - critter_id: props.critter?.critter_id ?? '' - }); - }} - /> - - ); - })} - - - ); - } - - if (props.section === ANIMAL_SECTION.CAPTURES) { - return ( - } - addBtn={getAddButton(SurveyAnimalsI18N.animalCaptureAddBtn)} - infoText={SurveyAnimalsI18N.animalCaptureHelp} - section={props.section} - critter={props.critter}> - - {props.critter.captures.map((capture) => ( - - handleOpenEditForm(capture)} - onClickDelete={async () => { - handleDelete('capture', critterbaseApi.capture.deleteCapture, capture.capture_id); - }} - /> - - ))} - - - ); - } - - return null; -}; diff --git a/app/src/features/surveys/view/survey-animals/AnimalSectionWrapper.tsx b/app/src/features/surveys/view/survey-animals/AnimalSectionWrapper.tsx deleted file mode 100644 index b490c5ae6e..0000000000 --- a/app/src/features/surveys/view/survey-animals/AnimalSectionWrapper.tsx +++ /dev/null @@ -1,102 +0,0 @@ -import Box from '@mui/material/Box'; -import grey from '@mui/material/colors/grey'; -import Divider from '@mui/material/Divider'; -import Paper from '@mui/material/Paper'; -import Stack from '@mui/material/Stack'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import { ICritterDetailedResponse } from 'interfaces/useCritterApi.interface'; -import { PropsWithChildren } from 'react'; -import { ANIMAL_SECTION } from './animal'; - -interface IAnimalSectionWrapperProps extends PropsWithChildren { - form?: JSX.Element; - section?: ANIMAL_SECTION; - infoText?: string; - critter?: ICritterDetailedResponse; - addBtn?: JSX.Element; -} -/** - * Wrapper for the selected section main content. - * - * This component renders beside the AnimalList navbar. - * In most cases it displays the currently selected critter + the attribute data cards. - * - * Note: All props can be undefined to easily handle the empty state. - * - * @param {IAnimalSectionWrapperProps} props - * @returns {*} - */ -export const AnimalSectionWrapper = (props: IAnimalSectionWrapperProps) => { - return ( - <> - {props.form} - - - - {props.critter ? `Animal Details > ${props.critter?.animal_id}` : 'No animal selected'} - - - - - {!props?.critter ? ( - - - No Animal Selected - - - ) : ( - - - - - {props.section} - - {props.addBtn} - - - - {props.infoText} - - {props.children} - - - )} - - - ); -}; diff --git a/app/src/features/surveys/view/survey-animals/GeneralAnimalSummary.tsx b/app/src/features/surveys/view/survey-animals/GeneralAnimalSummary.tsx deleted file mode 100644 index f2e6b57a61..0000000000 --- a/app/src/features/surveys/view/survey-animals/GeneralAnimalSummary.tsx +++ /dev/null @@ -1,89 +0,0 @@ -import { mdiContentCopy, mdiPencilOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import Divider from '@mui/material/Divider'; -import IconButton from '@mui/material/IconButton'; -import Paper from '@mui/material/Paper'; -import Toolbar from '@mui/material/Toolbar'; -import Typography from '@mui/material/Typography'; -import { DialogContext } from 'contexts/dialogContext'; -import { ICritterDetailedResponse } from 'interfaces/useCritterApi.interface'; -import { useContext } from 'react'; -import { setMessageSnackbar } from 'utils/Utils'; -import { DetailsWrapper } from '../SurveyDetails'; - -interface IGeneralDetail { - title: string; - value?: string | null; - valueEndIcon?: JSX.Element; -} - -interface GeneralAnimalSummaryProps { - /* - * Callback to be fired when edit action selected - */ - handleEdit: () => void; - critter: ICritterDetailedResponse; -} - -const GeneralAnimalSummary = (props: GeneralAnimalSummaryProps) => { - const dialogContext = useContext(DialogContext); - - const animalGeneralDetails: Array = [ - { title: 'Alias', value: props.critter?.animal_id }, - { title: 'Taxon', value: props.critter.itis_scientific_name }, - { title: 'Sex', value: props.critter.sex }, - { title: 'Wildlife Health ID', value: props.critter?.wlh_id }, - { - title: 'Critterbase ID', - value: props?.critter?.critter_id, - valueEndIcon: ( - { - navigator.clipboard.writeText(props?.critter?.critter_id ?? ''); - setMessageSnackbar('Copied Critter ID', dialogContext); - }}> - - - ) - } - ]; - - return ( - - - - - Animal Summary - - - - - - - - - Details - - {animalGeneralDetails.map((details) => - details.value !== undefined ? ( - - {details.title} - - {details.value} - {details.valueEndIcon} - - - ) : null - )} - - - - - - ); -}; - -export default GeneralAnimalSummary; diff --git a/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.test.tsx b/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.test.tsx deleted file mode 100644 index 1dc65f98b1..0000000000 --- a/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.test.tsx +++ /dev/null @@ -1,165 +0,0 @@ -import { AuthStateContext } from 'contexts/authStateContext'; -import { IProjectAuthStateContext, ProjectAuthStateContext } from 'contexts/projectAuthStateContext'; -import { IProjectContext, ProjectContext } from 'contexts/projectContext'; -import { ISurveyContext, SurveyContext } from 'contexts/surveyContext'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { DataLoader } from 'hooks/useDataLoader'; -import { useTelemetryApi } from 'hooks/useTelemetryApi'; -import { BrowserRouter } from 'react-router-dom'; -import { getMockAuthState, SystemAdminAuthState } from 'test-helpers/auth-helpers'; -import { cleanup, fireEvent, render, waitFor } from 'test-helpers/test-utils'; -import { SurveyAnimalsPage } from './SurveyAnimalsPage'; - -jest.mock('hooks/useQuery', () => ({ useQuery: () => ({ critter_id: 0 }) })); -jest.mock('../../../../hooks/useBioHubApi.ts'); -jest.mock('../../../../hooks/useTelemetryApi'); -jest.mock('../../../../hooks/useCritterbaseApi'); -const mockBiohubApi = useBiohubApi as jest.Mock; -const mockTelemetryApi = useTelemetryApi as jest.Mock; -const mockCritterbaseApi = useCritterbaseApi as jest.Mock; - -const mockUseBiohub = { - survey: { - getSurveyCritters: jest.fn(), - getDeploymentsInSurvey: jest.fn() - }, - taxonomy: { - getSpeciesFromIds: jest.fn() - } -}; - -const mockUseTelemetry = { - devices: { - getDeviceDetails: jest.fn() - } -}; - -const mockUseCritterbase = { - critters: { - getDetailedCritter: jest.fn() - }, - family: { - getAllFamilies: jest.fn() - }, - lookup: { - getTaxonMeasurements: jest.fn() - } -}; -const mockSurveyContext: ISurveyContext = { - artifactDataLoader: { - data: null, - load: jest.fn() - } as unknown as DataLoader, - surveyId: 1, - projectId: 1, - surveyDataLoader: { - data: { surveyData: { survey_details: { survey_name: 'name' } } }, - load: jest.fn() - } as unknown as DataLoader -} as unknown as ISurveyContext; - -const mockProjectAuthStateContext: IProjectAuthStateContext = { - getProjectParticipant: () => null, - hasProjectRole: () => true, - hasProjectPermission: () => true, - hasSystemRole: () => true, - getProjectId: () => 1, - hasLoadedParticipantInfo: true -}; - -const mockProjectContext: IProjectContext = { - artifactDataLoader: { - data: null, - load: jest.fn() - } as unknown as DataLoader, - projectId: 1, - projectDataLoader: { - data: { projectData: { project: { project_name: 'name' } } }, - load: jest.fn() - } as unknown as DataLoader -} as unknown as IProjectContext; - -const authState = getMockAuthState({ base: SystemAdminAuthState }); - -const page = ( - - - - - - - - - - - -); - -describe('SurveyAnimalsPage', () => { - beforeEach(async () => { - mockBiohubApi.mockImplementation(() => mockUseBiohub); - mockTelemetryApi.mockImplementation(() => mockUseTelemetry); - mockCritterbaseApi.mockImplementation(() => mockUseCritterbase); - mockUseBiohub.survey.getDeploymentsInSurvey.mockClear(); - mockUseBiohub.survey.getSurveyCritters.mockClear(); - mockUseTelemetry.devices.getDeviceDetails.mockClear(); - mockUseCritterbase.family.getAllFamilies.mockClear(); - mockUseCritterbase.lookup.getTaxonMeasurements.mockClear(); - }); - - afterEach(() => { - cleanup(); - }); - - it('should render the add critter dialog', async () => { - const screen = render(page); - - await waitFor(() => { - const addAnimalBtn = screen.getByRole('button', { name: 'Add' }); - expect(addAnimalBtn).toBeInTheDocument(); - }); - - await waitFor(() => { - fireEvent.click(screen.getByText('Add')); - }); - - await waitFor(() => { - expect(screen.getByText('Add Critter')).toBeInTheDocument(); - }); - - await waitFor(() => { - fireEvent.click(screen.getByText('Cancel')); - }); - }); - - it('should be able to select critter from navbar', async () => { - mockUseBiohub.survey.getSurveyCritters.mockResolvedValueOnce([ - { - critter_id: 'critter_uuid', - animal_id: 'test-critter-alias', - wlh_id: '123-45', - survey_critter_id: 1, - taxon: 'a', - created_at: 'a' - } - ]); - const screen = render(page); - await waitFor(() => { - const addAnimalBtn = screen.getByRole('button', { name: 'Add' }); - expect(addAnimalBtn).toBeInTheDocument(); - }); - - await waitFor(() => { - expect(screen.getByText('test-critter-alias')).toBeInTheDocument(); - }); - - await waitFor(() => { - fireEvent.click(screen.getByText('test-critter-alias')); - }); - - await waitFor(() => { - expect(screen.getByText('General')).toBeInTheDocument(); - }); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.tsx b/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.tsx deleted file mode 100644 index ecb8dd7392..0000000000 --- a/app/src/features/surveys/view/survey-animals/SurveyAnimalsPage.tsx +++ /dev/null @@ -1,86 +0,0 @@ -import { SurveyContext } from 'contexts/surveyContext'; -import { SurveySectionFullPageLayout } from 'features/surveys/components/layout/SurveySectionFullPageLayout'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { useQuery } from 'hooks/useQuery'; -import { useContext, useEffect, useState } from 'react'; -import { ANIMAL_FORM_MODE, ANIMAL_SECTION } from './animal'; -import AnimalList from './AnimalList'; -import { AnimalSection } from './AnimalSection'; -import GeneralAnimalForm from './form-sections/GeneralAnimalForm'; - -export const SurveyAnimalsPage = () => { - const biohubApi = useBiohubApi(); - const critterbaseApi = useCritterbaseApi(); - - const { surveyId, projectId } = useContext(SurveyContext); - - const { critter_id } = useQuery(); - - const survey_critter_id = Number(critter_id); - - const [selectedSection, setSelectedSection] = useState(ANIMAL_SECTION.GENERAL); - const [openAddCritter, setOpenAddCritter] = useState(false); - - const { - data: surveyCritters, - load: loadCritters, - refresh: refreshSurveyCritters, - isLoading: crittersLoading - } = useDataLoader(() => biohubApi.survey.getSurveyCritters(projectId, surveyId)); - - const { data: detailedCritter, refresh: refreshCritter } = useDataLoader(critterbaseApi.critters.getDetailedCritter); - - loadCritters(); - - useEffect(() => { - const getDetailedCritterOnMount = async () => { - if (detailedCritter) { - return; - } - const focusCritter = surveyCritters?.find((critter) => critter.survey_critter_id === Number(survey_critter_id)); - if (!focusCritter) { - return; - } - await refreshCritter(focusCritter.critter_id); - }; - getDetailedCritterOnMount(); - }, [surveyCritters, survey_critter_id, critterbaseApi.critters, detailedCritter, refreshCritter]); - - return ( - <> - { - setOpenAddCritter(false); - refreshSurveyCritters(); - }} - /> - setOpenAddCritter(true)} - refreshCritter={refreshCritter} - surveyCritters={surveyCritters} - isLoading={crittersLoading} - selectedSection={selectedSection} - onSelectSection={(section) => setSelectedSection(section)} - /> - } - mainComponent={ - - } - /> - - ); -}; diff --git a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTable.tsx b/app/src/features/surveys/view/survey-animals/SurveyAnimalsTable.tsx deleted file mode 100644 index e532c67a3b..0000000000 --- a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTable.tsx +++ /dev/null @@ -1,132 +0,0 @@ -import { GridColDef } from '@mui/x-data-grid'; -import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; -import { ProjectRoleGuard } from 'components/security/Guards'; -import { PROJECT_PERMISSION, SYSTEM_ROLE } from 'constants/roles'; -import { default as dayjs } from 'dayjs'; -import { ISimpleCritterWithInternalId } from 'interfaces/useSurveyApi.interface'; -import SurveyAnimalsTableActions from './SurveyAnimalsTableActions'; -import { IAnimalDeployment } from './telemetry-device/device'; - -interface ISurveyAnimalsTableEntry { - survey_critter_id: number; - critter_id: string; - animal_id: string | null; - itis_scientific_name: string; - deployments?: IAnimalDeployment[]; -} - -interface ISurveyAnimalsTableProps { - animalData: ISimpleCritterWithInternalId[]; - deviceData?: IAnimalDeployment[]; - onMenuOpen: (critter_id: number) => void; - onRemoveCritter: (critter_id: number) => void; - onEditCritter: (critter_id: number) => void; - onMapOpen: () => void; -} - -export const SurveyAnimalsTable = ({ - animalData, - deviceData, - onMenuOpen, - onRemoveCritter, - onEditCritter, - onMapOpen -}: ISurveyAnimalsTableProps): JSX.Element => { - const animalDeviceData: ISurveyAnimalsTableEntry[] = deviceData - ? [...animalData] // spreading this prevents this error "TypeError: Cannot assign to read only property '0' of object '[object Array]' in typescript" - .map((animal) => { - const deployments = deviceData.filter((device) => device.critter_id === animal.critter_id); - return { - ...animal, - deployments: deployments - }; - }) - : animalData; - - const columns: GridColDef[] = [ - { - field: 'itis_scientific_name', - headerName: 'Species', - flex: 1 - }, - { - field: 'animal_id', - headerName: 'Alias', - flex: 1 - }, - { - field: 'wlh_id', - headerName: 'WLH ID', - flex: 1, - renderCell: (params) => <>{params.value ? params.value : 'None'} - }, - { - field: 'current_devices', - headerName: 'Current Devices', - flex: 1, - valueGetter: (params) => { - const currentDeploys = params.row.deployments?.filter( - (device: IAnimalDeployment) => !device.attachment_end || dayjs(device.attachment_end).isAfter(dayjs()) - ); - return currentDeploys?.length - ? currentDeploys.map((device: IAnimalDeployment) => device.device_id).join(', ') - : 'No Devices'; - } - }, - { - field: 'previous_devices', - headerName: 'Previous Devices', - flex: 1, - valueGetter: (params) => { - const previousDeploys = params.row.deployments?.filter( - (device: IAnimalDeployment) => device.attachment_end && dayjs(device.attachment_end).isBefore(dayjs()) - ); - return previousDeploys?.length - ? previousDeploys.map((device: IAnimalDeployment) => device.device_id).join(', ') - : 'No Devices'; - } - }, - { - field: 'actions', - type: 'actions', - sortable: false, - flex: 1, - align: 'right', - maxWidth: 50, - renderCell: (params) => ( - - - - ) - } - ]; - - return ( - row.critter_id} - columns={columns} - pageSizeOptions={[5]} - rowSelection={false} - checkboxSelection={false} - hideFooter - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - disableVirtualization - sortingOrder={['asc', 'desc']} - data-testid="survey-animal-table" - /> - ); -}; diff --git a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.test.tsx b/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.test.tsx deleted file mode 100644 index 36f5a54bb5..0000000000 --- a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.test.tsx +++ /dev/null @@ -1,39 +0,0 @@ -import { fireEvent, render, waitFor } from 'test-helpers/test-utils'; -import SurveyAnimalsTableActions from './SurveyAnimalsTableActions'; - -describe('SurveyAnimalsTableActions', () => { - const onAddDevice = jest.fn(); - const onRemoveCritter = jest.fn(); - const onEditCritter = jest.fn(); - - it('all buttons should be clickable', async () => { - const { getByTestId } = render( - {}} - onEditCritter={onEditCritter} - onRemoveCritter={onRemoveCritter} - onMenuOpen={() => {}} - onMapOpen={() => {}} - /> - ); - - fireEvent.click(getByTestId('animal actions')); - - await waitFor(() => { - expect(getByTestId('animal-table-row-add-device')).toBeInTheDocument(); - expect(getByTestId('animal-table-row-remove-critter')).toBeInTheDocument(); - }); - - fireEvent.click(getByTestId('animal-table-row-add-device')); - expect(onAddDevice.mock.calls.length).toBe(1); - - fireEvent.click(getByTestId('animal-table-row-remove-critter')); - expect(onRemoveCritter.mock.calls.length).toBe(1); - - fireEvent.click(getByTestId('animal-table-row-edit-critter')); - expect(onEditCritter.mock.calls.length).toBe(1); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.tsx b/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.tsx deleted file mode 100644 index 240c000bd7..0000000000 --- a/app/src/features/surveys/view/survey-animals/SurveyAnimalsTableActions.tsx +++ /dev/null @@ -1,130 +0,0 @@ -import { mdiDotsVertical, mdiMapMarker, mdiPencilOutline, mdiPlus, mdiTrashCanOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import IconButton from '@mui/material/IconButton'; -import ListItemIcon from '@mui/material/ListItemIcon'; -import Menu from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; -import Typography from '@mui/material/Typography'; -import React, { useState } from 'react'; -import { IAnimalDeployment } from './telemetry-device/device'; - -type ICritterFn = (critter_id: number) => void; - -export interface ITableActionsMenuProps { - critter_id: number; - devices?: IAnimalDeployment[]; - onMenuOpen: ICritterFn; - onAddDevice?: ICritterFn; - onEditDevice?: ICritterFn; - onEditCritter: ICritterFn; - onRemoveCritter: ICritterFn; - onMapOpen: () => void; -} - -const SurveyAnimalsTableActions = (props: ITableActionsMenuProps) => { - const [anchorEl, setAnchorEl] = useState(null); - const open = Boolean(anchorEl); - - const handleClick = (event: React.MouseEvent) => { - setAnchorEl(event.currentTarget); - props.onMenuOpen(props.critter_id); - }; - - const handleClose = () => { - setAnchorEl(null); - }; - - return ( - <> - - - - - {props.onAddDevice ? ( - { - handleClose(); - props.onAddDevice?.(props.critter_id); - }} - data-testid="animal-table-row-add-device"> - - - - Add Telemetry Device - - ) : null} - - {props.devices?.length && props.onEditDevice ? ( - { - handleClose(); - props.onEditDevice?.(props.critter_id); - }} - data-testid="animal-table-row-edit-timespan"> - - - - Edit Telemetry Devices - - ) : null} - - { - handleClose(); - props.onEditCritter(props.critter_id); - }} - data-testid="animal-table-row-edit-critter"> - - - - Edit Animal - - - {!props.devices?.length && ( - { - handleClose(); - props.onRemoveCritter(props.critter_id); - }} - data-testid="animal-table-row-remove-critter"> - - - - Remove Animal - - )} - - {props.devices?.length ? ( - { - handleClose(); - props.onMapOpen(); - }} - data-testid="animal-table-row-view-telemetry"> - - - - View Telemetry - - ) : null} - - - ); -}; - -export default SurveyAnimalsTableActions; diff --git a/app/src/features/surveys/view/survey-animals/TextInputToggle.tsx b/app/src/features/surveys/view/survey-animals/TextInputToggle.tsx deleted file mode 100644 index 2f8aa599ca..0000000000 --- a/app/src/features/surveys/view/survey-animals/TextInputToggle.tsx +++ /dev/null @@ -1,49 +0,0 @@ -import { mdiPlus } from '@mdi/js'; -import Icon from '@mdi/react'; -import Button from '@mui/material/Button'; -import { ReactNode, useState } from 'react'; - -interface TextInputToggleProps { - label: string; - children: ReactNode; - //Additional props if you want the parent component to have control of the toggle state - toggleProps?: { - handleToggle: () => void; - toggleState: boolean; - }; -} - -/** - * Renders a toggle input. Button with label -> any component - * Used in animal form for toggle comment inputs - * - * @param {TextInputToggleProps} - * @return {*} - */ - -const TextInputToggle = ({ children, label, toggleProps }: TextInputToggleProps) => { - const [showInput, setShowInput] = useState(false); - const toggleInput = () => { - setShowInput((s) => !s); - }; - - const canShowInput = toggleProps?.toggleState === undefined ? showInput : toggleProps?.toggleState; - - return ( -
- {!canShowInput ? ( - - ) : ( - children - )} -
- ); -}; - -export default TextInputToggle; diff --git a/app/src/features/surveys/view/survey-animals/animal.ts b/app/src/features/surveys/view/survey-animals/animal.ts index ff6d0822d3..2e8d5fd962 100644 --- a/app/src/features/surveys/view/survey-animals/animal.ts +++ b/app/src/features/surveys/view/survey-animals/animal.ts @@ -1,7 +1,6 @@ import { DATE_LIMIT } from 'constants/dateTimeFormats'; import { default as dayjs } from 'dayjs'; import { - ICritterDetailedResponse, IQualitativeMeasurementCreate, IQualitativeMeasurementUpdate, IQuantitativeMeasurementCreate, @@ -9,12 +8,11 @@ import { } from 'interfaces/useCritterApi.interface'; import { PROJECTION_MODE } from 'utils/mapProjectionHelpers'; import yup from 'utils/YupSchema'; -import { AnyObjectSchema, InferType } from 'yup'; /** * Critterbase related enums. - * */ + export enum ANIMAL_FORM_MODE { ADD = 'add', EDIT = 'edit' @@ -32,77 +30,7 @@ export enum AnimalRelationship { PARENT = 'parents' } -export enum ANIMAL_SECTION { - GENERAL = 'General', - COLLECTION_UNITS = 'Ecological Units', - MARKINGS = 'Markings', - MEASUREMENTS = 'Measurements', - CAPTURES = 'Captures', - MORTALITY = 'Mortality', - FAMILY = 'Family' -} - -/** - * Shared props for animal section forms. - * example: MarkingAnimalForm - * - */ - -export type AnimalFormProps = - | { - /** - * When formMode 'ADD' formObject is undefined. - */ - formObject?: never; - /** - * The form mode -> Add / EDIT. - */ - formMode: ANIMAL_FORM_MODE.ADD; - /** - * The dialog open state. - */ - open: boolean; - /** - * Callback when dialog closes. - */ - handleClose: () => void; - /** - * Critterbase detailed critter object. - */ - critter: ICritterDetailedResponse; - } - | { - /** - * When formMode 'EDIT' formObject is defined. - */ - formObject: T; - formMode: ANIMAL_FORM_MODE.EDIT; - open: boolean; - handleClose: () => void; - critter: ICritterDetailedResponse; - }; - -/** - * Checks if property in schema is required. Used to keep required fields in sync with schema. - * ie: { required: true } -> { required: isReq(Schema, 'property_name') } - * - * @template T - AnyObjectSchema - * @param {T} schema - Yup Schema. - * @param {keyof T['fields']} key - Property of yup schema. - * @returns {boolean} indicator if required in schema. - */ -export const isRequiredInSchema = (schema: T, key: keyof T['fields']): boolean => { - return Boolean(schema.fields[key].exclusiveTests.required); -}; - -export const glt = (num: number, greater = true) => `Must be ${greater ? 'greater' : 'less'} than or equal to ${num}`; - -const req = 'Required'; -const mustBeNum = 'Must be a number'; -const numSchema = yup.number().typeError(mustBeNum); - -const latSchema = yup.number().min(-90, glt(-90)).max(90, glt(90, false)).typeError(mustBeNum); -const lonSchema = yup.number().min(-180, glt(-180)).max(180, glt(180, false)).typeError(mustBeNum); +const glt = (num: number, greater = true) => `Must be ${greater ? 'greater' : 'less'} than or equal to ${num}`; const dateSchema = yup .date() @@ -112,7 +40,6 @@ const dateSchema = yup /** * Critterbase create schemas. - * */ export const LocationSchema = yup.object().shape({ @@ -127,35 +54,35 @@ export const LocationSchema = yup.object().shape({ .number() .when('projection_mode', { is: (projection_mode: PROJECTION_MODE) => projection_mode === PROJECTION_MODE.WGS, - then: latSchema + then: yup.number().min(-90, glt(-90)).max(90, glt(90, false)).typeError('Must be a number') }) .when('projection_mode', { is: (projection_mode: PROJECTION_MODE) => projection_mode === PROJECTION_MODE.UTM, then: yup.number() }) - .required(req), + .required('Required'), longitude: yup .number() .when('projection_mode', { is: (projection_mode: PROJECTION_MODE) => projection_mode === PROJECTION_MODE.WGS, - then: lonSchema + then: yup.number().min(-180, glt(-180)).max(180, glt(180, false)).typeError('Must be a number') }) .when('projection_mode', { is: (projection_mode: PROJECTION_MODE) => projection_mode === PROJECTION_MODE.UTM, then: yup.number() }) - .required(req), - coordinate_uncertainty: yup.number().required(req), + .required('Required'), + coordinate_uncertainty: yup.number().required('Required'), coordinate_uncertainty_unit: yup.string() }); export const CreateCritterCaptureSchema = yup.object({ capture_id: yup.string().optional(), - critter_id: yup.string().required(req), + critter_id: yup.string().required('Required'), capture_location: LocationSchema.required(), release_location: LocationSchema.optional().default(undefined), capture_comment: yup.string().optional(), - capture_date: yup.string().required(req), + capture_date: yup.string().required('Required'), capture_time: yup.string().optional().nullable(), release_date: yup.string().optional().nullable(), release_time: yup.string().optional().nullable(), @@ -164,16 +91,16 @@ export const CreateCritterCaptureSchema = yup.object({ export const CreateCritterSchema = yup.object({ critter_id: yup.string().optional(), - itis_tsn: yup.number().required(req), - animal_id: yup.string().required(req), + itis_tsn: yup.number().required('Required'), + animal_id: yup.string().required('Required'), wlh_id: yup.string().optional().nullable(), - sex: yup.mixed().oneOf(Object.values(AnimalSex)).required(req), + sex: yup.mixed().oneOf(Object.values(AnimalSex)).required('Required'), critter_comment: yup.string().optional().nullable() }); export const CreateCritterMarkingSchema = yup.object({ marking_id: yup.string().optional(), - critter_id: yup.string().required(req), + critter_id: yup.string().required('Required'), marking_type_id: yup.string().required('Marking type is required'), taxon_marking_body_location_id: yup.string().required('Body location required'), primary_colour_id: yup.string().optional().nullable(), @@ -182,12 +109,12 @@ export const CreateCritterMarkingSchema = yup.object({ }); export const CreateCritterMeasurementSchema = yup.object({ - critter_id: yup.string().required().required(req), + critter_id: yup.string().required().required('Required'), measurement_qualitative_id: yup.string().optional().nullable(), measurement_quantitative_id: yup.string().optional().nullable(), taxon_measurement_id: yup.string().required('Type is required'), qualitative_option_id: yup.string().optional().nullable(), - value: numSchema.required(req).optional().nullable(), + value: yup.number().typeError('Must be a number').required('Required').optional().nullable(), measured_timestamp: dateSchema.required('Date is required').optional().nullable(), measurement_comment: yup.string().optional().nullable(), capture_id: yup.string().optional().nullable(), @@ -196,13 +123,13 @@ export const CreateCritterMeasurementSchema = yup.object({ export const CreateCritterCollectionUnitSchema = yup.object({ critter_collection_unit_id: yup.string().optional(), - critter_id: yup.string().required(req), + critter_id: yup.string().required('Required'), collection_unit_id: yup.string().required('Name is required'), collection_category_id: yup.string().required('Category is required') }); export const CreateCritterMortalitySchema = yup.object({ - critter_id: yup.string().required(req), + critter_id: yup.string().required('Required'), mortality_id: yup.string().optional().nullable(), location: LocationSchema.required(), mortality_timestamp: dateSchema.required('Mortality Date is required'), @@ -216,24 +143,24 @@ export const CreateCritterMortalitySchema = yup.object({ }); export const CreateCritterFamilySchema = yup.object({ - critter_id: yup.string().uuid().required(), + critterbase_critter_id: yup.string().uuid().required(), family_id: yup.string().optional(), family_label: yup.string().optional(), - relationship: yup.mixed().oneOf(Object.values(AnimalRelationship)).required(req) + relationship: yup.mixed().oneOf(Object.values(AnimalRelationship)).required('Required') }); /** * Critterbase schema infered types. * */ -export type ICreateCritter = InferType; - -export type ICreateCritterMarking = InferType; -export type ICreateCritterMeasurement = InferType; -export type ICreateCritterCollectionUnit = InferType & { key?: string }; -export type ICreateCritterCapture = InferType; -export type ICreateCritterFamily = InferType; -export type ICreateCritterMortality = InferType; +export type ICreateCritter = yup.InferType; + +export type ICreateCritterMarking = yup.InferType; +export type ICreateCritterMeasurement = yup.InferType; +export type ICreateCritterCollectionUnit = yup.InferType & { key?: string }; +export type ICreateCritterCapture = yup.InferType; +export type ICreateCritterFamily = yup.InferType; +export type ICreateCritterMortality = yup.InferType; /** * Adding data to a critters in bulk diff --git a/app/src/features/surveys/view/survey-animals/form-sections/CaptureAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/CaptureAnimalForm.tsx deleted file mode 100644 index 2f7b683b05..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/CaptureAnimalForm.tsx +++ /dev/null @@ -1,329 +0,0 @@ -import Box from '@mui/material/Box'; -import Checkbox from '@mui/material/Checkbox'; -import FormControlLabel from '@mui/material/FormControlLabel'; -import Grid from '@mui/material/Grid'; -import Stack from '@mui/material/Stack'; -import Switch from '@mui/material/Switch'; -import Typography from '@mui/material/Typography'; -import EditDialog from 'components/dialog/EditDialog'; -import CustomTextField from 'components/fields/CustomTextField'; -import SingleDateField from 'components/fields/SingleDateField'; -import { SurveyAnimalsI18N } from 'constants/i18n'; -import { Field, useFormikContext } from 'formik'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICaptureResponse } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; -import { getLatLngAsUtm, getUtmAsLatLng, PROJECTION_MODE } from 'utils/mapProjectionHelpers'; -import { - AnimalFormProps, - ANIMAL_FORM_MODE, - CreateCritterCaptureSchema, - ICreateCritterCapture, - isRequiredInSchema -} from '../animal'; -import FormLocationPreview from './LocationEntryForm'; - -/** - * This component renders a 'critter capture' create / edit dialog. - * - * Ties into the LocationEntryForm to display capture / release details on map. - * Handles additional conversion of UTM <--> WGS coordinates during edit and submission. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -export const CaptureAnimalForm = (props: AnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [loading, setLoading] = useState(false); - const [projectionMode, setProjectionMode] = useState(PROJECTION_MODE.WGS); - - const handleSave = async (values: ICreateCritterCapture) => { - setLoading(true); - try { - if (projectionMode === PROJECTION_MODE.UTM) { - if (values.release_location) { - const [latitude, longitude] = getUtmAsLatLng( - values.release_location.latitude, - values.release_location.longitude - ); - values = { ...values, release_location: { ...values.release_location, latitude, longitude } }; - } - const [latitude, longitude] = getUtmAsLatLng( - values.capture_location.latitude, - values.capture_location.longitude - ); - values = { ...values, capture_location: { ...values.capture_location, latitude, longitude } }; - } - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - await critterbaseApi.capture.createCapture(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created capture.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - await critterbaseApi.capture.updateCapture(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited capture.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter capture request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - return ( - - ) - }} - /> - ); -}; - -type CaptureFormProps = Pick, 'formMode'> & { - projectionMode: PROJECTION_MODE; - handleProjection: (projection: PROJECTION_MODE) => void; -}; - -const CaptureFormFields = (props: CaptureFormProps) => { - const { values, setValues, setFieldValue } = useFormikContext(); - - const [showRelease, setShowRelease] = useState(values.release_location); - - const isUtmProjection = props.projectionMode === PROJECTION_MODE.UTM; - - const disableUtmToggle = - !values.capture_location.latitude || - !values.capture_location.longitude || - (showRelease && !values?.release_location?.latitude) || - !values?.release_location?.longitude; - - const handleShowRelease = () => { - /** - * If release is currently showing wipe existing values in release_location. - * - */ - if (showRelease) { - setFieldValue('release_location', undefined); - setShowRelease(false); - return; - } - setValues({ - ...values, - release_location: { latitude: '', longitude: '', coordinate_uncertainty: '', coordinate_uncertainty_unit: 'm' } - }); - setShowRelease(true); - }; - - const handleProjectionChange = () => { - const switchProjection = isUtmProjection ? PROJECTION_MODE.WGS : PROJECTION_MODE.UTM; - - /** - * These projection conversions are expecting non null values for lat/lng. - * UI currently hides the UTM toggle when these values are not defined in the form. - * - */ - const [captureLat, captureLon] = !isUtmProjection - ? getLatLngAsUtm(values.capture_location.latitude, values.capture_location.longitude) - : getUtmAsLatLng(values.capture_location.latitude, values.capture_location.longitude); - - const [releaseLat, releaseLon] = !isUtmProjection - ? getLatLngAsUtm(values.release_location.latitude, values.release_location.longitude) - : getUtmAsLatLng(values.release_location.latitude, values.release_location.longitude); - - setValues({ - ...values, - capture_location: { - ...values.capture_location, - projection_mode: switchProjection, - latitude: captureLat, - longitude: captureLon - }, - release_location: { - ...values.release_location, - projection_mode: switchProjection, - latitude: releaseLat, - longitude: releaseLon - } - }); - - props.handleProjection(switchProjection); - }; - - return ( - - - - Event Dates - } - label="UTM" - /> - - - - - - - - - - - - - Capture Location - - - - - - - - - - - {props.formMode === ANIMAL_FORM_MODE.ADD ? ( - - } - label={SurveyAnimalsI18N.animalCaptureReleaseRadio} - /> - - ) : null} - - - - {showRelease ? ( - - Release Location - - - - - - - - - - - - - ) : null} - - - - Additional Information - - - - ); -}; - -export default CaptureAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.test.tsx b/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.test.tsx deleted file mode 100644 index 67280fb4ff..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.test.tsx +++ /dev/null @@ -1,43 +0,0 @@ -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICritterDetailedResponse } from 'interfaces/useCritterApi.interface'; -import { render, waitFor } from 'test-helpers/test-utils'; -import { ANIMAL_FORM_MODE } from '../animal'; -import CollectionUnitAnimalForm from './CollectionUnitAnimalForm'; - -jest.mock('hooks/useCritterbaseApi'); - -const mockUseCritterbaseApi = useCritterbaseApi as jest.Mock; - -const mockHandleClose = jest.fn(); - -const mockUseCritterbase = { - lookup: { - getSelectOptions: jest.fn() - } -}; - -describe('CollectionUnitForm', () => { - beforeEach(() => { - mockUseCritterbaseApi.mockImplementation(() => mockUseCritterbase); - mockUseCritterbase.lookup.getSelectOptions.mockClear(); - }); - it('should display two form inputs for category and name', async () => { - mockUseCritterbase.lookup.getSelectOptions.mockResolvedValueOnce([ - { id: 'a', value: 'a', label: 'category_label' } - ]); - - const { getByText } = render( - - ); - - await waitFor(() => { - expect(getByText('Category')).toBeInTheDocument(); - expect(getByText('Name')).toBeInTheDocument(); - }); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.tsx deleted file mode 100644 index 71a90f86f8..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/CollectionUnitAnimalForm.tsx +++ /dev/null @@ -1,111 +0,0 @@ -import Grid from '@mui/material/Grid'; -import EditDialog from 'components/dialog/EditDialog'; -import CbSelectField from 'components/fields/CbSelectField'; -import { Field, FieldProps } from 'formik'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICritterCollectionUnitResponse } from 'interfaces/useCritterApi.interface'; -import { get } from 'lodash-es'; -import { useState } from 'react'; -import { - AnimalFormProps, - ANIMAL_FORM_MODE, - CreateCritterCollectionUnitSchema, - ICreateCritterCollectionUnit, - isRequiredInSchema -} from '../animal'; - -/** - * This component renders a 'critter collection unit' create / edit dialog. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -export const CollectionUnitAnimalForm = (props: AnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - //Animals may have multiple collection units, but only one instance of each category. - //We use this and pass to the select component to ensure categories already used in the form can't be selected again. - const disabledCategories = props.critter.collection_units.reduce((acc: Record, curr) => { - if (curr.collection_category_id) { - acc[curr.collection_category_id] = true; - } - return acc; - }, {}); - - const [loading, setLoading] = useState(false); - - const handleSave = async (values: ICreateCritterCollectionUnit) => { - setLoading(true); - try { - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - await critterbaseApi.collectionUnit.createCritterCollectionUnit(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created ecological unit.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - await critterbaseApi.collectionUnit.updateCritterCollectionUnit(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited ecological unit.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter ecological unit request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - return ( - - - - - - - {({ form }: FieldProps) => ( - - )} - - - - ) - }} - /> - ); -}; - -export default CollectionUnitAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.test.tsx b/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.test.tsx deleted file mode 100644 index 533f37f741..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.test.tsx +++ /dev/null @@ -1,44 +0,0 @@ -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICritterDetailedResponse } from 'interfaces/useCritterApi.interface'; -import { render, waitFor } from 'test-helpers/test-utils'; -import { ANIMAL_FORM_MODE } from '../animal'; -import FamilyAnimalForm from './FamilyAnimalForm'; - -jest.mock('hooks/useCritterbaseApi'); - -const mockUseCritterbaseApi = useCritterbaseApi as jest.Mock; -const mockHandleClose = jest.fn(); - -const mockUseCritterbase = { - lookup: { - getSelectOptions: jest.fn() - }, - family: { - getAllFamilies: jest.fn() - } -}; - -describe('FamilyAnimalForm', () => { - beforeEach(() => { - mockUseCritterbaseApi.mockImplementation(() => mockUseCritterbase); - mockUseCritterbase.lookup.getSelectOptions.mockClear(); - mockUseCritterbase.family.getAllFamilies.mockClear(); - }); - it('should display both inputs for family form section', async () => { - mockUseCritterbase.lookup.getSelectOptions.mockResolvedValueOnce([{ id: 'a', value: 'a', label: 'family_1' }]); - mockUseCritterbase.family.getAllFamilies.mockResolvedValueOnce([{ family_id: 'a', family_label: 'family_1' }]); - const { getByText } = render( - - ); - - await waitFor(() => { - expect(getByText(/add family relationship/i)).toBeInTheDocument(); - expect(getByText(/child in/i)).toBeInTheDocument(); - }); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.tsx deleted file mode 100644 index 00f32bc50b..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/FamilyAnimalForm.tsx +++ /dev/null @@ -1,269 +0,0 @@ -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Checkbox from '@mui/material/Checkbox'; -import { grey } from '@mui/material/colors'; -import FormControlLabel from '@mui/material/FormControlLabel'; -import Grid from '@mui/material/Grid'; -import MenuItem from '@mui/material/MenuItem'; -import Paper from '@mui/material/Paper'; -import Typography from '@mui/material/Typography'; -import ComponentDialog from 'components/dialog/ComponentDialog'; -import EditDialog from 'components/dialog/EditDialog'; -import { CbSelectWrapper } from 'components/fields/CbSelectFieldWrapper'; -import CustomTextField from 'components/fields/CustomTextField'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { IFamilyChildResponse, IFamilyParentResponse } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; -import { - AnimalFormProps, - AnimalRelationship, - ANIMAL_FORM_MODE, - CreateCritterFamilySchema, - ICreateCritterFamily, - isRequiredInSchema -} from '../animal'; - -/** - * This component renders a 'critter family relationship' create / edit dialog. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -export const FamilyAnimalForm = (props: AnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [showFamilyStructure, setShowFamilyStructure] = useState(false); - const [createNewFamily, setCreateNewFamily] = useState(false); - const [loading, setLoading] = useState(false); - - const { data: familyHierarchy, load: loadHierarchy } = useDataLoader(critterbaseApi.family.getImmediateFamily); - const { - data: allFamilies, - load: loadFamilies, - refresh: refreshFamilies - } = useDataLoader(critterbaseApi.family.getAllFamilies); - - loadFamilies(); - - const initialValues = { - critter_id: props.critter.critter_id, - family_id: props?.formObject?.family_id, - family_label: props?.formObject?.family_label ?? '', - relationship: (props?.formObject as IFamilyParentResponse)?.parent_critter_id - ? AnimalRelationship.PARENT - : AnimalRelationship.CHILD - }; - - const handleSave = async (values: ICreateCritterFamily) => { - setLoading(true); - try { - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - if (values.family_label) { - const family = await critterbaseApi.family.createFamily(values.family_label); - values.family_id = family.family_id; - } - await critterbaseApi.family.createFamilyRelationship(values); - - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created family relationship.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - if (!values.family_id || !initialValues.family_id) { - throw new Error(`family_id should be defined`); - } - - if (values.family_label) { - await critterbaseApi.family.editFamily(initialValues.family_id, values.family_label); - } - - await critterbaseApi.family.deleteRelationship({ - family_id: initialValues.family_id, - critter_id: initialValues.critter_id, - relationship: initialValues.relationship - }); - - await critterbaseApi.family.createFamilyRelationship({ - family_id: values.family_id, - critter_id: values.critter_id, - relationship: values.relationship - }); - - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited family relationship.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter family relationship request failed.` }); - } finally { - refreshFamilies(); - props.handleClose(); - setLoading(false); - } - }; - - return ( - - - setCreateNewFamily((create) => !create)} - /> - } - label={ - props.formMode === ANIMAL_FORM_MODE.ADD - ? 'Would you like to create a new critter family?' - : 'Would you like to modify the family label?' - } - /> - - {createNewFamily ? ( - - - - ) : ( - - - {allFamilies?.map((family) => ( - - {family.family_label ? family.family_label : family.family_id} - - ))} - - - )} - - - - - Parent in - - - Child in - - - - - - {props?.formObject?.family_id ? ( - - ) : null} - - setShowFamilyStructure(false)}> - - - Family ID - - - {props?.formObject?.family_id} - - - Parents: -
    - {familyHierarchy?.parents.map((a) => ( -
  • - - - - Critter ID - - {a.critter_id} - - - - Animal ID - - {a.animal_id} - - -
    • - ))} -
- - - Children: -
    - {familyHierarchy?.children.map((critter) => ( -
  • - - - - Critter ID - - {critter.critter_id} - - - - Animal ID - - {critter.animal_id} - - -
    • - ))} -
- - - - - ) - }} - /> - ); -}; - -export default FamilyAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/GeneralAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/GeneralAnimalForm.tsx deleted file mode 100644 index 69f4ccb5be..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/GeneralAnimalForm.tsx +++ /dev/null @@ -1,135 +0,0 @@ -import Grid from '@mui/material/Grid'; -import HelpButtonTooltip from 'components/buttons/HelpButtonTooltip'; -import EditDialog from 'components/dialog/EditDialog'; -import CbSelectField from 'components/fields/CbSelectField'; -import CustomTextField from 'components/fields/CustomTextField'; -import { SpeciesAutoCompleteFormikField } from 'components/species/components/SpeciesAutoCompleteFormikField'; -import { SurveyAnimalsI18N } from 'constants/i18n'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { ICritterDetailedResponse, ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; -import { v4 } from 'uuid'; -import { AnimalSex, ANIMAL_FORM_MODE, CreateCritterSchema, ICreateCritter, isRequiredInSchema } from '../animal'; - -export type GeneralAnimalFormProps = - | { - formObject?: never; - formMode: ANIMAL_FORM_MODE.ADD; - open: boolean; - handleClose: () => void; - critter?: never; - projectId: number; - surveyId: number; - } - | { - formObject: T; - formMode: ANIMAL_FORM_MODE.EDIT; - open: boolean; - handleClose: () => void; - critter: ICritterDetailedResponse | ICritterSimpleResponse; - projectId?: never; - surveyId?: never; - }; - -/** - * This component renders a 'critter' create / edit dialog. - * Handles the basic properties of a Critterbase critter. - * - * @param {GeneralAnimalFormProps} props - * @returns {*} - */ -const GeneralAnimalForm = (props: GeneralAnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const biohubApi = useBiohubApi(); - const dialog = useDialogContext(); - - const [loading, setLoading] = useState(false); - - const handleSave = async (values: ICreateCritter) => { - setLoading(true); - try { - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - await biohubApi.survey.createCritterAndAddToSurvey(props.projectId, props.surveyId, values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created critter.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - await critterbaseApi.critters.updateCritter(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited critter.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - return ( - - - - - - - - - - - - - - - - - - - - - ) - }}> - ); -}; - -export default GeneralAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/LocationEntryForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/LocationEntryForm.tsx deleted file mode 100644 index b87903628f..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/LocationEntryForm.tsx +++ /dev/null @@ -1,111 +0,0 @@ -import Box from '@mui/material/Box'; -import Paper from '@mui/material/Paper'; -import Stack from '@mui/material/Stack'; -import ToggleButton from '@mui/material/ToggleButton'; -import ToggleButtonGroup from '@mui/material/ToggleButtonGroup'; -import Typography from '@mui/material/Typography'; -import AdditionalLayers from 'components/map/components/AdditionalLayers'; -import BaseLayerControls from 'components/map/components/BaseLayerControls'; -import { MapBaseCss } from 'components/map/components/MapBaseCss'; -import { MarkerIconColor, MarkerWithResizableRadius } from 'components/map/components/MarkerWithResizableRadius'; -import { MAP_DEFAULT_CENTER, MAP_DEFAULT_ZOOM } from 'constants/spatial'; -import { useFormikContext } from 'formik'; -import { LatLng } from 'leaflet'; -import { get } from 'lodash-es'; -import { useState } from 'react'; -import { LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; -import { getLatLngAsUtm, getUtmAsLatLng, PROJECTION_MODE } from 'utils/mapProjectionHelpers'; - -export interface IFormLocation { - title: string; - pingColour: MarkerIconColor; - fields: { - latitude: keyof T; - longitude: keyof T; - }; -} - -type FormLocationsPreviewProps = { - projection?: PROJECTION_MODE; - locations: IFormLocation[]; -}; - -export const FormLocationPreview = ({ - projection = PROJECTION_MODE.WGS, - locations -}: FormLocationsPreviewProps) => { - const { setFieldValue, values } = useFormikContext(); - - const [markerToggle, setMarkerToggle] = useState(null); - - const handleSetMarkerLocation = (coords: LatLng) => { - if (markerToggle === null) { - return; - } - let latitude = coords.lat; - let longitude = coords.lng; - - if (projection === PROJECTION_MODE.UTM && latitude && longitude) { - [latitude, longitude] = getLatLngAsUtm(latitude, longitude); - } - - setFieldValue(locations[markerToggle].fields.latitude as string, Number(latitude.toFixed(5))); - setFieldValue(locations[markerToggle].fields.longitude as string, Number(longitude.toFixed(5))); - - setMarkerToggle(null); - }; - - const renderMarker = (location: IFormLocation) => { - let latitude = get(values, location.fields.latitude); - let longitude = get(values, location.fields.longitude); - - if (projection === PROJECTION_MODE.UTM && latitude && longitude) { - [latitude, longitude] = getUtmAsLatLng(latitude, longitude); - } - - // Marking positions can be different than the fields if the projection is UTM. - const renderPosition = latitude && longitude ? new LatLng(latitude, longitude) : undefined; - - return ( - - ); - }; - - return ( - - - Location Preview - setMarkerToggle(value)} exclusive> - {locations.map((location, idx) => ( - - {`Set ${location.title} Location`} - - ))} - - - - - renderMarker(location))} /> - - - - - - - - ); -}; - -export default FormLocationPreview; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/MarkingAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/MarkingAnimalForm.tsx deleted file mode 100644 index 5e7e37848f..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/MarkingAnimalForm.tsx +++ /dev/null @@ -1,137 +0,0 @@ -import Grid from '@mui/material/Grid'; -import EditDialog from 'components/dialog/EditDialog'; -import CbSelectField from 'components/fields/CbSelectField'; -import CustomTextField from 'components/fields/CustomTextField'; -import FormikDevDebugger from 'components/formik/FormikDevDebugger'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { IMarkingResponse } from 'interfaces/useCritterApi.interface'; -import { useState } from 'react'; -import { - AnimalFormProps, - ANIMAL_FORM_MODE, - CreateCritterMarkingSchema, - ICreateCritterMarking, - isRequiredInSchema -} from '../animal'; - -/** - * This component renders a 'critter marking' create / edit dialog. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -export const MarkingAnimalForm = (props: AnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [loading, setLoading] = useState(false); - - const handleSave = async (values: ICreateCritterMarking) => { - setLoading(true); - try { - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - await critterbaseApi.marking.createMarking(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created marking.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - await critterbaseApi.marking.updateMarking(values); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited marking.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter marking request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - return ( - - - - - - - - - - - - - - - - - - - ) - }} - /> - ); -}; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/MeasurementAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/MeasurementAnimalForm.tsx deleted file mode 100644 index efe9b4f4dd..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/MeasurementAnimalForm.tsx +++ /dev/null @@ -1,213 +0,0 @@ -import Grid from '@mui/material/Grid'; -import MenuItem from '@mui/material/MenuItem'; -import EditDialog from 'components/dialog/EditDialog'; -import { CbSelectWrapper } from 'components/fields/CbSelectFieldWrapper'; -import CustomTextField from 'components/fields/CustomTextField'; -import SingleDateField from 'components/fields/SingleDateField'; -import { Field } from 'formik'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { - CBMeasurementType, - CBQualitativeMeasurementTypeDefinition, - CBQuantitativeMeasurementTypeDefinition, - IQualitativeMeasurementResponse, - IQuantitativeMeasurementResponse -} from 'interfaces/useCritterApi.interface'; -import { has, startCase } from 'lodash-es'; -import { useEffect, useMemo, useState } from 'react'; -import { - AnimalFormProps, - ANIMAL_FORM_MODE, - CreateCritterMeasurementSchema, - ICreateCritterMeasurement, - isRequiredInSchema -} from '../animal'; - -/** - * This component renders a 'critter measurement' create / edit dialog. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -export const MeasurementAnimalForm = ( - props: AnimalFormProps -) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [loading, setLoading] = useState(false); - const [measurementTypeDef, setMeasurementTypeDef] = useState(); - - const { data: measurements, load: loadMeasurements } = useDataLoader(() => - critterbaseApi.xref.getTaxonMeasurements(props.critter.itis_tsn) - ); - loadMeasurements(); - - const isQualitative = has(measurementTypeDef, 'options'); - - const measurementDefs = useMemo(() => { - return measurements ? [...measurements.qualitative, ...measurements.quantitative] : []; - }, [measurements]); - - useEffect(() => { - const foundMeasurementDef = measurementDefs.find( - (measurement) => measurement.taxon_measurement_id === props.formObject?.taxon_measurement_id - ); - setMeasurementTypeDef(foundMeasurementDef); - }, [measurementDefs, props?.formObject?.taxon_measurement_id]); - - const handleSave = async (values: ICreateCritterMeasurement) => { - setLoading(true); - try { - if (isQualitative) { - delete values.measurement_quantitative_id; - delete values.value; - - props.formMode === ANIMAL_FORM_MODE.ADD - ? await critterbaseApi.measurement.createQualitativeMeasurement(values) - : await critterbaseApi.measurement.updateQualitativeMeasurement(values); - } else { - delete values.measurement_qualitative_id; - delete values.qualitative_option_id; - values = { ...values, value: Number(values.value) }; - - props.formMode === ANIMAL_FORM_MODE.ADD - ? await critterbaseApi.measurement.createQuantitativeMeasurement(values) - : await critterbaseApi.measurement.updateQuantitativeMeasurement(values); - } - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created measurement.` }); - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter measurement request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - const validateQuantitativeMeasurement = async (val: '' | number) => { - const quantitativeTypeDef = measurementTypeDef as CBQuantitativeMeasurementTypeDefinition; - const min = quantitativeTypeDef?.min_value ?? 0; - const max = quantitativeTypeDef?.max_value; - const unit = quantitativeTypeDef?.unit ? quantitativeTypeDef.unit : ``; - if (val === '') { - return; - } - if (isNaN(val)) { - return `Must be a number`; - } - if (val < min) { - return `Measurement must be greater than ${min}${unit}`; - } - if (max && val > max) { - return `Measurement must be less than ${max}${unit}`; - } - }; - - return ( - - - - {measurementDefs?.map((measurementDef) => ( - setMeasurementTypeDef(measurementDef)}> - {startCase(measurementDef.measurement_name)} - - ))} - - - - {isQualitative ? ( - - {(measurementTypeDef as CBQualitativeMeasurementTypeDefinition)?.options?.map((qualitativeOption) => ( - - {startCase(qualitativeOption.option_label)} - - ))} - - ) : ( - - )} - - - - - - - - - ) - }} - /> - ); -}; - -export default MeasurementAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/form-sections/MortalityAnimalForm.tsx b/app/src/features/surveys/view/survey-animals/form-sections/MortalityAnimalForm.tsx deleted file mode 100644 index d55769a440..0000000000 --- a/app/src/features/surveys/view/survey-animals/form-sections/MortalityAnimalForm.tsx +++ /dev/null @@ -1,271 +0,0 @@ -import Box from '@mui/material/Box'; -import Grid from '@mui/material/Grid'; -import Stack from '@mui/material/Stack'; -import Typography from '@mui/material/Typography'; -import EditDialog from 'components/dialog/EditDialog'; -import CbSelectField from 'components/fields/CbSelectField'; -import CustomTextField from 'components/fields/CustomTextField'; -import SingleDateField from 'components/fields/SingleDateField'; -import { SpeciesAutoCompleteFormikField } from 'components/species/components/SpeciesAutoCompleteFormikField'; -import { Field, useFormikContext } from 'formik'; -import { useDialogContext } from 'hooks/useContext'; -import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; -import { IMortalityResponse } from 'interfaces/useCritterApi.interface'; -import { mapValues } from 'lodash-es'; -import { useState } from 'react'; -import { - AnimalFormProps, - ANIMAL_FORM_MODE, - CreateCritterMortalitySchema, - ICreateCritterMortality, - isRequiredInSchema -} from '../animal'; -import FormLocationPreview from './LocationEntryForm'; - -/** - * This component renders a 'critter mortality' create / edit dialog. - * - * @param {AnimalFormProps} props - Generic AnimalFormProps. - * @returns {*} - */ -const MortalityAnimalForm = (props: AnimalFormProps) => { - const critterbaseApi = useCritterbaseApi(); - const dialog = useDialogContext(); - - const [loading, setLoading] = useState(false); - - const handleSave = async (values: ICreateCritterMortality) => { - setLoading(true); - // Replaces empty strings with null values. - const patchedValues = mapValues(values, (value) => (value === '' ? null : value)); - - try { - if (props.formMode === ANIMAL_FORM_MODE.ADD) { - await critterbaseApi.mortality.createMortality(patchedValues); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully created mortality.` }); - } - if (props.formMode === ANIMAL_FORM_MODE.EDIT) { - await critterbaseApi.mortality.updateMortality(patchedValues); - dialog.setSnackbar({ open: true, snackbarMessage: `Successfully edited mortality.` }); - } - } catch (err) { - dialog.setSnackbar({ open: true, snackbarMessage: `Critter mortality request failed.` }); - } finally { - props.handleClose(); - setLoading(false); - } - }; - - return ( - - }} - /> - ); -}; - -/** - * This component renders the 'critter mortality' form fields. - * Nested inside MortalityAnimalForm to use the formikContext hook. - * - * @param {Pick, 'formObject'>} props - IMortalityResponse. - * @returns {*} - */ -const MortalityForm = (props: Pick, 'formObject'>) => { - const { setFieldValue } = useFormikContext(); - - const proximateTsn = props.formObject?.proximate_predated_by_itis_tsn; - const ultimateTsn = props.formObject?.ultimate_predated_by_itis_tsn; - - const [pcodTaxonDisabled, setPcodTaxonDisabled] = useState(!proximateTsn); //Controls whether you can select taxons from the PCOD Taxon dropdown. - const [ucodTaxonDisabled, setUcodTaxonDisabled] = useState(!ultimateTsn); //Controls whether you can select taxons from the UCOD Taxon dropdown. - - const handleCauseOfDeathReasonChange = (label: string, isProximateCOD: boolean) => { - const isDisabled = !label.includes('Predation'); - if (isProximateCOD) { - setPcodTaxonDisabled(isDisabled); - } else { - setUcodTaxonDisabled(isDisabled); - } - - if (isDisabled) { - setFieldValue('proximate_predated_by_itis_tsn', '', true); - } else { - setFieldValue('ultimate_predated_by_itis_tsn', '', true); - } - }; - return ( - - - Date of Event - - - - - Proximate Cause of Death - - - handleCauseOfDeathReasonChange(label, true)} - orderBy={'asc'} - label={'Reason'} - controlProps={{ - required: isRequiredInSchema(CreateCritterMortalitySchema, 'proximate_cause_of_death_id') - }} - id={`pcod-reason`} - route={'lookups/cods'} - /> - - - - - - - - - - - - Ultimate Cause of Death - - - { - handleCauseOfDeathReasonChange(label, false); - }} - label={'Reason'} - controlProps={{ - required: isRequiredInSchema(CreateCritterMortalitySchema, 'ultimate_cause_of_death_id') - }} - id={`ucod-reason`} - route={'lookups/cods'} - /> - - - - - - - - - - - - Mortality Location - - - - - - - - - - - - - - - - - Additional Details - - - - ); -}; - -export default MortalityAnimalForm; diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/DeploymentForm.tsx b/app/src/features/surveys/view/survey-animals/telemetry-device/DeploymentForm.tsx deleted file mode 100644 index c24595e6d0..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/DeploymentForm.tsx +++ /dev/null @@ -1,143 +0,0 @@ -import { mdiTrashCanOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import Grid from '@mui/material/Grid'; -import IconButton from '@mui/material/IconButton'; -import YesNoDialog from 'components/dialog/YesNoDialog'; -import SingleDateField from 'components/fields/SingleDateField'; -import { DialogContext } from 'contexts/dialogContext'; -import { SurveyContext } from 'contexts/surveyContext'; -import { Field, useFormikContext } from 'formik'; -import { IGetDeviceDetailsResponse } from 'hooks/telemetry/useDeviceApi'; -import { useBiohubApi } from 'hooks/useBioHubApi'; -import { useQuery } from 'hooks/useQuery'; -import { Fragment, useContext, useState } from 'react'; -import { dateRangesOverlap, setMessageSnackbar } from 'utils/Utils'; -import { ANIMAL_FORM_MODE } from '../animal'; -import { IAnimalTelemetryDevice, IDeploymentTimespan } from './device'; - -interface DeploymentFormSectionProps { - mode: ANIMAL_FORM_MODE; - deviceDetails?: IGetDeviceDetailsResponse; -} - -export const DeploymentForm = (props: DeploymentFormSectionProps): JSX.Element => { - const { mode, deviceDetails } = props; - - const biohubApi = useBiohubApi(); - const { critter_id: survey_critter_id } = useQuery(); - const { values, validateField } = useFormikContext(); - const { surveyId, projectId } = useContext(SurveyContext); - const dialogContext = useContext(DialogContext); - - const [deploymentIDToDelete, setDeploymentIDToDelete] = useState(null); - - const device = values; - const deployments = device.deployments; - - const handleRemoveDeployment = async (deployment_id: string) => { - try { - if (survey_critter_id === undefined) { - setMessageSnackbar('No critter set!', dialogContext); - } - await biohubApi.survey.removeDeployment(projectId, surveyId, Number(survey_critter_id), deployment_id); - const indexOfDeployment = deployments?.findIndex((deployment) => deployment.deployment_id === deployment_id); - if (indexOfDeployment !== undefined) { - deployments?.splice(indexOfDeployment); - } - setMessageSnackbar('Deployment deleted', dialogContext); - } catch (e) { - setMessageSnackbar('Failed to delete deployment.', dialogContext); - } - }; - - const deploymentOverlapTest = (deployment: IDeploymentTimespan) => { - if (!deviceDetails) { - return; - } - - if (!deployment.attachment_start) { - return; - } - const existingDeployment = deviceDetails.deployments.find( - (existingDeployment) => - deployment.deployment_id !== existingDeployment.deployment_id && - dateRangesOverlap( - deployment.attachment_start, - deployment.attachment_end, - existingDeployment.attachment_start, - existingDeployment.attachment_end - ) - ); - if (!existingDeployment) { - return; - } - return `This will conflict with an existing deployment for the device running from ${ - existingDeployment.attachment_start - } until ${existingDeployment.attachment_end ?? 'indefinite.'}`; - }; - - return ( - <> - - {deployments?.map((deploy, i) => { - return ( - - - validateField(`deployments.${i}.attachment_start`) }} - validate={() => deploymentOverlapTest(deploy)} - /> - - - validateField(`deployments.${i}.attachment_end`) }} - validate={() => deploymentOverlapTest(deploy)} - /> - - {mode === ANIMAL_FORM_MODE.EDIT && ( - - { - setDeploymentIDToDelete(String(deploy.deployment_id)); - }}> - - - - )} - - ); - })} - - - {/* Delete Dialog */} - setDeploymentIDToDelete(null)} - onNo={() => setDeploymentIDToDelete(null)} - onYes={async () => { - if (deploymentIDToDelete) { - await handleRemoveDeployment(deploymentIDToDelete); - } - setDeploymentIDToDelete(null); - }} - /> - - ); -}; diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryDeviceForm.tsx b/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryDeviceForm.tsx deleted file mode 100644 index f7ef3f7a11..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryDeviceForm.tsx +++ /dev/null @@ -1,158 +0,0 @@ -import Box from '@mui/material/Box'; -import Grid from '@mui/material/Grid'; -import Typography from '@mui/material/Typography'; -import CustomTextField from 'components/fields/CustomTextField'; -import TelemetrySelectField from 'components/fields/TelemetrySelectField'; -import FormikDevDebugger from 'components/formik/FormikDevDebugger'; -import { AttachmentType } from 'constants/attachments'; -import { Field, useFormikContext } from 'formik'; -import useDataLoader from 'hooks/useDataLoader'; -import { useTelemetryApi } from 'hooks/useTelemetryApi'; -import { useEffect } from 'react'; -import { ANIMAL_FORM_MODE } from '../animal'; -import { DeploymentForm } from './DeploymentForm'; -import { IAnimalTelemetryDevice } from './device'; -import TelemetryFileUpload from './TelemetryFileUpload'; - -export interface ITelemetryDeviceFormProps { - mode: ANIMAL_FORM_MODE; -} - -const TelemetryDeviceForm = (props: ITelemetryDeviceFormProps) => { - const { mode } = props; - - const telemetryApi = useTelemetryApi(); - const { values: device } = useFormikContext(); - - const { data: deviceDetails, refresh, isReady } = useDataLoader(telemetryApi.devices.getDeviceDetails); - - const canRenderFileUpload = - isReady && ((device.device_make === 'Vectronic' && !deviceDetails?.keyXStatus) || device.device_make === 'Lotek'); - - useEffect(() => { - if (device.device_id && device.device_make) { - refresh(device.device_id, device.device_make); - } - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [device.device_id, device.device_make]); - - if (!device) { - return <>; - } - - return ( - <> - - - Device Metadata - - - - - - - - - - - - { - const codeVals = await telemetryApi.devices.getCodeValues('frequency_unit'); - return codeVals.map((a) => a.description); - }} - /> - - - - - - - - - - - - {canRenderFileUpload && ( - - - Upload Attachment - - {device.device_make === 'Vectronic' && ( - <> - {`Vectronic KeyX File (Optional)`} - - - )} - {device.device_make === 'Lotek' && ( - <> - {`Lotek Config File (Optional)`} - - - )} - - )} - - - Deployments - - - - - - ); -}; - -export default TelemetryDeviceForm; diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.test.tsx b/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.test.tsx deleted file mode 100644 index 03d286c94c..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.test.tsx +++ /dev/null @@ -1,20 +0,0 @@ -import { AttachmentType } from 'constants/attachments'; -import { ConfigContext, IConfig } from 'contexts/configContext'; -import { Formik } from 'formik'; -import { render } from 'test-helpers/test-utils'; -import TelemetryFileUpload from './TelemetryFileUpload'; - -describe('TelemetryFileUpload component', () => { - it('should render with correct props', async () => { - const { getByTestId } = render( - - - - - - ); - - const fileUploadComponent = getByTestId('drop-zone-input'); - expect(fileUploadComponent).toBeInTheDocument(); - }); -}); diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.tsx b/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.tsx deleted file mode 100644 index 845bf0562c..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryFileUpload.tsx +++ /dev/null @@ -1,41 +0,0 @@ -import FileUpload, { IReplaceHandler } from 'components/file-upload/FileUpload'; -import { IFileHandler, UploadFileStatus } from 'components/file-upload/FileUploadItem'; -import { AttachmentType, ProjectSurveyAttachmentValidExtensions } from 'constants/attachments'; -import { useFormikContext } from 'formik'; -import React from 'react'; -import { IAnimalTelemetryDeviceFile } from './device'; - -export const TelemetryFileUpload: React.FC<{ attachmentType: AttachmentType; fileKey: string; typeKey: string }> = ( - props -) => { - const { setFieldValue } = useFormikContext<{ formValues: IAnimalTelemetryDeviceFile[] }>(); - const fileHandler: IFileHandler = (file) => { - setFieldValue(props.fileKey, file); - setFieldValue(props.typeKey, props.attachmentType); - }; - - const replaceHandler: IReplaceHandler = () => { - setFieldValue(props.fileKey, null); - setFieldValue(props.typeKey, props.attachmentType); - }; - - return ( - - ); -}; - -export default TelemetryFileUpload; diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryMap.tsx b/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryMap.tsx deleted file mode 100644 index 5da5ef7adf..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/TelemetryMap.tsx +++ /dev/null @@ -1,151 +0,0 @@ -import Box from '@mui/material/Box'; -import Paper from '@mui/material/Paper'; -import Typography from '@mui/material/Typography'; -import AdditionalLayers from 'components/map/components/AdditionalLayers'; -import BaseLayerControls from 'components/map/components/BaseLayerControls'; -import { SetMapBounds } from 'components/map/components/Bounds'; -import { MapBaseCss } from 'components/map/styles/MapBaseCss'; -import { MAP_DEFAULT_CENTER, MAP_DEFAULT_ZOOM } from 'constants/spatial'; -import { default as dayjs } from 'dayjs'; -import { Feature } from 'geojson'; -import L, { LatLng } from 'leaflet'; -import { useMemo, useState } from 'react'; -import { GeoJSON, LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; -import { uuidToColor } from 'utils/Utils'; -import { v4 } from 'uuid'; -import { IAnimalDeployment, ITelemetryPointCollection } from './device'; - -interface ITelemetryMapProps { - telemetryData?: ITelemetryPointCollection; - deploymentData?: IAnimalDeployment[]; -} - -type ColourDeployment = IAnimalDeployment & { colour: string; fillColour: string }; - -interface ILegend { - hasData: boolean; - colourMap: ColourDeployment[]; -} - -const Legend = ({ hasData, colourMap }: ILegend) => { - return ( -
-
- - {hasData ? ( - colourMap.map((deploymentAndColour) => ( - - - {`Device ID: ${deploymentAndColour.device_id}, deployed from ${dayjs( - deploymentAndColour.attachment_start - ).format('DD-MM-YYYY')} to ${ - deploymentAndColour.attachment_end - ? dayjs(deploymentAndColour.attachment_end).format('DD-MM-YYYY') - : 'indefinite' - }`} - - )) - ) : ( - {`No telemetry available for this animal's deployment(s).`} - )} - -
-
- ); -}; - -const TelemetryMap = ({ deploymentData, telemetryData }: ITelemetryMapProps): JSX.Element => { - const [legendColours, setLegendColours] = useState([]); - - const features = useMemo(() => { - const featureCollections = telemetryData; - if (!featureCollections || !deploymentData) { - return []; - } - const result: Feature[] = []; - const colourMap: Record = {}; - const fillColourMap: Record = {}; - const legendColours: ColourDeployment[] = []; - deploymentData.forEach((deployment) => { - const { fillColor, outlineColor } = uuidToColor(deployment.deployment_id); - fillColourMap[deployment.deployment_id] = fillColor; - colourMap[deployment.deployment_id] = outlineColor; - legendColours.push({ ...deployment, colour: fillColor, fillColour: outlineColor }); - }); - setLegendColours(legendColours); - for (const featureCollection of Object.values(featureCollections)) { - for (const feature of featureCollection.features) { - if (!feature.properties) { - feature.properties = {}; - } - feature.properties.colour = colourMap[feature.properties.deployment_id]; - feature.properties.fillColour = fillColourMap[feature.properties.deployment_id]; - result.push(feature); - } - } - result.sort((a, b) => a.geometry.type.localeCompare(b.geometry.type)); - return result; - }, [telemetryData, deploymentData]); - - const mapBounds = useMemo(() => { - const bounds = new L.LatLngBounds([]); - telemetryData?.points.features.forEach((feature) => { - if (feature.geometry.type === 'Point') { - const [lon, lat] = feature.geometry.coordinates; - if (lon > -140 && lon < -110 && lat > 45 && lat < 60) { - //We filter points that are clearly bad values out of the map bounds so that we don't wind up too zoomed out due to one wrong point. - //These values are still present on the map if you move around though. - bounds.extend([lat, lon]); - } - } - }); - if (bounds.isValid()) { - return bounds; - } else { - return undefined; - } - }, [telemetryData?.points.features]); - - const point = (_feature: Feature, latlng: LatLng) => { - return new L.CircleMarker(latlng, { radius: 5, fillOpacity: 1 }); - }; - - return ( - - - - ( - - )), - 0} colourMap={legendColours} /> - ]} - /> - - - - - ); -}; - -export default TelemetryMap; diff --git a/app/src/features/surveys/view/survey-animals/telemetry-device/device.ts b/app/src/features/surveys/view/survey-animals/telemetry-device/device.ts deleted file mode 100644 index 19360b0ad7..0000000000 --- a/app/src/features/surveys/view/survey-animals/telemetry-device/device.ts +++ /dev/null @@ -1,84 +0,0 @@ -import { AttachmentType } from 'constants/attachments'; -import { FeatureCollection } from 'geojson'; -import yup from 'utils/YupSchema'; -import { InferType } from 'yup'; - -export type IAnimalDeployment = InferType; - -export type IDeploymentTimespan = InferType; - -export type IAnimalTelemetryDevice = InferType; - -export type ICreateAnimalDeployment = InferType; - -export type ITelemetryPointCollection = { points: FeatureCollection; tracks: FeatureCollection }; - -const req = 'Required.'; -const mustBeNum = 'Must be a number'; -const mustBePos = 'Must be positive'; -const mustBeInt = 'Must be an integer'; -const maxInt = 2147483647; -const numSchema = yup.number().typeError(mustBeNum).min(0, mustBePos); -const intSchema = numSchema.max(maxInt, `Must be less than ${maxInt}`).integer(mustBeInt).required(req); - -export const AnimalDeploymentTimespanSchema = yup.object({}).shape({ - deployment_id: yup.string(), - attachment_start: yup.string().isValidDateString().required(req).typeError(req), - attachment_end: yup.string().isValidDateString().isEndDateSameOrAfterStartDate('attachment_start').nullable() -}); - -export const AnimalTelemetryDeviceSchema = yup.object({}).shape({ - device_id: intSchema, - device_make: yup.string().required(req), - frequency: numSchema.nullable(), - frequency_unit: yup.string().nullable(), - device_model: yup.string().nullable(), - deployments: yup.array(AnimalDeploymentTimespanSchema) -}); - -export const AnimalDeploymentSchema = yup.object({}).shape({ - assignment_id: yup.string().required(), - collar_id: yup.string().required(), - critter_id: yup.string().required(), - attachment_start: yup.string().isValidDateString().required(), - attachment_end: yup.string().isValidDateString().isEndDateSameOrAfterStartDate('attachment_start'), - deployment_id: yup.string().required(), - device_id: yup.number().required(), - device_make: yup.string().required(), - device_model: yup.string(), - frequency: numSchema, - frequency_unit: yup.string() -}); - -export const CreateAnimalDeployment = yup.object({ - critter_id: yup.string().uuid().required(req), // Critterbase critter_id - device_id: intSchema, - device_make: yup.string().required(req), - frequency: numSchema.optional(), - frequency_unit: yup.string().optional(), - device_model: yup.string().optional(), - attachment_start: yup.string().isValidDateString(), - attachment_end: yup.string().isValidDateString().isEndDateSameOrAfterStartDate('attachment_start') -}); - -export interface IAnimalTelemetryDeviceFile extends IAnimalTelemetryDevice { - attachmentFile?: File; - attachmentType?: AttachmentType; -} - -export class Device implements Omit { - device_id: number; - device_make: string; - device_model: string | null; - frequency: number | null; - frequency_unit: string | null; - collar_id: string; - constructor(obj: Record) { - this.device_id = Number(obj.device_id); - this.device_make = String(obj.device_make); - this.device_model = obj.device_model ? String(obj.device_model) : null; - this.frequency = obj.frequency ? Number(obj.frequency) : null; - this.frequency_unit = obj.frequency_unit ? String(obj.frequency_unit) : null; - this.collar_id = String(obj.collar_id); - } -} diff --git a/app/src/features/surveys/view/survey-spatial/SurveySpatialContainer.tsx b/app/src/features/surveys/view/survey-spatial/SurveySpatialContainer.tsx new file mode 100644 index 0000000000..cec15b59b0 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/SurveySpatialContainer.tsx @@ -0,0 +1,84 @@ +import { mdiEye, mdiPaw, mdiWifiMarker } from '@mdi/js'; +import Paper from '@mui/material/Paper'; +import { TelemetryDataContextProvider } from 'contexts/telemetryDataContext'; +import { SurveySpatialAnimal } from 'features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimal'; +import { SurveySpatialObservation } from 'features/surveys/view/survey-spatial/components/observation/SurveySpatialObservation'; +import { + SurveySpatialDatasetViewEnum, + SurveySpatialToolbar +} from 'features/surveys/view/survey-spatial/components/SurveySpatialToolbar'; +import { SurveySpatialTelemetry } from 'features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetry'; +import { useObservationsContext, useTaxonomyContext } from 'hooks/useContext'; +import { isEqual } from 'lodash-es'; +import { useEffect, useState } from 'react'; + +/** + * Container component for displaying survey spatial data. + * It includes a toolbar to switch between different dataset views + * (observations, animals, telemetry) and fetches and catches necessary taxonomic data. + * + * @returns {JSX.Element} The rendered component. + */ +export const SurveySpatialContainer = (): JSX.Element => { + const observationsContext = useObservationsContext(); + const taxonomyContext = useTaxonomyContext(); + + const [activeView, setActiveView] = useState(SurveySpatialDatasetViewEnum.OBSERVATIONS); + + // Fetch and cache all taxonomic data required for the observations. + useEffect(() => { + const cacheTaxonomicData = async () => { + if (observationsContext.observationsDataLoader.data) { + // Fetch all unique ITIS TSNs from observations to retrieve taxonomic names + const taxonomicIds = [ + ...new Set(observationsContext.observationsDataLoader.data.surveyObservations.map((item) => item.itis_tsn)) + ].filter((tsn): tsn is number => tsn !== null); + + await taxonomyContext.cacheSpeciesTaxonomyByIds(taxonomicIds); + } + }; + + cacheTaxonomicData(); + // Should not re-run this effect on `taxonomyContext` changes + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [observationsContext.observationsDataLoader.data]); + + return ( + + {/* Toolbar for switching between different dataset views */} + + + {/* Display the corresponding dataset view based on the selected active view */} + {isEqual(SurveySpatialDatasetViewEnum.OBSERVATIONS, activeView) && } + {isEqual(SurveySpatialDatasetViewEnum.TELEMETRY, activeView) && ( + + + + )} + {isEqual(SurveySpatialDatasetViewEnum.ANIMALS, activeView) && } + + ); +}; diff --git a/app/src/features/surveys/view/components/spatial-data/SurveySpatialToolbar.tsx b/app/src/features/surveys/view/survey-spatial/components/SurveySpatialToolbar.tsx similarity index 82% rename from app/src/features/surveys/view/components/spatial-data/SurveySpatialToolbar.tsx rename to app/src/features/surveys/view/survey-spatial/components/SurveySpatialToolbar.tsx index 194d06a963..285d71a019 100644 --- a/app/src/features/surveys/view/components/spatial-data/SurveySpatialToolbar.tsx +++ b/app/src/features/surveys/view/survey-spatial/components/SurveySpatialToolbar.tsx @@ -1,4 +1,4 @@ -import { mdiBroadcast, mdiChevronDown, mdiCog, mdiEye } from '@mdi/js'; +import { mdiChevronDown, mdiCog, mdiEye, mdiPaw, mdiWifiMarker } from '@mdi/js'; import Icon from '@mdi/react'; import Box from '@mui/material/Box'; import Button from '@mui/material/Button'; @@ -19,7 +19,7 @@ import { Link as RouterLink } from 'react-router-dom'; export enum SurveySpatialDatasetViewEnum { OBSERVATIONS = 'OBSERVATIONS', TELEMETRY = 'TELEMETRY', - MARKED_ANIMALS = 'MARKED_ANIMALS' + ANIMALS = 'ANIMALS' } interface ISurveySpatialDatasetView { @@ -29,13 +29,21 @@ interface ISurveySpatialDatasetView { isLoading: boolean; } -interface ISurveySptialToolbarProps { - updateDatasetView: (view: SurveySpatialDatasetViewEnum) => void; - views: ISurveySpatialDatasetView[]; +interface ISurveySpatialToolbarProps { activeView: SurveySpatialDatasetViewEnum; + setActiveView: (view: SurveySpatialDatasetViewEnum) => void; + views: ISurveySpatialDatasetView[]; } -const SurveySpatialToolbar = (props: ISurveySptialToolbarProps) => { +/** + * Toolbar that buttons (tabs) to switch between different views of the survey data (observations, animals, telemetry). + * + * @param {ISurveySpatialToolbarProps} props + * @return {*} + */ +export const SurveySpatialToolbar = (props: ISurveySpatialToolbarProps) => { + const { activeView, setActiveView, views } = props; + const [anchorEl, setAnchorEl] = useState(null); const updateDatasetView = (_event: React.MouseEvent, view: SurveySpatialDatasetViewEnum) => { @@ -43,7 +51,7 @@ const SurveySpatialToolbar = (props: ISurveySptialToolbarProps) => { return; } - props.updateDatasetView(view); + setActiveView(view); }; const handleMenuClick = (event: React.MouseEvent) => { @@ -85,13 +93,19 @@ const SurveySpatialToolbar = (props: ISurveySptialToolbarProps) => { }}> - + Observations + + + + + Animals + - + Telemetry @@ -126,7 +140,7 @@ const SurveySpatialToolbar = (props: ISurveySptialToolbarProps) => { { letterSpacing: '0.02rem' } }}> - {props.views.map((view) => ( + {views.map((view) => ( { ); }; - -export default SurveySpatialToolbar; diff --git a/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimal.tsx b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimal.tsx new file mode 100644 index 0000000000..8fb5799d49 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimal.tsx @@ -0,0 +1,103 @@ +import Box from '@mui/material/Box'; +import { IStaticLayer } from 'components/map/components/StaticLayers'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; +import { SurveySpatialAnimalCapturePopup } from 'features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalCapturePopup'; +import { SurveySpatialAnimalMortalityPopup } from 'features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalMortalityPopup'; +import { SurveySpatialAnimalTable } from 'features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalTable'; +import { SurveySpatialMap } from 'features/surveys/view/survey-spatial/components/map/SurveySpatialMap'; +import SurveyMapTooltip from 'features/surveys/view/SurveyMapTooltip'; +import { useSurveyContext } from 'hooks/useContext'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { useEffect, useMemo } from 'react'; +import { coloredCustomMortalityMarker } from 'utils/mapUtils'; + +/** + * Component for displaying animal capture points on a map and in a table. + * Retrieves and displays data related to animal captures for a specific survey. + */ +export const SurveySpatialAnimal = () => { + const surveyContext = useSurveyContext(); + + const crittersApi = useCritterbaseApi(); + + const critterIds = useMemo( + () => surveyContext.critterDataLoader.data?.map((critter) => critter.critterbase_critter_id) ?? [], + [surveyContext.critterDataLoader.data] + ); + + // Data loader for fetching animal capture data for the map ONLY. Table data is fetched separately in `SurveySpatialAnimalTable.tsx` + const geometryDataLoader = useDataLoader((critter_ids: string[]) => + crittersApi.critters.getMultipleCrittersGeometryByIds(critter_ids) + ); + + useEffect(() => { + if (!critterIds.length) { + return; + } + + geometryDataLoader.load(critterIds); + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [critterIds]); + + const captureLayer: IStaticLayer = { + layerName: 'Animal Captures', + layerOptions: { + fillColor: SURVEY_MAP_LAYER_COLOURS.CAPTURE_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + color: SURVEY_MAP_LAYER_COLOURS.CAPTURE_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR + }, + features: + geometryDataLoader.data?.captures.map((capture) => ({ + id: capture.capture_id, + key: `capture-${capture.capture_id}`, + geoJSON: { + type: 'Feature', + geometry: { + type: 'Point', + coordinates: [capture.coordinates[1], capture.coordinates[0]] + }, + properties: {} + } + })) ?? [], + popup: (feature) => , + tooltip: (feature) => + }; + + const mortalityLayer: IStaticLayer = { + layerName: 'Animal Mortalities', + layerOptions: { + fillColor: SURVEY_MAP_LAYER_COLOURS.MORTALITY_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + color: SURVEY_MAP_LAYER_COLOURS.MORTALITY_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + marker: coloredCustomMortalityMarker + }, + features: + geometryDataLoader.data?.mortalities.map((mortality) => ({ + id: mortality.mortality_id, + key: `mortality-${mortality.mortality_id}`, + geoJSON: { + type: 'Feature', + geometry: { + type: 'Point', + coordinates: [mortality.coordinates[1], mortality.coordinates[0]] + }, + properties: {} + } + })) ?? [], + popup: (feature) => , + tooltip: (feature) => + }; + + return ( + <> + {/* Display map with animal capture points */} + + + + + {/* Display data table with animal capture details */} + + + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalCapturePopup.tsx b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalCapturePopup.tsx new file mode 100644 index 0000000000..ca3506ce35 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalCapturePopup.tsx @@ -0,0 +1,60 @@ +import { IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { ICaptureResponse } from 'interfaces/useCritterApi.interface'; +import { Popup } from 'react-leaflet'; + +export interface ISurveySpatialAnimalCapturePopupProps { + feature: IStaticLayerFeature; +} + +/** + * Renders a popup for animal capture data on the map. + * + * @param {ISurveySpatialAnimalCapturePopupProps} props + * @return {*} + */ +export const SurveySpatialAnimalCapturePopup = (props: ISurveySpatialAnimalCapturePopupProps) => { + const { feature } = props; + + const critterbaseApi = useCritterbaseApi(); + + const captureDataLoader = useDataLoader((captureId) => critterbaseApi.capture.getCapture(captureId)); + + const getCaptureMetadata = (capture: ICaptureResponse) => { + return [ + { label: 'Capture ID', value: String(capture.capture_id) }, + { label: 'Date', value: dayjs(capture.capture_date).format(DATE_FORMAT.LongDateTimeFormat) }, + { label: 'Time', value: String(capture.capture_time ?? '') }, + { + label: 'Coordinates', + value: [capture.release_location?.latitude ?? null, capture.release_location?.longitude ?? null] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + } + ]; + }; + + return ( + { + captureDataLoader.load(String(feature.id)); + } + }}> + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalMortalityPopup.tsx b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalMortalityPopup.tsx new file mode 100644 index 0000000000..393890c9d5 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalMortalityPopup.tsx @@ -0,0 +1,59 @@ +import { IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; +import { IMortalityResponse } from 'interfaces/useCritterApi.interface'; +import { Popup } from 'react-leaflet'; + +export interface ISurveySpatialAnimalMortalityPopupProps { + feature: IStaticLayerFeature; +} + +/** + * Renders a popup for animal mortality data on the map. + * + * @param {ISurveySpatialAnimalMortalityPopupProps} props + * @return {*} + */ +export const SurveySpatialAnimalMortalityPopup = (props: ISurveySpatialAnimalMortalityPopupProps) => { + const { feature } = props; + + const critterbaseApi = useCritterbaseApi(); + + const mortalityDataLoader = useDataLoader((mortalityId) => critterbaseApi.mortality.getMortality(mortalityId)); + + const getMortalityMetadata = (mortality: IMortalityResponse) => { + return [ + { label: 'Mortality ID', value: String(mortality.mortality_id) }, + { label: 'Date', value: dayjs(mortality.mortality_timestamp).format(DATE_FORMAT.LongDateTimeFormat) }, + { + label: 'Coordinates', + value: [mortality.location?.latitude ?? null, mortality.location?.longitude ?? null] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + } + ]; + }; + + return ( + { + mortalityDataLoader.load(String(feature.id)); + } + }}> + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalTable.tsx b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalTable.tsx new file mode 100644 index 0000000000..e8d184f511 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/animal/SurveySpatialAnimalTable.tsx @@ -0,0 +1,117 @@ +import { mdiArrowTopRight } from '@mdi/js'; +import { GridColDef } from '@mui/x-data-grid'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { useSurveyContext } from 'hooks/useContext'; +import { useCritterbaseApi } from 'hooks/useCritterbaseApi'; +import useDataLoader from 'hooks/useDataLoader'; + +// Set height so the skeleton loader matches table rows +const rowHeight = 52; + +/** + * Interface defining the structure of animal data used in the table. + */ +interface IAnimalData { + id: number; + animal_id: string; + scientificName: string; +} + +/** + * Props interface for SurveySpatialAnimalTable component. + */ +interface ISurveyDataAnimalTableProps { + isLoading: boolean; +} + +/** + * Component for displaying animal data in a table, fetching data via context and API hooks. + * Renders a table with animal nicknames and scientific names, with loading skeleton when data is loading. + */ +export const SurveySpatialAnimalTable = (props: ISurveyDataAnimalTableProps) => { + const surveyContext = useSurveyContext(); + const critterbaseApi = useCritterbaseApi(); + + // Fetch critter data loader from survey context + const animals = surveyContext.critterDataLoader.data ?? []; + + // DataLoader to fetch detailed critter data based on IDs from context + const animalsDataLoader = useDataLoader(() => + critterbaseApi.critters.getMultipleCrittersByIds(animals.map((animal) => animal.critterbase_critter_id)) + ); + + // Load data if animals data is available + if (animals.length) { + animalsDataLoader.load(); + } + + // Map fetched data to table data structure + const rows: IAnimalData[] = + animalsDataLoader.data?.map((item) => ({ + id: item.critter_id, + animal_id: item.animal_id ?? '', + scientificName: item.itis_scientific_name, + status: !!item.mortality?.length + })) ?? []; + + // Define columns for the data grid + const columns: GridColDef[] = [ + { + field: 'animal_id', + headerName: 'Nickname', + flex: 1 + }, + { + field: 'scientificName', + headerName: 'Species', + flex: 1, + renderCell: (params) => // Render scientific name with custom typography component + } + ]; + + return ( + 0 && (props.isLoading || animalsDataLoader.isLoading || !animalsDataLoader.isReady)} + isLoadingFallback={} + isLoadingFallbackDelay={100} + hasNoData={!animals.length || !rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.id} + columns={columns} + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 5 } + } + }} + pageSizeOptions={[5]} + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + disableColumnSelector + disableColumnFilter + disableColumnMenu + disableVirtualization + sortingOrder={['asc', 'desc']} + data-testid="survey-animals-data-table" + /> + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/map/SurveySpatialMap.tsx b/app/src/features/surveys/view/survey-spatial/components/map/SurveySpatialMap.tsx new file mode 100644 index 0000000000..ce916ecbc1 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/map/SurveySpatialMap.tsx @@ -0,0 +1,42 @@ +import { IStaticLayer } from 'components/map/components/StaticLayers'; +import { useSamplingSiteStaticLayer } from 'features/surveys/view/survey-spatial/components/map/useSamplingSiteStaticLayer'; +import { useStudyAreaStaticLayer } from 'features/surveys/view/survey-spatial/components/map/useStudyAreaStaticLayer'; +import SurveyMap from 'features/surveys/view/SurveyMap'; +import { useMemo } from 'react'; + +/** + * Props interface for SurveySpatialMap component. + */ +interface ISurveyDataMapProps { + /** + * Array of additional static layers to be added to the map. + */ + staticLayers: IStaticLayer[]; + /** + * Loading indicator to control map skeleton loader. + */ + isLoading: boolean; +} + +/** + * Component for displaying survey-related spatial data on a map. + * + * Automatically includes the study area and sampling site static layers. + * + * @param {ISurveyDataMapProps} props + * @return {*} + */ +export const SurveySpatialMap = (props: ISurveyDataMapProps) => { + const { staticLayers, isLoading } = props; + + const studyAreaStaticLayer = useStudyAreaStaticLayer(); + + const samplingSiteStaticLayer = useSamplingSiteStaticLayer(); + + const allStaticLayers = useMemo( + () => [studyAreaStaticLayer, samplingSiteStaticLayer, ...staticLayers], + [samplingSiteStaticLayer, staticLayers, studyAreaStaticLayer] + ); + + return ; +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/map/useSamplingSiteStaticLayer.tsx b/app/src/features/surveys/view/survey-spatial/components/map/useSamplingSiteStaticLayer.tsx new file mode 100644 index 0000000000..9fdf33aa54 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/map/useSamplingSiteStaticLayer.tsx @@ -0,0 +1,64 @@ +import { IStaticLayer } from 'components/map/components/StaticLayers'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import SurveyMapTooltip from 'features/surveys/view/SurveyMapTooltip'; +import { useSurveyContext } from 'hooks/useContext'; +import { Popup } from 'react-leaflet'; + +/** + * Hook to get the sampling site static layer. + * + * @return {*} {IStaticLayer} + */ +export const useSamplingSiteStaticLayer = (): IStaticLayer => { + const surveyContext = useSurveyContext(); + + const samplingSiteStaticLayer: IStaticLayer = { + layerName: 'Sampling Sites', + layerOptions: { + color: SURVEY_MAP_LAYER_COLOURS.SAMPLING_SITE_COLOUR, + fillColor: SURVEY_MAP_LAYER_COLOURS.SAMPLING_SITE_COLOUR + }, + features: + surveyContext.sampleSiteDataLoader.data?.sampleSites.flatMap((site) => { + return { + id: site.survey_sample_site_id, + key: `sampling-site-${site.survey_sample_site_id}`, + geoJSON: site.geojson + }; + }) ?? [], + popup: (feature) => { + const sampleSite = surveyContext.sampleSiteDataLoader.data?.sampleSites.find( + (item) => item.survey_sample_site_id === feature.id + ); + + const metadata = []; + + if (sampleSite) { + metadata.push({ + label: 'Name', + value: sampleSite.name + }); + + metadata.push({ + label: 'Description', + value: sampleSite.description + }); + } + + return ( + + + + ); + }, + tooltip: (feature) => + }; + + return samplingSiteStaticLayer; +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/map/useStudyAreaStaticLayer.tsx b/app/src/features/surveys/view/survey-spatial/components/map/useStudyAreaStaticLayer.tsx new file mode 100644 index 0000000000..66e8d839b3 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/map/useStudyAreaStaticLayer.tsx @@ -0,0 +1,66 @@ +import { IStaticLayer } from 'components/map/components/StaticLayers'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import SurveyMapTooltip from 'features/surveys/view/SurveyMapTooltip'; +import { useSurveyContext } from 'hooks/useContext'; +import { Popup } from 'react-leaflet'; + +/** + * Hook to get the study area static layer. + * + * @return {*} {IStaticLayer} + */ +export const useStudyAreaStaticLayer = (): IStaticLayer => { + const surveyContext = useSurveyContext(); + + const studyAreaStaticLayer: IStaticLayer = { + layerName: 'Study Areas', + layerOptions: { + color: SURVEY_MAP_LAYER_COLOURS.STUDY_AREA_COLOUR, + fillColor: SURVEY_MAP_LAYER_COLOURS.STUDY_AREA_COLOUR + }, + features: + surveyContext.surveyDataLoader.data?.surveyData.locations.flatMap((location) => { + return location.geojson.map((feature) => { + return { + id: location.survey_location_id, + key: `study-area-${location.survey_location_id}`, + geoJSON: feature + }; + }); + }) ?? [], + popup: (feature) => { + const location = surveyContext.surveyDataLoader.data?.surveyData.locations.find( + (item) => item.survey_location_id === feature.id + ); + + const metadata = []; + + if (location) { + metadata.push({ + label: 'Name', + value: location.name + }); + + metadata.push({ + label: 'Description', + value: location.description + }); + } + + return ( + + + + ); + }, + tooltip: (feature) => + }; + + return studyAreaStaticLayer; +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservation.tsx b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservation.tsx new file mode 100644 index 0000000000..34836bdf3a --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservation.tsx @@ -0,0 +1,74 @@ +import Box from '@mui/material/Box'; +import { IStaticLayer, IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; +import SurveyObservationTabularDataContainer from 'features/surveys/view/components/data-container/SurveyObservationTabularDataContainer'; +import { SurveySpatialMap } from 'features/surveys/view/survey-spatial/components/map/SurveySpatialMap'; +import { SurveySpatialObservationPointPopup } from 'features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationPointPopup'; +import SurveyMapTooltip from 'features/surveys/view/SurveyMapTooltip'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { IGetSurveyObservationsGeometryResponse } from 'interfaces/useObservationApi.interface'; +import { useEffect, useMemo } from 'react'; +import { coloredCustomObservationMarker } from 'utils/mapUtils'; + +/** + * Component to display survey observation data on a map and in a table. + */ +export const SurveySpatialObservation = () => { + const surveyContext = useSurveyContext(); + const { surveyId, projectId } = surveyContext; + const biohubApi = useBiohubApi(); + + const observationsGeometryDataLoader = useDataLoader(() => + biohubApi.observation.getObservationsGeometry(projectId, surveyId) + ); + + useEffect(() => { + observationsGeometryDataLoader.load(); + }, [observationsGeometryDataLoader]); + + const observations: IGetSurveyObservationsGeometryResponse | undefined = observationsGeometryDataLoader.data; + + const observationPoints: IStaticLayerFeature[] = useMemo(() => { + return ( + observations?.surveyObservationsGeometry.map((item) => ({ + id: Number(item.survey_observation_id), + key: `observation-${item.survey_observation_id}`, + geoJSON: { + type: 'Feature', + properties: {}, + geometry: item.geometry + } + })) ?? [] + ); + }, [observations?.surveyObservationsGeometry]); + + const observationLayer: IStaticLayer = { + layerName: 'Species Observations', + layerOptions: { + fillColor: SURVEY_MAP_LAYER_COLOURS.OBSERVATIONS_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + color: SURVEY_MAP_LAYER_COLOURS.OBSERVATIONS_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + marker: coloredCustomObservationMarker + }, + features: observationPoints, + popup: (feature) => { + return ; + }, + tooltip: (feature) => + }; + + return ( + <> + {/* Display map with observation points */} + + + + + {/* Display data table with observation details */} + + + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationPointPopup.tsx b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationPointPopup.tsx new file mode 100644 index 0000000000..8e17ef5285 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationPointPopup.tsx @@ -0,0 +1,70 @@ +import { IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useSurveyContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { ObservationRecord } from 'interfaces/useObservationApi.interface'; +import { Popup } from 'react-leaflet'; +import { getFormattedDate } from 'utils/Utils'; + +interface ISurveySpatialObservationPointPopupProps { + feature: IStaticLayerFeature; +} + +/** + * Renders a popup for observation data on the map. + * + * @param {ISurveySpatialObservationPointPopupProps} props + * @return {*} + */ +export const SurveySpatialObservationPointPopup = (props: ISurveySpatialObservationPointPopupProps) => { + const { feature } = props; + + const surveyContext = useSurveyContext(); + const biohubApi = useBiohubApi(); + + const observationDataLoader = useDataLoader((observationId: number) => + biohubApi.observation.getObservationRecord(surveyContext.projectId, surveyContext.surveyId, observationId) + ); + + const getObservationMetadata = (observation: ObservationRecord) => { + return [ + { label: 'Taxon ID', value: String(observation.itis_tsn) }, + { label: 'Count', value: String(observation.count) }, + { + label: 'Coords', + value: [observation.latitude, observation.longitude] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + }, + { + label: 'Date', + value: getFormattedDate( + observation.observation_time ? DATE_FORMAT.LongDateTimeFormat : DATE_FORMAT.MediumDateFormat, + `${observation.observation_date} ${observation.observation_time}` + ) + } + ]; + }; + + return ( + { + observationDataLoader.load(Number(feature.id)); + } + }}> + + + ); +}; diff --git a/app/src/features/surveys/view/components/spatial-data/SurveySpatialObservationDataTable.tsx b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationTable.tsx similarity index 52% rename from app/src/features/surveys/view/components/spatial-data/SurveySpatialObservationDataTable.tsx rename to app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationTable.tsx index 0605ddd16a..a47dc7181a 100644 --- a/app/src/features/surveys/view/components/spatial-data/SurveySpatialObservationDataTable.tsx +++ b/app/src/features/surveys/view/survey-spatial/components/observation/SurveySpatialObservationTable.tsx @@ -1,12 +1,9 @@ import { mdiArrowTopRight } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import grey from '@mui/material/colors/grey'; -import Skeleton from '@mui/material/Skeleton'; -import Stack from '@mui/material/Stack'; -import Typography from '@mui/material/Typography'; -import { GridColDef, GridOverlay, GridSortModel } from '@mui/x-data-grid'; +import { GridColDef, GridSortModel } from '@mui/x-data-grid'; import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; import { SurveyContext } from 'contexts/surveyContext'; import dayjs from 'dayjs'; import { useBiohubApi } from 'hooks/useBioHubApi'; @@ -14,7 +11,7 @@ import { useTaxonomyContext } from 'hooks/useContext'; import useDataLoader from 'hooks/useDataLoader'; import { useContext, useEffect, useState } from 'react'; -// Set height so we the skeleton loader will match table rows +// Set height so the skeleton loader will match table rows const rowHeight = 52; interface IObservationTableRow { @@ -31,66 +28,38 @@ interface IObservationTableRow { longitude: number | null; } -interface ISurveySpatialObservationDataTableProps { +interface ISurveyDataObservationTableProps { isLoading: boolean; } -// Skeleton Loader template -const SkeletonRow = () => ( - - - - - - - - - - - -); - -const SurveySpatialObservationDataTable = (props: ISurveySpatialObservationDataTableProps) => { +/** + * Component to display observation data in a table with server-side pagination and sorting. + * + * @param {ISurveyDataObservationTableProps} props - Component properties. + * @returns {JSX.Element} The rendered component. + */ +export const SurveySpatialObservationTable = (props: ISurveyDataObservationTableProps) => { const biohubApi = useBiohubApi(); const surveyContext = useContext(SurveyContext); const taxonomyContext = useTaxonomyContext(); const [totalRows, setTotalRows] = useState(0); const [page, setPage] = useState(0); - const [pageSize, setPageSize] = useState(5); + const [pageSize, setPageSize] = useState(10); const [sortModel, setSortModel] = useState([]); - const [tableData, setTableData] = useState([]); + const [rows, setTableData] = useState([]); const [tableColumns, setTableColumns] = useState[]>([]); const paginatedDataLoader = useDataLoader((page: number, limit: number, sort?: string, order?: 'asc' | 'desc') => biohubApi.observation.getObservationRecords(surveyContext.projectId, surveyContext.surveyId, { - page: page + 1, // this fixes an off by one error between the front end and the back end + page: page + 1, // This fixes an off-by-one error between the front end and the back end limit, sort, order }) ); - // page information has changed, fetch more data + // Page information has changed, fetch more data useEffect(() => { if (sortModel.length > 0) { if (sortModel[0].sort) { @@ -99,10 +68,10 @@ const SurveySpatialObservationDataTable = (props: ISurveySpatialObservationDataT } else { paginatedDataLoader.refresh(page, pageSize); } - // Should not re-run this effect on `paginatedDataLoader.refresh` changes // eslint-disable-next-line react-hooks/exhaustive-deps }, [page, pageSize, sortModel]); + // Update table data and columns when new data is loaded useEffect(() => { if (paginatedDataLoader.data) { setTotalRows(paginatedDataLoader.data.pagination.total); @@ -132,9 +101,7 @@ const SurveySpatialObservationDataTable = (props: ISurveySpatialObservationDataT headerName: 'Species', flex: 1, minWidth: 200, - renderCell: (params) => { - return {params.row.itis_scientific_name}; - } + renderCell: (params) => {params.row.itis_scientific_name} }, { field: 'survey_sample_site_name', @@ -192,69 +159,48 @@ const SurveySpatialObservationDataTable = (props: ISurveySpatialObservationDataT }, [paginatedDataLoader.data, taxonomyContext]); return ( - <> - {props.isLoading ? ( - - - - - - ) : ( - { - setPage(model.page); - setPageSize(model.pageSize); - }} - pageSizeOptions={[5]} - paginationMode="server" - sortingMode="server" - sortModel={sortModel} - onSortModelChange={(model) => setSortModel(model)} - loading={paginatedDataLoader.isLoading} - getRowId={(row) => row.survey_observation_id} - columns={tableColumns} - rowSelection={false} - checkboxSelection={false} - disableColumnSelector - disableColumnFilter - disableColumnMenu - disableVirtualization - data-testid="survey-spatial-observation-data-table" - noRowsOverlay={ - - - - Add observations after sampling information  - - - - After adding sampling information, add observations and assign them to a sampling period - - - - } - sx={{ - '& .MuiDataGrid-virtualScroller': { - height: '250px', - overflowY: 'auto !important' - }, - '& .MuiDataGrid-overlay': { - height: '250px', - display: 'flex', - justifyContent: 'center', - alignItems: 'center' - } - }} + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + - )} - + } + hasNoDataFallbackDelay={100}> + { + setPage(model.page); + setPageSize(model.pageSize); + }} + pageSizeOptions={[10, 25, 50]} + paginationMode="server" + sortingMode="server" + sortModel={sortModel} + onSortModelChange={(model) => setSortModel(model)} + loading={paginatedDataLoader.isLoading} + getRowId={(row) => row.survey_observation_id} + columns={tableColumns} + rowSelection={false} + autoHeight={false} + checkboxSelection={false} + disableColumnSelector + disableColumnFilter + disableColumnMenu + disableVirtualization + data-testid="survey-spatial-observation-data-table" + /> + ); }; - -export default SurveySpatialObservationDataTable; diff --git a/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetry.tsx b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetry.tsx new file mode 100644 index 0000000000..3737f7bc89 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetry.tsx @@ -0,0 +1,140 @@ +import Box from '@mui/material/Box'; +import { IStaticLayer, IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; +import { SurveySpatialMap } from 'features/surveys/view/survey-spatial/components/map/SurveySpatialMap'; +import { SurveySpatialTelemetryPopup } from 'features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryPopup'; +import { SurveySpatialTelemetryTable } from 'features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryTable'; +import SurveyMapTooltip from 'features/surveys/view/SurveyMapTooltip'; +import { Position } from 'geojson'; +import { useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import { ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; +import { IAnimalDeployment, ITelemetry } from 'interfaces/useTelemetryApi.interface'; +import { useCallback, useEffect, useMemo } from 'react'; + +/** + * Component to display telemetry data on a map and in a table. + * + * @returns {JSX.Element} The rendered component. + */ +export const SurveySpatialTelemetry = () => { + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const deploymentDataLoader = telemetryDataContext.deploymentsDataLoader; + const telemetryDataLoader = telemetryDataContext.telemetryDataLoader; + + // Load deployments data + useEffect(() => { + deploymentDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [surveyContext.projectId, surveyContext.surveyId]); + + // Load telemetry data for all deployments + useEffect(() => { + if (!deploymentDataLoader.data?.length) { + // No deployments data, therefore no telemetry data to load + return; + } + + telemetryDataLoader.load(deploymentDataLoader.data?.map((deployment) => deployment.bctw_deployment_id) ?? []); + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [deploymentDataLoader.data]); + + const isLoading = + deploymentDataLoader.isLoading || + !deploymentDataLoader.isReady || + ((telemetryDataLoader.isLoading || !telemetryDataLoader.isReady) && !!deploymentDataLoader.data?.length); + + /** + * Combines telemetry, deployment, and critter data into a single list of telemetry points. + * + * @param {ITelemetry[]} telemetry The telemetry data. + * @param {IAnimalDeployment[]} deployments The deployment data. + * @param {ICritterSimpleResponse[]} critters The critter data. + * @returns {IStaticLayerFeature[]} The combined list of telemetry points. + */ + const combineTelemetryData = useCallback( + ( + telemetry: ITelemetry[], + deployments: IAnimalDeployment[], + critters: ICritterSimpleResponse[] + ): IStaticLayerFeature[] => { + return ( + telemetry + ?.filter((telemetry) => telemetry.latitude !== undefined && telemetry.longitude !== undefined) + .reduce( + ( + acc: { + deployment: IAnimalDeployment; + critter: ICritterSimpleResponse; + telemetry: ITelemetry; + }[], + telemetry: ITelemetry + ) => { + const deployment = deployments.find( + (animalDeployment) => animalDeployment.bctw_deployment_id === telemetry.deployment_id + ); + + const critter = critters.find((detailedCritter) => detailedCritter.critter_id === deployment?.critter_id); + + if (critter && deployment) { + acc.push({ deployment, critter, telemetry }); + } + + return acc; + }, + [] + ) + .map(({ telemetry }) => { + return { + id: telemetry.id, + key: `telemetry-id-${telemetry.id}`, + geoJSON: { + type: 'Feature', + properties: {}, + geometry: { + type: 'Point', + coordinates: [telemetry.longitude, telemetry.latitude] as Position + } + } + }; + }) ?? [] + ); + }, + [] + ); + + const telemetryPoints: IStaticLayerFeature[] = useMemo(() => { + const telemetry = telemetryDataLoader.data ?? []; + const deployments = deploymentDataLoader.data ?? []; + const critters = surveyContext.critterDataLoader.data ?? []; + + return combineTelemetryData(telemetry, deployments, critters); + }, [combineTelemetryData, surveyContext.critterDataLoader.data, deploymentDataLoader.data, telemetryDataLoader.data]); + + const telemetryLayer: IStaticLayer = { + layerName: 'Telemetry', + layerOptions: { + fillColor: SURVEY_MAP_LAYER_COLOURS.TELEMETRY_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + color: SURVEY_MAP_LAYER_COLOURS.TELEMETRY_COLOUR ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + opacity: 0.75 + }, + features: telemetryPoints, + popup: (feature) => , + tooltip: (feature) => + }; + + return ( + <> + {/* Display map with telemetry points */} + + + + + {/* Display data table with telemetry details */} + + + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryPopup.tsx b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryPopup.tsx new file mode 100644 index 0000000000..609dcaff08 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryPopup.tsx @@ -0,0 +1,101 @@ +import { IStaticLayerFeature } from 'components/map/components/StaticLayers'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import dayjs from 'dayjs'; +import { SurveyMapPopup } from 'features/surveys/view/SurveyMapPopup'; +import { useSurveyContext, useTelemetryDataContext } from 'hooks/useContext'; +import { Popup } from 'react-leaflet'; + +export interface ISurveySpatialTelemetryPopupProps { + feature: IStaticLayerFeature; +} + +/** + * Renders a popup for telemetry data on the map. + * + * TODO: This currently relies on the telemetry, deployment, and critter data loaders to already be loaded. The + * improvement would be to fetch that data when the popup is opened, based on the provided feature ID. + * + * @param {ISurveySpatialTelemetryPopupProps} props + * @return {*} + */ +export const SurveySpatialTelemetryPopup = (props: ISurveySpatialTelemetryPopupProps) => { + const { feature } = props; + + const surveyContext = useSurveyContext(); + const telemetryDataContext = useTelemetryDataContext(); + + const deploymentDataLoader = telemetryDataContext.deploymentsDataLoader; + const telemetryDataLoader = telemetryDataContext.telemetryDataLoader; + + const getTelemetryMetadata = () => { + const telemetryId = feature.id; + + const telemetryRecord = telemetryDataLoader.data?.find((telemetry) => telemetry.id === telemetryId); + + if (!telemetryRecord) { + return [{ label: 'Telemetry ID', value: telemetryId }]; + } + + const deploymentRecord = deploymentDataLoader.data?.find( + (deployment) => deployment.bctw_deployment_id === telemetryRecord.deployment_id + ); + + if (!deploymentRecord) { + return [ + { label: 'Telemetry ID', value: telemetryId }, + { + label: 'Location', + value: [telemetryRecord.latitude, telemetryRecord.longitude] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + }, + { label: 'Date', value: dayjs(telemetryRecord?.acquisition_date).toISOString() } + ]; + } + + const critterRecord = surveyContext.critterDataLoader.data?.find( + (critter) => critter.critter_id === deploymentRecord.critter_id + ); + + if (!critterRecord) { + return [ + { label: 'Telemetry ID', value: telemetryId }, + { label: 'Device ID', value: String(deploymentRecord.device_id) }, + { + label: 'Location', + value: [telemetryRecord.latitude, telemetryRecord.longitude] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + }, + { label: 'Date', value: dayjs(telemetryRecord?.acquisition_date).toISOString() } + ]; + } + + return [ + { label: 'Telemetry ID', value: telemetryId }, + { label: 'Device ID', value: String(deploymentRecord.device_id) }, + { label: 'Nickname', value: critterRecord.animal_id ?? '' }, + { + label: 'Location', + value: [telemetryRecord?.latitude, telemetryRecord?.longitude] + .filter((coord): coord is number => coord !== null) + .map((coord) => coord.toFixed(6)) + .join(', ') + }, + { label: 'Date', value: dayjs(telemetryRecord?.acquisition_date).format(DATE_FORMAT.LongDateTimeFormat) } + ]; + }; + + return ( + + + + ); +}; diff --git a/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryTable.tsx b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryTable.tsx new file mode 100644 index 0000000000..1f35e17b73 --- /dev/null +++ b/app/src/features/surveys/view/survey-spatial/components/telemetry/SurveySpatialTelemetryTable.tsx @@ -0,0 +1,211 @@ +import { mdiArrowTopRight } from '@mdi/js'; +import Typography from '@mui/material/Typography'; +import { GridColDef } from '@mui/x-data-grid'; +import { StyledDataGrid } from 'components/data-grid/StyledDataGrid'; +import { LoadingGuard } from 'components/loading/LoadingGuard'; +import { SkeletonTable } from 'components/loading/SkeletonLoaders'; +import { NoDataOverlay } from 'components/overlay/NoDataOverlay'; +import { DATE_FORMAT } from 'constants/dateTimeFormats'; +import { SurveyContext } from 'contexts/surveyContext'; +import dayjs from 'dayjs'; +import { ScientificNameTypography } from 'features/surveys/animals/components/ScientificNameTypography'; +import { useBiohubApi } from 'hooks/useBioHubApi'; +import { useTelemetryDataContext } from 'hooks/useContext'; +import useDataLoader from 'hooks/useDataLoader'; +import { IAnimalDeploymentWithCritter } from 'interfaces/useSurveyApi.interface'; +import { useContext, useEffect, useMemo } from 'react'; + +// Set height so the skeleton loader will match table rows +const rowHeight = 52; + +interface ITelemetryData { + id: number; + critter_id: number | null; + device_id: number; + frequency: number | null; + frequency_unit: string | null; + // start: string; + end: string; + itis_scientific_name: string; +} + +interface ISurveyDataTelemetryTableProps { + isLoading: boolean; +} + +/** + * Component to display telemetry data in a table format. + * + * @param {ISurveyDataTelemetryTableProps} props - The component props. + * @param {boolean} props.isLoading - Indicates if the data is currently loading. + * @returns {JSX.Element} The rendered component. + */ +export const SurveySpatialTelemetryTable = (props: ISurveyDataTelemetryTableProps) => { + const surveyContext = useContext(SurveyContext); + const telemetryDataContext = useTelemetryDataContext(); + + const biohubApi = useBiohubApi(); + + const critterDataLoader = useDataLoader(biohubApi.survey.getSurveyCritters); + const deploymentDataLoader = telemetryDataContext.deploymentsDataLoader; + const frequencyUnitDataLoader = useDataLoader(() => biohubApi.telemetry.getCodeValues('frequency_unit')); + + useEffect(() => { + deploymentDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + critterDataLoader.load(surveyContext.projectId, surveyContext.surveyId); + frequencyUnitDataLoader.load(); + }, [ + critterDataLoader, + deploymentDataLoader, + frequencyUnitDataLoader, + surveyContext.projectId, + surveyContext.surveyId + ]); + + /** + * Merges critters with associated deployments + * + * @returns {ICritterDeployment[]} Critter deployments + */ + const critterDeployments: IAnimalDeploymentWithCritter[] = useMemo(() => { + const critterDeployments: IAnimalDeploymentWithCritter[] = []; + const critters = critterDataLoader.data ?? []; + const deployments = deploymentDataLoader.data ?? []; + + if (!critters.length || !deployments.length) { + return []; + } + + const critterMap = new Map(critters.map((critter) => [critter.critterbase_critter_id, critter])); + + deployments.forEach((deployment) => { + const critter = critterMap.get(String(deployment.critterbase_critter_id)); + if (critter) { + critterDeployments.push({ critter, deployment }); + } + }); + + return critterDeployments; + }, [critterDataLoader.data, deploymentDataLoader.data]); + + /** + * Memoized calculation of table rows based on critter deployments data. + * Formats dates and combines necessary fields for display. + */ + const rows: ITelemetryData[] = useMemo(() => { + return critterDeployments.map((item) => { + return { + // Critters in this table may use multiple devices across multiple timespans + id: item.deployment.deployment_id, + critter_id: item.critter.critter_id, + animal_id: item.critter.animal_id, + device_id: item.deployment.device_id, + // start: dayjs(item.deployment.attachment_start).format(DATE_FORMAT.MediumDateFormat), + end: item.deployment.attachment_end_date + ? dayjs(item.deployment.attachment_end_date).format(DATE_FORMAT.MediumDateFormat) + : '', + frequency: item.deployment.frequency ?? null, + frequency_unit: item.deployment.frequency_unit + ? frequencyUnitDataLoader.data?.find((frequencyCode) => frequencyCode.id === item.deployment.frequency_unit) + ?.code ?? null + : null, + itis_scientific_name: item.critter.itis_scientific_name + }; + }); + }, [critterDeployments, frequencyUnitDataLoader.data]); + + // Define table columns + const columns: GridColDef[] = [ + { + field: 'animal_id', + headerName: 'Nickname', + flex: 1 + }, + { + field: 'itis_scientific_name', + headerName: 'Species', + flex: 1, + renderCell: (param) => { + return ( + + ); + } + }, + { + field: 'device_id', + headerName: 'Device ID', + flex: 1 + }, + { + field: 'frequency', + headerName: 'Frequency', + flex: 1, + renderCell: (param) => { + return ( + + {param.row.frequency}  + + {param.row.frequency_unit} + + + ); + } + }, + { + field: 'start', + headerName: 'Start Date', + flex: 1 + }, + { + field: 'end', + headerName: 'End Date', + flex: 1 + } + ]; + + return ( + } + isLoadingFallbackDelay={100} + hasNoData={!rows.length} + hasNoDataFallback={ + + } + hasNoDataFallbackDelay={100}> + row.id} + columns={columns} + initialState={{ + pagination: { + paginationModel: { page: 1, pageSize: 5 } + } + }} + pageSizeOptions={[5]} + rowSelection={false} + checkboxSelection={false} + disableRowSelectionOnClick + disableColumnSelector + disableColumnFilter + disableColumnMenu + disableVirtualization + sortingOrder={['asc', 'desc']} + data-testid="survey-spatial-telemetry-data-table" + /> + + ); +}; diff --git a/app/src/hooks/api/useAnalyticsApi.test.ts b/app/src/hooks/api/useAnalyticsApi.test.ts new file mode 100644 index 0000000000..cf7d72e18a --- /dev/null +++ b/app/src/hooks/api/useAnalyticsApi.test.ts @@ -0,0 +1,65 @@ +import axios from 'axios'; +import MockAdapter from 'axios-mock-adapter'; +import { IObservationCountByGroup } from 'interfaces/useAnalyticsApi.interface'; +import useAnalyticsApi from './useAnalyticsApi'; + +describe('useAnalyticsApi', () => { + let mock: MockAdapter; + + beforeEach(() => { + mock = new MockAdapter(axios); + }); + + afterEach(() => { + mock.restore(); + }); + + it('getObservationCountByGroup works as expected', async () => { + const response: IObservationCountByGroup[] = [ + { + id: '123-456-789', + row_count: 10, + individual_count: 40, + individual_percentage: 1, + itis_tsn: 123456, + observation_date: '2021-01-01', + survey_sample_site_id: 1, + survey_sample_method_id: 2, + survey_sample_period_id: 3, + qualitative_measurements: [ + { + taxon_measurement_id: '66', + measurement_name: 'a', + option: { + option_id: '1', + option_label: 'x' + } + } + ], + quantitative_measurements: [ + { + taxon_measurement_id: '77', + measurement_name: 'b', + value: 1 + } + ] + } + ]; + + mock.onGet('/api/analytics/observations').reply(200, response); + + const surveyIds = [1, 2]; + const groupByColumns = ['a', 'b']; + const groupByQuantitativeMeasurements = ['c', 'd']; + const groupByQualitativeMeasurements = ['e', 'f']; + + const result = await useAnalyticsApi(axios).getObservationCountByGroup( + surveyIds, + groupByColumns, + groupByQuantitativeMeasurements, + groupByQualitativeMeasurements + ); + + expect(result).toEqual(response); + }); +}); diff --git a/app/src/hooks/api/useAnalyticsApi.ts b/app/src/hooks/api/useAnalyticsApi.ts new file mode 100644 index 0000000000..b45ae447c3 --- /dev/null +++ b/app/src/hooks/api/useAnalyticsApi.ts @@ -0,0 +1,36 @@ +import { AxiosInstance } from 'axios'; +import { IObservationCountByGroup } from 'interfaces/useAnalyticsApi.interface'; + +/** + * Returns a set of supported api methods for working with survey analytics + * + * @param {AxiosInstance} axios + * @return {*} object whose properties are supported api methods. + */ +const useAnalyticsApi = (axios: AxiosInstance) => { + /** + * Create a new project survey + * + * @param {number[]} surveyIds + * @param {string[]} groupByColumns + * @param {string[]} groupByQualitativeMeasurements + * @param {string[]} groupByQuantitativeMeasurements + * @return {*} + */ + const getObservationCountByGroup = async ( + surveyIds: number[], + groupByColumns: string[], + groupByQuantitativeMeasurements: string[], + groupByQualitativeMeasurements: string[] + ): Promise => { + const { data } = await axios.get('/api/analytics/observations', { + params: { surveyIds, groupByColumns, groupByQuantitativeMeasurements, groupByQualitativeMeasurements } + }); + + return data; + }; + + return { getObservationCountByGroup }; +}; + +export default useAnalyticsApi; diff --git a/app/src/hooks/api/useAnimalApi.ts b/app/src/hooks/api/useAnimalApi.ts index 2889d79abb..9adf107fee 100644 --- a/app/src/hooks/api/useAnimalApi.ts +++ b/app/src/hooks/api/useAnimalApi.ts @@ -1,6 +1,6 @@ import { AxiosInstance } from 'axios'; import { IAnimalsAdvancedFilters } from 'features/summary/tabular-data/animal/AnimalsListFilterForm'; -import { IFindAnimalsResponse } from 'interfaces/useAnimalApi.interface'; +import { IFindAnimalsResponse, IGetCaptureMortalityGeometryResponse } from 'interfaces/useAnimalApi.interface'; import qs from 'qs'; import { ApiPaginationRequestOptions } from 'types/misc'; @@ -14,6 +14,25 @@ import { ApiPaginationRequestOptions } from 'types/misc'; * @return {*} object whose properties are supported api methods. */ const useAnimalApi = (axios: AxiosInstance) => { + /** + * Fetches all geojson capture and mortalities points for all animals in survey + * the given survey. + * + * @param {number} projectId + * @param {number} surveyId + * @return {*} {Promise} + */ + const getCaptureMortalityGeometry = async ( + projectId: number, + surveyId: number + ): Promise => { + const { data } = await axios.get( + `/api/project/${projectId}/survey/${surveyId}/critters/spatial` + ); + + return data; + }; + /** * Get animals for a system user id. * @@ -35,7 +54,7 @@ const useAnimalApi = (axios: AxiosInstance) => { return data; }; - return { findAnimals }; + return { getCaptureMortalityGeometry, findAnimals }; }; export default useAnimalApi; diff --git a/app/src/hooks/api/useAxios.ts b/app/src/hooks/api/useAxios.ts index e40b59af12..c49c586679 100644 --- a/app/src/hooks/api/useAxios.ts +++ b/app/src/hooks/api/useAxios.ts @@ -63,7 +63,6 @@ const useAxios = (baseUrl?: string): AxiosInstance => { authRefreshAttemptsRef.current++; // Attempt to refresh the keycloak token - // Note: updateToken called with an arbitrarily large number of seconds to guarantee the update is executed const user = await auth.signinSilent(); if (!user) { diff --git a/app/src/hooks/api/useObservationApi.ts b/app/src/hooks/api/useObservationApi.ts index 3d53ab2ee6..525d6e483f 100644 --- a/app/src/hooks/api/useObservationApi.ts +++ b/app/src/hooks/api/useObservationApi.ts @@ -1,5 +1,9 @@ import { AxiosInstance, AxiosProgressEvent, CancelTokenSource } from 'axios'; import { IObservationsAdvancedFilters } from 'features/summary/tabular-data/observation/ObservationsListFilterForm'; +import { + CBQualitativeMeasurementTypeDefinition, + CBQuantitativeMeasurementTypeDefinition +} from 'interfaces/useCritterApi.interface'; import { IGetSurveyObservationsGeometryResponse, IGetSurveyObservationsResponse, @@ -8,6 +12,7 @@ import { SupplementaryObservationCountData } from 'interfaces/useObservationApi.interface'; import { EnvironmentTypeIds } from 'interfaces/useReferenceApi.interface'; +import { IPartialTaxonomy } from 'interfaces/useTaxonomyApi.interface'; import qs from 'qs'; import { ApiPaginationRequestOptions } from 'types/misc'; @@ -121,6 +126,43 @@ const useObservationApi = (axios: AxiosInstance) => { return data; }; + /** + * Retrieves species observed in a given survey + * + * @param {number} projectId + * @param {number} surveyId + * @return {*} {Promise} + */ + const getObservedSpecies = async (projectId: number, surveyId: number): Promise => { + const { data } = await axios.get( + `/api/project/${projectId}/survey/${surveyId}/observations/taxon` + ); + + return data; + }; + + /** + * Retrieves all measurements associated with all observation records + * + * @param {number} projectId + * @param {number} surveyId + * @return {*} {Promise} + */ + const getObservationMeasurementDefinitions = async ( + projectId: number, + surveyId: number + ): Promise<{ + qualitative_measurements: CBQualitativeMeasurementTypeDefinition[]; + quantitative_measurements: CBQuantitativeMeasurementTypeDefinition[]; + }> => { + const { data } = await axios.get<{ + qualitative_measurements: CBQualitativeMeasurementTypeDefinition[]; + quantitative_measurements: CBQuantitativeMeasurementTypeDefinition[]; + }>(`/api/project/${projectId}/survey/${surveyId}/observations/measurements`); + + return data; + }; + /** * Retrieves all survey observation records for the given survey * @@ -295,8 +337,10 @@ const useObservationApi = (axios: AxiosInstance) => { insertUpdateObservationRecords, getObservationRecords, getObservationRecord, + getObservedSpecies, findObservations, getObservationsGeometry, + getObservationMeasurementDefinitions, deleteObservationRecords, deleteObservationMeasurements, deleteObservationEnvironments, diff --git a/app/src/hooks/api/useProjectApi.test.ts b/app/src/hooks/api/useProjectApi.test.ts index c644f4b985..363e4ba6a3 100644 --- a/app/src/hooks/api/useProjectApi.test.ts +++ b/app/src/hooks/api/useProjectApi.test.ts @@ -6,7 +6,7 @@ import { IProjectIUCNForm } from 'features/projects/components/ProjectIUCNForm'; import { IProjectObjectivesForm } from 'features/projects/components/ProjectObjectivesForm'; import { ICreateProjectRequest, IFindProjectsResponse, UPDATE_GET_ENTITIES } from 'interfaces/useProjectApi.interface'; import { getProjectForViewResponse } from 'test-helpers/project-helpers'; -import { ISurveyPermitForm } from '../../features/surveys/SurveyPermitForm'; +import { ISurveyPermitForm } from '../../features/surveys/components/permit/SurveyPermitForm'; import useProjectApi from './useProjectApi'; describe('useProjectApi', () => { @@ -66,7 +66,8 @@ describe('useProjectApi', () => { end_date: '2021-12-31', regions: [], focal_species: [123, 456], - types: [1, 2, 3] + types: [1, 2, 3], + members: [{ system_user_id: 1, display_name: 'John doe' }] } ], pagination: { diff --git a/app/src/hooks/api/useStandardsApi.ts b/app/src/hooks/api/useStandardsApi.ts index 75ecaf5f15..e27190cdbe 100644 --- a/app/src/hooks/api/useStandardsApi.ts +++ b/app/src/hooks/api/useStandardsApi.ts @@ -1,5 +1,6 @@ import { AxiosInstance } from 'axios'; -import { IGetSpeciesStandardsResponse } from 'interfaces/useStandardsApi.interface'; +import { IEnvironmentStandards, IMethodStandard, ISpeciesStandards } from 'interfaces/useStandardsApi.interface'; +import qs from 'qs'; /** * Returns information about what data can be uploaded for a given species, @@ -12,16 +13,52 @@ const useStandardsApi = (axios: AxiosInstance) => { /** * Fetch species standards * - * @return {*} {Promise} + * @return {*} {Promise} */ - const getSpeciesStandards = async (tsn: number): Promise => { + const getSpeciesStandards = async (tsn: number): Promise => { const { data } = await axios.get(`/api/standards/taxon/${tsn}`); return data; }; + /** + * Fetch method standards + * + * @param {string} keyword + * @return {*} {Promise} + */ + const getMethodStandards = async (keyword?: string): Promise => { + const params = { keyword }; + + const { data } = await axios.get('/api/standards/methods', { + params, + paramsSerializer: (params) => qs.stringify(params) + }); + + return data; + }; + + /** + * Fetch environment standards + * + * @param {string} keyword + * @return {*} {Promise} + */ + const getEnvironmentStandards = async (keyword?: string): Promise => { + const params = { keyword }; + + const { data } = await axios.get('/api/standards/environment', { + params, + paramsSerializer: (params) => qs.stringify(params) + }); + + return data; + }; + return { - getSpeciesStandards + getSpeciesStandards, + getEnvironmentStandards, + getMethodStandards }; }; diff --git a/app/src/hooks/api/useSurveyApi.test.ts b/app/src/hooks/api/useSurveyApi.test.ts index a9763f8a4a..7cd6dd2ff3 100644 --- a/app/src/hooks/api/useSurveyApi.test.ts +++ b/app/src/hooks/api/useSurveyApi.test.ts @@ -1,7 +1,6 @@ import axios from 'axios'; import MockAdapter from 'axios-mock-adapter'; import { AnimalSex, ICreateCritter } from 'features/surveys/view/survey-animals/animal'; -import { IAnimalDeployment } from 'features/surveys/view/survey-animals/telemetry-device/device'; import { ICreateSurveyRequest, ICreateSurveyResponse, @@ -9,6 +8,7 @@ import { IFindSurveysResponse, SurveyBasicFieldsObject } from 'interfaces/useSurveyApi.interface'; +import { IAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; import { ApiPaginationResponseParams } from 'types/misc'; import { v4 } from 'uuid'; import useSurveyApi from './useSurveyApi'; @@ -27,6 +27,7 @@ describe('useSurveyApi', () => { const projectId = 1; const surveyId = 1; const critterId = 1; + const deploymentId = 1; describe('createSurvey', () => { it('creates a survey', async () => { @@ -93,19 +94,21 @@ describe('useSurveyApi', () => { }); }); - describe('addDeployment', () => { + describe('createDeployment', () => { it('should add deployment to survey critter', async () => { mock.onPost(`/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/deployments`).reply(201, 1); - const result = await useSurveyApi(axios).addDeployment(projectId, surveyId, critterId, { + const result = await useSurveyApi(axios).createDeployment(projectId, surveyId, critterId, { device_id: 1, - device_make: 'ATS', + device_make: 22, device_model: 'E', frequency: 1, - frequency_unit: 'Hz', - attachment_start: '2023-01-01', - attachment_end: undefined, - critter_id: v4() + frequency_unit: 33, + critterbase_start_capture_id: '', + critterbase_end_capture_id: '', + critterbase_end_mortality_id: '', + attachment_end_date: '', + attachment_end_time: '' }); expect(result).toBe(1); @@ -117,15 +120,22 @@ describe('useSurveyApi', () => { const response: IAnimalDeployment = { assignment_id: v4(), collar_id: v4(), - critter_id: v4(), - attachment_start: '2023-01-01', - attachment_end: '2023-01-01', - deployment_id: v4(), + critterbase_critter_id: v4(), + critter_id: 123, + critterbase_start_capture_id: '', + critterbase_end_capture_id: '', + critterbase_end_mortality_id: '', + attachment_start_date: '', + attachment_start_time: '', + attachment_end_date: '', + attachment_end_time: '', + deployment_id: 123, + bctw_deployment_id: v4(), device_id: 123, - device_make: '', + device_make: 22, device_model: 'a', frequency: 1, - frequency_unit: 'Hz' + frequency_unit: 33 }; mock.onGet(`/api/project/${projectId}/survey/${surveyId}/deployments`).reply(200, [response]); @@ -140,11 +150,19 @@ describe('useSurveyApi', () => { describe('updateDeployment', () => { it('should update a deployment', async () => { - mock.onPatch(`/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/deployments`).reply(200, 1); - const result = await useSurveyApi(axios).updateDeployment(projectId, surveyId, critterId, { - attachment_end: undefined, - deployment_id: 'a', - attachment_start: 'a' + mock.onPut(`/api/project/${projectId}/survey/${surveyId}/deployments/${deploymentId}`).reply(200, 1); + const result = await useSurveyApi(axios).updateDeployment(projectId, surveyId, deploymentId, { + critter_id: 1, + critterbase_start_capture_id: '', + critterbase_end_capture_id: '', + critterbase_end_mortality_id: '', + attachment_end_date: '', + attachment_end_time: '', + frequency: 10.5, + frequency_unit: 44, + device_id: 1, + device_make: 22, + device_model: '' }); expect(result).toBe(1); @@ -155,7 +173,7 @@ describe('useSurveyApi', () => { it('should get critters', async () => { const response = [ { - critter_id: 'critter' + critterbase_critter_id: 'critter' } as IDetailedCritterWithInternalId ]; @@ -168,18 +186,4 @@ describe('useSurveyApi', () => { expect(result).toEqual(response); }); }); - - describe('uploadSurveyKeyx', () => { - it('should upload a keyx file', async () => { - const file = new File([''], 'file.keyx', { type: 'application/keyx' }); - const response = { - attachmentId: 'attachment', - revision_count: 1 - }; - mock.onPost(`/api/project/${projectId}/survey/${surveyId}/attachments/keyx/upload`).reply(201, response); - - const result = await useSurveyApi(axios).uploadSurveyKeyx(projectId, surveyId, file); - expect(result).toEqual(response); - }); - }); }); diff --git a/app/src/hooks/api/useSurveyApi.ts b/app/src/hooks/api/useSurveyApi.ts index 3187b31704..a9df91cb9d 100644 --- a/app/src/hooks/api/useSurveyApi.ts +++ b/app/src/hooks/api/useSurveyApi.ts @@ -4,12 +4,7 @@ import { IReportMetaForm } from 'components/attachments/ReportMetaForm'; import { ISurveyCritter } from 'contexts/animalPageContext'; import { ISurveyAdvancedFilters } from 'features/summary/list-data/survey/SurveysListFilterForm'; import { ICreateCritter } from 'features/surveys/view/survey-animals/animal'; -import { - IAnimalDeployment, - ICreateAnimalDeployment, - IDeploymentTimespan, - ITelemetryPointCollection -} from 'features/surveys/view/survey-animals/telemetry-device/device'; +import { ICritterDetailedResponse, ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; import { IGetReportDetails, IUploadAttachmentResponse } from 'interfaces/useProjectApi.interface'; import { ICreateSurveyRequest, @@ -18,9 +13,13 @@ import { IGetSurveyAttachmentsResponse, IGetSurveyForUpdateResponse, IGetSurveyForViewResponse, - ISimpleCritterWithInternalId, - SurveyUpdateObject + IUpdateSurveyRequest } from 'interfaces/useSurveyApi.interface'; +import { + IAllTelemetryPointCollection, + IAnimalDeployment, + ICreateAnimalDeploymentPostData +} from 'interfaces/useTelemetryApi.interface'; import qs from 'qs'; import { ApiPaginationRequestOptions } from 'types/misc'; @@ -126,10 +125,10 @@ const useSurveyApi = (axios: AxiosInstance) => { * * @param {number} projectId * @param {number} surveyId - * @param {SurveyUpdateObject} surveyData + * @param {IUpdateSurveyRequest} surveyData * @return {*} {Promise} */ - const updateSurvey = async (projectId: number, surveyId: number, surveyData: SurveyUpdateObject): Promise => { + const updateSurvey = async (projectId: number, surveyId: number, surveyData: IUpdateSurveyRequest): Promise => { const { data } = await axios.put(`/api/project/${projectId}/survey/${surveyId}/update`, surveyData); return data; @@ -165,39 +164,6 @@ const useSurveyApi = (axios: AxiosInstance) => { return data; }; - /** - * Upload survey keyx files. - * - * @param {number} projectId - * @param {number} surveyId - * @param {File} file - * @param {CancelTokenSource} [cancelTokenSource] - * @param {(progressEvent: AxiosProgressEvent) => void} [onProgress] - * @return {*} {Promise} - */ - const uploadSurveyKeyx = async ( - projectId: number, - surveyId: number, - file: File, - cancelTokenSource?: CancelTokenSource, - onProgress?: (progressEvent: AxiosProgressEvent) => void - ): Promise => { - const req_message = new FormData(); - - req_message.append('media', file); - - const { data } = await axios.post( - `/api/project/${projectId}/survey/${surveyId}/attachments/keyx/upload`, - req_message, - { - cancelToken: cancelTokenSource?.token, - onUploadProgress: onProgress - } - ); - - return data; - }; - /** * Upload survey reports. * @@ -392,20 +358,55 @@ const useSurveyApi = (axios: AxiosInstance) => { * * @param {number} projectId * @param {number} surveyId - * @returns {ISimpleCritterWithInternalId[]} + * @returns {ICritterSimpleResponse[]} */ - const getSurveyCritters = async (projectId: number, surveyId: number): Promise => { + const getSurveyCritters = async (projectId: number, surveyId: number): Promise => { const { data } = await axios.get(`/api/project/${projectId}/survey/${surveyId}/critters`); return data; }; + /** + * Retrieve a list of critters associated with the given survey with details taken from critterbase. + * + * @param {number} projectId + * @param {number} surveyId + * @param {number} critterId + * @return {*} {Promise} + */ + const getCritterById = async ( + projectId: number, + surveyId: number, + critterId: number + ): Promise => { + const { data } = await axios.get( + `/api/project/${projectId}/survey/${surveyId}/critters/${critterId}?format=detailed` + ); + return data; + }; + + /** + * Retrieve a list of critters associated with the given survey with details from critterbase, including + * additional information such as captures and mortality + * + * @param {number} projectId + * @param {number} surveyId + * @return {*} {Promise} + */ + const getSurveyCrittersDetailed = async ( + projectId: number, + surveyId: number + ): Promise => { + const { data } = await axios.get(`/api/project/${projectId}/survey/${surveyId}/critters?format=detailed`); + return data; + }; + /** * Create a critter and add it to the list of critters associated with this survey. This will create a new critter in Critterbase. * * @param {number} projectId * @param {number} surveyId - * @param {Critter} critter Critter payload type - * @returns Count of affected rows + * @param {ICreateCritter} critter + * @return {*} {Promise} */ const createCritterAndAddToSurvey = async ( projectId: number, @@ -421,8 +422,8 @@ const useSurveyApi = (axios: AxiosInstance) => { * * @param {number} projectId * @param {number} surveyId - * @param {number} critterId - * @returns {*} + * @param {number[]} critterIds + * @return {*} {Promise} */ const removeCrittersFromSurvey = async ( projectId: number, @@ -436,20 +437,20 @@ const useSurveyApi = (axios: AxiosInstance) => { }; /** - * Add a new deployment with associated device hardware metadata. Must include critterbase critter id. + * Create a new deployment with associated device hardware metadata. Must include critterbase critter id. * * @param {number} projectId * @param {number} surveyId * @param {number} critterId - * @param {IAnimalTelemetryDevice & {critter_id: string}} body - * @returns {*} + * @param {Omit} body + * @return {*} {Promise<{ deploymentId: number }>} */ - const addDeployment = async ( + const createDeployment = async ( projectId: number, surveyId: number, - critterId: number, // Survey critter_id - body: ICreateAnimalDeployment // Critterbase critter_id - ): Promise => { + critterId: number, + body: Omit + ): Promise<{ deploymentId: number }> => { const { data } = await axios.post( `/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/deployments`, body @@ -462,20 +463,17 @@ const useSurveyApi = (axios: AxiosInstance) => { * * @param {number} projectId * @param {number} surveyId - * @param {number} critterId - * @param {IDeploymentTimespan} body - * @returns {*} + * @param {number} deploymentId + * @param {ICreateAnimalDeploymentPostData} body + * @return {*} {Promise} */ const updateDeployment = async ( projectId: number, surveyId: number, - critterId: number, - body: IDeploymentTimespan + deploymentId: number, + body: ICreateAnimalDeploymentPostData ): Promise => { - const { data } = await axios.patch( - `/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/deployments`, - body - ); + const { data } = await axios.put(`/api/project/${projectId}/survey/${surveyId}/deployments/${deploymentId}`, body); return data; }; @@ -484,22 +482,41 @@ const useSurveyApi = (axios: AxiosInstance) => { * * @param {number} projectId * @param {number} surveyId - * @returns {*} + * @return {*} {Promise} */ const getDeploymentsInSurvey = async (projectId: number, surveyId: number): Promise => { const { data } = await axios.get(`/api/project/${projectId}/survey/${surveyId}/deployments`); return data; }; + /** + * Get deployment by Id, using the integer Id from SIMS instead of the BCTW GUID + * + * @param {number} projectId + * @param {number} surveyId + * @param {number} deploymentId + * @return {*} {Promise} + */ + const getDeploymentById = async ( + projectId: number, + surveyId: number, + deploymentId: number + ): Promise => { + const { data } = await axios.get(`/api/project/${projectId}/survey/${surveyId}/deployments/${deploymentId}`); + return data; + }; + /** * Get all telemetry points for a critter in a survey within a given time span. * + * TODO: Unused? + * * @param {number} projectId * @param {number} surveyId * @param {number} critterId * @param {string} startDate * @param {string} endDate - * @return {*} {Promise} + * @return {*} {Promise} */ const getCritterTelemetry = async ( projectId: number, @@ -507,26 +524,27 @@ const useSurveyApi = (axios: AxiosInstance) => { critterId: number, startDate: string, endDate: string - ): Promise => { + ): Promise => { const { data } = await axios.get( `/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/telemetry?startDate=${startDate}&endDate=${endDate}` ); return data; }; + /** - * Removes a deployment. Will trigger removal in both SIMS and BCTW. + * Ends a deployment. Will trigger removal in both SIMS and BCTW. * * @param {number} projectId * @param {number} surveyId * @param {number} critterId - * @param {string} deploymentId - * @returns {*} + * @param {number} deploymentId + * @return {*} {Promise} */ - const removeDeployment = async ( + const endDeployment = async ( projectId: number, surveyId: number, critterId: number, - deploymentId: string + deploymentId: number ): Promise => { const { data } = await axios.delete( `/api/project/${projectId}/survey/${surveyId}/critters/${critterId}/deployments/${deploymentId}` @@ -534,14 +552,26 @@ const useSurveyApi = (axios: AxiosInstance) => { return data; }; + /** + * Deletes a deployment. Will trigger deletion in SIMS and invalidates the deployment in BCTW. + * + * @param {number} projectId + * @param {number} surveyId + * @param {number} deploymentId + * @return {*} {Promise} + */ + const deleteDeployment = async (projectId: number, surveyId: number, deploymentId: number): Promise => { + const { data } = await axios.delete(`/api/project/${projectId}/survey/${surveyId}/deployments/${deploymentId}`); + return data; + }; + /** * Bulk upload Critters from CSV. * - * @async - * @param {File} file - Critters CSV. + * @param {File} file * @param {number} projectId * @param {number} surveyId - * @returns {Promise} + * @return {*} {Promise<{ survey_critter_ids: number[] }>} */ const importCrittersFromCsv = async ( file: File, @@ -563,9 +593,9 @@ const useSurveyApi = (axios: AxiosInstance) => { getSurveysBasicFieldsByProjectId, getSurveyForUpdate, findSurveys, + getDeploymentById, updateSurvey, uploadSurveyAttachments, - uploadSurveyKeyx, uploadSurveyReports, updateSurveyReportMetadata, getSurveyReportDetails, @@ -576,11 +606,14 @@ const useSurveyApi = (axios: AxiosInstance) => { getSurveyCritters, createCritterAndAddToSurvey, removeCrittersFromSurvey, - addDeployment, + createDeployment, + getSurveyCrittersDetailed, getDeploymentsInSurvey, + getCritterById, updateDeployment, getCritterTelemetry, - removeDeployment, + endDeployment, + deleteDeployment, importCrittersFromCsv }; }; diff --git a/app/src/hooks/api/useTaxonomyApi.ts b/app/src/hooks/api/useTaxonomyApi.ts index 6aa8d92d52..23635a87e1 100644 --- a/app/src/hooks/api/useTaxonomyApi.ts +++ b/app/src/hooks/api/useTaxonomyApi.ts @@ -1,5 +1,5 @@ import { useConfigContext } from 'hooks/useContext'; -import { IPartialTaxonomy, ITaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import { IPartialTaxonomy, ITaxonomy, ITaxonomyHierarchy } from 'interfaces/useTaxonomyApi.interface'; import { startCase } from 'lodash-es'; import qs from 'qs'; import useAxios from './useAxios'; @@ -32,6 +32,25 @@ const useTaxonomyApi = () => { return parseSearchResponse(data.searchResponse); }; + /** + * Retrieves parent taxons for multiple TSNs + * + * @param {number[]} tsns + * @return {*} {Promise} + */ + const getTaxonHierarchyByTSNs = async (tsns: number[]): Promise => { + const { data } = await apiAxios.get('/api/taxonomy/taxon/tsn/hierarchy', { + params: { + tsn: [...new Set(tsns)] + }, + paramsSerializer: (params) => { + return qs.stringify(params); + } + }); + + return data; + }; + /** * Search for taxon records by search terms. * @@ -59,13 +78,20 @@ const useTaxonomyApi = () => { return { getSpeciesFromIds, - searchSpeciesByTerms + searchSpeciesByTerms, + getTaxonHierarchyByTSNs }; }; /** * Parses the taxon search response into start case. * + * The case of scientific names should not be modified. Genus names and higher are capitalized while + * species-level and subspecies-level names (the second and third words in a species/subspecies name) are not capitalized. + * Example: Ursus americanus, Rangifier tarandus caribou, Mammalia, Alces alces. + * + * The case of common names is less standardized and often just preference. + * * @template T * @param {T[]} searchResponse - Array of Taxonomy objects * @returns {T[]} Correctly cased Taxonomy @@ -74,7 +100,7 @@ const parseSearchResponse = (searchResponse: T[]): T return searchResponse.map((taxon) => ({ ...taxon, commonNames: taxon.commonNames.map((commonName) => startCase(commonName)), - scientificName: startCase(taxon.scientificName) + scientificName: taxon.scientificName })); }; diff --git a/app/src/hooks/api/useTelemetryApi.test.ts b/app/src/hooks/api/useTelemetryApi.test.ts index 8c66b9bb2a..2d518c4b2c 100644 --- a/app/src/hooks/api/useTelemetryApi.test.ts +++ b/app/src/hooks/api/useTelemetryApi.test.ts @@ -45,4 +45,43 @@ describe('useTelemetryApi', () => { expect(result).toEqual(mockResponse); }); + + describe('getCodeValues', () => { + it('should return a list of code values', async () => { + const mockCodeValues = { + code_header_title: 'code_header_title', + code_header_name: 'code_header_name', + id: 123, + description: 'description', + long_description: 'long_description' + }; + + mock.onGet('/api/telemetry/code?codeHeader=code_header_name').reply(200, [mockCodeValues]); + const result = await useTelemetryApi(axios).getCodeValues('code_header_name'); + expect(result).toEqual([mockCodeValues]); + }); + + it('should catch errors', async () => { + mock.onGet('/api/telemetry/code?codeHeader=code_header_name').reply(500, 'error'); + const result = await useTelemetryApi(axios).getCodeValues('code_header_name'); + expect(result).toEqual([]); + }); + }); + + describe('uploadTelemetryDeviceCredentialFile', () => { + it('should upload a keyx file', async () => { + const projectId = 1; + const surveyId = 2; + + const file = new File([''], 'file.keyx', { type: 'application/keyx' }); + const response = { + attachmentId: 'attachment', + revision_count: 1 + }; + mock.onPost(`/api/project/${projectId}/survey/${surveyId}/attachments/telemetry`).reply(201, response); + + const result = await useTelemetryApi(axios).uploadTelemetryDeviceCredentialFile(projectId, surveyId, file); + expect(result).toEqual(response); + }); + }); }); diff --git a/app/src/hooks/api/useTelemetryApi.ts b/app/src/hooks/api/useTelemetryApi.ts index 08f51bd1ce..62d2d9e22b 100644 --- a/app/src/hooks/api/useTelemetryApi.ts +++ b/app/src/hooks/api/useTelemetryApi.ts @@ -1,7 +1,15 @@ -import { AxiosInstance } from 'axios'; -import { ITelemetryAdvancedFilters } from 'features/summary/tabular-data/telemetry/TelemetryListFilterForm'; - -import { IFindTelemetryResponse } from 'interfaces/useTelemetryApi.interface'; +import { AxiosInstance, AxiosProgressEvent, CancelTokenSource } from 'axios'; +import { IAllTelemetryAdvancedFilters } from 'features/summary/tabular-data/telemetry/TelemetryListFilterForm'; +import { IUploadAttachmentResponse } from 'interfaces/useProjectApi.interface'; +import { + IAllTelemetry, + ICodeResponse, + ICreateManualTelemetry, + IFindTelemetryResponse, + IManualTelemetry, + IUpdateManualTelemetry, + TelemetryDeviceKeyFile +} from 'interfaces/useTelemetryApi.interface'; import qs from 'qs'; import { ApiPaginationRequestOptions } from 'types/misc'; @@ -16,12 +24,12 @@ const useTelemetryApi = (axios: AxiosInstance) => { * Get telemetry for a system user id. * * @param {ApiPaginationRequestOptions} [pagination] - * @param {ITelemetryAdvancedFilters} filterFieldData + * @param {IAllTelemetryAdvancedFilters} filterFieldData * @return {*} {Promise} */ const findTelemetry = async ( pagination?: ApiPaginationRequestOptions, - filterFieldData?: ITelemetryAdvancedFilters + filterFieldData?: IAllTelemetryAdvancedFilters ): Promise => { const params = { ...pagination, @@ -33,7 +41,180 @@ const useTelemetryApi = (axios: AxiosInstance) => { return data; }; - return { findTelemetry }; + /** + * Get list of manual and vendor telemetry by deployment ids + * + * @param {string[]} deploymentIds BCTW deployment ids + * @return {*} {Promise} + */ + const getAllTelemetryByDeploymentIds = async (deploymentIds: string[]): Promise => { + const { data } = await axios.get('/api/telemetry/deployments', { + params: { + bctwDeploymentIds: deploymentIds + } + }); + return data; + }; + + /** + * Bulk create Manual Telemetry + * + * @param {ICreateManualTelemetry[]} manualTelemetry Manual Telemetry create objects + * @return {*} {Promise} + */ + const createManualTelemetry = async ( + manualTelemetry: ICreateManualTelemetry[] + ): Promise => { + const { data } = await axios.post('/api/telemetry/manual', manualTelemetry); + return data; + }; + + /** + * Bulk update Manual Telemetry + * + * @param {IUpdateManualTelemetry[]} manualTelemetry Manual Telemetry update objects + * @return {*} + */ + const updateManualTelemetry = async (manualTelemetry: IUpdateManualTelemetry[]) => { + const { data } = await axios.patch('/api/telemetry/manual', manualTelemetry); + return data; + }; + + /** + * Delete manual telemetry records + * + * @param {string[]} telemetryIds Manual Telemetry ids to delete + * @return {*} + */ + const deleteManualTelemetry = async (telemetryIds: string[]) => { + const { data } = await axios.post('/api/telemetry/manual/delete', telemetryIds); + return data; + }; + + /** + * Uploads a telemetry CSV for import. + * + * @param {number} projectId + * @param {number} surveyId + * @param {File} file + * @param {CancelTokenSource} [cancelTokenSource] + * @param {(progressEvent: AxiosProgressEvent) => void} [onProgress] + * @return {*} {Promise<{ submission_id: number }>} + */ + const uploadCsvForImport = async ( + projectId: number, + surveyId: number, + file: File, + cancelTokenSource?: CancelTokenSource, + onProgress?: (progressEvent: AxiosProgressEvent) => void + ): Promise<{ submission_id: number }> => { + const formData = new FormData(); + + formData.append('media', file); + + const { data } = await axios.post<{ submission_id: number }>( + `/api/project/${projectId}/survey/${surveyId}/telemetry/upload`, + formData, + { + cancelToken: cancelTokenSource?.token, + onUploadProgress: onProgress + } + ); + return data; + }; + + /** + * Begins processing an uploaded telemetry CSV for import + * + * @param {number} submissionId + * @return {*} + */ + const processTelemetryCsvSubmission = async (submissionId: number) => { + const { data } = await axios.post('/api/telemetry/manual/process', { + submission_id: submissionId + }); + + return data; + }; + + /** + * Returns a list of code values for a given code header. + * + * @param {string} codeHeader + * @return {*} {Promise} + */ + const getCodeValues = async (codeHeader: string): Promise => { + try { + const { data } = await axios.get(`/api/telemetry/code?codeHeader=${codeHeader}`); + return data; + } catch (e) { + if (e instanceof Error) { + console.error(e.message); + } + } + return []; + }; + + /** + * Upload a telemetry device credential file. + * + * @param {number} projectId + * @param {number} surveyId + * @param {File} file + * @param {CancelTokenSource} [cancelTokenSource] + * @param {(progressEvent: AxiosProgressEvent) => void} [onProgress] + * @return {*} {Promise} + */ + const uploadTelemetryDeviceCredentialFile = async ( + projectId: number, + surveyId: number, + file: File, + cancelTokenSource?: CancelTokenSource, + onProgress?: (progressEvent: AxiosProgressEvent) => void + ): Promise => { + const req_message = new FormData(); + + req_message.append('media', file); + + const { data } = await axios.post( + `/api/project/${projectId}/survey/${surveyId}/attachments/telemetry`, + req_message, + { + cancelToken: cancelTokenSource?.token, + onUploadProgress: onProgress + } + ); + + return data; + }; + + /** + * Get all uploaded telemetry device credential key files. + * + * @param {number} projectId + * @param {number} surveyId + * @return {*} {Promise} + */ + const getTelemetryDeviceKeyFiles = async (projectId: number, surveyId: number): Promise => { + const { data } = await axios.get<{ telemetryAttachments: TelemetryDeviceKeyFile[] }>( + `/api/project/${projectId}/survey/${surveyId}/attachments/telemetry` + ); + + return data.telemetryAttachments; + }; + + return { + findTelemetry, + getAllTelemetryByDeploymentIds, + createManualTelemetry, + updateManualTelemetry, + deleteManualTelemetry, + uploadCsvForImport, + processTelemetryCsvSubmission, + getCodeValues, + uploadTelemetryDeviceCredentialFile, + getTelemetryDeviceKeyFiles + }; }; export default useTelemetryApi; diff --git a/app/src/hooks/cb_api/useCritterApi.tsx b/app/src/hooks/cb_api/useCritterApi.tsx index 8ced897d93..8a40403043 100644 --- a/app/src/hooks/cb_api/useCritterApi.tsx +++ b/app/src/hooks/cb_api/useCritterApi.tsx @@ -1,5 +1,6 @@ import { AxiosInstance } from 'axios'; import { IBulkCreate, IBulkUpdate, ICreateCritter } from 'features/surveys/view/survey-animals/animal'; +import { IGetCaptureMortalityGeometryResponse } from 'interfaces/useAnimalApi.interface'; import { ICritterDetailedResponse, ICritterSimpleResponse } from 'interfaces/useCritterApi.interface'; const useCritterApi = (axios: AxiosInstance) => { @@ -69,16 +70,33 @@ const useCritterApi = (axios: AxiosInstance) => { * * @async * @param {string[]} critter_ids - Critter identifiers. - * @returns {Promise} + * @returns {Promise} + */ + // TODO: Fix critterbase bug. This endpoint returns an empty array when ?format=detailed. + const getMultipleCrittersByIds = async (critter_ids: string[]): Promise => { + const { data } = await axios.post(`/api/critterbase/critters?format=detailed`, { critter_ids }); + return data; + }; + + /** + * Get capture and mortality geometry for multiple critter Ids. + * + * @async + * @param {string[]} critter_ids - Critter identifiers. + * @returns {Promise} */ - const getMultipleCrittersByIds = async (critter_ids: string[]): Promise => { - const { data } = await axios.post(`/api/critterbase/critters`, { critter_ids }); + // TODO: Fix critterbase bug. This endpoint returns an empty array when ?format=detailed. + const getMultipleCrittersGeometryByIds = async ( + critter_ids: string[] + ): Promise => { + const { data } = await axios.post(`/api/critterbase/critters/spatial`, { critter_ids }); return data; }; return { getDetailedCritter, getMultipleCrittersByIds, + getMultipleCrittersGeometryByIds, createCritter, updateCritter, bulkCreate, diff --git a/app/src/hooks/cb_api/useFamilyApi.test.tsx b/app/src/hooks/cb_api/useFamilyApi.test.tsx deleted file mode 100644 index e9f9d0b293..0000000000 --- a/app/src/hooks/cb_api/useFamilyApi.test.tsx +++ /dev/null @@ -1,42 +0,0 @@ -import axios from 'axios'; -import MockAdapter from 'axios-mock-adapter'; -import { v4 } from 'uuid'; -import { useFamilyApi } from './useFamilyApi'; - -describe('useFamily', () => { - let mock: MockAdapter; - - beforeEach(() => { - mock = new MockAdapter(axios); - }); - - afterEach(() => { - mock.restore(); - }); - - const family = { - family_id: v4(), - family_label: 'fam' - }; - - const immediateFamily = { - parents: [], - children: [] - }; - - it('should return a list of families', async () => { - mock.onGet('/api/critterbase/family').reply(200, [family]); - const result = await useFamilyApi(axios).getAllFamilies(); - expect(Array.isArray(result)).toBe(true); - expect(result.length).toBe(1); - expect(result[0].family_id).toBeDefined(); - }); - - it('should return an immediate family by id', async () => { - const familyId = v4(); - mock.onGet('/api/critterbase/family/' + familyId).reply(200, immediateFamily); - const result = await useFamilyApi(axios).getImmediateFamily(familyId); - expect(Array.isArray(result.parents)).toBe(true); - expect(Array.isArray(result.children)).toBe(true); - }); -}); diff --git a/app/src/hooks/cb_api/useFamilyApi.tsx b/app/src/hooks/cb_api/useFamilyApi.tsx deleted file mode 100644 index 15f293c90c..0000000000 --- a/app/src/hooks/cb_api/useFamilyApi.tsx +++ /dev/null @@ -1,140 +0,0 @@ -import { AxiosInstance } from 'axios'; -import { AnimalRelationship } from 'features/surveys/view/survey-animals/animal'; -import { IFamilyChildResponse, IFamilyParentResponse } from 'interfaces/useCritterApi.interface'; -import { v4 } from 'uuid'; - -interface ICritterStub { - critter_id: string; - animal_id: string | null; -} - -export type IFamily = { - family_id: string; - family_label: string; -}; - -export type IImmediateFamily = { - parents: ICritterStub[]; - siblings: ICritterStub[]; - children: ICritterStub[]; -}; - -type CreateFamilyRelationshipPayload = { - relationship: AnimalRelationship; - family_label?: string; - family_id?: string; - critter_id: string; -}; - -export const useFamilyApi = (axios: AxiosInstance) => { - /** - * Get all Critterbase families. - * - * @async - * @returns {Promise} Critter families. - */ - const getAllFamilies = async (): Promise => { - const { data } = await axios.get('/api/critterbase/family'); - - return data; - }; - - /** - * Get immediate family of a specific critter. - * - * @async - * @param {string} family_id - Family primary key identifier. - * @returns {Promise} The critters parents, children and siblings. - */ - const getImmediateFamily = async (family_id: string): Promise => { - const { data } = await axios.get(`/api/critterbase/family/${family_id}`); - - return data; - }; - - /** - * Create a new family. - * Families must be created before parents or children can be added. - * - * @async - * @param {string} label - The family's label. example: `caribou-2024-skeena-family` - * @returns {Promise} Critter family. - */ - const createFamily = async (label: string): Promise => { - const { data } = await axios.post(`/api/critterbase/family/create`, { family_id: v4(), family_label: label }); - - return data; - }; - - /** - * Edit a family label. - * - * @async - * @param {string} family_id - The id of the family. - * @param {string} label - New family label. example: `caribou-2025-skeena-family-v2` - * @returns {Promise} Critter family. - */ - const editFamily = async (family_id: string, label: string) => { - const { data } = await axios.patch(`/api/critterbase/family/${family_id}`, { family_label: label }); - - return data; - }; - - /** - * Create (parent or child) relationship of a family. - * - * @async - * @param {CreateFamilyRelationshipPayload} payload - Create relationship payload. - * @returns {Promise} - */ - const createFamilyRelationship = async ( - payload: CreateFamilyRelationshipPayload - ): Promise => { - if (payload.relationship === AnimalRelationship.CHILD) { - const { data } = await axios.post(`/api/critterbase/family/children`, { - family_id: payload.family_id, - child_critter_id: payload.critter_id - }); - - return data; - } - - const { data } = await axios.post(`/api/critterbase/family/parents`, { - family_id: payload.family_id, - parent_critter_id: payload.critter_id - }); - - return data; - }; - - /** - * Delete a relationship (parent or child) of a family. - * - * @async - * @param {*} params - * @returns {Promise} Either parent or child delete response. - */ - const deleteRelationship = async (params: { - relationship: AnimalRelationship; - family_id: string; - critter_id: string; - }): Promise => { - const payload = - params.relationship === AnimalRelationship.CHILD - ? { family_id: params.family_id, child_critter_id: params.critter_id } - : { family_id: params.family_id, parent_critter_id: params.critter_id }; - - const { data } = await axios.delete(`/api/critterbase/family/${params.relationship}`, { data: payload }); - - return data; - }; - - return { - getAllFamilies, - getImmediateFamily, - editFamily, - deleteRelationship, - createFamily, - createFamilyRelationship - }; -}; diff --git a/app/src/hooks/cb_api/useXrefApi.tsx b/app/src/hooks/cb_api/useXrefApi.tsx index 14056c47ad..dcd8723fa7 100644 --- a/app/src/hooks/cb_api/useXrefApi.tsx +++ b/app/src/hooks/cb_api/useXrefApi.tsx @@ -5,6 +5,7 @@ import { ICollectionCategory, ICollectionUnit } from 'interfaces/useCritterApi.interface'; +import qs from 'qs'; export const useXrefApi = (axios: AxiosInstance) => { /** @@ -21,13 +22,21 @@ export const useXrefApi = (axios: AxiosInstance) => { /** * Get measurement definitions by search term. * - * @param {string} searchTerm + * @param {string} name + * @param {string[]} tsns * @return {*} {Promise} */ const getMeasurementTypeDefinitionsBySearchTerm = async ( - searchTerm: string + name: string, + tsns?: number[] ): Promise => { - const { data } = await axios.get(`/api/critterbase/xref/taxon-measurements/search?name=${searchTerm}`); + const t = tsns?.map((tsn) => Number(tsn)); + const { data } = await axios.get(`/api/critterbase/xref/taxon-measurements/search`, { + params: { name, tsns: t }, + paramsSerializer: (params) => { + return qs.stringify(params); + } + }); return data; }; @@ -38,12 +47,18 @@ export const useXrefApi = (axios: AxiosInstance) => { * @return {*} {Promise} */ const getTsnCollectionCategories = async (tsn: number): Promise => { - const { data } = await axios.get(`/api/critterbase/xref/taxon-collection-categories?tsn=${tsn}`); + const { data } = await axios.get('/api/critterbase/xref/taxon-collection-categories', { + params: { tsn }, + paramsSerializer: (params) => { + return qs.stringify(params); + } + }); + return data; }; /** - * Get collection (ie. ecological) units that are available for a given taxon + * Get collection (ie. ecological) units values for a given collection unit * * @param {string} unit_id * @return {*} {Promise} diff --git a/app/src/hooks/telemetry/useDeviceApi.test.tsx b/app/src/hooks/telemetry/useDeviceApi.test.tsx deleted file mode 100644 index 8d94d662c7..0000000000 --- a/app/src/hooks/telemetry/useDeviceApi.test.tsx +++ /dev/null @@ -1,86 +0,0 @@ -import axios from 'axios'; -import MockAdapter from 'axios-mock-adapter'; -import { Device } from 'features/surveys/view/survey-animals/telemetry-device/device'; -import { useDeviceApi } from './useDeviceApi'; - -describe('useDeviceApi', () => { - let mock: MockAdapter; - - beforeEach(() => { - mock = new MockAdapter(axios); - }); - - afterEach(() => { - mock.restore(); - }); - - const mockVendors = ['vendor1', 'vendor2']; - - const mockCodeValues = { - code_header_title: 'code_header_title', - code_header_name: 'code_header_name', - id: 123, - description: 'description', - long_description: 'long_description' - }; - - describe('getCollarVendors', () => { - it('should return a list of vendors', async () => { - mock.onGet('/api/telemetry/vendors').reply(200, mockVendors); - const result = await useDeviceApi(axios).getCollarVendors(); - expect(result).toEqual(mockVendors); - }); - - it('should catch errors', async () => { - mock.onGet('/api/telemetry/vendors').reply(500, 'error'); - const result = await useDeviceApi(axios).getCollarVendors(); - expect(result).toEqual([]); - }); - }); - - describe('getCodeValues', () => { - it('should return a list of code values', async () => { - mock.onGet('/api/telemetry/code?codeHeader=code_header_name').reply(200, [mockCodeValues]); - const result = await useDeviceApi(axios).getCodeValues('code_header_name'); - expect(result).toEqual([mockCodeValues]); - }); - - it('should catch errors', async () => { - mock.onGet('/api/telemetry/code?codeHeader=code_header_name').reply(500, 'error'); - const result = await useDeviceApi(axios).getCodeValues('code_header_name'); - expect(result).toEqual([]); - }); - }); - - describe('getDeviceDetails', () => { - it('should return device deployment details', async () => { - mock.onGet(`/api/telemetry/device/${123}`).reply(200, { device: undefined, deployments: [] }); - const result = await useDeviceApi(axios).getDeviceDetails(123, 'Vectronic'); - expect(result.deployments.length).toBe(0); - }); - - it('should catch errors', async () => { - mock.onGet(`/api/telemetry/device/${123}`).reply(500, 'error'); - const result = await useDeviceApi(axios).getDeviceDetails(123, 'Vectronic'); - expect(result.deployments.length).toBe(0); - expect(result.device).toBeUndefined(); - expect(result.keyXStatus).toBe(false); - }); - }); - - describe('upsertCollar', () => { - it('should upsert a collar', async () => { - const device = new Device({ device_id: 123, collar_id: 'abc' }); - mock.onPost(`/api/telemetry/device`).reply(200, { device_id: 123, collar_id: 'abc' }); - const result = await useDeviceApi(axios).upsertCollar(device); - expect(result.device_id).toBe(123); - }); - - it('should catch errors', async () => { - const device = new Device({ device_id: 123, collar_id: 'abc' }); - mock.onPost(`/api/telemetry/device`).reply(500, 'error'); - const result = await useDeviceApi(axios).upsertCollar(device); - expect(result).toEqual({}); - }); - }); -}); diff --git a/app/src/hooks/telemetry/useDeviceApi.tsx b/app/src/hooks/telemetry/useDeviceApi.tsx deleted file mode 100644 index 50f454e6b0..0000000000 --- a/app/src/hooks/telemetry/useDeviceApi.tsx +++ /dev/null @@ -1,105 +0,0 @@ -import { AxiosInstance } from 'axios'; -import { Device, IAnimalDeployment } from 'features/surveys/view/survey-animals/telemetry-device/device'; - -interface ICodeResponse { - code_header_title: string; - code_header_name: string; - id: number; - code: string; - description: string; - long_description: string; -} - -export interface IGetDeviceDetailsResponse { - device: Record | undefined; - keyXStatus: boolean; - deployments: Omit[]; -} - -/** - * Returns a set of functions for making device-related API calls. - * - * @param {AxiosInstance} axios - * @return {*} - */ -const useDeviceApi = (axios: AxiosInstance) => { - /** - * Returns a list of supported collar vendors. - * - * @return {*} {Promise} - */ - const getCollarVendors = async (): Promise => { - try { - const { data } = await axios.get('/api/telemetry/vendors'); - return data; - } catch (e) { - if (e instanceof Error) { - console.error(e.message); - } - } - return []; - }; - - /** - * Returns a list of code values for a given code header. - * - * @param {string} codeHeader - * @return {*} {Promise} - */ - const getCodeValues = async (codeHeader: string): Promise => { - try { - const { data } = await axios.get(`/api/telemetry/code?codeHeader=${codeHeader}`); - return data; - } catch (e) { - if (e instanceof Error) { - console.error(e.message); - } - } - return []; - }; - - /** - * Returns details for a given device. - * - * @param {number} deviceId - * @param {string} deviceMake - * @return {*} {Promise} - */ - const getDeviceDetails = async (deviceId: number, deviceMake: string): Promise => { - try { - const { data } = await axios.get(`/api/telemetry/device/${deviceId}?make=${deviceMake}`); - return data; - } catch (e) { - if (e instanceof Error) { - console.error(e.message); - } - } - return { device: undefined, keyXStatus: false, deployments: [] }; - }; - - /** - * Allows you to update a collar in bctw, invalidating the old record. - * @param {Device} body - * @returns {*} - */ - const upsertCollar = async (body: Device): Promise => { - try { - const { data } = await axios.post(`/api/telemetry/device`, body); - return data; - } catch (e) { - if (e instanceof Error) { - console.error(e.message); - } - } - return {}; - }; - - return { - getDeviceDetails, - getCollarVendors, - getCodeValues, - upsertCollar - }; -}; - -export { useDeviceApi }; diff --git a/app/src/hooks/useBioHubApi.ts b/app/src/hooks/useBioHubApi.ts index 2443e19f5e..0115bd2df5 100644 --- a/app/src/hooks/useBioHubApi.ts +++ b/app/src/hooks/useBioHubApi.ts @@ -3,6 +3,7 @@ import useReferenceApi from 'hooks/api/useReferenceApi'; import { useConfigContext } from 'hooks/useContext'; import { useMemo } from 'react'; import useAdminApi from './api/useAdminApi'; +import useAnalyticsApi from './api/useAnalyticsApi'; import useAnimalApi from './api/useAnimalApi'; import useAxios from './api/useAxios'; import useCodesApi from './api/useCodesApi'; @@ -31,6 +32,8 @@ export const useBiohubApi = () => { const config = useConfigContext(); const apiAxios = useAxios(config.API_HOST); + const analytics = useAnalyticsApi(apiAxios); + const project = useProjectApi(apiAxios); const projectParticipants = useProjectParticipationApi(apiAxios); @@ -71,6 +74,7 @@ export const useBiohubApi = () => { return useMemo( () => ({ + analytics, project, projectParticipants, taxonomy, diff --git a/app/src/hooks/useContext.tsx b/app/src/hooks/useContext.tsx index e07c93c36b..39da771e41 100644 --- a/app/src/hooks/useContext.tsx +++ b/app/src/hooks/useContext.tsx @@ -8,7 +8,8 @@ import { IObservationsTableContext, ObservationsTableContext } from 'contexts/ob import { IProjectContext, ProjectContext } from 'contexts/projectContext'; import { ISurveyContext, SurveyContext } from 'contexts/surveyContext'; import { ITaxonomyContext, TaxonomyContext } from 'contexts/taxonomyContext'; -import { ITelemetryTableContext, TelemetryTableContext } from 'contexts/telemetryTableContext'; +import { ITelemetryDataContext, TelemetryDataContext } from 'contexts/telemetryDataContext'; +import { IAllTelemetryTableContext, TelemetryTableContext } from 'contexts/telemetryTableContext'; import { useContext } from 'react'; /** @@ -148,11 +149,28 @@ export const useObservationsTableContext = (): IObservationsTableContext => { }; /** - * Returns an instance of `IObservationsTableContext` from `ObservationsTableContext`. + * Returns an instance of `ITelemetryDataContext` from `TelemetryDataContext`. * - * @return {*} {IObservationsTableContext} + * @return {*} {ITelemetryDataContext} */ -export const useTelemetryTableContext = (): ITelemetryTableContext => { +export const useTelemetryDataContext = (): ITelemetryDataContext => { + const context = useContext(TelemetryDataContext); + + if (!context) { + throw Error( + 'TelemetryDataContext is undefined, please verify you are calling useTelemetryDataContext() as child of an component.' + ); + } + + return context; +}; + +/** + * Returns an instance of `ITelemetryTableContext` from `TelemetryTableContext`. + * + * @return {*} {ITelemetryTableContext} + */ +export const useTelemetryTableContext = (): IAllTelemetryTableContext => { const context = useContext(TelemetryTableContext); if (!context) { @@ -165,7 +183,7 @@ export const useTelemetryTableContext = (): ITelemetryTableContext => { }; /** - * Returns an instance of `ITaxonomyContext` from `SurveyContext`. + * Returns an instance of `ITaxonomyContext` from `TaxonomyContext`. * * @return {*} {ITaxonomyContext} */ @@ -184,7 +202,7 @@ export const useTaxonomyContext = (): ITaxonomyContext => { /** * Returns an instance of `IAnimalPageContext` from `AnimalPageContext`. * - * @return {*} {ISurveyContext} + * @return {*} {IAnimalPageContext} */ export const useAnimalPageContext = (): IAnimalPageContext => { const context = useContext(AnimalPageContext); diff --git a/app/src/hooks/useCritterbaseApi.ts b/app/src/hooks/useCritterbaseApi.ts index d142fcce4d..308455853c 100644 --- a/app/src/hooks/useCritterbaseApi.ts +++ b/app/src/hooks/useCritterbaseApi.ts @@ -6,7 +6,6 @@ import { useAuthentication } from './cb_api/useAuthenticationApi'; import { useCaptureApi } from './cb_api/useCaptureApi'; import { useCollectionUnitApi } from './cb_api/useCollectionUnitApi'; import { useCritterApi } from './cb_api/useCritterApi'; -import { useFamilyApi } from './cb_api/useFamilyApi'; import { useLookupApi } from './cb_api/useLookupApi'; import { useMarkingApi } from './cb_api/useMarkingApi'; import { useMeasurementApi } from './cb_api/useMeasurementApi'; @@ -27,8 +26,6 @@ export const useCritterbaseApi = () => { const lookup = useLookupApi(apiAxios); - const family = useFamilyApi(apiAxios); - const xref = useXrefApi(apiAxios); const marking = useMarkingApi(apiAxios); @@ -46,7 +43,6 @@ export const useCritterbaseApi = () => { critters, authentication, lookup, - family, xref, marking, collectionUnit, diff --git a/app/src/hooks/useTelemetryApi.ts b/app/src/hooks/useTelemetryApi.ts deleted file mode 100644 index dbf2f1ea5e..0000000000 --- a/app/src/hooks/useTelemetryApi.ts +++ /dev/null @@ -1,179 +0,0 @@ -import { AxiosProgressEvent, CancelTokenSource } from 'axios'; -import { useConfigContext } from 'hooks/useContext'; -import useAxios from './api/useAxios'; -import { useDeviceApi } from './telemetry/useDeviceApi'; - -export interface ICritterDeploymentResponse { - critter_id: string; - device_id: number; - deployment_id: string; - survey_critter_id: string; - alias: string; - attachment_start: string; - attachment_end?: string; - taxon: string; -} - -export interface IUpdateManualTelemetry { - telemetry_manual_id: string; - latitude: number; - longitude: number; - acquisition_date: string; -} -export interface ICreateManualTelemetry { - deployment_id: string; - latitude: number; - longitude: number; - acquisition_date: string; -} - -export interface IManualTelemetry extends ICreateManualTelemetry { - telemetry_manual_id: string; -} - -export interface IVendorTelemetry extends ICreateManualTelemetry { - telemetry_id: string; -} - -export interface ITelemetry { - id: string; - deployment_id: string; - telemetry_manual_id: string; - telemetry_id: number | null; - latitude: number; - longitude: number; - acquisition_date: string; - telemetry_type: string; -} - -export const useTelemetryApi = () => { - const config = useConfigContext(); - const axios = useAxios(config.API_HOST); - const devices = useDeviceApi(axios); - - /** - * Get list of manual and vendor telemetry by deployment ids - * - * @param {string[]} deploymentIds BCTW deployment ids - * @return {*} {Promise} - */ - const getAllTelemetryByDeploymentIds = async (deploymentIds: string[]): Promise => { - const { data } = await axios.post('/api/telemetry/deployments', deploymentIds); - return data; - }; - - /** - * Get a list of vendor retrieved telemetry by deployment ids - * - * @param {string[]} deploymentIds Vendor telemetry deployment ids - * @return {*} {Promise} - */ - const getVendorTelemetryByDeploymentIds = async (deploymentIds: string[]): Promise => { - const { data } = await axios.post('/api/telemetry/vendor/deployments', deploymentIds); - return data; - }; - - /** - * Get a list of manually created telemetry by deployment ids - * - * @param {string[]} deploymentIds Manual Telemetry deployment ids - * @return {*} {Promise} - */ - const getManualTelemetryByDeploymentIds = async (deploymentIds: string[]): Promise => { - const { data } = await axios.post('/api/telemetry/manual/deployments', deploymentIds); - return data; - }; - - /** - * Bulk create Manual Telemetry - * - * @param {ICreateManualTelemetry[]} manualTelemetry Manual Telemetry create objects - * @return {*} {Promise} - */ - const createManualTelemetry = async ( - manualTelemetry: ICreateManualTelemetry[] - ): Promise => { - const { data } = await axios.post('/api/telemetry/manual', manualTelemetry); - return data; - }; - - /** - * Bulk update Manual Telemetry - * - * @param {IUpdateManualTelemetry[]} manualTelemetry Manual Telemetry update objects - * @return {*} - */ - const updateManualTelemetry = async (manualTelemetry: IUpdateManualTelemetry[]) => { - const { data } = await axios.patch('/api/telemetry/manual', manualTelemetry); - return data; - }; - - /** - * Delete manual telemetry records - * - * @param {string[]} telemetryIds Manual Telemetry ids to delete - * @return {*} - */ - const deleteManualTelemetry = async (telemetryIds: string[]) => { - const { data } = await axios.post('/api/telemetry/manual/delete', telemetryIds); - return data; - }; - - /** - * Uploads a telemetry CSV for import. - * - * @param {number} projectId - * @param {number} surveyId - * @param {File} file - * @param {CancelTokenSource} [cancelTokenSource] - * @param {(progressEvent: AxiosProgressEvent) => void} [onProgress] - * @return {*} {Promise<{ submission_id: number }>} - */ - const uploadCsvForImport = async ( - projectId: number, - surveyId: number, - file: File, - cancelTokenSource?: CancelTokenSource, - onProgress?: (progressEvent: AxiosProgressEvent) => void - ): Promise<{ submission_id: number }> => { - const formData = new FormData(); - - formData.append('media', file); - - const { data } = await axios.post<{ submission_id: number }>( - `/api/project/${projectId}/survey/${surveyId}/telemetry/upload`, - formData, - { - cancelToken: cancelTokenSource?.token, - onUploadProgress: onProgress - } - ); - return data; - }; - - /** - * Begins processing an uploaded telemetry CSV for import - * - * @param {number} submissionId - * @return {*} - */ - const processTelemetryCsvSubmission = async (submissionId: number) => { - const { data } = await axios.post(`/api/telemetry/manual/process`, { - submission_id: submissionId - }); - - return data; - }; - - return { - devices, - getAllTelemetryByDeploymentIds, - getManualTelemetryByDeploymentIds, - createManualTelemetry, - updateManualTelemetry, - getVendorTelemetryByDeploymentIds, - deleteManualTelemetry, - uploadCsvForImport, - processTelemetryCsvSubmission - }; -}; diff --git a/app/src/interfaces/useAdminApi.interface.ts b/app/src/interfaces/useAdminApi.interface.ts index 2f2140928d..41bc926d27 100644 --- a/app/src/interfaces/useAdminApi.interface.ts +++ b/app/src/interfaces/useAdminApi.interface.ts @@ -29,6 +29,8 @@ export interface IGetAccessRequestsListResponse { description: string; notes: string; create_date: string; + update_date: string | null; + updated_by: string | null; data: IAccessRequestDataObject; } diff --git a/app/src/interfaces/useAnalyticsApi.interface.ts b/app/src/interfaces/useAnalyticsApi.interface.ts new file mode 100644 index 0000000000..1e15f26046 --- /dev/null +++ b/app/src/interfaces/useAnalyticsApi.interface.ts @@ -0,0 +1,31 @@ +interface IQualitativeMeasurementGroup { + taxon_measurement_id: string; + measurement_name: string; + option: { + option_id: string; + option_label: string; + }; +} + +interface IQuantitativeMeasurementGroup { + taxon_measurement_id: string; + measurement_name: string; + value: number; +} + +export interface IObservationCountByGroup { + /** + * Randomly generated unique ID for the group. + */ + id: string; + row_count: number; + individual_count: number; + individual_percentage: number; + itis_tsn?: number; + observation_date?: string; + survey_sample_site_id?: number; + survey_sample_method_id?: number; + survey_sample_period_id?: number; + qualitative_measurements: IQualitativeMeasurementGroup[]; + quantitative_measurements: IQuantitativeMeasurementGroup[]; +} diff --git a/app/src/interfaces/useAnimalApi.interface.ts b/app/src/interfaces/useAnimalApi.interface.ts index 02b9243480..61cbc9f397 100644 --- a/app/src/interfaces/useAnimalApi.interface.ts +++ b/app/src/interfaces/useAnimalApi.interface.ts @@ -22,3 +22,27 @@ export interface IFindAnimalsResponse { animals: IFindAnimalObj[]; pagination: ApiPaginationResponseParams; } + +/** + * Interface representing the geometry of a mortality event. + */ +interface ICaptureGeometry { + capture_id: string; + coordinates: [number, number]; +} + +/** + * Interface representing the geometry of a mortality event. + */ +interface IMortalityGeometry { + mortality_id: string; + coordinates: [number, number]; +} + +/** + * Interface representing combined capture and mortality geometries + */ +export interface IGetCaptureMortalityGeometryResponse { + captures: ICaptureGeometry[]; + mortalities: IMortalityGeometry[]; +} diff --git a/app/src/interfaces/useCodesApi.interface.ts b/app/src/interfaces/useCodesApi.interface.ts index eed3a36d6c..92310c26b4 100644 --- a/app/src/interfaces/useCodesApi.interface.ts +++ b/app/src/interfaces/useCodesApi.interface.ts @@ -34,7 +34,6 @@ export interface IGetAllCodeSetsResponse { project_roles: CodeSet; administrative_activity_status_type: CodeSet; intended_outcomes: CodeSet<{ id: number; name: string; description: string }>; - vantage_codes: CodeSet; survey_jobs: CodeSet; site_selection_strategies: CodeSet; survey_progress: CodeSet<{ id: number; name: string; description: string }>; diff --git a/app/src/interfaces/useCritterApi.interface.ts b/app/src/interfaces/useCritterApi.interface.ts index 810e8a6d0f..f913f7cfdd 100644 --- a/app/src/interfaces/useCritterApi.interface.ts +++ b/app/src/interfaces/useCritterApi.interface.ts @@ -1,4 +1,4 @@ -import { ICreateCritterCollectionUnit } from 'features/surveys/view/survey-animals/animal'; +import { AnimalSex, ICreateCritterCollectionUnit } from 'features/surveys/view/survey-animals/animal'; import { Feature } from 'geojson'; import { IPartialTaxonomy } from './useTaxonomyApi.interface'; @@ -6,7 +6,7 @@ export interface ICritterCreate { critter_id?: string; wlh_id?: string | null; animal_id?: string | null; - sex: string; + sex: AnimalSex; itis_tsn: number; responsible_region_nr_id?: string | null; critter_comment?: string | null; @@ -16,6 +16,7 @@ export interface ICreateEditAnimalRequest { critter_id?: string; nickname: string; species: IPartialTaxonomy | null; + sex: AnimalSex; ecological_units: ICreateCritterCollectionUnit[]; wildlife_health_id: string | null; critter_comment: string | null; @@ -103,6 +104,11 @@ export interface IEditMortalityRequest extends IMarkings, IMeasurementsUpdate { mortality: IMortalityPostData; } +export interface ICollectionUnitMultiTsnResponse { + tsn: number; + categories: ICollectionCategory[]; +} + export interface ICollectionCategory { collection_category_id: string; category_name: string; @@ -269,7 +275,8 @@ export type IFamilyChildResponse = { }; export type ICritterDetailedResponse = { - critter_id: string; + critter_id: number; + critterbase_critter_id: string; itis_tsn: number; itis_scientific_name: string; wlh_id: string | null; @@ -290,7 +297,8 @@ export type ICritterDetailedResponse = { }; export interface ICritterSimpleResponse { - critter_id: string; + critter_id: number; + critterbase_critter_id: string; wlh_id: string | null; animal_id: string | null; sex: string; @@ -386,6 +394,6 @@ export type CBMeasurementSearchByTsnResponse = { * Response object when searching for measurement type definitions by search term. */ export type CBMeasurementSearchByTermResponse = { - qualitative: (CBQualitativeMeasurementTypeDefinition & { tsnHierarchy: number[] })[]; - quantitative: (CBQuantitativeMeasurementTypeDefinition & { tsnHierarchy: number[] })[]; + qualitative: CBQualitativeMeasurementTypeDefinition[]; + quantitative: CBQuantitativeMeasurementTypeDefinition[]; }; diff --git a/app/src/interfaces/useObservationApi.interface.ts b/app/src/interfaces/useObservationApi.interface.ts index 05a861f614..aa0e695c8d 100644 --- a/app/src/interfaces/useObservationApi.interface.ts +++ b/app/src/interfaces/useObservationApi.interface.ts @@ -13,11 +13,13 @@ export interface IGetSurveyObservationsResponse { pagination: ApiPaginationResponseParams; } +export interface IGetSurveyObservationsGeometryObject { + survey_observation_id: number; + geometry: GeoJSON.Point; +} + export interface IGetSurveyObservationsGeometryResponse { - surveyObservationsGeometry: { - survey_observation_id: number; - geometry: GeoJSON.Point; - }[]; + surveyObservationsGeometry: IGetSurveyObservationsGeometryObject[]; supplementaryObservationData: SupplementaryObservationData; } diff --git a/app/src/interfaces/useProjectApi.interface.ts b/app/src/interfaces/useProjectApi.interface.ts index 38adfe2455..384cbf0690 100644 --- a/app/src/interfaces/useProjectApi.interface.ts +++ b/app/src/interfaces/useProjectApi.interface.ts @@ -130,6 +130,10 @@ export interface IProjectsListItemData { * The types of the surveys in the project. */ types: number[]; + /** + * Members of the project + */ + members: { system_user_id: number; display_name: string }[]; } export interface IProjectUserRoles { diff --git a/app/src/interfaces/useSamplingSiteApi.interface.ts b/app/src/interfaces/useSamplingSiteApi.interface.ts index 675839738c..33799d4129 100644 --- a/app/src/interfaces/useSamplingSiteApi.interface.ts +++ b/app/src/interfaces/useSamplingSiteApi.interface.ts @@ -117,6 +117,7 @@ export interface IGetSampleMethodRecord { export interface IGetSampleMethodDetails extends IGetSampleMethodRecord { technique: { method_technique_id: number; + method_lookup_id: number; name: string; description: string; attractants: number[]; diff --git a/app/src/interfaces/useStandardsApi.interface.ts b/app/src/interfaces/useStandardsApi.interface.ts index fc58fd85ab..09069b72c3 100644 --- a/app/src/interfaces/useStandardsApi.interface.ts +++ b/app/src/interfaces/useStandardsApi.interface.ts @@ -4,13 +4,26 @@ import { ICollectionUnit } from './useCritterApi.interface'; +interface IStandardNameDescription { + name: string; + description: string; +} + +interface IQualitativeAttributeStandard extends IStandardNameDescription { + options: IStandardNameDescription[]; +} + +interface IQuantitativeAttributeStandard extends IStandardNameDescription { + unit: string; +} + /** * Data standards for a taxon * * @export - * @interface IGetSpeciesStandardsResponse + * @interface ISpeciesStandards */ -export interface IGetSpeciesStandardsResponse { +export interface ISpeciesStandards { tsn: number; scientificName: string; measurements: { @@ -22,5 +35,27 @@ export interface IGetSpeciesStandardsResponse { key: string; value: string; }[]; - ecological_units: ICollectionUnit[]; + ecologicalUnits: ICollectionUnit[]; +} + +/** + * Data standards for methods + * + * @export + * @interface IMethodStandard + */ +export interface IMethodStandard extends IStandardNameDescription { + method_lookup_id: number; + attributes: { qualitative: IQualitativeAttributeStandard[]; quantitative: IQuantitativeAttributeStandard[] }; +} + +/** + * Data standards for environments + * + * @export + * @interface IEnvironmentStandards + */ +export interface IEnvironmentStandards { + qualitative: IQualitativeAttributeStandard[]; + quantitative: IQuantitativeAttributeStandard[]; } diff --git a/app/src/interfaces/useSurveyApi.interface.ts b/app/src/interfaces/useSurveyApi.interface.ts index 6059106f18..fd99d9a7fe 100644 --- a/app/src/interfaces/useSurveyApi.interface.ts +++ b/app/src/interfaces/useSurveyApi.interface.ts @@ -8,9 +8,12 @@ import { import { IGeneralInformationForm } from 'features/surveys/components/general-information/GeneralInformationForm'; import { ISurveyLocationForm } from 'features/surveys/components/locations/StudyAreaForm'; import { IPurposeAndMethodologyForm } from 'features/surveys/components/methodology/PurposeAndMethodologyForm'; -import { IBlockData } from 'features/surveys/components/sampling-strategy/blocks/BlockForm'; +import { ISurveyPermitForm } from 'features/surveys/components/permit/SurveyPermitForm'; +import { ISpeciesForm, ITaxonomyWithEcologicalUnits } from 'features/surveys/components/species/SpeciesForm'; +import { ISurveyPartnershipsForm } from 'features/surveys/view/components/SurveyPartnershipsForm'; import { Feature } from 'geojson'; import { ITaxonomy } from 'interfaces/useTaxonomyApi.interface'; +import { IAnimalDeployment } from 'interfaces/useTelemetryApi.interface'; import { ApiPaginationResponseParams, StringBoolean } from 'types/misc'; import { ICritterDetailedResponse, ICritterSimpleResponse } from './useCritterApi.interface'; @@ -27,7 +30,12 @@ export interface ICreateSurveyRequest IAgreementsForm, IParticipantsJobForm, ISurveyLocationForm, - ISurveyBlockForm {} + ISurveyBlockForm, + ISurveyPartnershipsForm, + ISurveySiteSelectionForm, + ISpeciesForm, + Omit, + Omit {} /** * Create survey response object. @@ -47,17 +55,10 @@ export interface IGetSurveyStratumForm { export interface IPostSurveyStratum { survey_stratum_id: number | null; name: string; - description?: string; + description: string | null; } export interface ISurveySiteSelectionForm { - site_selection: { - strategies: string[]; - stratums: IGetSurveyStratum[]; - }; -} - -export interface ISurveySiteSelectionUpdateObject { site_selection: { strategies: string[]; stratums: IPostSurveyStratum[]; @@ -91,7 +92,6 @@ export interface IGetSurveyForViewResponseDetails { export interface IGetSurveyForViewResponsePurposeAndMethodology { intended_outcome_ids: number[]; additional_details: string; - vantage_code_ids: number[]; } export interface IGetSurveyForViewResponseProprietor { @@ -176,40 +176,37 @@ export interface SurveyBasicFieldsObject { types: number[]; } -export type SurveyUpdateObject = ISurveyUpdateObject & ISurveySiteSelectionUpdateObject; - -interface ISurveyUpdateObject extends ISurveyLocationForm { - survey_details?: { +export type IUpdateSurveyRequest = ISurveyLocationForm & { + survey_details: { survey_name: string; + progress_id: number; start_date: string; end_date: string; survey_types: number[]; revision_count: number; }; - species?: { - focal_species: ITaxonomy[]; - ancillary_species: ITaxonomy[]; + species: { + focal_species: ITaxonomyWithEcologicalUnits[]; }; - permit?: { + permit: { permits: { - permit_id?: number; + permit_id?: number | null; permit_number: string; permit_type: string; }[]; }; - funding_sources?: { + funding_sources: { funding_source_id: number; amount: number; revision_count: number; }[]; - partnerships?: IGetSurveyForUpdateResponsePartnerships; - purpose_and_methodology?: { + partnerships: IGetSurveyForUpdateResponsePartnerships; + purpose_and_methodology: { intended_outcome_ids: number[]; additional_details: string; - vantage_code_ids: number[]; revision_count: number; }; - proprietor?: { + proprietor: { survey_data_proprietary: StringBoolean; proprietary_data_category: number; proprietor_name: string; @@ -217,9 +214,25 @@ interface ISurveyUpdateObject extends ISurveyLocationForm { category_rationale: string; disa_required: StringBoolean; }; - participants?: IGetSurveyParticipant[]; - blocks: IBlockData[]; -} + participants: IGetSurveyParticipant[]; + blocks: { + survey_block_id?: number | null; + name: string; + description: string; + }[]; + site_selection: { + strategies: string[]; + stratums: { + survey_stratum_id: number | null; + name: string; + description: string | null; + }[]; + }; + agreements: { + sedis_procedures_accepted: StringBoolean; + foippa_requirements_accepted: StringBoolean; + }; +}; export interface SurveySupplementaryData { survey_metadata_publish: { @@ -269,7 +282,6 @@ export interface IGetSurveyForViewResponse { export interface IGetSpecies { focal_species: ITaxonomy[]; - ancillary_species: ITaxonomy[]; } export interface IGetSurveyAttachment { @@ -335,22 +347,126 @@ export interface IUpdateAgreementsForm { } export interface IGetSurveyForUpdateResponse { - surveyData: SurveyUpdateObject; + surveyData: { + survey_details: { + id: number; + project_id: number; + uuid: string; + survey_name: string; + start_date: string; + end_date: string; + progress_id: number; + survey_types: number[]; + revision_count: number; + }; + species: { + focal_species: ITaxonomyWithEcologicalUnits[]; + }; + permit: { + permits: { + permit_id: number; + permit_number: string; + permit_type: string; + }[]; + }; + funding_sources: { + funding_source_id: number; + survey_id: number; + survey_funding_source_id: number; + amount: number; + funding_source_name: string; + start_date: string | null; + end_date: string | null; + description: string | null; + revision_count: number; + }[]; + partnerships: IGetSurveyForUpdateResponsePartnerships; + purpose_and_methodology: { + intended_outcome_ids: number[]; + additional_details: string; + revision_count: number; + }; + proprietor: { + proprietor_type_name: string; + proprietor_type_id: number; + first_nations_name: string | null; + first_nations_id: number; + category_rationale: string; + proprietor_name: string; + disa_required: StringBoolean; + survey_data_proprietary: StringBoolean; + proprietary_data_category: number; + }; + locations: { + survey_id: number; + survey_location_id: number; + name: string; + description: string; + geometry: null; + geography: string; + geojson: Feature[]; + revision_count: number; + }[]; + participants: { + system_user_id: number; + user_identifier: string; + user_guid: string; + record_end_date: string | null; + identity_source: string; + role_ids: number[]; + role_names: string[]; + email: string; + display_name: string; + given_name: string | null; + family_name: string | null; + agency: string | null; + survey_participation_id: number; + survey_id: number; + survey_job_id: number; + survey_job_name: string; + }[]; + site_selection: { + strategies: string[]; + stratums: { + survey_stratum_id: number; + survey_id: number; + name: string; + description: 's1111'; + sample_stratum_count: number; + revision_count: number; + }[]; + }; + blocks: { + survey_block_id: number; + survey_id: number; + name: string; + description: string; + sample_block_count: number; + revision_count: number; + }[]; + agreements: { + sedis_procedures_accepted: StringBoolean; + foippa_requirements_accepted: StringBoolean; + }; + }; } -export interface ISimpleCritterWithInternalId extends ICritterSimpleResponse { - survey_critter_id: number; +export interface IDetailedCritterWithInternalId extends ICritterDetailedResponse { + critter_id: number; //The internal critter_id in the SIMS DB. Called this to distinguish against the critterbase UUID of the same name. } -export interface IDetailedCritterWithInternalId extends ICritterDetailedResponse { - survey_critter_id: number; //The internal critter_id in the SIMS DB. Called this to distinguish against the critterbase UUID of the same name. +export interface IAnimalDeploymentWithCritter { + deployment: IAnimalDeployment; + critter: ICritterSimpleResponse; } export type IEditSurveyRequest = IGeneralInformationForm & + ISpeciesForm & IPurposeAndMethodologyForm & - ISurveyFundingSourceForm & ISurveyLocationForm & IProprietaryDataForm & IUpdateAgreementsForm & { partnerships: IGetSurveyForViewResponsePartnerships } & ISurveySiteSelectionForm & IParticipantsJobForm & - ISurveyBlockForm; + ISurveyBlockForm & + ISurveyPermitForm & + ISurveyFundingSourceForm; diff --git a/app/src/interfaces/useTaxonomyApi.interface.ts b/app/src/interfaces/useTaxonomyApi.interface.ts index 27ce499345..83edf013bc 100644 --- a/app/src/interfaces/useTaxonomyApi.interface.ts +++ b/app/src/interfaces/useTaxonomyApi.interface.ts @@ -1,14 +1,3 @@ -export interface IItisSearchResponse { - commonNames: string[]; - kingdom: string; - name: string; - parentTSN: string; - scientificName: string; - tsn: string; - updateDate: string; - usage: string; -} - export type ITaxonomy = { tsn: number; commonNames: string[]; @@ -21,3 +10,5 @@ export type ITaxonomy = { // to return the extra `rank` and `kingdom` fields, which are currently only available in some of the BioHub taxonomy // endpoints. export type IPartialTaxonomy = Partial & Pick; + +export type ITaxonomyHierarchy = Pick & { hierarchy: number[] }; diff --git a/app/src/interfaces/useTelemetryApi.interface.ts b/app/src/interfaces/useTelemetryApi.interface.ts index c04bf5e3b5..c2a4349e76 100644 --- a/app/src/interfaces/useTelemetryApi.interface.ts +++ b/app/src/interfaces/useTelemetryApi.interface.ts @@ -1,4 +1,7 @@ +import { DeploymentFormYupSchema } from 'features/surveys/telemetry/deployments/components/form/DeploymentForm'; +import { FeatureCollection } from 'geojson'; import { ApiPaginationResponseParams } from 'types/misc'; +import yup from 'utils/YupSchema'; export interface IFindTelementryObj { telemetry_id: string; @@ -24,3 +27,188 @@ export interface IFindTelemetryResponse { telemetry: IFindTelementryObj[]; pagination: ApiPaginationResponseParams; } + +export interface ICritterDeploymentResponse { + critter_id: string; + device_id: number; + deployment_id: string; + survey_critter_id: string; + alias: string; + attachment_start: string; + attachment_end?: string; + taxon: string; +} + +export interface IUpdateManualTelemetry { + telemetry_manual_id: string; + latitude: number; + longitude: number; + acquisition_date: string; +} +export interface ICreateManualTelemetry { + deployment_id: string; + latitude: number; + longitude: number; + acquisition_date: string; +} + +export interface IManualTelemetry extends ICreateManualTelemetry { + telemetry_manual_id: string; +} + +export interface IAllTelemetry { + id: string; + deployment_id: string; + telemetry_manual_id: string; + telemetry_id: number | null; + device_id: string; + latitude: number; + longitude: number; + acquisition_date: string; + telemetry_type: string; +} + +export type IAnimalDeployment = { + // BCTW properties + + /** + * The ID of a BCTW collar animal assignment (aka: deployment) record. + */ + assignment_id: string; + /** + * The ID of a BCTW collar record. + */ + collar_id: string; + /** + * The ID of a BCTW critter record. Should match a critter_id in Critterbase. + */ + critter_id: number; + /** + * The ID of a BCTW device. + */ + device_id: number; + /** + * The time the deployment started. + */ + attachment_start_date: string | null; + /** + * The time the deployment started. + */ + attachment_start_time: string | null; + /** + * The time the deployment ended. + */ + attachment_end_date: string | null; + /** + * The time the deployment ended. + */ + attachment_end_time: string | null; + /** + * The ID of a BCTW deployment record. + */ + bctw_deployment_id: string; + /** + * The ID of a BCTW device make record. + */ + device_make: number; + /** + * The model of the device. + */ + device_model: string | null; + /** + * The frequency of the device. + */ + frequency: number | null; + /** + * The ID of a BCTW frequency unit record. + */ + frequency_unit: number | null; + + // SIMS properties + + /** + * SIMS deployment record ID + */ + deployment_id: number; + /** + * Critterbase critter ID + */ + critterbase_critter_id: string; + /** + * Critterbase capture ID for the start of the deployment. + */ + critterbase_start_capture_id: string; + /** + * Critterbase capture ID for the end of the deployment. + */ + critterbase_end_capture_id: string | null; + /** + * Critterbase mortality ID for the end of the deployment. + */ + critterbase_end_mortality_id: string | null; +}; + +export type ICreateAnimalDeployment = yup.InferType; + +export interface ICreateAnimalDeploymentPostData extends Omit { + device_id: number; +} + +export type IAllTelemetryPointCollection = { points: FeatureCollection; tracks: FeatureCollection }; + +export interface ITelemetry { + id: string; + /** + * Either the telemetry_manual_id or telemetry_id (depending on the type of telemetry: manual vs vendor). + */ + deployment_id: string; + /** + * The telemetry_manual_id if the telemetry was manually created. + * Will be null if the telemetry was retrieved from a vendor. + */ + telemetry_manual_id: string | null; + /** + * The telemetry_id if the telemetry was retrieved from a vendor. + * Will be null if the telemetry was manually created. + */ + telemetry_id: number | null; + /** + * The latitude of the telemetry. + */ + latitude: number; + /** + * The longitude of the telemetry. + */ + longitude: number; + /** + * The acquisition date of the telemetry. + */ + acquisition_date: string; + /** + * The type of telemetry. + * Will either be 'MANUAL' (for manual telementry) or the name of the vendor (for vendor telemetry). + */ + telemetry_type: string; +} + +export interface ICodeResponse { + code_header_title: string; + code_header_name: string; + id: number; + code: string; + description: string; + long_description: string; +} + +export type TelemetryDeviceKeyFile = { + survey_telemetry_credential_attachment_id: number; + uuid: string; + file_name: string; + file_type: string; + file_size: number; + create_date: string; + update_date: string | null; + title: string | null; + description: string | null; + key: string; +}; diff --git a/app/src/test-helpers/code-helpers.ts b/app/src/test-helpers/code-helpers.ts index ea54c4efa8..8af0951dda 100644 --- a/app/src/test-helpers/code-helpers.ts +++ b/app/src/test-helpers/code-helpers.ts @@ -35,10 +35,6 @@ export const codes: IGetAllCodeSetsResponse = { { id: 2, name: 'Actioned' }, { id: 3, name: 'Rejected' } ], - vantage_codes: [ - { id: 1, name: 'Vantage Code 1' }, - { id: 2, name: 'Vantage Code 2' } - ], intended_outcomes: [ { id: 1, name: 'Intended Outcome 1', description: 'Description 1' }, { id: 2, name: 'Intended Outcome 2', description: 'Description 2' } diff --git a/app/src/test-helpers/survey-helpers.ts b/app/src/test-helpers/survey-helpers.ts index b8d0dff493..078318156d 100644 --- a/app/src/test-helpers/survey-helpers.ts +++ b/app/src/test-helpers/survey-helpers.ts @@ -20,8 +20,7 @@ export const surveyObject: SurveyViewObject = { blocks: [], purpose_and_methodology: { intended_outcome_ids: [1], - additional_details: 'details', - vantage_code_ids: [1, 2] + additional_details: 'details' }, proprietor: { proprietary_data_category_name: 'proprietor type', @@ -65,15 +64,6 @@ export const surveyObject: SurveyViewObject = { rank: 'species', kingdom: 'animalia' } - ], - ancillary_species: [ - { - tsn: 2, - commonNames: ['focal species 2'], - scientificName: 'scientific name 2', - rank: 'species', - kingdom: 'animalia' - } ] }, site_selection: { diff --git a/app/src/themes/appTheme.ts b/app/src/themes/appTheme.ts index 1afe273e4c..cd82c81de1 100644 --- a/app/src/themes/appTheme.ts +++ b/app/src/themes/appTheme.ts @@ -210,7 +210,8 @@ const appTheme = createTheme({ MuiDialogTitle: { styleOverrides: { root: { - paddingTop: '24px' + paddingTop: '24px', + paddingBottom: '8px' } } }, diff --git a/app/src/types/yup.d.ts b/app/src/types/yup.d.ts index 0fe155bc6c..0bece13fb3 100644 --- a/app/src/types/yup.d.ts +++ b/app/src/types/yup.d.ts @@ -111,17 +111,6 @@ declare module 'yup' { message: string ): yup.StringSchema, string | undefined>; - /** - * Determine if the object of focal and ancillary species has duplicates - * - * @param {string} message='Focal and Ancillary species must be unique' - error message if this check fails - * @return {*} {(yup.StringSchema, string | undefined>)} - * @memberof ArraySchema - */ - isUniqueFocalAncillarySpecies( - message: string - ): yup.StringSchema, string | undefined>; - /** * Determine if the author array contains unique `first_name`/`last_name` pairs. * diff --git a/app/src/utils/Utils.tsx b/app/src/utils/Utils.tsx index 4f99945381..994630cd65 100644 --- a/app/src/utils/Utils.tsx +++ b/app/src/utils/Utils.tsx @@ -461,9 +461,10 @@ export const firstOrNull = (arr: T[]): T | null => (arr.length > 0 ? arr[0] * @param seed * @returns */ -export const getRandomHexColor = (seed: number, min = 100, max = 170): string => { +export const getRandomHexColor = (seed: number, min = 120, max = 180): string => { const randomChannel = (): string => { - const x = Math.sin(seed++) * 10000; + // Change the multiplier to change the colour boldness + const x = Math.sin(seed++) * 1000; return (Math.floor((x - Math.floor(x)) * (max - min + 1)) + min).toString(16).padStart(2, '0'); }; diff --git a/app/src/utils/YupSchema.ts b/app/src/utils/YupSchema.ts index 09a5a55561..cbe50cd099 100644 --- a/app/src/utils/YupSchema.ts +++ b/app/src/utils/YupSchema.ts @@ -26,24 +26,6 @@ yup.addMethod(yup.array, 'isUniqueIUCNClassificationDetail', function (message: }); }); -yup.addMethod(yup.array, 'isUniqueFocalAncillarySpecies', function (message: string) { - return this.test('is-unique-focal-ancillary-species', message, function (values) { - if (!values || !values.length) { - return true; - } - - let hasDuplicates = false; - - this.parent.focal_species.forEach((species: number) => { - if (values.includes(species)) { - hasDuplicates = true; - } - }); - - return !hasDuplicates; - }); -}); - yup.addMethod( yup.string, 'isValidDateString', diff --git a/app/src/utils/mapUtils.ts b/app/src/utils/mapUtils.ts index 6481cd67be..453ffb95e0 100644 --- a/app/src/utils/mapUtils.ts +++ b/app/src/utils/mapUtils.ts @@ -1,54 +1,84 @@ -import { Feature } from 'geojson'; +import { SURVEY_MAP_LAYER_COLOURS } from 'constants/colours'; import L, { LatLng } from 'leaflet'; -export const MapDefaultBlue = '#3388ff'; - -export const DefaultMapValues = { - zoom: 5, - center: [55, -128] -}; - -export interface INonEditableGeometries { - feature: Feature; - popupComponent?: JSX.Element; -} - -export interface IClusteredPointGeometries { - coordinates: number[]; - popupComponent?: JSX.Element; -} -export interface MapPointProps { +export interface ColoredCustomMarkerProps { latlng: LatLng; fillColor?: string; borderColor?: string; } -export const coloredPoint = (point: MapPointProps): L.CircleMarker => { - return new L.CircleMarker(point.latlng, { +/** + * Returns a custom map marker for symbolizing points. + * + * @param {ColoredCustomMarkerProps} point + * @return {*} {L.CircleMarker} + */ +export const coloredCustomMarker = (props: ColoredCustomMarkerProps): L.CircleMarker => { + return new L.CircleMarker(props.latlng, { radius: 6, fillOpacity: 1, - fillColor: point.fillColor ?? MapDefaultBlue, - color: point.borderColor ?? '#ffffff', + fillColor: props.fillColor ?? SURVEY_MAP_LAYER_COLOURS.DEFAULT_COLOUR, + color: props.borderColor ?? '#ffffff', weight: 1 }); }; /** - * Returns custom map marker for symbolizing observations + * Util function for creating a custom map marker for symbolizing observation points. * - * @param fillColor - * @returns + * @param {string} [color] */ -export const generateCustomPointMarkerUrl = (fillColor?: string) => +const _generateCustomObservationMarkerUrl = (color?: string) => 'data:image/svg+xml;base64,' + btoa( `` ); -export const coloredCustomPointMarker = (point: MapPointProps): L.Marker => { - return new L.Marker(point.latlng, { - icon: L.icon({ iconUrl: generateCustomPointMarkerUrl(point?.fillColor), iconSize: [20, 15], iconAnchor: [12, 12] }) +/** + * Util function for creating a custom map marker for symbolizing animal mortality points. + * + * @param {string} [color] + */ +const _generateCustomMortalityMarkerUrl = (color?: string) => + 'data:image/svg+xml;base64,' + + btoa( + ` + + ` + ); + +/** + * Returns custom map marker for symbolizing observation points. + * + * @param {ColoredCustomMarkerProps} props + * @return {*} {L.Marker} + */ +export const coloredCustomObservationMarker = (props: ColoredCustomMarkerProps): L.Marker => { + return new L.Marker(props.latlng, { + icon: L.icon({ + iconUrl: _generateCustomObservationMarkerUrl(props.fillColor), + iconSize: [20, 15], + iconAnchor: [12, 12] + }) + }); +}; + +/** + * Returns custom map marker for symbolizing animal mortality points. + * + * @param {ColoredCustomMarkerProps} props + * @return {*} {L.Marker} + */ +export const coloredCustomMortalityMarker = (props: ColoredCustomMarkerProps): L.Marker => { + return new L.Marker(props.latlng, { + icon: L.icon({ + iconUrl: _generateCustomMortalityMarkerUrl(props.fillColor), + iconSize: [20, 15], + iconAnchor: [12, 12] + }) }); }; diff --git a/app/src/utils/spatial-utils.test.ts b/app/src/utils/spatial-utils.test.ts new file mode 100644 index 0000000000..7f4456b85b --- /dev/null +++ b/app/src/utils/spatial-utils.test.ts @@ -0,0 +1,269 @@ +import { SAMPLING_SITE_SPATIAL_TYPE } from 'constants/spatial'; +import { Feature, Point } from 'geojson'; +import { getSamplingSiteSpatialType } from 'utils/spatial-utils'; +import { getCoordinatesFromGeoJson, isGeoJsonPointFeature, isValidCoordinates } from './spatial-utils'; + +describe('isValidCoordinates', () => { + it('returns true when the latitude and longitude values are valid', () => { + const latitude = 0; + const longitude = 0; + + const response = isValidCoordinates(latitude, longitude); + + expect(response).toEqual(true); + }); + + it('returns false when the latitude is less than -90', () => { + const latitude = -91; + const longitude = 0; + + const response = isValidCoordinates(latitude, longitude); + + expect(response).toEqual(false); + }); + + it('returns false when the latitude is greater than 90', () => { + const latitude = 91; + const longitude = 0; + + const response = isValidCoordinates(latitude, longitude); + + expect(response).toEqual(false); + }); + + it('returns false when the longitude is less than -180', () => { + const latitude = 0; + const longitude = -181; + + const response = isValidCoordinates(latitude, longitude); + + expect(response).toEqual(false); + }); + + it('returns false when the longitude is greater than 180', () => { + const latitude = 0; + const longitude = 181; + + const response = isValidCoordinates(latitude, longitude); + + expect(response).toEqual(false); + }); + + it('returns false when the latitude is undefined', () => { + const longitude = 0; + + const response = isValidCoordinates(undefined, longitude); + + expect(response).toEqual(false); + }); + + it('returns false when the longitude is undefined', () => { + const latitude = 0; + + const response = isValidCoordinates(latitude, undefined); + + expect(response).toEqual(false); + }); +}); + +describe('getCoordinatesFromGeoJson', () => { + it('returns the latitude and longitude values from a GeoJson Point Feature', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'Point', + coordinates: [11, 22] + }, + properties: {} + }; + + const response = getCoordinatesFromGeoJson(feature); + + expect(response).toEqual({ latitude: 22, longitude: 11 }); + }); +}); + +describe('isGeoJsonPointFeature', () => { + it('returns true when the feature is a GeoJson Point Feature', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'Point', + coordinates: [0, 0] + }, + properties: {} + }; + + const response = isGeoJsonPointFeature(feature); + + expect(response).toEqual(true); + }); + + it('returns false when the feature is not a GeoJson Point Feature', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'LineString', + coordinates: [ + [0, 0], + [1, 1] + ] + }, + properties: {} + }; + + const response = isGeoJsonPointFeature(feature); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is undefined', () => { + const response = isGeoJsonPointFeature(undefined); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is null', () => { + const response = isGeoJsonPointFeature(null); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is an empty object', () => { + const response = isGeoJsonPointFeature({}); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is an empty array', () => { + const response = isGeoJsonPointFeature([]); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is a string', () => { + const response = isGeoJsonPointFeature('string'); + + expect(response).toEqual(false); + }); + + it('returns false when the feature is a number', () => { + const response = isGeoJsonPointFeature(1); + + expect(response).toEqual(false); + }); +}); + +describe('getSamplingSiteSpatialType', () => { + it('maps MultiLineString to Transect', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'MultiLineString', + coordinates: [[[0, 0]], [[1, 1]]] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.TRANSECT); + }); + + it('maps LineString to Transect', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'LineString', + coordinates: [ + [0, 0], + [1, 1] + ] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.TRANSECT); + }); + + it('maps Point to Point', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'Point', + coordinates: [0, 0] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.POINT); + }); + + it('maps MultiPoint to Point', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'MultiPoint', + coordinates: [ + [0, 0], + [1, 1] + ] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.POINT); + }); + + it('maps Polygon to Area', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'Polygon', + coordinates: [ + [ + [0, 0], + [1, 1], + [0, 1], + [0, 0] + ] + ] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.AREA); + }); + + it('maps MultiPolygon to Area', () => { + const feature: Feature = { + type: 'Feature', + geometry: { + type: 'MultiPolygon', + coordinates: [ + [ + [ + [0, 0], + [1, 1], + [0, 1], + [0, 0] + ] + ] + ] + }, + properties: {} + }; + + const response = getSamplingSiteSpatialType(feature); + + expect(response).toEqual(SAMPLING_SITE_SPATIAL_TYPE.AREA); + }); +}); diff --git a/app/src/utils/spatial-utils.ts b/app/src/utils/spatial-utils.ts index 9cce878245..0b088e5cf5 100644 --- a/app/src/utils/spatial-utils.ts +++ b/app/src/utils/spatial-utils.ts @@ -1,48 +1,26 @@ +import { SAMPLING_SITE_SPATIAL_TYPE } from 'constants/spatial'; import { Feature, Point } from 'geojson'; -import { isDefined } from 'utils/Utils'; +import { isDefined } from './Utils'; /** - * Get a point feature from the given latitude and longitude. + * Checks whether a latitude-longitude pair of coordinates is valid. * - * @template Return00PointType - * @param {{ - * latitude?: number; // Latitude of the point - * longitude?: number; // Longitude of the point - * properties?: Record; // Properties of the point feature - * return00Point?: Return00PointType; // By default, if latitude or longitude is not defined, return null. If this is - * set to true, the default value for latitude and longitude will be 0, and a non-null point feature will be returned. - * }} params - * @return {*} {(Return00PointType extends true ? Feature : Feature | null)} - */ -export const getPointFeature = (params: { - latitude?: number; - longitude?: number; - properties?: Record; - return00Point?: Return00PointType; -}): Return00PointType extends true ? Feature : Feature | null => { - if (!params.return00Point && (!isDefined(params.latitude) || !isDefined(params.longitude))) { - return null as Return00PointType extends true ? Feature : Feature | null; - } - - return { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [params.longitude ?? 0, params.latitude ?? 0] - }, - properties: { ...params.properties } - }; -}; - -/** - * Checks whether a latitude-longitude pair of coordinates is valid + * A valid latitude is between -90 and 90 degrees, inclusive. + * A valid longitude is between -180 and 180 degrees, inclusive. * - * @param {number} latitude - * @param {number} longitude - * @returns boolean + * @param {(number | undefined)} latitude + * @param {(number | undefined)} longitude + * @return {*} {boolean} */ export const isValidCoordinates = (latitude: number | undefined, longitude: number | undefined) => { - return latitude && longitude && latitude > -90 && latitude < 90 && longitude > -180 && longitude < 180 ? true : false; + return ( + isDefined(latitude) && + isDefined(longitude) && + latitude >= -90 && + latitude <= 90 && + longitude >= -180 && + longitude <= 180 + ); }; /** @@ -52,18 +30,42 @@ export const isValidCoordinates = (latitude: number | undefined, longitude: numb * @return {*} {{ latitude: number; longitude: number }} */ export const getCoordinatesFromGeoJson = (feature: Feature): { latitude: number; longitude: number } => { - const lon = feature.geometry.coordinates[0]; - const lat = feature.geometry.coordinates[1]; + const longitude = feature.geometry.coordinates[0]; + const latitude = feature.geometry.coordinates[1]; - return { latitude: lat as number, longitude: lon as number }; + return { latitude, longitude }; }; /** * Checks if the given feature is a GeoJson Feature containing a Point. * - * @param {(Feature | any)} [feature] + * @param {(unknown)} [feature] * @return {*} {feature is Feature} */ -export const isGeoJsonPointFeature = (feature?: Feature | any): feature is Feature => { - return (feature as Feature)?.geometry.type === 'Point'; +export const isGeoJsonPointFeature = (feature?: unknown): feature is Feature => { + return (feature as Feature)?.geometry?.type === 'Point'; +}; + +/** + * Get the spatial type of a sampling site feature (Point, Transect, Area, etc). + * + * @param {Feature} feature + * @return {*} {(SAMPLING_SITE_SPATIAL_TYPE | null)} + */ +export const getSamplingSiteSpatialType = (feature: Feature): SAMPLING_SITE_SPATIAL_TYPE | null => { + const geometryType = feature.geometry.type; + + if (['MultiLineString', 'LineString'].includes(geometryType)) { + return SAMPLING_SITE_SPATIAL_TYPE.TRANSECT; + } + + if (['Point', 'MultiPoint'].includes(geometryType)) { + return SAMPLING_SITE_SPATIAL_TYPE.POINT; + } + + if (['Polygon', 'MultiPolygon'].includes(geometryType)) { + return SAMPLING_SITE_SPATIAL_TYPE.AREA; + } + + return null; }; diff --git a/docker-compose.yml b/compose.yml similarity index 96% rename from docker-compose.yml rename to compose.yml index 0bd03d55cd..8d1955a247 100644 --- a/docker-compose.yml +++ b/compose.yml @@ -1,5 +1,3 @@ -version: "3.5" - services: ## Build postgres docker image db: @@ -80,8 +78,15 @@ services: - MAX_REQ_BODY_SIZE=${MAX_REQ_BODY_SIZE} - MAX_UPLOAD_NUM_FILES=${MAX_UPLOAD_NUM_FILES} - MAX_UPLOAD_FILE_SIZE=${MAX_UPLOAD_FILE_SIZE} - # Logging and Validation + # Logging - LOG_LEVEL=${LOG_LEVEL} + - LOG_LEVEL_FILE=${LOG_LEVEL_FILE} + - LOG_FILE_DIR=${LOG_FILE_DIR} + - LOG_FILE_NAME=${LOG_FILE_NAME} + - LOG_FILE_DATE_PATTERN=${LOG_FILE_DATE_PATTERN} + - LOG_FILE_MAX_SIZE=${LOG_FILE_MAX_SIZE} + - LOG_FILE_MAX_FILES=${LOG_FILE_MAX_FILES} + # API Validation - API_RESPONSE_VALIDATION_ENABLED=${API_RESPONSE_VALIDATION_ENABLED} - DATABASE_RESPONSE_VALIDATION_ENABLED=${DATABASE_RESPONSE_VALIDATION_ENABLED} # Clamav diff --git a/database/.docker/db/Dockerfile b/database/.docker/db/Dockerfile index b0808f9bfa..effd413ed7 100644 --- a/database/.docker/db/Dockerfile +++ b/database/.docker/db/Dockerfile @@ -1,5 +1,5 @@ # ######################################################################################################## -# This DockerFile is used for local development (via docker-compose) only. +# This DockerFile is used for local development (via compose.yml) only. # ######################################################################################################## ARG POSTGRES_VERSION=12.5 diff --git a/database/.docker/db/Dockerfile.setup b/database/.docker/db/Dockerfile.setup index 6bb7575574..40c77c4659 100644 --- a/database/.docker/db/Dockerfile.setup +++ b/database/.docker/db/Dockerfile.setup @@ -1,5 +1,5 @@ # ######################################################################################################## -# This DockerFile is used for both Openshift deployments and local development (via docker-compose). +# This DockerFile is used for both Openshift deployments and local development (via compose.yml). # ######################################################################################################## FROM node:20 diff --git a/database/.pipeline/config.js b/database/.pipeline/config.js index e126db6e77..5f53a1826b 100644 --- a/database/.pipeline/config.js +++ b/database/.pipeline/config.js @@ -97,6 +97,25 @@ const phases = { memoryLimit: '5Gi', replicas: '1' }, + 'test-spi': { + namespace: 'af2668-test', + name: `${name}-spi`, + phase: 'test-spi', + changeId: deployChangeId, + suffix: '-test-spi', + instance: `${name}-spi-test-spi`, + version: `${version}`, + tag: `test-spi-${version}`, + nodeEnv: 'production', + tz: config.timezone.db, + dbSetupDockerfilePath: dbSetupDockerfilePath, + volumeCapacity: '20Gi', + cpuRequest: '50m', + cpuLimit: '2000m', + memoryRequest: '100Mi', + memoryLimit: '5Gi', + replicas: '1' + }, prod: { namespace: 'af2668-prod', name: `${name}`, diff --git a/database/src/migrations/20240722000002_remove_duplicate_users.ts b/database/src/migrations/20240722000002_remove_duplicate_users.ts index 97b5c23c68..3b453c24e6 100644 --- a/database/src/migrations/20240722000002_remove_duplicate_users.ts +++ b/database/src/migrations/20240722000002_remove_duplicate_users.ts @@ -12,8 +12,7 @@ import { Knex } from 'knex'; * - administrative_activity: Delete duplicate administrative_activity records. * * Updates/fixes several constraints: - * - system_user_nuk1: Don't allow more than 1 active record with the same user_guid. - * - system_user_nuk2: Don't allow more than 1 active record with the same user_identifier (case-insensitive) AND user_identity_source_id. + * - system_user_uk2: Don't allow more than 1 record with the same user_identifier (case-insensitive) AND user_identity_source_id. * * Does not update the following tables: * - audit_log: This table tracks the history of all changes to the database, including changes from this migration. @@ -40,6 +39,7 @@ export async function up(knex: Knex): Promise { -- Drop constraint temporarily (added back at the end) ALTER TABLE project_participation DROP CONSTRAINT IF EXISTS project_participation_uk2; + ---------------------------------------------------------------------------------------- -- Find AND migrate duplicate system_user_ids ---------------------------------------------------------------------------------------- @@ -173,7 +173,7 @@ export async function up(knex: Knex): Promise { WHERE sp.system_user_id = ANY(w_system_user_3.duplicate_system_user_ids) ), -- Update duplicate system_user_ids in the webform_draft table to the canonical system_user_id - w_end_date_duplicate_webform_draft as ( + w_update_duplicate_webform_draft as ( UPDATE webform_draft SET system_user_id = wsu3.system_user_id @@ -181,18 +181,15 @@ export async function up(knex: Knex): Promise { WHERE webform_draft.system_user_id = ANY(wsu3.duplicate_system_user_ids) ), -- Delete duplicate system_user_role records for duplicate system_user_ids - w_end_date_duplicate_system_user_role AS ( + w_delete_duplicate_system_user_role AS ( DELETE FROM system_user_role USING w_system_user_3 wsu3 WHERE system_user_role.system_user_id = ANY(wsu3.duplicate_system_user_ids) ), - -- End date all duplicate system_user records for duplicate system_user_ids - w_end_date_duplicate_system_user AS ( - UPDATE system_user su - SET - record_end_date = NOW(), - notes = 'Duplicate user record; merged into system_user_id ' || wsu3.system_user_id || '.' - FROM w_system_user_3 wsu3 + -- Delete duplicate system_user records for duplicate system_user_ids + w_delete_duplicate_system_user AS ( + DELETE FROM system_user su + USING w_system_user_3 wsu3 WHERE su.system_user_id = ANY(wsu3.duplicate_system_user_ids) ), -- Update the user details for the canonical system user record @@ -245,17 +242,17 @@ export async function up(knex: Knex): Promise { -- Add updated constraints ---------------------------------------------------------------------------------------- - -- Don't allow more than 1 active record with the same user_guid. - CREATE UNIQUE INDEX system_user_nuk1 ON system_user (user_guid, (record_end_date is null)) WHERE record_end_date is null; - - -- Don't allow more than 1 active record with the same user_identifier (case-insensitive) AND user_identity_source_id. - CREATE UNIQUE INDEX system_user_nuk2 ON system_user(LOWER(user_identifier), user_identity_source_id, (record_end_date is null)) WHERE record_end_date is null; + -- Don't allow more than 1 record with the same user_identifier (case-insensitive) AND user_identity_source_id. + CREATE UNIQUE INDEX system_user_uk2 ON system_user(LOWER(user_identifier), user_identity_source_id); -- Don't allow the same system user to have more than one project role within a project. ALTER TABLE biohub.project_participation ADD CONSTRAINT project_participation_uk1 UNIQUE (system_user_id, project_id); -- Don't allow the same system user to have more than one survey role within a survey. ALTER TABLE biohub.survey_participation ADD CONSTRAINT survey_participation_uk1 UNIQUE (system_user_id, survey_id); + + -- Don't allow duplicate user_guid values + CREATE UNIQUE INDEX system_user_uk1 ON system_user (user_guid); `); } diff --git a/database/src/migrations/20240802000000_deployment_capture.ts b/database/src/migrations/20240802000000_deployment_capture.ts new file mode 100644 index 0000000000..455c01ca3f --- /dev/null +++ b/database/src/migrations/20240802000000_deployment_capture.ts @@ -0,0 +1,33 @@ +import { Knex } from 'knex'; + +/** + * Adds capture_id references to the deployment table to track the start and end of deployments + * + * @export + * @param {Knex} knex + * @return {*} {Promise} + */ +export async function up(knex: Knex): Promise { + await knex.raw(`--sql + + -- Set the search path + SET SEARCH_PATH = biohub, biohub_dapi_v1; + + -- Drop the view if it exists + DROP VIEW IF EXISTS biohub_dapi_v1.deployment; + + -- Add columns to the deployment table + ALTER TABLE biohub.deployment ADD COLUMN critterbase_start_capture_id UUID; + ALTER TABLE biohub.deployment ADD COLUMN critterbase_end_capture_id UUID; + ALTER TABLE biohub.deployment ADD COLUMN critterbase_end_mortality_id UUID; + + -- Recreate the view + CREATE OR REPLACE VIEW biohub_dapi_v1.deployment AS + SELECT * FROM biohub.deployment; + + `); +} + +export async function down(knex: Knex): Promise { + await knex.raw(``); +} diff --git a/database/src/migrations/20240802161900_drop_vantage_codes.ts b/database/src/migrations/20240802161900_drop_vantage_codes.ts new file mode 100644 index 0000000000..6dae62be2c --- /dev/null +++ b/database/src/migrations/20240802161900_drop_vantage_codes.ts @@ -0,0 +1,74 @@ +import { Knex } from 'knex'; + +/** + * Drop survey vantage code + * + * @export + * @param {Knex} knex + * @return {*} {Promise} + */ +export async function up(knex: Knex): Promise { + await knex.raw(`--sql + ---------------------------------------------------------------------------------------- + -- Drop survey vantage + ---------------------------------------------------------------------------------------- + SET SEARCH_PATH=biohub_dapi_v1; + + DROP VIEW IF EXISTS survey; + DROP VIEW IF EXISTS vantage; + DROP VIEW IF EXISTS survey_vantage; + + ---------------------------------------------------------------------------------------- + -- Alter tables/data + ---------------------------------------------------------------------------------------- + SET SEARCH_PATH=biohub; + + DROP TABLE survey_vantage; + DROP TABLE vantage; + + ---------------------------------------------------------------------------------------- + -- Truncate tables because no survey_type data has been meaningful as of the migration date + ---------------------------------------------------------------------------------------- + DELETE FROM survey_type; + DELETE FROM survey_intended_outcome; + DELETE FROM type; + DELETE FROM intended_outcome; + + ---------------------------------------------------------------------------------------- + -- Update survey type codes + ---------------------------------------------------------------------------------------- + INSERT INTO + type (name, record_effective_date) + VALUES + ('Telemetry', now()), + ('Species observations', now()), + ('Animal captures', now()), + ('Animal mortalities', now()), + ('Habitat features', now()); + + ---------------------------------------------------------------------------------------- + -- Update ecological variables (intended outcomes) codes + ---------------------------------------------------------------------------------------- + INSERT INTO + intended_outcome (name, description, record_effective_date) + VALUES + ('Survival or mortality', 'The survival or mortality of individuals in a population, including causes of death.', now()), + ('Birth or recruitment', 'The number of individuals born into a population.', now()), + ('Geographic distribution or dispersal', 'The geographic distribution of one or more populations, including movement and dispersals patterns.', now()), + ('Population size', 'The abundance or density of one or more populations.', now()), + ('Population structure', 'The structure or composition of a population.', now()), + ('Community structure', 'The structure or composition of a community, which includes multiple populations.', now()), + ('Species diversity', 'The number of species.', now()); + + ---------------------------------------------------------------------------------------- + -- Update views + ---------------------------------------------------------------------------------------- + SET SEARCH_PATH=biohub_dapi_v1; + + CREATE OR REPLACE VIEW survey as SELECT * FROM biohub.survey; + `); +} + +export async function down(knex: Knex): Promise { + await knex.raw(``); +} diff --git a/database/src/migrations/20240809140000_study_species_units.ts b/database/src/migrations/20240809140000_study_species_units.ts new file mode 100644 index 0000000000..5b51403485 --- /dev/null +++ b/database/src/migrations/20240809140000_study_species_units.ts @@ -0,0 +1,62 @@ +import { Knex } from 'knex'; + +/** + * Create new tables: + * - study_species_unit + * + * @export + * @param {Knex} knex + * @return {*} {Promise} + */ +export async function up(knex: Knex): Promise { + await knex.raw(`--sql + SET SEARCH_PATH=biohub; + + ----------------------------------------------------------------------------------------------------------------- + -- CREATE study_species_unit table for associating collection units / ecological units with a survey + ----------------------------------------------------------------------------------------------------------------- + CREATE TABLE study_species_unit ( + study_species_unit_id integer GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1), + study_species_id integer NOT NULL, + critterbase_collection_category_id UUID NOT NULL, + critterbase_collection_unit_id UUID NOT NULL, + create_date timestamptz(6) DEFAULT now() NOT NULL, + create_user integer NOT NULL, + update_date timestamptz(6), + update_user integer, + revision_count integer DEFAULT 0 NOT NULL, + CONSTRAINT study_species_unit_pk PRIMARY KEY (study_species_unit_id) + ); + + COMMENT ON TABLE study_species_unit IS 'This table is intended to track ecological units of interest for focal species in a survey.'; + COMMENT ON COLUMN study_species_unit.study_species_unit_id IS 'Primary key to the table.'; + COMMENT ON COLUMN study_species_unit.study_species_id IS 'Foreign key to the study_species table.'; + COMMENT ON COLUMN study_species_unit.critterbase_collection_category_id IS 'UUID of an external critterbase collection category.'; + COMMENT ON COLUMN study_species_unit.critterbase_collection_unit_id IS 'UUID of an external critterbase collection unit.'; + COMMENT ON COLUMN study_species_unit.create_date IS 'The datetime the record was created.'; + COMMENT ON COLUMN study_species_unit.create_user IS 'The id of the user who created the record as identified in the system user table.'; + COMMENT ON COLUMN study_species_unit.update_date IS 'The datetime the record was updated.'; + COMMENT ON COLUMN study_species_unit.update_user IS 'The id of the user who updated the record as identified in the system user table.'; + COMMENT ON COLUMN study_species_unit.revision_count IS 'Revision count used for concurrency control.'; + + -- add foreign key constraint + ALTER TABLE study_species_unit ADD CONSTRAINT study_species_unit_fk1 FOREIGN KEY (study_species_id) REFERENCES study_species(study_species_id); + + -- add indexes for foreign keys + CREATE INDEX study_species_unit_idx1 ON study_species_unit(study_species_id); + + -- add triggers for user data + CREATE TRIGGER audit_study_species_unit BEFORE INSERT OR UPDATE OR DELETE ON biohub.study_species_unit FOR EACH ROW EXECUTE PROCEDURE tr_audit_trigger(); + CREATE TRIGGER journal_study_species_unit AFTER INSERT OR UPDATE OR DELETE ON biohub.study_species_unit FOR EACH ROW EXECUTE PROCEDURE tr_journal_trigger(); + + ---------------------------------------------------------------------------------------- + -- Create measurement table views + ---------------------------------------------------------------------------------------- + SET SEARCH_PATH=biohub_dapi_v1; + CREATE OR REPLACE VIEW study_species_unit AS SELECT * FROM biohub.study_species_unit; + `); +} + +export async function down(knex: Knex): Promise { + await knex.raw(``); +} diff --git a/database/src/migrations/20240823000000_add_telemetry_credential_attachments_table.ts b/database/src/migrations/20240823000000_add_telemetry_credential_attachments_table.ts new file mode 100644 index 0000000000..5b7986c1d3 --- /dev/null +++ b/database/src/migrations/20240823000000_add_telemetry_credential_attachments_table.ts @@ -0,0 +1,137 @@ +import { Knex } from 'knex'; + +// Manual step 2 (see JSDoc comment below) +// UPDATE survey_telemetry_credential_attachment SET key = REGEXP_REPLACE(key, '(.*/\d+/surveys/\d+/)([^/]+\.pdf)', '\1telemetry-credentials/\2'); + +/** + * Create 1 new table for storing telemetry device credential attachments (ex: device KeyX or Cfg files). + * - survey_telemetry_credential_attachment + * + * Migrate existing survey attachments with file_type 'keyx' to the new survey_telemetry_credential_attachment table. + * + * Manual steps after running this migration: + * + * 1. Move all keyx files in S3 from '...surveys/{surveyId}/' to + * 'surveys/{surveyId}/telemetry-credentials/} + */ +export async function up(knex: Knex): Promise { + await knex.raw(`--sql + SET SEARCH_PATH=biohub; + + ---------------------------------------------------------------------------------------- + -- Create table + ---------------------------------------------------------------------------------------- + + CREATE TABLE survey_telemetry_credential_attachment ( + survey_telemetry_credential_attachment_id integer GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1), + uuid uuid DEFAULT public.gen_random_uuid(), + survey_id integer NOT NULL, + file_type varchar(300) NOT NULL, + file_name varchar(300), + title varchar(300), + description varchar(250), + key varchar(1000) NOT NULL, + file_size integer, + create_date timestamptz(6) DEFAULT now() NOT NULL, + create_user integer NOT NULL, + update_date timestamptz(6), + update_user integer, + revision_count integer DEFAULT 0 NOT NULL, + CONSTRAINT survey_telemetry_credential_attachment_pk PRIMARY KEY (survey_telemetry_credential_attachment_id) + ); + + COMMENT ON COLUMN survey_telemetry_credential_attachment.survey_telemetry_credential_attachment_id IS 'System generated surrogate primary key identifier.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.uuid IS 'The universally unique identifier for the record.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.survey_id IS 'Foreign key to the survey table.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.file_type IS 'The attachment type. Attachment type examples include keyx, cfg, etc.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.file_name IS 'The name of the file attachment.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.title IS 'The title of the file.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.description IS 'The description of the record.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.key IS 'The identifying key to the file in the storage system.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.file_size IS 'The size of the file in bytes.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.create_date IS 'The datetime the record was created.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.create_user IS 'The id of the user who created the record as identified in the system user table.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.update_date IS 'The datetime the record was updated.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.update_user IS 'The id of the user who updated the record as identified in the system user table.'; + COMMENT ON COLUMN survey_telemetry_credential_attachment.revision_count IS 'Revision count used for concurrency control.'; + COMMENT ON TABLE survey_telemetry_credential_attachment IS 'A list of telemetry device credential files (ex: device credential files like Keyx or Cfg).'; + + + -- Add foreign key constraints + ALTER TABLE survey_telemetry_credential_attachment + ADD CONSTRAINT survey_telemetry_credential_attachment_fk1 + FOREIGN KEY (survey_id) + REFERENCES survey(survey_id); + + -- Add indexes for foreign keys + CREATE INDEX survey_telemetry_credential_attachment_idx1 ON survey_telemetry_credential_attachment(survey_id); + + ---------------------------------------------------------------------------------------- + -- Create audit and journal triggers + ---------------------------------------------------------------------------------------- + + CREATE TRIGGER audit_survey_telemetry_credential_attachment BEFORE INSERT OR UPDATE OR DELETE ON survey_telemetry_credential_attachment FOR EACH ROW EXECUTE PROCEDURE tr_audit_trigger(); + CREATE TRIGGER journal_survey_telemetry_credential_attachment AFTER INSERT OR UPDATE OR DELETE ON survey_telemetry_credential_attachment FOR EACH ROW EXECUTE PROCEDURE tr_journal_trigger(); + + ---------------------------------------------------------------------------------------- + -- Migrate existing survey attachments with file_type 'keyx' to the new + -- survey_telemetry_credential_attachment table. + ---------------------------------------------------------------------------------------- + + INSERT INTO survey_telemetry_credential_attachment + ( + survey_id, + file_type, + file_name, + title, + description, + key, + file_size, + create_user, + create_date, + update_user, + update_date, + revision_count + ) + SELECT + survey_id, + 'KeyX', + file_name, + title, + description, + key, + file_size, + create_user, + create_date, + update_user, + update_date, + revision_count + FROM + survey_attachment + WHERE + file_type = 'keyx'; + + -- Remove the migrated records from the survey_attachment table + DELETE FROM survey_attachment + WHERE file_type = 'keyx'; + + ---------------------------------------------------------------------------------------- + -- Create view + ---------------------------------------------------------------------------------------- + + SET SEARCH_PATH=biohub_dapi_v1; + + CREATE OR REPLACE VIEW survey_telemetry_credential_attachment as SELECT * FROM biohub.survey_telemetry_credential_attachment; + `); +} + +export async function down(knex: Knex): Promise { + await knex.raw(``); +} diff --git a/database/src/procedures/api_patch_system_user.ts b/database/src/procedures/api_patch_system_user.ts index d8c126529c..8803be960e 100644 --- a/database/src/procedures/api_patch_system_user.ts +++ b/database/src/procedures/api_patch_system_user.ts @@ -9,7 +9,8 @@ import { Knex } from 'knex'; * - Second using `p_user_identifier` and `p_user_identity_source_name` * 2. If no user is found, return null * 3. If a user is found, update the system user record with the latest information passed to this function if any of - * the incoming values are not the same as the existing values + * the incoming values are not the same as the existing values (if all incoming values are the same as the existing then + * no update is performed). * * @export * @param {Knex} knex @@ -36,7 +37,6 @@ export async function seed(knex: Knex): Promise { AS $$ DECLARE _system_user system_user%rowtype; - _user_identity_source_id user_identity_source.user_identity_source_id%type; BEGIN -- Attempt to find user based on guid SELECT * INTO _system_user FROM system_user @@ -46,14 +46,15 @@ export async function seed(knex: Knex): Promise { -- Otherwise, attempt to find user based on identifier and identity source IF NOT found THEN - SELECT user_identity_source_id INTO strict _user_identity_source_id FROM user_identity_source - WHERE LOWER(name) = LOWER(p_user_identity_source_name) - AND record_end_date IS NULL; - SELECT * INTO _system_user FROM system_user - WHERE user_identity_source_id = _user_identity_source_id - AND LOWER(user_identifier) = LOWER(p_user_identifier) - LIMIT 1; + WHERE user_identity_source_id = ( + SELECT user_identity_source_id FROM user_identity_source + WHERE LOWER(name) = LOWER(p_user_identity_source_name) + AND record_end_date IS NULL + ) + AND LOWER(user_identifier) = LOWER(p_user_identifier) + AND record_end_date IS NULL + LIMIT 1; END IF; -- If no user found, return and do nothing @@ -73,13 +74,13 @@ export async function seed(knex: Knex): Promise { WHERE system_user_id = _system_user.system_user_id AND ( - user_guid != p_system_user_guid OR - user_identifier != p_user_identifier OR - email != p_email OR - display_name != p_display_name OR - given_name != p_given_name OR - family_name != p_family_name OR - agency != p_agency + user_guid IS DISTINCT FROM p_system_user_guid OR + user_identifier IS DISTINCT FROM p_user_identifier OR + email IS DISTINCT FROM p_email OR + display_name IS DISTINCT FROM p_display_name OR + given_name IS DISTINCT FROM p_given_name OR + family_name IS DISTINCT FROM p_family_name OR + agency IS DISTINCT FROM p_agency ); -- Return system user id of patched record diff --git a/database/src/procedures/delete_survey_procedure.ts b/database/src/procedures/delete_survey_procedure.ts index 16d446fd39..460257526a 100644 --- a/database/src/procedures/delete_survey_procedure.ts +++ b/database/src/procedures/delete_survey_procedure.ts @@ -119,9 +119,6 @@ export async function seed(knex: Knex): Promise { DELETE FROM survey_funding_source WHERE survey_id = p_survey_id; - DELETE FROM survey_vantage - WHERE survey_id = p_survey_id; - DELETE FROM survey_spatial_component WHERE survey_id = p_survey_id; diff --git a/database/src/seeds/03_basic_project_survey_setup.ts b/database/src/seeds/03_basic_project_survey_setup.ts index b98018b086..1ec5a7b19a 100644 --- a/database/src/seeds/03_basic_project_survey_setup.ts +++ b/database/src/seeds/03_basic_project_survey_setup.ts @@ -18,16 +18,11 @@ const focalTaxonIdOptions = [ { itis_tsn: 180543, itis_scientific_name: 'Ursus arctos' } // Grizzly bear ]; -const ancillaryTaxonIdOptions = [ - { itis_tsn: 180703, itis_scientific_name: 'Alces alces' }, // Moose - { itis_tsn: 180596, itis_scientific_name: 'Canis lupus' }, // Wolf - { itis_tsn: 180713, itis_scientific_name: 'Oreamnos americanus' }, // Rocky Mountain goat - { itis_tsn: 180543, itis_scientific_name: 'Ursus arctos' } // Grizzly bear -]; - const surveyRegionsA = ['Kootenay-Boundary Natural Resource Region', 'West Coast Natural Resource Region']; const surveyRegionsB = ['Cariboo Natural Resource Region', 'South Coast Natural Resource Region']; +const identitySources = ['IDIR', 'BCEIDBUSINESS', 'BCEIDBASIC']; + /** * Add spatial transform * @@ -51,6 +46,11 @@ export async function seed(knex: Knex): Promise { `); } + // Insert access requests + for (let i = 0; i < 8; i++) { + await knex.raw(`${insertAccessRequest()}`); + } + // Check if at least 1 project already exists const checkProjectsResponse = await knex.raw(checkAnyProjectExists()); @@ -75,12 +75,10 @@ export async function seed(knex: Knex): Promise { ${insertSurveyTypeData(surveyId)} ${insertSurveyPermitData(surveyId)} ${insertSurveyFocalSpeciesData(surveyId)} - ${insertSurveyAncillarySpeciesData(surveyId)} ${insertSurveyFundingData(surveyId)} ${insertSurveyProprietorData(surveyId)} ${insertSurveyFirstNationData(surveyId)} ${insertSurveyStakeholderData(surveyId)} - ${insertSurveyVantageData(surveyId)} ${insertSurveyParticipationData(surveyId)} ${insertSurveyLocationData(surveyId)} ${insertSurveySiteStrategy(surveyId)} @@ -179,22 +177,6 @@ const insertSurveyParticipationData = (surveyId: number) => ` ; `; -/** - * SQL to insert Survey Vantage data - * - */ -const insertSurveyVantageData = (surveyId: number) => ` - INSERT into survey_vantage - ( - survey_id, - vantage_id - ) - VALUES ( - ${surveyId}, - (select vantage_id from vantage order by random() limit 1) - ); -`; - /** * SQL to insert Survey Proprietor data * @@ -271,23 +253,6 @@ const insertSurveyFocalSpeciesData = (surveyId: number) => { `; }; -const insertSurveyAncillarySpeciesData = (surveyId: number) => { - const ancillarySpecies = ancillaryTaxonIdOptions[Math.floor(Math.random() * ancillaryTaxonIdOptions.length)]; - return ` - INSERT into study_species - ( - survey_id, - itis_tsn, - is_focal - ) - VALUES ( - ${surveyId}, - ${ancillarySpecies.itis_tsn}, - 'N' - ); - `; -}; - /** * SQL to insert Survey permit data * @@ -771,3 +736,37 @@ const insertSurveyRegionData = (surveyId: string, region: string) => ` WHERE region_name = $$${region}$$; `; + +/** + * SQL to insert system access requests + * + */ +const insertAccessRequest = () => ` + INSERT INTO administrative_activity + ( + administrative_activity_status_type_id, + administrative_activity_type_id, + reported_system_user_id, + assigned_system_user_id, + description, + data, + notes + ) + VALUES ( + (SELECT administrative_activity_status_type_id FROM administrative_activity_status_type ORDER BY random() LIMIT 1), + (SELECT administrative_activity_type_id FROM administrative_activity_type WHERE name = 'System Access'), + (SELECT system_user_id FROM system_user ORDER BY random() LIMIT 1), + (SELECT system_user_id FROM system_user ORDER BY random() LIMIT 1), + $$${faker.lorem.sentences(2)}$$, + jsonb_build_object( + 'reason', '${faker.lorem.sentences(1)}', + 'userGuid', '${faker.string.uuid()}', + 'name', '${faker.lorem.words(2)}', + 'username', '${faker.lorem.words(1)}', + 'email', 'default', + 'identitySource', '${identitySources[faker.number.int({ min: 0, max: identitySources.length - 1 })]}', + 'displayName', '${faker.lorem.words(1)}' + ), + $$${faker.lorem.sentences(2)}$$ + ); + `; diff --git a/env_config/env.docker b/env_config/env.docker index face12d12c..b78a07268b 100644 --- a/env_config/env.docker +++ b/env_config/env.docker @@ -5,11 +5,11 @@ # # These env vars are automatically read by the makefile (when running make commands). # -# Newly added environment variables need to be added to the docker-compose file, +# Newly added environment variables need to be added to the compose.yml file, # under whichever service needs them (api, app, etc) # # Exposed Ports/URLs -# - Certain ports/urls are exposed in docker-compose and may conflict with other +# - Certain ports/urls are exposed in compose.yml and may conflict with other # docker-containers if they are exposing the same ports/urls. # # - If conflicts arise, modify the conflicting values in your `.env` and re-build. @@ -46,9 +46,27 @@ API_HOST=localhost API_PORT=6100 API_TZ=America/Vancouver -# See `api/utils/logger.ts` for details on LOG_LEVEL +# ------------------------------------------------------------------------------ +# API - Logging +# ------------------------------------------------------------------------------ +# See `api/utils/logger.ts` for details on LOG_LEVEL and LOG_LEVEL_FILE + +# Log level when logging to the console LOG_LEVEL=debug +# Log level when logging to a persistent file (See `api/data`) +LOG_LEVEL_FILE=debug +# See https://github.com/winstonjs/winston-daily-rotate-file for param details +LOG_FILE_DIR=data/logs +LOG_FILE_NAME=sims-api-%DATE%.log +LOG_FILE_DATE_PATTERN=YYYY-MM-DD-HH +LOG_FILE_MAX_SIZE=50m +LOG_FILE_MAX_FILES=14d + +# ------------------------------------------------------------------------------ +# API - Validation +# ------------------------------------------------------------------------------ + # Control whether or not api response validation is enabled API_RESPONSE_VALIDATION_ENABLED=true