From 637ae9c01beecbc7d5c5f1cc99dc918584caa451 Mon Sep 17 00:00:00 2001 From: Kjartan Einarsson Date: Mon, 25 Mar 2024 14:06:50 -0700 Subject: [PATCH 1/7] initial clean --- api/src/constants/artifacts.ts | 11 - api/src/constants/attachments.ts | 4 - api/src/constants/roles.ts | 12 - .../json-schema/transformation-schema.test.ts | 287 ----------- api/src/json-schema/transformation-schema.ts | 221 --------- api/src/json-schema/validation-schema.test.ts | 241 --------- api/src/json-schema/validation-schema.ts | 457 ------------------ 7 files changed, 1233 deletions(-) delete mode 100644 api/src/constants/artifacts.ts delete mode 100644 api/src/constants/attachments.ts delete mode 100644 api/src/json-schema/transformation-schema.test.ts delete mode 100644 api/src/json-schema/transformation-schema.ts delete mode 100644 api/src/json-schema/validation-schema.test.ts delete mode 100644 api/src/json-schema/validation-schema.ts diff --git a/api/src/constants/artifacts.ts b/api/src/constants/artifacts.ts deleted file mode 100644 index 0f34ce86f..000000000 --- a/api/src/constants/artifacts.ts +++ /dev/null @@ -1,11 +0,0 @@ -export enum ARTIFACT_TYPE { - ARCHIVE = 'Archive', - AUDIO = 'Audio', - DATA = 'Data', - IMAGE = 'Image', - OTHER = 'Other', - REPORT = 'Report', - SPATIAL = 'Spatial', - SPREADSHEET = 'Spreadsheet', - VIDEO = 'Video' -} diff --git a/api/src/constants/attachments.ts b/api/src/constants/attachments.ts deleted file mode 100644 index 7c47db481..000000000 --- a/api/src/constants/attachments.ts +++ /dev/null @@ -1,4 +0,0 @@ -export enum ATTACHMENT_TYPE { - REPORT = 'Report', - OTHER = 'Other' -} diff --git a/api/src/constants/roles.ts b/api/src/constants/roles.ts index 2e3455c4e..dd4f0dec7 100644 --- a/api/src/constants/roles.ts +++ b/api/src/constants/roles.ts @@ -8,15 +8,3 @@ export enum SYSTEM_ROLE { SYSTEM_ADMIN = 'System Administrator', DATA_ADMINISTRATOR = 'Data Administrator' } - -/** - * Project level roles. - * - * @export - * @enum {number} - */ -export enum PROJECT_ROLE { - PROJECT_LEAD = 'Project Lead', - PROJECT_EDITOR = 'Editor', - PROJECT_VIEWER = 'Viewer' -} diff --git a/api/src/json-schema/transformation-schema.test.ts b/api/src/json-schema/transformation-schema.test.ts deleted file mode 100644 index ca4b2322c..000000000 --- a/api/src/json-schema/transformation-schema.test.ts +++ /dev/null @@ -1,287 +0,0 @@ -import Ajv from 'ajv'; -import { expect } from 'chai'; -import { describe } from 'mocha'; -import { submissionTransformationSchema } from './transformation-schema'; - -// Useful online json-schema validator: https://www.jsonschemavalidator.net/ - -describe('submissionTransformationSchema', () => { - const ajv = new Ajv(); - - it('is valid schema', () => { - expect(ajv.validateSchema(submissionTransformationSchema)).to.be.true; - }); -}); - -describe('example submission transformation schema', () => { - const exampleSchema = { - flatten: [ - { - fileName: 'Effort & Site Conditions', - uniqueId: ['Survey Area', 'Block ID/SU ID', 'Stratum'] - }, - { - fileName: 'Observations', - uniqueId: ['Waypoint'], - parent: { - fileName: 'Effort & Site Conditions', - uniqueId: ['Survey Area', 'Block ID/SU ID', 'Stratum'] - } - }, - { - fileName: 'UTM_LatLong', - uniqueId: ['Waypoint'], - parent: { - fileName: 'Observations', - uniqueId: ['Waypoint'] - } - }, - { - fileName: 'Strata Metadata', - uniqueId: ['Stratum'], - parent: { - fileName: 'Observations', - uniqueId: ['Stratum'] - } - } - ], - transform: [ - { - condition: { - if: { - columns: ['Lone Cows'], - not: true - } - }, - transformations: [ - { - fields: { - id: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum', 'Waypoint'], - separator: ':' - }, - eventID: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum'], - separator: ':' - }, - eventDate: { - columns: ['Date'] - }, - verbatimCoordinatesUTM: { - columns: ['UTM Zone', 'Easting', 'Northing'] - }, - verbatimCoordinatesLatLong: { - columns: ['lat', 'long'] - }, - occurrenceID: { - columns: ['Waypoint'], - unique: 'occ' - }, - individualCount: { - columns: ['Lone Cows'] - }, - vernacularName: { - columns: ['Species'] - }, - lifestage: { - value: 'Adult' - }, - sex: { - value: 'Female' - } - } - } - ] - }, - { - condition: { - if: { - columns: ['Cow W/1 calf'] - } - }, - transformations: [ - { - fields: { - id: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum', 'Waypoint'], - separator: ':' - }, - eventID: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum'], - separator: ':' - }, - eventDate: { - columns: ['Date'] - }, - verbatimCoordinatesUTM: { - columns: ['UTM Zone', 'Easting', 'Northing'] - }, - verbatimCoordinatesLatLong: { - columns: ['lat', 'long'] - }, - occurrenceID: { - columns: ['Waypoint'], - unique: 'occ' - }, - individualCount: { - columns: ['Cow W/1 calf'] - }, - vernacularName: { - columns: ['Species'] - }, - lifestage: { - value: 'Adult' - }, - sex: { - value: 'Female' - }, - resourceID: { - columns: ['Waypoint'], - unique: 'occ' - }, - relatedResourceID: { - value: '' - }, - relationshipOfResource: { - value: 'mother of' - } - } - }, - { - fields: { - id: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum', 'Waypoint'], - separator: ':' - }, - eventID: { - columns: ['Survey Area', 'Block ID/SU ID', 'Stratum'], - separator: ':' - }, - eventDate: { - columns: ['Date'] - }, - verbatimCoordinatesUTM: { - columns: ['UTM Zone', 'Easting', 'Northing'] - }, - verbatimCoordinatesLatLong: { - columns: ['lat', 'long'] - }, - occurrenceID: { - columns: ['Waypoint'], - unique: 'occ' - }, - individualCount: { - value: 1 - }, - vernacularName: { - columns: ['Species'] - }, - lifestage: { - value: 'Yearling' - }, - sex: { - value: 'Unknown' - }, - resourceID: { - columns: ['Waypoint'], - unique: 'occ' - }, - relatedResourceID: { - value: '' - }, - relationshipOfResource: { - value: 'offspring of' - } - } - } - ], - postTransformations: [ - { - relationship: { - spreadColumn: 'individualCount', - uniqueIdColumn: 'occurrenceID' - } - } - ] - } - ], - parse: [ - { - fileName: 'event', - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['eventID'] }, target: 'eventID' }, - { source: { columns: ['eventDate'] }, target: 'eventDate' }, - { - source: { columns: ['verbatimCoordinatesUTM', 'verbatimCoordinatesLatLong'] }, - target: 'verbatimCoordinates' - } - ] - }, - { - fileName: 'occurrence', - conditionalFields: ['individualCount'], - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['occurrenceID'] }, target: 'occurrenceID' }, - { source: { columns: ['individualCount'] }, target: 'individualCount' }, - { source: { columns: ['vernacularName'] }, target: 'taxonID' }, - { source: { columns: ['lifeStage'] }, target: 'lifeStage' }, - { source: { columns: ['sex'] }, target: 'sex' }, - { source: { value: 'Approved' }, target: 'Status' } - ] - }, - { - fileName: 'taxon', - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['occurrenceID'] }, target: 'occurrenceID' }, - { source: { columns: ['vernacularName'] }, target: 'vernacularName' } - ] - }, - { - fileName: 'resourcerelationship', - conditionalFields: ['resourceID'], - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['resourceID'] }, target: 'resourceID' }, - { source: { columns: ['relatedResourceID'] }, target: 'relatedResourceID' }, - { source: { columns: ['relationshipOfResource'] }, target: 'relationshipOfResource' } - ] - }, - { - fileName: 'measurementorfact', - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['eventID'] }, target: 'measurementID' }, - { source: { value: 'Habitat Description' }, target: 'measurementType' }, - { source: { columns: ['effort_habitat_description'] }, target: 'measurementValue' } - ] - }, - { - fileName: 'measurementorfact', - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['occurrenceID'] }, target: 'measurementID' }, - { source: { value: 'Stratum' }, target: 'measurementType' }, - { source: { columns: ['summary_stratum'] }, target: 'measurementValue' } - ] - }, - { - fileName: 'measurementorfact', - columns: [ - { source: { columns: ['id'] }, target: 'id' }, - { source: { columns: ['occurrenceID'] }, target: 'measurementID' }, - { source: { value: 'Activity' }, target: 'measurementType' }, - { source: { columns: ['observation_activity'] }, target: 'measurementValue' } - ] - } - ] - }; - - const ajv = new Ajv(); - - it('validates against submissionTransformationSchema', () => { - expect(ajv.validate(submissionTransformationSchema, exampleSchema), JSON.stringify(ajv.errors)).to.be.true; - }); -}); diff --git a/api/src/json-schema/transformation-schema.ts b/api/src/json-schema/transformation-schema.ts deleted file mode 100644 index ec8ab8d67..000000000 --- a/api/src/json-schema/transformation-schema.ts +++ /dev/null @@ -1,221 +0,0 @@ -export const submissionTransformationSchema = { - description: 'Occurrence Submission Transformation Schema', - type: 'object', - required: ['flatten', 'transform', 'parse'], - properties: { - name: { - description: 'The name of the submission file', - type: 'string' - }, - description: { - description: 'The description of the submission file', - type: 'string' - }, - flatten: { - type: 'array', - items: { - type: 'object', - required: ['fileName', 'uniqueId'], - properties: { - fileName: { - type: 'string' - }, - uniqueId: { - type: 'array', - items: { - type: 'string' - } - }, - parent: { - type: 'object', - properties: { - fileName: { - type: 'string' - }, - uniqueId: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - } - }, - transform: { - type: 'array', - items: { - type: 'object', - required: ['transformations'], - properties: { - condition: { - type: 'object', - properties: { - if: { - type: 'object', - required: ['columns'], - properties: { - columns: { - type: 'array', - items: { - type: 'string' - } - }, - not: { - type: 'boolean' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - transformations: { - type: 'array', - items: { - type: 'object', - required: ['fields'], - properties: { - fields: { - type: 'object', - patternProperties: { - '^.*$': { - type: 'object', - oneOf: [ - { - type: 'object', - required: ['columns'], - properties: { - columns: { - type: 'array', - items: { - type: 'string' - } - }, - separator: { - type: 'string' - }, - unique: { - type: 'string' - } - }, - additionalProperties: false - }, - { - type: 'object', - required: ['value'], - properties: { - value: { - type: ['string', 'number'] - } - }, - additionalProperties: false - } - ] - } - }, - additionalProperties: false - } - }, - additionalProperties: false - } - }, - postTransformations: { - type: 'array', - items: { - anyOf: [ - { - type: 'object', - properties: { - relationship: { - type: 'object', - properties: { - spreadColumn: { - type: 'string' - }, - uniqueIdColumn: { - type: 'string' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - } - ] - } - } - }, - additionalProperties: false - } - }, - parse: { - type: 'array', - items: { - type: 'object', - required: ['fileName', 'columns'], - properties: { - fileName: { - type: 'string' - }, - columns: { - type: 'array', - items: { - type: 'object', - properties: { - source: { - oneOf: [ - { - type: 'object', - required: ['columns'], - properties: { - columns: { - type: 'array', - items: { - type: 'string' - } - }, - separator: { - type: 'string' - }, - unique: { - type: 'string' - } - }, - additionalProperties: false - }, - { - type: 'object', - required: ['value'], - properties: { - value: { - type: ['string', 'number'] - } - }, - additionalProperties: false - } - ] - }, - target: { - type: 'string' - } - }, - additionalProperties: false - } - }, - conditionalFields: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - } - }, - additionalProperties: false -}; diff --git a/api/src/json-schema/validation-schema.test.ts b/api/src/json-schema/validation-schema.test.ts deleted file mode 100644 index 907335ac7..000000000 --- a/api/src/json-schema/validation-schema.test.ts +++ /dev/null @@ -1,241 +0,0 @@ -import Ajv from 'ajv'; -import { expect } from 'chai'; -import { describe } from 'mocha'; -import { submissionValidationSchema } from './validation-schema'; - -// Useful online json-schema validator: https://www.jsonschemavalidator.net/ - -describe('submissionValidationSchema', () => { - const ajv = new Ajv(); - - it('is valid schema', () => { - expect(ajv.validateSchema(submissionValidationSchema)).to.be.true; - }); -}); - -describe('example submission validation schema', () => { - const exampleSchema2 = { - name: 'Example Submission Validation Schema', - description: 'An example submission validation schema.', - files: [ - { - name: 'event', - description: 'The Event file for this submission. Should contain information about events.', - columns: [ - { - name: 'eventID', - validations: [] - }, - { - name: 'parentEventID', - validations: [] - }, - { - name: 'samplingProtocol', - validations: [] - }, - { - name: 'geodeticDatum', - validations: [] - }, - { - name: 'verbatimCoordinates', - validations: [ - { - column_format_validator: { - reg_exp: '^9N \\d{6} \\d{7}$', - expected_format: '9N 12345 123456' - } - } - ] - }, - { - name: 'verbatimElevation', - validations: [] - }, - { - name: 'coordinateUncertaintyInMeters', - validations: [] - }, - { - name: 'coordinatePrecision', - validations: [] - }, - { - name: 'verbatimLocality', - validations: [] - }, - { - name: 'locationRemarks', - validations: [] - } - ], - validations: [ - { - file_required_columns_validator: { - required_columns: [ - 'eventID', - 'parentEventID', - 'eventDate', - 'samplingProtocol', - 'geodeticDatum', - 'verbatimCoordinates', - 'verbatimElevation', - 'coordinateUncertaintyInMeters', - 'coordinatePrecision', - 'verbatimLocality', - 'locationRemarks' - ] - } - } - ] - }, - { - name: 'occurrence', - description: 'The Occurrence file for this submission. Should contain information about occurrences.', - columns: [ - { - name: 'sex', - desciption: 'The sex of the observed taxon.', - validations: [ - { - column_code_validator: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - allowed_code_values: [ - { - name: 'male', - description: 'A male' - }, - { - name: 'female', - description: 'A female' - }, - { - name: 'unclassified', - description: 'An unclassified sex' - } - ] - } - } - ] - }, - { - name: 'lifeStage', - desciption: 'The life stage of the observed taxon.', - validations: [ - { - column_code_validator: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - allowed_code_values: [ - { - name: 'adult', - description: 'An adult' - }, - { - name: 'juvenile', - description: 'A child' - } - ] - } - } - ] - }, - { - name: 'individualCount', - desciption: 'The occurrence count.', - validations: [ - { - column_format_validator: { - name: '', - description: '', - reg_exp: '^\\d.*$', - expected_format: 'A positive integer' - } - } - ] - } - ], - validations: [ - { - file_required_columns_validator: { - name: '', - description: '', - required_columns: [ - 'eventID', - 'occurrenceID', - 'basisOfRecord', - 'type', - 'taxonID', - 'sex', - 'lifeStage', - 'individualCount', - 'identifiedBy', - 'organismQuantity', - 'organismQuantityType' - ] - } - }, - { - file_recommended_columns_validator: { - name: '', - description: '', - recommended_columns: ['occurrenceRemarks'] - } - } - ] - }, - { - name: 'measurementorfact', - description: - 'The Measurement Or Fact file for this submission. Should contain information about measurements and facts.', - columns: [], - validations: [] - }, - { - name: 'resourcerelationship', - description: - 'The Resource Relationship file for this submission. Should contain information about resource relationships.', - columns: [], - validations: [] - }, - { - name: 'taxon', - description: 'The Taxon file for this submission. Should contain information about taxonomy.', - columns: [], - validations: [] - } - ], - validations: [ - { - submission_required_files_validator: { - name: '', - description: '', - required_files: ['event', 'occurrence', 'taxon'] - } - }, - { - mimetype_validator: { - name: '', - description: '', - reg_exps: ['application/zip', 'application/x-zip-compressed', 'application/x-rar-compressed'] - } - } - ] - }; - - const ajv = new Ajv(); - - it('validates against submissionValidationSchema', () => { - expect(ajv.validate(submissionValidationSchema, exampleSchema2), JSON.stringify(ajv.errors)).to.be.true; - }); -}); diff --git a/api/src/json-schema/validation-schema.ts b/api/src/json-schema/validation-schema.ts deleted file mode 100644 index 895621467..000000000 --- a/api/src/json-schema/validation-schema.ts +++ /dev/null @@ -1,457 +0,0 @@ -export const submissionValidationSchema = { - description: 'Occurrence Submission Validation Schema', - type: 'object', - properties: { - name: { - description: 'The name of the submission file', - type: 'string' - }, - description: { - description: 'The description of the submission file', - type: 'string' - }, - files: { - description: 'An array of files/sheets within the submission file', - type: 'array', - items: [ - { - $ref: '#/$defs/file' - } - ] - }, - defaultFile: { - description: 'A fall-back file definition to use when no files/sheets match items in the files array', - $ref: '#/$defs/file' - }, - validations: { - description: 'An array of validations to apply against the submission file', - type: 'array', - items: { - $ref: '#/$defs/submission_validation' - } - } - }, - $defs: { - file: { - description: 'A single file/sheet within a submission file', - type: 'object', - required: ['name', 'columns'], - properties: { - name: { - description: 'The name of the file/sheet', - type: 'string' - }, - description: { - description: 'The description of the file/sheet', - type: 'string' - }, - columns: { - description: 'An array of columns within the file', - type: 'array', - items: { - $ref: '#/$defs/column' - } - }, - validations: { - description: 'An array of validations to apply against the file/sheet', - type: 'array', - items: { - $ref: '#/$defs/file_validation' - } - } - }, - additionalProperties: false - }, - column: { - description: 'An single column within a file/sheet', - type: 'object', - required: ['name'], - properties: { - name: { - description: 'The name of the column', - type: 'string' - }, - description: { - description: 'The description of the column', - type: 'string' - }, - validations: { - description: 'An array of validations to apply against the column', - type: 'array', - items: { - $ref: '#/$defs/column_validation' - } - } - }, - additionalProperties: false - }, - submission_validation: { - title: 'Submission File Validation', - description: 'The validators that can be applied against a submission file.', - anyOf: [ - { - $ref: '#/$defs/submission_required_files_validator' - }, - { - $ref: '#/$defs/mimetype_validator' - } - ] - }, - file_validation: { - title: 'File/Sheet Validation', - description: 'The validators that can be applied against a file/sheet within a submission file.', - anyOf: [ - { - $ref: '#/$defs/file_required_columns_validator' - }, - { - $ref: '#/$defs/file_recommended_columns_validator' - }, - { - $ref: '#/$defs/file_duplicate_columns_validator' - }, - { - $ref: '#/$defs/file_valid_columns_validator' - } - ] - }, - column_validation: { - title: 'Column Validation', - description: 'The validators that can be applied against a column within a file/sheet.', - anyOf: [ - { - $ref: '#/$defs/column_format_validator' - }, - { - $ref: '#/$defs/column_code_validator' - }, - { - $ref: '#/$defs/column_range_validator' - }, - { - $ref: '#/$defs/column_unique_validator' - }, - { - $ref: '#/$defs/column_key_validator' - }, - { - $ref: '#/$defs/column_numeric_validator' - } - ] - }, - submission_required_files_validator: { - description: 'Validates that this submission file contains required files/sheets', - type: 'object', - properties: { - submission_required_files_validator: { - type: 'object', - required: ['required_files'], - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - required_files: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - mimetype_validator: { - description: 'Validates that the mimetype of this submission/file is in an allowed set of values', - type: 'object', - properties: { - mimetype_validator: { - type: 'object', - required: ['reg_exps'], - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - reg_exps: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - file_required_columns_validator: { - description: 'Validates that this file/sheet contains required columns', - type: 'object', - properties: { - file_required_columns_validator: { - type: 'object', - required: ['required_columns'], - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - required_columns: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - file_recommended_columns_validator: { - description: 'Validates that this file/sheet contains recommended columns', - type: 'object', - properties: { - file_recommended_columns_validator: { - type: 'object', - required: ['recommended_columns'], - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - recommended_columns: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - file_duplicate_columns_validator: { - description: 'Validates that this file/sheet contains recommended columns', - type: 'object', - properties: { - file_duplicate_columns_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - file_valid_columns_validator: { - description: 'Validates that this file/sheet contains only valid (known) columns', - type: 'object', - properties: { - file_valid_columns_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - valid_columns: { - type: 'array', - items: { - type: 'string' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - column_format_validator: { - description: 'Validates that this column value matches a regex', - type: 'object', - properties: { - column_format_validator: { - type: 'object', - required: ['reg_exp', 'expected_format'], - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - reg_exp: { - type: 'string' - }, - reg_exp_flags: { - type: 'string' - }, - expected_format: { - type: 'string' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - - column_numeric_validator: { - description: 'Validates that this column is a number', - type: 'object', - properties: { - column_numeric_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - column_range_validator: { - description: 'Validates that this column value matches a number range', - type: 'object', - properties: { - column_range_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - min_value: { - type: 'number' - }, - max_value: { - type: 'number' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - column_code_validator: { - description: 'Validates that this column value is in an allowed set of values', - type: 'object', - properties: { - column_code_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - allowed_code_values: { - type: 'array', - items: { - $ref: '#/$defs/code_value' - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - column_unique_validator: { - description: 'Validates that this column value is unique within this column', - type: 'object', - properties: { - column_unique_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - is_unique: { - type: 'boolean' - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - column_key_validator: { - description: 'Validates that this column value has a matching counterpart in the target `file` and `column`', - type: 'object', - properties: { - column_key_validator: { - type: 'object', - properties: { - name: { - type: 'string' - }, - description: { - type: 'string' - }, - parent_key: { - type: 'object', - properties: { - file: { - type: 'string' - }, - column: { - type: 'string' - } - } - } - }, - additionalProperties: false - } - }, - additionalProperties: false - }, - code_value: { - description: 'Validates that this column value has a matching counterpart in the target `file` and `column`', - type: 'object', - required: ['name'], - properties: { - name: { - type: ['string', 'number'] - }, - description: { - type: 'string' - } - }, - additionalProperties: false - } - }, - additionalProperties: false -}; From 7593715827a4f7d14d0110c4142c87d68e54773f Mon Sep 17 00:00:00 2001 From: Kjartan Einarsson Date: Mon, 25 Mar 2024 16:41:50 -0700 Subject: [PATCH 2/7] remove unused endpoints --- .../access-request/count.test.ts | 82 ------ .../administrative/access-request/count.ts | 81 ------ .../access-request/update.test.ts | 109 -------- .../administrative/access-request/update.ts | 150 ----------- .../administrative/activity/create.test.ts | 62 ----- .../paths/administrative/activity/create.ts | 84 ------ .../administrative/activity/list.test.ts | 102 ------- api/src/paths/administrative/activity/list.ts | 153 ----------- .../administrative/activity/update.test.ts | 79 ------ .../paths/administrative/activity/update.ts | 98 ------- .../administrative/security/categories.ts | 136 ---------- .../{submissionId}/messages.test.ts | 79 ------ .../submission/{submissionId}/messages.ts | 252 ------------------ 13 files changed, 1467 deletions(-) delete mode 100644 api/src/paths/administrative/access-request/count.test.ts delete mode 100644 api/src/paths/administrative/access-request/count.ts delete mode 100644 api/src/paths/administrative/access-request/update.test.ts delete mode 100644 api/src/paths/administrative/access-request/update.ts delete mode 100644 api/src/paths/administrative/activity/create.test.ts delete mode 100644 api/src/paths/administrative/activity/create.ts delete mode 100644 api/src/paths/administrative/activity/list.test.ts delete mode 100644 api/src/paths/administrative/activity/list.ts delete mode 100644 api/src/paths/administrative/activity/update.test.ts delete mode 100644 api/src/paths/administrative/activity/update.ts delete mode 100644 api/src/paths/administrative/security/categories.ts delete mode 100644 api/src/paths/administrative/submission/{submissionId}/messages.test.ts delete mode 100644 api/src/paths/administrative/submission/{submissionId}/messages.ts diff --git a/api/src/paths/administrative/access-request/count.test.ts b/api/src/paths/administrative/access-request/count.test.ts deleted file mode 100644 index 68ba76731..000000000 --- a/api/src/paths/administrative/access-request/count.test.ts +++ /dev/null @@ -1,82 +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 { HTTP400 } from '../../../errors/http-error'; -import { AdministrativeService } from '../../../services/administrative-service'; -import * as userIdentifier from '../../../utils/keycloak-utils'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as count from './count'; - -chai.use(sinonChai); - -describe('count', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw a 400 error when no user identifier', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - sinon.stub(userIdentifier, 'getUserIdentifier').returns(null); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = count.getPendingAccessRequestsCount(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTP400).message).to.equal('Missing required userIdentifier'); - } - }); - - it('should return 0 on success (no rowCount)', async () => { - const dbConnectionObj = getMockDBConnection({ systemUserId: () => 1 }); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - sinon.stub(userIdentifier, 'getUserIdentifier').returns('string'); - - const getPendingAccessRequestCountStub = sinon - .stub(AdministrativeService.prototype, 'getPendingAccessRequestCount') - .resolves(0); - - const requestHandler = count.getPendingAccessRequestsCount(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(getPendingAccessRequestCountStub).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql(0); - }); - - it('should return rowCount on success', async () => { - const dbConnectionObj = getMockDBConnection({ systemUserId: () => 1 }); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - sinon.stub(userIdentifier, 'getUserIdentifier').returns('string'); - - const getPendingAccessRequestCountStub = sinon - .stub(AdministrativeService.prototype, 'getPendingAccessRequestCount') - .resolves(2); - - const requestHandler = count.getPendingAccessRequestsCount(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(getPendingAccessRequestCountStub).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql(2); - }); -}); diff --git a/api/src/paths/administrative/access-request/count.ts b/api/src/paths/administrative/access-request/count.ts deleted file mode 100644 index 7991f4346..000000000 --- a/api/src/paths/administrative/access-request/count.ts +++ /dev/null @@ -1,81 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection } from '../../../database/db'; -import { HTTP400 } from '../../../errors/http-error'; -import { hasPendingAdministrativeActivitiesResponseObject } from '../../../openapi/schemas/administrative-activity'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { getUserIdentifier } from '../../../utils/keycloak-utils'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/access-request/count'); - -export const GET: Operation = [getPendingAccessRequestsCount()]; - -GET.apiDoc = { - description: 'Has one or more pending Administrative Activities.', - tags: ['access request'], - security: [ - { - Bearer: [] - } - ], - requestBody: { - description: 'Administrative Activity get request object.', - content: { - 'application/json': { - schema: { - title: 'Administrative Activity request object', - type: 'object', - properties: {} - } - } - } - }, - responses: { - 200: { - description: '`Has Pending Administrative Activities` get response object.', - content: { - 'application/json': { - schema: { - ...(hasPendingAdministrativeActivitiesResponseObject as object) - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Get all projects. - * - * @returns {RequestHandler} - */ -export function getPendingAccessRequestsCount(): RequestHandler { - return async (req, res) => { - const connection = getAPIUserDBConnection(); - const administrativeService = new AdministrativeService(connection); - - try { - const userIdentifier = getUserIdentifier(req['keycloak_token']); - - if (!userIdentifier) { - throw new HTTP400('Missing required userIdentifier'); - } - - await connection.open(); - - const result = await administrativeService.getPendingAccessRequestCount(userIdentifier); - await connection.commit(); - - return res.status(200).json(result); - } catch (error) { - defaultLog.error({ label: 'getPendingAccessRequestsCount', message: 'error', error }); - - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/access-request/update.test.ts b/api/src/paths/administrative/access-request/update.test.ts deleted file mode 100644 index f51460f7e..000000000 --- a/api/src/paths/administrative/access-request/update.test.ts +++ /dev/null @@ -1,109 +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 { SystemUserExtended } from '../../../repositories/user-repository'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { GCNotifyService } from '../../../services/gcnotify-service'; -import { UserService } from '../../../services/user-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as update from './update'; - -chai.use(sinonChai); - -describe('updateAccessRequest', () => { - afterEach(() => { - sinon.restore(); - }); - - it('re-throws any error that is thrown', async () => { - const mockDBConnection = getMockDBConnection({ - open: () => { - throw new Error('test error'); - } - }); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.body = { - userIdentifier: 1, - identitySource: 'identitySource', - requestId: 1, - requestStatusTypeId: 1, - roleIds: [1, 3] - }; - - const requestHandler = update.updateAccessRequest(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('test error'); - } - }); - - it('adds new system roles and updates administrative activity', async () => { - const mockDBConnection = getMockDBConnection(); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestId = 1; - const requestStatusTypeId = 2; - const roleIdsToAdd = [1, 3]; - - mockReq.body = { - userIdentifier: 'username', - identitySource: 'identitySource', - requestId: requestId, - requestStatusTypeId: requestStatusTypeId, - roleIds: roleIdsToAdd - }; - - const systemUserId = 4; - const existingRoleIds = [1, 2]; - const mockSystemUser: SystemUserExtended = { - system_user_id: systemUserId, - user_identity_source_id: 2, - user_identifier: 'username', - user_guid: '', - record_end_date: '', - record_effective_date: '2023-12-08', - create_date: '2023-12-08 14:37:41.315999-08', - create_user: 1, - update_date: null, - update_user: null, - revision_count: 0, - identity_source: 'identitySource', - role_ids: existingRoleIds, - role_names: [] - }; - const ensureSystemUserStub = sinon.stub(UserService.prototype, 'ensureSystemUser').resolves(mockSystemUser); - - const addSystemRolesStub = sinon.stub(UserService.prototype, 'addUserSystemRoles'); - - const updateAdministrativeActivityStub = sinon.stub( - AdministrativeService.prototype, - 'updateAdministrativeActivity' - ); - - const sendApprovalEmailStub = sinon.stub(GCNotifyService.prototype, 'sendApprovalEmail'); - - const requestHandler = update.updateAccessRequest(); - - await requestHandler(mockReq, mockRes, mockNext); - - const expectedRoleIdsToAdd = [3]; - - expect(ensureSystemUserStub).to.have.been.calledOnce; - expect(addSystemRolesStub).to.have.been.calledWith(systemUserId, expectedRoleIdsToAdd); - expect(updateAdministrativeActivityStub).to.have.been.calledWith(requestId, requestStatusTypeId); - expect(sendApprovalEmailStub).to.have.been.calledWith(requestStatusTypeId, 'username', 'identitySource'); - }); -}); diff --git a/api/src/paths/administrative/access-request/update.ts b/api/src/paths/administrative/access-request/update.ts deleted file mode 100644 index d2f9c6945..000000000 --- a/api/src/paths/administrative/access-request/update.ts +++ /dev/null @@ -1,150 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { SYSTEM_IDENTITY_SOURCE } from '../../../constants/database'; -import { SYSTEM_ROLE } from '../../../constants/roles'; -import { getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { GCNotifyService } from '../../../services/gcnotify-service'; -import { UserService } from '../../../services/user-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/access-request/update'); - -export const PUT: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN], - discriminator: 'SystemRole' - } - ] - }; - }), - updateAccessRequest() -]; - -PUT.apiDoc = { - description: "Update a user's system access request and add any specified system roles to the user.", - tags: ['user'], - security: [ - { - Bearer: [] - } - ], - requestBody: { - content: { - 'application/json': { - schema: { - type: 'object', - required: ['userGuid', 'userIdentifier', 'identitySource', 'requestId', 'requestStatusTypeId'], - properties: { - userGuid: { - type: 'string', - description: 'The GUID for the user.' - }, - userIdentifier: { - type: 'string', - description: 'The user identifier for the user.' - }, - identitySource: { - type: 'string', - enum: [ - SYSTEM_IDENTITY_SOURCE.IDIR, - SYSTEM_IDENTITY_SOURCE.BCEID_BASIC, - SYSTEM_IDENTITY_SOURCE.BCEID_BUSINESS - ] - }, - requestId: { - type: 'number', - description: 'The id of the access request to update.' - }, - requestStatusTypeId: { - type: 'number', - description: 'The status type id to set for the access request.' - }, - roleIds: { - type: 'array', - items: { - type: 'number' - }, - description: - 'An array of role ids to add, if the access-request was approved. Ignored if the access-request was denied.' - } - } - } - } - } - }, - responses: { - 200: { - description: 'Add system user roles to user OK.' - }, - ...defaultErrorResponses - } -}; - -/** - * Updates an access request. - * - * key steps performed: - * - Get the user by their user identifier - * - If user is not found, add them - * - Determine if there are any new roles to add, and add them if there are - * - Update the administrative activity record status - * - * @return {*} {RequestHandler} - */ -export function updateAccessRequest(): RequestHandler { - return async (req, res) => { - defaultLog.debug({ label: 'updateAccessRequest', message: 'params', req_body: req.body }); - - const userGuid = req.body?.userGuid; - const userIdentifier = req.body?.userIdentifier; - const identitySource = req.body?.identitySource; - const administrativeActivityId = Number(req.body?.requestId); - const administrativeActivityStatusTypeId = Number(req.body?.requestStatusTypeId); - const roleIds: number[] = req.body?.roleIds || []; - - const connection = getDBConnection(req['keycloak_token']); - const gcnotifyService = new GCNotifyService(connection); - const administrativeService = new AdministrativeService(connection); - - try { - await connection.open(); - - const userService = new UserService(connection); - - // Get the system user (adding or activating them if they already existed). - const systemUserObject = await userService.ensureSystemUser(userGuid, userIdentifier, identitySource); - - // Filter out any system roles that have already been added to the user - const rolesIdsToAdd = roleIds.filter((roleId) => !systemUserObject.role_ids.includes(roleId)); - - if (rolesIdsToAdd?.length) { - // Add any missing roles (if any) - await userService.addUserSystemRoles(systemUserObject.system_user_id, rolesIdsToAdd); - } - - // Update the access request record status - await administrativeService.updateAdministrativeActivity( - administrativeActivityId, - administrativeActivityStatusTypeId - ); - - //if the access request is an approval send Approval email - await gcnotifyService.sendApprovalEmail(administrativeActivityStatusTypeId, userIdentifier, identitySource); - - await connection.commit(); - - return res.status(200).send(); - } catch (error) { - defaultLog.error({ label: 'updateAccessRequest', message: 'error', error }); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/activity/create.test.ts b/api/src/paths/administrative/activity/create.test.ts deleted file mode 100644 index 93a95e18d..000000000 --- a/api/src/paths/administrative/activity/create.test.ts +++ /dev/null @@ -1,62 +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 { HTTP500 } from '../../../errors/http-error'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { GCNotifyService } from '../../../services/gcnotify-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as create from './create'; - -chai.use(sinonChai); - -describe('create', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw a 400 error when no system user id', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub(), - systemUserId: () => 0 - }); - - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = create.createAdministrativeActivity(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTP500).message).to.equal('Failed to identify system user ID'); - } - }); - - it('should return 200 when create completes', async () => { - const dbConnectionObj = getMockDBConnection({ systemUserId: () => 1 }); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const createAdministrativeActivityStub = sinon - .stub(AdministrativeService.prototype, 'createAdministrativeActivity') - .resolves({ id: 1, create_date: 'date' }); - - sinon.stub(GCNotifyService.prototype, 'sendAccessRequestReceivedEmail').resolves(); - - const requestHandler = create.createAdministrativeActivity(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(createAdministrativeActivityStub).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql({ id: 1, date: 'date' }); - }); -}); diff --git a/api/src/paths/administrative/activity/create.ts b/api/src/paths/administrative/activity/create.ts deleted file mode 100644 index 82c617294..000000000 --- a/api/src/paths/administrative/activity/create.ts +++ /dev/null @@ -1,84 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection } from '../../../database/db'; -import { HTTP500 } from '../../../errors/http-error'; -import { administrativeActivityResponseObject } from '../../../openapi/schemas/administrative-activity'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { GCNotifyService } from '../../../services/gcnotify-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/activity/list'); - -export const POST: Operation = [createAdministrativeActivity()]; - -POST.apiDoc = { - description: 'Create a new Administrative Activity.', - tags: ['admin'], - security: [ - { - Bearer: [] - } - ], - requestBody: { - description: 'Administrative Activity post request object.', - content: { - 'application/json': { - schema: { - title: 'Administrative Activity request object', - type: 'object', - properties: {} - } - } - } - }, - responses: { - 200: { - description: 'Administrative activity post response object.', - content: { - 'application/json': { - schema: { - ...(administrativeActivityResponseObject as object) - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Creates a new access request record. - * - * @returns {RequestHandler} - */ -export function createAdministrativeActivity(): RequestHandler { - return async (req, res) => { - const connection = getAPIUserDBConnection(); - const administrativeService = new AdministrativeService(connection); - const gcNotifyService = new GCNotifyService(connection); - try { - await connection.open(); - - const systemUserId = connection.systemUserId(); - - if (!systemUserId) { - throw new HTTP500('Failed to identify system user ID'); - } - - const response = await administrativeService.createAdministrativeActivity(systemUserId, req?.body); - - await connection.commit(); - - await gcNotifyService.sendAccessRequestReceivedEmail(); - - return res.status(200).json({ id: response.id, date: response.create_date }); - } catch (error) { - defaultLog.error({ label: 'administrativeActivity', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/activity/list.test.ts b/api/src/paths/administrative/activity/list.test.ts deleted file mode 100644 index f490f42ee..000000000 --- a/api/src/paths/administrative/activity/list.test.ts +++ /dev/null @@ -1,102 +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 { AdministrativeService } from '../../../services/administrative-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as list from './list'; - -chai.use(sinonChai); - -describe('getAdministrativeActivities', () => { - afterEach(() => { - sinon.restore(); - }); - - it('re-throws any error that is thrown', async () => { - const mockDBConnection = getMockDBConnection({ - open: () => { - throw new Error('test error'); - } - }); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = list.getAdministrativeActivities(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('test error'); - } - }); - - it('should return the rows on success (empty)', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { type: 'string' }; - - const mockGetAdministrativeActivities = sinon - .stub(AdministrativeService.prototype, 'getAdministrativeActivities') - .resolves([]); - - const requestHandler = list.getAdministrativeActivities(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockGetAdministrativeActivities).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql([]); - }); - - it('should return the rows on success (not empty)', async () => { - const data = { - id: 1, - type: 2, - type_name: 'type name', - status: 3, - status_name: 'status name', - description: 'description', - data: 'data', - notes: 'notes', - create_date: '2020/04/04' - }; - - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { type: 'string' }; - - const mockGetAdministrativeActivities = sinon - .stub(AdministrativeService.prototype, 'getAdministrativeActivities') - .resolves([data]); - - const requestHandler = list.getAdministrativeActivities(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockGetAdministrativeActivities).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql([data]); - }); -}); diff --git a/api/src/paths/administrative/activity/list.ts b/api/src/paths/administrative/activity/list.ts deleted file mode 100644 index 4e3d1584d..000000000 --- a/api/src/paths/administrative/activity/list.ts +++ /dev/null @@ -1,153 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { SYSTEM_ROLE } from '../../../constants/roles'; -import { getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/activity/list'); - -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN], - discriminator: 'SystemRole' - } - ] - }; - }), - getAdministrativeActivities() -]; - -export enum ADMINISTRATIVE_ACTIVITY_STATUS_TYPE { - PENDING = 'Pending', - ACTIONED = 'Actioned', - REJECTED = 'Rejected' -} - -export const getAllAdministrativeActivityStatusTypes = (): string[] => - Object.values(ADMINISTRATIVE_ACTIVITY_STATUS_TYPE); - -GET.apiDoc = { - description: 'Get a list of administrative activities based on the provided criteria.', - tags: ['admin'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - in: 'query', - name: 'type', - schema: { - type: 'string', - enum: ['System Access'] - } - }, - { - in: 'query', - name: 'status', - schema: { - type: 'array', - items: { - type: 'string', - enum: getAllAdministrativeActivityStatusTypes() - } - } - } - ], - responses: { - 200: { - description: 'List of administrative activities.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - properties: { - id: { - type: 'number', - description: 'Administrative activity row ID' - }, - type: { - type: 'number', - description: 'Administrative activity type ID' - }, - type_name: { - type: 'string', - description: 'Administrative activity type name' - }, - status: { - type: 'number', - description: 'Administrative activity status type ID' - }, - status_name: { - type: 'string', - description: 'Administrative activity status type name' - }, - description: { - type: 'string' - }, - notes: { - type: 'string' - }, - data: { - type: 'object', - description: 'JSON data blob containing additional information about the activity record', - properties: { - // Don't specify as this is a JSON blob column - } - }, - create_date: { - type: 'string' - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Get all administrative activities for the specified type, or all if no type is provided. - * - * @returns {RequestHandler} - */ -export function getAdministrativeActivities(): RequestHandler { - return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); - const administrativeService = new AdministrativeService(connection); - - try { - const administrativeActivityTypeName = (req.query?.type as string) || ''; - - const administrativeActivityStatusTypes: string[] = - (req.query?.status as string[]) || getAllAdministrativeActivityStatusTypes(); - - await connection.open(); - - const response = await administrativeService.getAdministrativeActivities( - administrativeActivityTypeName, - administrativeActivityStatusTypes - ); - - await connection.commit(); - - return res.status(200).json(response); - } catch (error) { - defaultLog.error({ label: 'getAdministrativeActivities', message: 'error', error }); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/activity/update.test.ts b/api/src/paths/administrative/activity/update.test.ts deleted file mode 100644 index d4e928d40..000000000 --- a/api/src/paths/administrative/activity/update.test.ts +++ /dev/null @@ -1,79 +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 { AdministrativeService } from '../../../services/administrative-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as update from './update'; - -chai.use(sinonChai); - -describe('update', () => { - afterEach(() => { - sinon.restore(); - }); - - const sampleReq = { - keycloak_token: {}, - body: { - id: 1, - status: 2 - } - } as any; - - it('re-throws any error that is thrown', async () => { - const mockDBConnection = getMockDBConnection({ - open: () => { - throw new Error('test error'); - } - }); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.body = { - userIdentifier: 1, - identitySource: 'identitySource', - requestId: 1, - requestStatusTypeId: 1, - roleIds: [1, 3] - }; - - const requestHandler = update.getUpdateAdministrativeActivityHandler(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('test error'); - } - }); - - it('should return 200 after update is completed', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.body = sampleReq.body; - - const mockUpdateAdministrativeActivity = sinon - .stub(AdministrativeService.prototype, 'updateAdministrativeActivity') - .resolves(); - - const requestHandler = update.getUpdateAdministrativeActivityHandler(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockUpdateAdministrativeActivity).to.have.been.calledOnce; - expect(mockRes.statusValue).to.equal(200); - }); -}); diff --git a/api/src/paths/administrative/activity/update.ts b/api/src/paths/administrative/activity/update.ts deleted file mode 100644 index 2c796ceaf..000000000 --- a/api/src/paths/administrative/activity/update.ts +++ /dev/null @@ -1,98 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { SYSTEM_ROLE } from '../../../constants/roles'; -import { getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { AdministrativeService } from '../../../services/administrative-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/activity/update'); - -export const PUT: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN], - discriminator: 'SystemRole' - } - ] - }; - }), - getUpdateAdministrativeActivityHandler() -]; - -PUT.apiDoc = { - description: 'Update an existing administrative activity.', - tags: ['admin'], - security: [ - { - Bearer: [] - } - ], - requestBody: { - description: 'Administrative activity request object.', - content: { - 'application/json': { - schema: { - title: 'Administrative activity put object', - type: 'object', - required: ['id', 'status'], - properties: { - id: { - title: 'administrative activity record ID', - type: 'number' - }, - status: { - title: 'administrative activity status type code ID', - type: 'number' - } - } - } - } - } - }, - responses: { - ...defaultErrorResponses - } -}; - -/** - * Get a request handler to update an existing administrative activity. - * - * @returns {RequestHandler} - */ -export function getUpdateAdministrativeActivityHandler(): RequestHandler { - return async (req, res) => { - defaultLog.debug({ - label: 'getUpdateAdministrativeActivityHandler', - message: 'params', - req_body: req.body - }); - - const administrativeActivityId = Number(req.body?.id); - const administrativeActivityStatusTypeId = Number(req.body?.status); - - const connection = getDBConnection(req['keycloak_token']); - const administrativeService = new AdministrativeService(connection); - - try { - await connection.open(); - - await administrativeService.updateAdministrativeActivity( - administrativeActivityId, - administrativeActivityStatusTypeId - ); - - await connection.commit(); - - return res.status(200).send(); - } catch (error) { - defaultLog.error({ label: 'getUpdateAdministrativeActivityHandler', message: 'error', error }); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/security/categories.ts b/api/src/paths/administrative/security/categories.ts deleted file mode 100644 index d984b50fe..000000000 --- a/api/src/paths/administrative/security/categories.ts +++ /dev/null @@ -1,136 +0,0 @@ -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 { SecurityService } from '../../../services/security-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/security/categories'); - -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN], - discriminator: 'SystemRole' - } - ] - }; - }), - getActiveSecurityCategories() -]; - -GET.apiDoc = { - description: - 'Get all active security rules with their associated categories. A security category is active if it has not been end-dated.', - tags: ['security'], - security: [ - { - Bearer: [] - } - ], - responses: { - 200: { - description: 'Security Categories.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - required: [ - 'security_category_id', - 'name', - 'description', - 'record_effective_date', - 'record_end_date', - 'create_date', - 'create_user', - 'update_date', - 'update_user', - 'revision_count' - ], - properties: { - security_category_id: { - type: 'integer' - }, - name: { - type: 'string' - }, - description: { - type: 'string' - }, - record_effective_date: { - type: 'string' - }, - record_end_date: { - type: 'string', - nullable: true - }, - create_date: { - type: 'string' - }, - create_user: { - type: 'integer' - }, - update_date: { - type: 'string', - nullable: true - }, - update_user: { - type: 'integer', - minimum: 1, - nullable: true - }, - revision_count: { - type: 'integer' - } - }, - additionalProperties: false - } - } - } - } - }, - 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 getActiveSecurityCategories(): RequestHandler { - return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); - const service = new SecurityService(connection); - - try { - await connection.open(); - - const data = await service.getActiveSecurityCategories(); - - await connection.commit(); - - return res.status(200).json(data); - } catch (error) { - defaultLog.error({ label: 'getActiveSecurityCategories', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/administrative/submission/{submissionId}/messages.test.ts b/api/src/paths/administrative/submission/{submissionId}/messages.test.ts deleted file mode 100644 index 414907209..000000000 --- a/api/src/paths/administrative/submission/{submissionId}/messages.test.ts +++ /dev/null @@ -1,79 +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 { SubmissionService } from '../../../../services/submission-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../__mocks__/db'; -import { createSubmissionMessages } from './messages'; - -chai.use(sinonChai); - -describe('createSubmissionMessages', () => { - afterEach(() => { - sinon.restore(); - }); - - it('re-throws any error that is thrown', async () => { - const mockDBConnection = getMockDBConnection({ - open: () => { - throw new Error('test error'); - } - }); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const requestHandler = createSubmissionMessages(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('test error'); - } - }); - - it('should return an array of Reviewed submission objects', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const submissionId = 1; - const messages = [ - { - submission_message_type_id: 2, - label: 'label', - message: 'message', - data: { - dataField: 'dataField' - } - } - ]; - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - submissionId: String(submissionId) - }; - mockReq.body = { - messages - }; - - const createMessagesStub = sinon.stub(SubmissionService.prototype, 'createMessages').resolves(undefined); - - const requestHandler = createSubmissionMessages(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(createMessagesStub).to.have.been.calledOnceWith(submissionId, messages); - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.be.undefined; - }); -}); diff --git a/api/src/paths/administrative/submission/{submissionId}/messages.ts b/api/src/paths/administrative/submission/{submissionId}/messages.ts deleted file mode 100644 index 7df95de2d..000000000 --- a/api/src/paths/administrative/submission/{submissionId}/messages.ts +++ /dev/null @@ -1,252 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { SYSTEM_ROLE } from '../../../../constants/roles'; -import { getDBConnection } from '../../../../database/db'; -import { defaultErrorResponses } from '../../../../openapi/schemas/http-responses'; -import { SubmissionMessageRecord } from '../../../../repositories/submission-repository'; -import { authorizeRequestHandler } from '../../../../request-handlers/security/authorization'; -import { SubmissionService } from '../../../../services/submission-service'; -import { getLogger } from '../../../../utils/logger'; - -const defaultLog = getLogger('paths/administrative/submission/reviewed'); - -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN, SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - getSubmissionMessages() -]; - -GET.apiDoc = { - description: 'Get messages for a submission.', - tags: ['admin'], - security: [ - { - Bearer: [] - } - ], - parameters: [ - { - description: 'Submission ID', - in: 'path', - name: 'submissionId', - schema: { - type: 'integer', - minimum: 1 - }, - required: true - } - ], - responses: { - 200: { - description: 'Array of messages for a submission.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - properties: { - submission_message_id: { - type: 'integer', - minimum: 1 - }, - submission_message_type_id: { - type: 'integer', - minimum: 1 - }, - submission_feature_id: { - type: 'integer', - minimum: 1 - }, - label: { - type: 'string', - maxLength: 250 - }, - message: { - type: 'string', - maxLength: 500 - }, - data: { - type: 'object', - properties: {} - }, - create_date: { - type: 'string' - }, - create_user: { - type: 'integer', - minimum: 1 - }, - update_date: { - type: 'string' - }, - update_user: { - type: 'integer', - minimum: 1 - }, - revision_count: { - type: 'integer', - maximum: 0 - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Get messages for a submission. - * - * @returns {RequestHandler} - */ -export function getSubmissionMessages(): RequestHandler { - return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); - - const submissionId = Number(req.params.submissionId); - - try { - await connection.open(); - - const service = new SubmissionService(connection); - const response = await service.getMessages(submissionId); - - await connection.commit(); - - return res.status(200).json(response); - } catch (error) { - defaultLog.error({ label: 'getSubmissionMessages', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} - -export const POST: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN, SYSTEM_ROLE.DATA_ADMINISTRATOR], - discriminator: 'SystemRole' - } - ] - }; - }), - getSubmissionMessages() -]; - -POST.apiDoc = { - description: 'Creates new messages for a submission.', - tags: ['admin'], - security: [ - { - Bearer: [] - } - ], - requestBody: { - content: { - 'application/json': { - schema: { - type: 'object', - required: ['messages'], - properties: { - messages: { - type: 'array', - items: { - type: 'object', - required: ['submission_message_type_id', 'label', 'message'], - properties: { - submission_message_type_id: { - type: 'integer', - minimum: 1 - }, - label: { - type: 'string', - maxLength: 250 - }, - message: { - type: 'string', - maxLength: 500 - }, - data: { - type: 'object', - properties: {} - } - } - }, - minItems: 1 - } - } - } - } - } - }, - parameters: [ - { - description: 'Submission ID', - in: 'path', - name: 'submissionId', - schema: { - type: 'integer', - minimum: 1 - }, - required: true - } - ], - responses: { - 200: { - description: 'Create submission messages OK' - }, - ...defaultErrorResponses - } -}; - -/** - * Create submission messages for a submission. - * - * @returns {RequestHandler} - */ -export function createSubmissionMessages(): RequestHandler { - return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); - - const submissionId = Number(req.params.submissionId); - - const messages = req.body.messages as Pick< - SubmissionMessageRecord, - 'submission_message_type_id' | 'label' | 'message' | 'data' - >[]; - - try { - await connection.open(); - - const service = new SubmissionService(connection); - const response = await service.createMessages(submissionId, messages); - - await connection.commit(); - - return res.status(200).json(response); - } catch (error) { - defaultLog.error({ label: 'getSubmissionMessages', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} From 707e32921a7994d17aaaf74f4620665cb559bf16 Mon Sep 17 00:00:00 2001 From: Kjartan Einarsson Date: Wed, 27 Mar 2024 14:36:06 -0700 Subject: [PATCH 3/7] remove unused endpoints/services/repos/utils --- api/package-lock.json | 121 +- api/src/errors/api-error.test.ts | 6 +- api/src/errors/api-error.ts | 13 - .../schemas/administrative-activity.test.ts | 12 - .../schemas/administrative-activity.ts | 25 - .../artifact/{artifactId}/getSignedUrl.ts | 2 +- api/src/paths/dwc/eml/search.test.ts | 185 -- api/src/paths/dwc/eml/search.ts | 100 -- .../paths/dwc/submission/{datasetId}/get.ts | 2 +- api/src/paths/gcnotify/send.ts | 2 +- api/src/queue/queue-registry.ts | 35 +- .../administrative-repository.test.ts | 199 --- .../repositories/administrative-repository.ts | 224 --- .../templates/SIMS-handlebar-template.ts | 280 --- .../services/administrative-service.test.ts | 95 -- api/src/services/administrative-service.ts | 75 - api/src/services/artifact-service.ts | 11 - api/src/services/dwc-service.test.ts | 1500 ----------------- api/src/services/dwc-service.ts | 779 --------- api/src/services/eml-service.test.ts | 509 ------ api/src/services/eml-service.ts | 317 ---- api/src/services/es-service.test.ts | 29 - api/src/services/es-service.ts | 84 - api/src/services/gcnotify-service.ts | 81 +- api/src/services/spatial-service.test.ts | 159 -- api/src/services/spatial-service.ts | 69 - api/src/services/validation-service.ts | 29 - app/src/AppRouter.tsx | 7 - app/src/features/search/SearchPage.tsx | 256 --- app/src/features/search/SearchRouter.tsx | 26 - app/src/hooks/api/useDatasetApi.test.ts | 18 - app/src/hooks/api/useDatasetApi.ts | 13 - app/src/hooks/api/useSearchApi.test.ts | 17 - app/src/hooks/api/useSearchApi.ts | 27 +- 34 files changed, 101 insertions(+), 5206 deletions(-) delete mode 100644 api/src/openapi/schemas/administrative-activity.test.ts delete mode 100644 api/src/openapi/schemas/administrative-activity.ts delete mode 100644 api/src/paths/dwc/eml/search.test.ts delete mode 100644 api/src/paths/dwc/eml/search.ts delete mode 100644 api/src/repositories/administrative-repository.test.ts delete mode 100644 api/src/repositories/administrative-repository.ts delete mode 100644 api/src/repositories/templates/SIMS-handlebar-template.ts delete mode 100644 api/src/services/administrative-service.test.ts delete mode 100644 api/src/services/administrative-service.ts delete mode 100644 api/src/services/dwc-service.test.ts delete mode 100644 api/src/services/dwc-service.ts delete mode 100644 api/src/services/eml-service.test.ts delete mode 100644 api/src/services/eml-service.ts delete mode 100644 api/src/services/es-service.test.ts delete mode 100644 api/src/services/es-service.ts delete mode 100644 app/src/features/search/SearchPage.tsx delete mode 100644 app/src/features/search/SearchRouter.tsx diff --git a/api/package-lock.json b/api/package-lock.json index 9fda741dc..8f3989254 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -678,6 +678,36 @@ "strip-ansi": "^7.0.1" } }, + "string-width-cjs": { + "version": "npm:string-width@4.2.3", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", + "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "requires": { + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "dependencies": { + "ansi-regex": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", + "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==" + }, + "emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" + }, + "strip-ansi": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "requires": { + "ansi-regex": "^5.0.1" + } + } + } + }, "strip-ansi": { "version": "7.1.0", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", @@ -686,6 +716,21 @@ "ansi-regex": "^6.0.1" } }, + "strip-ansi-cjs": { + "version": "npm:strip-ansi@6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "requires": { + "ansi-regex": "^5.0.1" + }, + "dependencies": { + "ansi-regex": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", + "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==" + } + } + }, "wrap-ansi": { "version": "8.1.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz", @@ -695,6 +740,54 @@ "string-width": "^5.0.1", "strip-ansi": "^7.0.1" } + }, + "wrap-ansi-cjs": { + "version": "npm:wrap-ansi@7.0.0", + "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", + "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==", + "requires": { + "ansi-styles": "^4.0.0", + "string-width": "^4.1.0", + "strip-ansi": "^6.0.0" + }, + "dependencies": { + "ansi-regex": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", + "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==" + }, + "ansi-styles": { + "version": "4.3.0", + "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", + "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==", + "requires": { + "color-convert": "^2.0.1" + } + }, + "emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" + }, + "string-width": { + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", + "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "requires": { + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + } + }, + "strip-ansi": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "requires": { + "ansi-regex": "^5.0.1" + } + } + } } } }, @@ -8968,16 +9061,6 @@ "strip-ansi": "^6.0.1" } }, - "string-width-cjs": { - "version": "npm:string-width@4.2.3", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", - "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", - "requires": { - "emoji-regex": "^8.0.0", - "is-fullwidth-code-point": "^3.0.0", - "strip-ansi": "^6.0.1" - } - }, "string.prototype.padend": { "version": "3.1.5", "resolved": "https://registry.npmjs.org/string.prototype.padend/-/string.prototype.padend-3.1.5.tgz", @@ -9035,14 +9118,6 @@ "ansi-regex": "^5.0.1" } }, - "strip-ansi-cjs": { - "version": "npm:strip-ansi@6.0.1", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", - "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", - "requires": { - "ansi-regex": "^5.0.1" - } - }, "strip-bom": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/strip-bom/-/strip-bom-2.0.0.tgz", @@ -10110,16 +10185,6 @@ "strip-ansi": "^6.0.0" } }, - "wrap-ansi-cjs": { - "version": "npm:wrap-ansi@7.0.0", - "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", - "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==", - "requires": { - "ansi-styles": "^4.0.0", - "string-width": "^4.1.0", - "strip-ansi": "^6.0.0" - } - }, "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", diff --git a/api/src/errors/api-error.test.ts b/api/src/errors/api-error.test.ts index d8a6da002..4817989ae 100644 --- a/api/src/errors/api-error.test.ts +++ b/api/src/errors/api-error.test.ts @@ -1,6 +1,6 @@ import { expect } from 'chai'; import { describe } from 'mocha'; -import { ApiErrorType, ApiExecuteSQLError, ApiGeneralError, ApiUnknownError } from './api-error'; +import { ApiErrorType, ApiExecuteSQLError, ApiGeneralError } from './api-error'; describe('ApiError', () => { describe('No error value provided', () => { @@ -14,10 +14,6 @@ describe('ApiError', () => { expect(new ApiGeneralError(message).name).to.equal(ApiErrorType.GENERAL); }); - it('Creates Api Unknown error', function () { - expect(new ApiUnknownError(message).name).to.equal(ApiErrorType.UNKNOWN); - }); - it('Creates Api execute SQL error', function () { expect(new ApiExecuteSQLError(message).name).to.equal(ApiErrorType.EXECUTE_SQL); }); diff --git a/api/src/errors/api-error.ts b/api/src/errors/api-error.ts index 701581391..4ee0edab6 100644 --- a/api/src/errors/api-error.ts +++ b/api/src/errors/api-error.ts @@ -38,19 +38,6 @@ export class ApiGeneralError extends ApiError { } } -/** - * API encountered an unknown/unexpected error. - * - * @export - * @class ApiUnknownError - * @extends {ApiError} - */ -export class ApiUnknownError extends ApiError { - constructor(message: string, errors?: (string | Record)[]) { - super(ApiErrorType.UNKNOWN, message, errors); - } -} - /** * API executed a query against the database, but the response was missing data, or indicated the query failed. * diff --git a/api/src/openapi/schemas/administrative-activity.test.ts b/api/src/openapi/schemas/administrative-activity.test.ts deleted file mode 100644 index 33a6edc94..000000000 --- a/api/src/openapi/schemas/administrative-activity.test.ts +++ /dev/null @@ -1,12 +0,0 @@ -import Ajv from 'ajv'; -import { expect } from 'chai'; -import { describe } from 'mocha'; -import { administrativeActivityResponseObject } from './administrative-activity'; - -describe('administrativeActivityResponseObject', () => { - const ajv = new Ajv(); - - it('is valid openapi v3 schema', () => { - expect(ajv.validateSchema(administrativeActivityResponseObject)).to.be.true; - }); -}); diff --git a/api/src/openapi/schemas/administrative-activity.ts b/api/src/openapi/schemas/administrative-activity.ts deleted file mode 100644 index bf87fc9b4..000000000 --- a/api/src/openapi/schemas/administrative-activity.ts +++ /dev/null @@ -1,25 +0,0 @@ -/** - * Response object for creating an access request - */ -export const administrativeActivityResponseObject = { - title: 'Administrative Activity Response Object', - type: 'object', - required: ['id', 'date'], - properties: { - id: { - type: 'number' - }, - date: { - type: 'string', - description: 'The date this administrative activity was made' - } - } -}; - -/** - * Response object for GET 'has pending administrative activities' operation - */ -export const hasPendingAdministrativeActivitiesResponseObject = { - title: '`Has Pending Administrative Activities` Response Object', - type: 'number' -}; diff --git a/api/src/paths/artifact/{artifactId}/getSignedUrl.ts b/api/src/paths/artifact/{artifactId}/getSignedUrl.ts index d56e712f5..5c4304a47 100644 --- a/api/src/paths/artifact/{artifactId}/getSignedUrl.ts +++ b/api/src/paths/artifact/{artifactId}/getSignedUrl.ts @@ -5,7 +5,7 @@ import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; import { SecurityService } from '../../../services/security-service'; import { getLogger } from '../../../utils/logger'; -const defaultLog = getLogger('paths/dwc/eml/get'); +const defaultLog = getLogger('paths/artifact/{artifactId}/getSignedUrl'); export const GET: Operation = [getArtifactSignedUrl()]; diff --git a/api/src/paths/dwc/eml/search.test.ts b/api/src/paths/dwc/eml/search.test.ts deleted file mode 100644 index aee667026..000000000 --- a/api/src/paths/dwc/eml/search.test.ts +++ /dev/null @@ -1,185 +0,0 @@ -import { SearchHit } from '@elastic/elasticsearch/lib/api/types'; -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../database/db'; -import { ESService } from '../../../services/es-service'; -import { SubmissionService } from '../../../services/submission-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as search from './search'; -import { GET } from './search'; - -chai.use(sinonChai); - -describe('search', () => { - describe('openApiSchema', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - const basicRequest = { - headers: { - 'content-type': 'application/json' - }, - body: {}, - params: {}, - query: {} - }; - - describe('should throw an error when', () => { - it('has invalid type', async () => { - const request = { ...basicRequest, query: { terms: false } }; - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].message).to.equal('must be string'); - }); - }); - - describe('should succeed when', () => { - it('has valid no value', async () => { - const request = { ...basicRequest, query: { terms: '' } }; - const response = requestValidator.validateRequest(request); - - expect(response).to.equal(undefined); - }); - - it('has valid single keyword value', async () => { - const request = { ...basicRequest, query: { terms: 'test' } }; - const response = requestValidator.validateRequest(request); - - expect(response).to.equal(undefined); - }); - - it('has valid single search value', async () => { - const request = { ...basicRequest, query: { terms: 'test' } }; - const response = requestValidator.validateRequest(request); - - expect(response).to.equal(undefined); - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - - describe('should throw an error when', () => { - it('has null value', async () => { - const apiResponse = null; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('has array with invalid key value: id', async () => { - const apiResponse = [{ id1: 1 }]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'id'"); - }); - - it('has array with invalid value: id', async () => { - const apiResponse = [{ id: 14, source: {}, fields: {} }]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'observation_count'"); - }); - it('has array with invalid value: source', async () => { - const apiResponse = [{ id: 'test', source: 1, fields: {} }]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'observation_count'"); - }); - }); - - describe('should succeed when', () => { - it('has empty valid values', async () => { - const apiResponse: never[] = []; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - - it('has valid values', async () => { - const apiResponse = [ - { id: 'test1', source: {}, observation_count: 1 }, - { id: 'test2', source: {}, observation_count: 2 } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - }); - }); - }); - - describe('searchInElasticSearch', () => { - afterEach(() => { - sinon.restore(); - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { - terms: 'search-term' - }; - - sinon.stub(ESService.prototype, 'keywordSearchEml').throws(new Error('test error')); - - const requestHandler = search.searchInElasticSearch(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as Error).message).to.equal('test error'); - expect(dbConnectionObj.release).to.have.been.calledOnce; - expect(dbConnectionObj.rollback).to.have.been.calledOnce; - } - }); - - it('returns search results when Elastic Search service succeeds with valid data', async () => { - const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { - terms: 'search-term' - }; - - sinon - .stub(SubmissionService.prototype, 'findSubmissionRecordsWithSpatialCount') - .onCall(0) - .resolves([ - { id: 'test_uuid1', source: {}, observation_count: 14 }, - { id: 'test_uuid2', source: {}, observation_count: 23 } - ]); - - const keywordSearchEmlStub = sinon.stub(ESService.prototype, 'keywordSearchEml').resolves([ - { _id: '123', _source: {}, fields: {} }, - { _id: '456', _source: {}, fields: {} } - ] as unknown as SearchHit[]); - - const requestHandler = search.searchInElasticSearch(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(keywordSearchEmlStub).to.have.been.calledOnceWith('search-term'); - expect(mockRes.jsonValue).eql([ - { id: 'test_uuid1', source: {}, observation_count: 14 }, - { id: 'test_uuid2', source: {}, observation_count: 23 } - ]); - }); - }); -}); diff --git a/api/src/paths/dwc/eml/search.ts b/api/src/paths/dwc/eml/search.ts deleted file mode 100644 index a8eacab8f..000000000 --- a/api/src/paths/dwc/eml/search.ts +++ /dev/null @@ -1,100 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { ESService } from '../../../services/es-service'; -import { SubmissionService } from '../../../services/submission-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/eml/search'); - -export const GET: Operation = [searchInElasticSearch()]; - -GET.apiDoc = { - description: 'searches submission files with elastic search', - tags: ['eml', 'search'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'submission search parameters.', - in: 'query', - name: 'terms', - required: false, - schema: { - type: 'string' - } - } - ], - responses: { - 200: { - description: 'Submission search response object.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - required: ['id', 'source', 'observation_count'], - properties: { - id: { - type: 'string' - }, - source: { - type: 'object' - }, - observation_count: { - type: 'number' - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Search for meta data in Elastic Search. - * - * @returns {RequestHandler} - */ -export function searchInElasticSearch(): RequestHandler { - return async (req, res) => { - const queryString = String(req.query.terms) || '*'; - - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - try { - await connection.open(); - - const elasticService = new ESService(); - - const submissionService = new SubmissionService(connection); - - const responseFromES = await elasticService.keywordSearchEml(queryString); - - const datasetIdsFromES = responseFromES.map((item) => item._id); - - const result = await submissionService.findSubmissionRecordsWithSpatialCount(datasetIdsFromES); - - // Remove null items, which indicates the provided elastic search dataset id had no matching database record. - const filteredResult = result.filter((item: any) => !!item); - - await connection.commit(); - - res.status(200).json(filteredResult); - } catch (error) { - defaultLog.error({ label: 'keywordSearchEml', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/{datasetId}/get.ts b/api/src/paths/dwc/submission/{datasetId}/get.ts index 3df0d4eec..5b853cbe8 100644 --- a/api/src/paths/dwc/submission/{datasetId}/get.ts +++ b/api/src/paths/dwc/submission/{datasetId}/get.ts @@ -5,7 +5,7 @@ import { defaultErrorResponses } from '../../../../openapi/schemas/http-response import { SubmissionService } from '../../../../services/submission-service'; import { getLogger } from '../../../../utils/logger'; -const defaultLog = getLogger('paths/dwc/eml/get'); +const defaultLog = getLogger('paths/dwc/submission/{datasetId}/get'); export const GET: Operation = [getMetadataByDatasetId()]; diff --git a/api/src/paths/gcnotify/send.ts b/api/src/paths/gcnotify/send.ts index 17f1cd6c0..cd156d3da 100644 --- a/api/src/paths/gcnotify/send.ts +++ b/api/src/paths/gcnotify/send.ts @@ -8,7 +8,7 @@ import { authorizeRequestHandler } from '../../request-handlers/security/authori import { GCNotifyService } from '../../services/gcnotify-service'; import { getLogger } from '../../utils/logger'; -const defaultLog = getLogger('paths/gcnotify'); +const defaultLog = getLogger('paths/gcnotify/send'); export const POST: Operation = [ authorizeRequestHandler(() => { diff --git a/api/src/queue/queue-registry.ts b/api/src/queue/queue-registry.ts index 0a78bdbfa..cb9620cf0 100644 --- a/api/src/queue/queue-registry.ts +++ b/api/src/queue/queue-registry.ts @@ -1,6 +1,5 @@ import { getAPIUserDBConnection } from '../database/db'; import { ISubmissionJobQueueRecord } from '../repositories/submission-job-queue-repository'; -import { DarwinCoreService } from '../services/dwc-service'; import { SubmissionJobQueueService } from '../services/submission-job-queue-service'; import { getLogger } from '../utils/logger'; @@ -13,13 +12,8 @@ export const DWC_DATASET_SUBMISSION_JOB = 'dwc_dataset_submission_job'; /** * Translates a string to a queue-job compatible function. */ -export const QueueJobRegistry = { - registry: [ - { - name: DWC_DATASET_SUBMISSION_JOB, - generator: jobQueueAttemptsWrapper(dwcDatasetSubmissionJob) - } - ], +export const QueueJobRegistry: { registry: any[]; findMatchingJob: (name: string) => QueueJob | undefined } = { + registry: [], /** * Find a job in the registry. * @@ -59,28 +53,3 @@ export function jobQueueAttemptsWrapper(queueJob: QueueJob): QueueJob { return queueJob(jobQueueRecord); }; } - -/** - * Function that runs the Darwin Core intake job. - * - * @export - * @param {ISubmissionJobQueueRecord} jobQueueRecord - */ -export async function dwcDatasetSubmissionJob(jobQueueRecord: ISubmissionJobQueueRecord) { - const connection = getAPIUserDBConnection(); - - try { - await connection.open(); - - const darwinCoreService = new DarwinCoreService(connection); - // Run darwin core intake job - - await darwinCoreService.intakeJob(jobQueueRecord); - } catch (error) { - defaultLog.error({ label: 'dwcDatasetSubmissionJob', message: 'error', error }); - throw error; - } finally { - await connection.commit(); - connection.release(); - } -} diff --git a/api/src/repositories/administrative-repository.test.ts b/api/src/repositories/administrative-repository.test.ts deleted file mode 100644 index 2066305e2..000000000 --- a/api/src/repositories/administrative-repository.test.ts +++ /dev/null @@ -1,199 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import { QueryResult } from 'pg'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { ApiExecuteSQLError } from '../errors/api-error'; -import { getMockDBConnection } from '../__mocks__/db'; -import { AdministrativeRepository, IAdministrativeActivity } from './administrative-repository'; - -chai.use(sinonChai); - -describe('AdministrativeRepository', () => { - describe('getAdministrativeActivities', async () => { - afterEach(() => { - sinon.restore(); - }); - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - try { - await administrativeRepository.getAdministrativeActivities('string', ['string']); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiExecuteSQLError).message).to.equal('Failed to get Administrative activities'); - } - }); - - it('should return rows if succeeds', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [{ id: 1 } as unknown as IAdministrativeActivity] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.getAdministrativeActivities('string', ['string']); - - expect(result).to.be.eql([{ id: 1 }]); - }); - }); - - describe('checkIfAccessRequestIsApproval', async () => { - afterEach(() => { - sinon.restore(); - }); - it('should return false if request is not Approved', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.checkIfAccessRequestIsApproval(1); - - expect(result).to.eql(false); - }); - - it('should return true if request is Approved', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [{ name: 'Actioned' }] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.checkIfAccessRequestIsApproval(1); - - expect(result).to.be.eql(true); - }); - }); - - describe('createAdministrativeActivity', async () => { - afterEach(() => { - sinon.restore(); - }); - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - try { - await administrativeRepository.createAdministrativeActivity(1, ['string']); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiExecuteSQLError).message).to.equal('Failed to submit administrative activity'); - } - }); - - it('should return rows if succeeds', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [{ id: 1 } as unknown as IAdministrativeActivity] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.createAdministrativeActivity(1, ['string']); - - expect(result).to.be.eql({ id: 1 }); - }); - }); - - describe('getPendingAccessRequestCount', async () => { - afterEach(() => { - sinon.restore(); - }); - it('should return 0 if no requests found', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.getPendingAccessRequestCount('string'); - expect(result).to.be.eql(0); - }); - - it('should return number of requests found', async () => { - const mockQueryResponse = { - rowCount: 2 - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.getPendingAccessRequestCount('string'); - - expect(result).to.be.eql(2); - }); - }); - - describe('updateAdministrativeActivity', async () => { - afterEach(() => { - sinon.restore(); - }); - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - try { - await administrativeRepository.updateAdministrativeActivity(1, 1); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiExecuteSQLError).message).to.equal('Failed to update administrative activity'); - } - }); - - it('should return rows if succeeds', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [{ id: 1 } as unknown as IAdministrativeActivity] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const administrativeRepository = new AdministrativeRepository(mockDBConnection); - - const result = await administrativeRepository.updateAdministrativeActivity(1, 1); - - expect(result).to.be.eql({ id: 1 }); - }); - }); -}); diff --git a/api/src/repositories/administrative-repository.ts b/api/src/repositories/administrative-repository.ts deleted file mode 100644 index 1817144b7..000000000 --- a/api/src/repositories/administrative-repository.ts +++ /dev/null @@ -1,224 +0,0 @@ -import SQL from 'sql-template-strings'; -import { ApiExecuteSQLError } from '../errors/api-error'; -import { BaseRepository } from './base-repository'; - -export interface IAdministrativeActivity { - id: number; - type: number; - type_name: string; - status: number; - status_name: string; - description: string; - notes: string; - data: string; - create_date: string; -} - -export interface ICreateAdministrativeActivity { - id: number; - create_date: string; -} - -export class AdministrativeRepository extends BaseRepository { - /** - * Get all Administrative Activities - * - * @param {string} administrativeActivityTypeName - * @param {string[]} administrativeActivityStatusTypes - * @return {*} {Promise} - * @memberof AdministrativeRepository - */ - async getAdministrativeActivities( - administrativeActivityTypeName: string, - administrativeActivityStatusTypes: string[] - ): Promise { - //TODO: turn sql to knex query - const sqlStatement = SQL` - SELECT - aa.administrative_activity_id as id, - aat.administrative_activity_type_id as type, - aat.name as type_name, - aast.administrative_activity_status_type_id as status, - aast.name as status_name, - aa.description, - aa.data, - aa.notes, - aa.create_date - FROM - administrative_activity aa - LEFT OUTER JOIN - administrative_activity_status_type aast - ON - aa.administrative_activity_status_type_id = aast.administrative_activity_status_type_id - LEFT OUTER JOIN - administrative_activity_type aat - ON - aa.administrative_activity_type_id = aat.administrative_activity_type_id - WHERE - 1 = 1 - `; - - if (administrativeActivityTypeName) { - sqlStatement.append(SQL` - AND - aat.name = ${administrativeActivityTypeName} - `); - } - - if (administrativeActivityStatusTypes?.length) { - sqlStatement.append(SQL` - AND - aast.name IN ( - `); - - // Add first element - sqlStatement.append(SQL`${administrativeActivityStatusTypes[0]}`); - - for (let idx = 1; idx < administrativeActivityStatusTypes.length; idx++) { - // Add subsequent elements, which get a comma prefix - sqlStatement.append(SQL`, ${administrativeActivityStatusTypes[idx]}`); - } - - sqlStatement.append(SQL`)`); - } - - sqlStatement.append(`;`); - - const response = await this.connection.sql(sqlStatement); - - if (response.rowCount <= 0) { - throw new ApiExecuteSQLError('Failed to get Administrative activities', [ - 'AdministrativeRepository->getAdministrativeActivities', - 'rowCount was null or undefined, expected rowCount >= 1' - ]); - } - - const result = (response && response.rowCount && response.rows) || []; - - return result; - } - - /** - * Check access request if actioned - * - * @param {number} adminActivityTypeId - * @return {*} {Promise} - * @memberof AdministrativeRepository - */ - async checkIfAccessRequestIsApproval(adminActivityTypeId: number): Promise { - const adminActivityStatusTypeSQLStatment = SQL` - SELECT - * - FROM - administrative_activity_status_type - WHERE - administrative_activity_status_type_id = ${adminActivityTypeId}; - `; - - const response = await this.connection.sql(adminActivityStatusTypeSQLStatment); - - if (response.rows?.[0]?.name === 'Actioned') { - return true; - } - return false; - } - - /** - * Create Administrative Activity - * - * @param {number} systemUserId - * @param {*} data - * @return {*} {Promise} - * @memberof AdministrativeRepository - */ - async createAdministrativeActivity(systemUserId: number, data: any): Promise { - const postAdministrativeActivitySQLStatement = SQL` - INSERT INTO administrative_activity ( - reported_system_user_id, - administrative_activity_type_id, - administrative_activity_status_type_id, - data - ) VALUES ( - ${systemUserId}, - 1, - 1, - ${data} - ) - RETURNING - administrative_activity_id as id, - create_date::timestamptz; - `; - - const response = await this.connection.sql(postAdministrativeActivitySQLStatement); - - const result = (response && response.rows && response.rows[0]) || null; - - if (!result || !result.id) { - throw new ApiExecuteSQLError('Failed to submit administrative activity'); - } - - return result; - } - - /** - * Get count of pending access requests - * - * @param {string} userIdentifier - * @return {*} {Promise} - * @memberof AdministrativeRepository - */ - async getPendingAccessRequestCount(userIdentifier: string): Promise { - const sqlStatement = SQL` - SELECT - * - FROM - administrative_activity aa - LEFT OUTER JOIN - administrative_activity_status_type aast - ON - aa.administrative_activity_status_type_id = aast.administrative_activity_status_type_id - WHERE - (aa.data -> 'username')::text = '"' || ${userIdentifier} || '"' - AND aast.name = 'Pending'; - `; - - const response = await this.connection.sql(sqlStatement); - - const result = (response && response.rowCount) || 0; - - return result; - } - - /** - * Update an existing administrative activity. - * - * @param {number} administrativeActivityId - * @param {number} administrativeActivityStatusTypeId - * @param {IDBConnection} connection - */ - async updateAdministrativeActivity( - administrativeActivityId: number, - administrativeActivityStatusTypeId: number - ): Promise<{ id: number }> { - const sqlStatement = SQL` - UPDATE - administrative_activity - SET - administrative_activity_status_type_id = ${administrativeActivityStatusTypeId} - WHERE - administrative_activity_id = ${administrativeActivityId} - RETURNING - administrative_activity_id as id; - `; - - const response = await this.connection.sql<{ id: number }>(sqlStatement); - - const result = (response && response.rowCount && response.rows[0]) || null; - - if (!result) { - throw new ApiExecuteSQLError('Failed to update administrative activity'); - } - - return result; - } -} diff --git a/api/src/repositories/templates/SIMS-handlebar-template.ts b/api/src/repositories/templates/SIMS-handlebar-template.ts deleted file mode 100644 index b0620da08..000000000 --- a/api/src/repositories/templates/SIMS-handlebar-template.ts +++ /dev/null @@ -1,280 +0,0 @@ -export const simsHandlebarsTemplate_HEADER = ` - - {{#if eml:eml.dataset.title}} -
-

{{eml:eml.dataset.title}}

- {{#each eml:eml.additionalMetadata as | amd |}} - {{#with (lookup amd.metadata "types") as | projectType | ~}} - {{#ifCond amd.describes '===' @root.eml:eml.dataset.[@_id]}} -
Inventory {{projectType.type}}
- {{/ifCond}} - {{/with}} - {{/each}} -
- {{/if}} -`; - -export const simsHandlebarsTemplate_DETAILS = ` -
- - -
-
- - - {{#each eml:eml.dataset.project.abstract.section as | section |}} - {{#ifCond section.title '===' "Objectives"}} -
-
- Project Objectives -
-
- {{section.para}} -
-
- {{/ifCond}} - {{/each}} - - - {{#if eml:eml.dataset.project.studyAreaDescription.coverage.temporalCoverage.rangeOfDates}} -
-
- Timeline -
-
- {{formatDate eml:eml.dataset.project.studyAreaDescription.coverage.temporalCoverage.rangeOfDates.beginDate.calendarDate 'YYYY-MM-DD' 'MMM YYYY'}} - {{formatDate eml:eml.dataset.project.studyAreaDescription.coverage.temporalCoverage.rangeOfDates.endDate.calendarDate 'YYYY-MM-DD' 'MMM YYYY'}} -
-
- {{/if}} - - - {{#each eml:eml.additionalMetadata as | amd |}} - {{#each amd.metadata as | metadata |}} - {{#ifCond @key '===' "projectTypes"}} -
-
- Project Type -
-
- {{metadata.projectType}} -
-
- {{/ifCond}} - {{/each}} - {{/each}} - - - {{#each eml:eml.additionalMetadata as | amd |}} - {{#each amd.metadata as | metadata |}} - {{#ifCond @key '===' "projectActivities"}} -
-
- Activities -
-
- {{#if (isAnArray metadata.projectActivity)}} - {{#each metadata.projectActivity as | activities |}} - {{activities.name}}{{#unless @last}}, {{/unless}} - {{/each}} - {{else}} - {{metadata.projectActivity.name}} - {{/if}} -
-
- {{/ifCond}} - {{/each}} - {{/each}} - - - {{#if eml:eml.dataset.contact}} -
-
- Project Coordinator -
-
- -
-
- {{/if}} - - - {{#if eml:eml.dataset.project.funding.section}} -
-
- Funding Sources -
-
- {{#each eml:eml.dataset.project.funding.section as | funding |}} - {{funding.para}}{{#unless @last}}, {{/unless}} - {{/each}} -
-
- {{/if}} - - - {{#each eml:eml.additionalMetadata as | amd |}} - {{#each amd.metadata as | metadata |}} - {{#ifCond @key '===' "partnerships"}} - {{#ifCond metadata '!==' ""}} -
-
- Partners -
-
- {{#if (isAnArray metadata.partnership)}} - {{#each metadata.partnership as | partnership |}} - {{partnership.name}}{{#unless @last}}, {{/unless}} - {{/each}} - {{else}} - {{metadata.partnership.name}} - {{/if}} -
-
- {{/ifCond}} - {{/ifCond}} - {{/each}} - {{/each}} - - - {{#each eml:eml.additionalMetadata as | amd |}} - {{#each amd.metadata as | metadata |}} - {{#ifCond @key '===' "IUCNConservationActions"}} - {{#ifCond metadata '!==' ""}} -
-
- Conservation Activities -
-
- {{#if (isAnArray metadata.IUCNConservationAction)}} -
    - {{#each metadata.IUCNConservationAction as | actions |}} -
  • - {{actions.IUCNConservationActionLevel1Classification}} > {{actions.IUCNConservationActionLevel2SubClassification}} > {{actions.IUCNConservationActionLevel3SubClassification}} -
    • - {{/each}} -
- {{else}} -
    -
  • - {{metadata.IUCNConservationAction.IUCNConservationActionLevel1Classification}} > {{metadata.IUCNConservationAction.IUCNConservationActionLevel2SubClassification}} > {{metadata.IUCNConservationAction.IUCNConservationActionLevel3SubClassification}} -
    • -
- {{/if}} -
-
- {{/ifCond}} - {{/ifCond}} - {{/each}} - {{/each}} - - {{#each eml:eml.dataset.project.abstract.section as | section |}} - {{#ifCond section.title '===' "Intended Outcomes"}} -
-
- Intended Outcomes: -
-
- {{section.para}} -
-
- {{/ifCond}} - {{/each}} - - {{#each eml:eml.dataset.project.designDescription.description.section as | section |}} - {{#ifCond section.title '===' "Field Method"}} -
-
- Field Method: -
-
- {{section.para}} -
-
- {{/ifCond}} - {{/each}} -
-
- - -
- {{#each eml:eml.additionalMetadata as | amd |}} - {{#with (lookup amd.metadata "projectAttachments") as | attachments | ~}} - -
-
- Documents -
-
- -
- - {{#each attachments.projectAttachment as | a |}} -
- {{a.file_name}} - {{#if a.is_secure}} - (secured) - {{else}} - (public) - {{/if}} -
- {{/each}} - - {{#if attachments.projectAttachment.file_name}} - {{attachments.projectAttachment.file_name}} - {{#if attachments.projectAttachment.is_secure}} - (secured) - {{else}} - (public) - {{/if}} - {{/if}} -
- - {{/with}} - {{/each}} -
- - -
- {{#each eml:eml.additionalMetadata as | amd |}} - - {{#with (lookup amd.metadata "projectReportAttachments") as | attachments | ~}} -
-
- Reports -
-
-
- - {{#each attachments.projectReportAttachment as | a |}} - - {{#if a.file_name}} -
- {{a.file_name}} - {{#if a.is_secure}} - (secured) - {{else}} - (public) - {{/if}} -
- {{/if}} - {{/each}} - - - {{#if attachments.projectReportAttachment.file_name}} - {{attachments.projectReportAttachment.file_name}} - {{#if attachments.projectReportAttachment.is_secure}} - (secured) - {{else}} - (public) - {{/if}} - {{/if}} -
- {{/with}} - {{/each}} -
-
-`; diff --git a/api/src/services/administrative-service.test.ts b/api/src/services/administrative-service.test.ts deleted file mode 100644 index 1fc9abb4f..000000000 --- a/api/src/services/administrative-service.test.ts +++ /dev/null @@ -1,95 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { - AdministrativeRepository, - IAdministrativeActivity, - ICreateAdministrativeActivity -} from '../repositories/administrative-repository'; -import { getMockDBConnection } from '../__mocks__/db'; -import { AdministrativeService } from './administrative-service'; - -chai.use(sinonChai); - -describe('administrativeService', () => { - describe('updateAdministrativeActivity', () => { - afterEach(() => { - sinon.restore(); - }); - - const dbConnectionObj = getMockDBConnection(); - const administrativeService = new AdministrativeService(dbConnectionObj); - - it('should return id value', async () => { - const AdministrativeRepositoryStub = sinon - .stub(AdministrativeRepository.prototype, 'updateAdministrativeActivity') - .resolves({ id: 1 }); - - const result = await administrativeService.updateAdministrativeActivity(1, 2); - - expect(result).to.eql({ id: 1 }); - expect(AdministrativeRepositoryStub).to.have.been.calledOnce; - }); - }); - - describe('getPendingAccessRequestCount', () => { - afterEach(() => { - sinon.restore(); - }); - - const dbConnectionObj = getMockDBConnection(); - const administrativeService = new AdministrativeService(dbConnectionObj); - - it('should return id value', async () => { - const AdministrativeRepositoryStub = sinon - .stub(AdministrativeRepository.prototype, 'getPendingAccessRequestCount') - .resolves(1); - - const result = await administrativeService.getPendingAccessRequestCount('string'); - - expect(result).to.eql(1); - expect(AdministrativeRepositoryStub).to.have.been.calledOnce; - }); - }); - - describe('createAdministrativeActivity', () => { - afterEach(() => { - sinon.restore(); - }); - - const dbConnectionObj = getMockDBConnection(); - const administrativeService = new AdministrativeService(dbConnectionObj); - - it('should return id value', async () => { - const AdministrativeRepositoryStub = sinon - .stub(AdministrativeRepository.prototype, 'createAdministrativeActivity') - .resolves({ id: 1 } as unknown as ICreateAdministrativeActivity); - - const result = await administrativeService.createAdministrativeActivity(1, 'string'); - - expect(result).to.eql({ id: 1 }); - expect(AdministrativeRepositoryStub).to.have.been.calledOnce; - }); - }); - - describe('getAdministrativeActivities', () => { - afterEach(() => { - sinon.restore(); - }); - - const dbConnectionObj = getMockDBConnection(); - const administrativeService = new AdministrativeService(dbConnectionObj); - - it('should return id value', async () => { - const AdministrativeRepositoryStub = sinon - .stub(AdministrativeRepository.prototype, 'getAdministrativeActivities') - .resolves([{ id: 1 } as unknown as IAdministrativeActivity]); - - const result = await administrativeService.getAdministrativeActivities('string', ['string']); - - expect(result).to.eql([{ id: 1 }]); - expect(AdministrativeRepositoryStub).to.have.been.calledOnce; - }); - }); -}); diff --git a/api/src/services/administrative-service.ts b/api/src/services/administrative-service.ts deleted file mode 100644 index 7664da35f..000000000 --- a/api/src/services/administrative-service.ts +++ /dev/null @@ -1,75 +0,0 @@ -import { IDBConnection } from '../database/db'; -import { - AdministrativeRepository, - IAdministrativeActivity, - ICreateAdministrativeActivity -} from '../repositories/administrative-repository'; -import { DBService } from './db-service'; - -export class AdministrativeService extends DBService { - administrativeRepository: AdministrativeRepository; - - constructor(connection: IDBConnection) { - super(connection); - - this.administrativeRepository = new AdministrativeRepository(connection); - } - - /** - * Get all Administrative Activities - * - * @param {string} administrativeActivityTypeName - * @param {string[]} administrativeActivityStatusTypes - * @return {*} {Promise} - * @memberof AdministrativeService - */ - async getAdministrativeActivities( - administrativeActivityTypeName: string, - administrativeActivityStatusTypes: string[] - ): Promise { - return this.administrativeRepository.getAdministrativeActivities( - administrativeActivityTypeName, - administrativeActivityStatusTypes - ); - } - - /** - * Create Administrative Activity - * - * @param {number} systemUserId - * @param {*} data - * @return {*} {Promise} - * @memberof AdministrativeService - */ - async createAdministrativeActivity(systemUserId: number, data: any): Promise { - return this.administrativeRepository.createAdministrativeActivity(systemUserId, data); - } - - /** - * Get count of pending access requests - * - * @param {string} userIdentifier - * @return {*} {Promise} - * @memberof AdministrativeService - */ - async getPendingAccessRequestCount(userIdentifier: string): Promise { - return this.administrativeRepository.getPendingAccessRequestCount(userIdentifier); - } - - /** - * Update an existing administrative activity. - * - * @param {number} administrativeActivityId - * @param {number} administrativeActivityStatusTypeId - * @param {IDBConnection} connection - */ - async updateAdministrativeActivity( - administrativeActivityId: number, - administrativeActivityStatusTypeId: number - ): Promise<{ id: number }> { - return this.administrativeRepository.updateAdministrativeActivity( - administrativeActivityId, - administrativeActivityStatusTypeId - ); - } -} diff --git a/api/src/services/artifact-service.ts b/api/src/services/artifact-service.ts index 2c9c17247..aa7d43cc0 100644 --- a/api/src/services/artifact-service.ts +++ b/api/src/services/artifact-service.ts @@ -29,17 +29,6 @@ export class ArtifactService extends DBService { this.submissionService = new SubmissionService(connection); } - /** - * Retrieves an array of of new primary keys for an artifact record. - * - * @param {number} [count=1] The number of artifact primary keys to generate (by default, only 1). - * @returns {*} {Promise} The array of artifact primary keys - * @memberof ArtifactRepository - */ - async getNextArtifactIds(count = 1): Promise { - return this.artifactRepository.getNextArtifactIds(count); - } - /** * Inserts a new artifact record * diff --git a/api/src/services/dwc-service.test.ts b/api/src/services/dwc-service.test.ts deleted file mode 100644 index 6589634e3..000000000 --- a/api/src/services/dwc-service.test.ts +++ /dev/null @@ -1,1500 +0,0 @@ -import { Client } from '@elastic/elasticsearch'; -import { WriteResponseBase } from '@elastic/elasticsearch/lib/api/types'; -import { S3 } from 'aws-sdk'; -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import { QueryResult } from 'pg'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { ApiExecuteSQLError, ApiGeneralError } from '../errors/api-error'; -import { - ISourceTransformModel, - ISubmissionJobQueueRecord, - ISubmissionModel, - SUBMISSION_STATUS_TYPE -} from '../repositories/submission-repository'; -import * as fileUtils from '../utils/file-utils'; -import { CSVWorksheet } from '../utils/media/csv/csv-file'; -import * as dwcUtils from '../utils/media/dwc/dwc-archive-file'; -import { DWCArchive } from '../utils/media/dwc/dwc-archive-file'; -import { ArchiveFile, MediaFile } from '../utils/media/media-file'; -import * as mediaUtils from '../utils/media/media-utils'; -import { getMockDBConnection } from '../__mocks__/db'; -import { DarwinCoreService } from './dwc-service'; -import { EMLService } from './eml-service'; -import { ElasticSearchIndices, ESService } from './es-service'; -import { SpatialService } from './spatial-service'; -import { SubmissionService } from './submission-service'; - -chai.use(sinonChai); - -describe.skip('DarwinCoreService', () => { - afterEach(() => { - sinon.restore(); - }); - - describe.skip('intakeJob', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - - const mediaFileStub = sinon.createStubInstance(MediaFile); - const bufferStub = sinon.createStubInstance(Buffer); - bufferStub.toString.returns( - '' - ); - mediaFileStub.buffer = bufferStub as unknown as Buffer; - - const mockDWCAFile = { - submission_id: 1, - eml: { - emlFile: mediaFileStub - }, - worksheets: {} - } as unknown as DWCArchive; - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const step1 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_1').resolves({ submission_metadata_id: 1 }); - const step2 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_2').resolves(mockDWCAFile); - const step3 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_3').resolves(); - const step4 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_4').resolves(); - const step5 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_5').resolves(); - const step6 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_6').resolves(); - const step7 = sinon - .stub(DarwinCoreService.prototype, 'intakeJob_step_7') - .resolves({ submission_observation_id: 1 }); - const step8 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_8').resolves(); - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - submission_id: 1, - //source_transform_id: 3, - uuid: '123-456-789' - }); - const step9 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_9').resolves({}); - const step10 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_10').resolves(); - const step11 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_11').resolves(); - const step12 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_12').resolves(); - const step13 = sinon.stub(DarwinCoreService.prototype, 'intakeJob_step_13').resolves(); - const submissionStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - - await service.intakeJob(mockJobQueue); - - expect(step1).to.be.calledOnce; - expect(step2).to.be.calledOnce; - expect(step3).to.be.calledOnce; - expect(step4).to.be.calledOnce; - expect(step5).to.be.calledOnce; - expect(step6).to.be.calledOnce; - expect(step7).to.be.calledOnce; - expect(step8).to.be.calledOnce; - expect(step9).to.be.calledOnce; - expect(step10).to.be.calledOnce; - expect(step11).to.be.calledOnce; - expect(step12).to.be.calledOnce; - expect(step13).to.be.calledOnce; - expect(submissionStatus).to.be.calledOnce; - }); - }); - - describe.skip('intakeJob_step_1', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should insert metadata record', async () => { - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return { rowCount: 1, rows: [{ submission_metadata_id: 1 }] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - - const response = await service.intakeJob_step_1(1); - expect(response).to.be.eql({ submission_metadata_id: 1 }); - }); - - it('should fail with `Inserting new Metadata record` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - sinon.stub(SubmissionService.prototype, 'insertSubmissionMetadataRecord').throws(); - const errorInsert = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_1(1); - } catch (error) { - expect(errorInsert).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Inserting new Metadata record'); - } - }); - }); - - describe.skip('intakeJob_step_2', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return DWCArchive', async () => { - const mockDBConnection = getMockDBConnection(); - const dwcArchive = { - eml: { - buffer: Buffer.from('test') - }, - worksheets: { - test1: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet, - test2: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet - } - } as unknown as DWCArchive; - - const service = new DarwinCoreService(mockDBConnection); - - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - submission_id: 1, - //source_transform_id: 3, - uuid: 'uuid' - }); - const metadata = sinon - .stub(SubmissionService.prototype, 'updateSubmissionMetadataEMLSource') - .resolves({ submission_metadata_id: 1 }); - - sinon.stub(DarwinCoreService.prototype, 'getAndPrepFileFromS3').resolves(dwcArchive); - const response = await service.intakeJob_step_2( - { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: null, - job_end_timestamp: null, - key: 's3 path' - } as unknown as ISubmissionJobQueueRecord, - 1 - ); - - expect(response).to.be.eql(dwcArchive); - expect(metadata).to.be.calledOnce; - }); - - it('should throw `File eml is empty` error', async () => { - const mockDBConnection = getMockDBConnection(); - const dwcArchive = { - eml: undefined, - worksheets: { - test1: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet, - test2: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet - } - } as unknown as DWCArchive; - - const service = new DarwinCoreService(mockDBConnection); - - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - submission_id: 1, - //source_transform_id: 3, - uuid: 'uuid' - }); - const metadata = sinon - .stub(SubmissionService.prototype, 'updateSubmissionMetadataEMLSource') - .resolves({ submission_metadata_id: 1 }); - sinon.stub(DarwinCoreService.prototype, 'getAndPrepFileFromS3').resolves(dwcArchive); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_2( - { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: null, - job_end_timestamp: null, - key: 's3 key' - } as unknown as ISubmissionJobQueueRecord, - 1 - ); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect(metadata).not.to.be.called; - expect((error as ApiGeneralError).errors).to.equal('Accessing S3 File, file eml is empty'); - } - }); - - it('should throw `No S3 Key` error', async () => { - const mockDBConnection = getMockDBConnection(); - const dwcArchive = { - eml: undefined, - worksheets: { - test1: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet, - test2: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet - } - } as unknown as DWCArchive; - - const service = new DarwinCoreService(mockDBConnection); - - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - submission_id: 1, - //source_transform_id: 3, - uuid: 'uuid' - }); - const metadata = sinon - .stub(SubmissionService.prototype, 'updateSubmissionMetadataEMLSource') - .resolves({ submission_metadata_id: 1 }); - sinon.stub(DarwinCoreService.prototype, 'getAndPrepFileFromS3').resolves(dwcArchive); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_2( - { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: null, - job_end_timestamp: null, - key: '' - } as unknown as ISubmissionJobQueueRecord, - 1 - ); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect(metadata).not.to.be.called; - expect((error as ApiGeneralError).errors).to.equal('No S3 Key given'); - } - }); - - it('should throw `Accessing S3 File` error', async () => { - const mockDBConnection = getMockDBConnection(); - const dwcArchive = { - eml: { - buffer: Buffer.from('test') - }, - worksheets: { - test1: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet, - test2: { - getRowObjects: () => { - return [ - { id: 1, name: 'test' }, - { id: 2, name: 'test' } - ]; - } - } as unknown as CSVWorksheet - } - } as unknown as DWCArchive; - - const service = new DarwinCoreService(mockDBConnection); - - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').throws(); - const metadata = sinon.stub(SubmissionService.prototype, 'updateSubmissionMetadataEMLSource').resolves(); - sinon.stub(DarwinCoreService.prototype, 'getAndPrepFileFromS3').resolves(dwcArchive); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_2( - { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: null, - job_end_timestamp: null - } as unknown as ISubmissionJobQueueRecord, - 1 - ); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect(metadata).not.to.be.called; - expect((error as ApiGeneralError).message).to.equal('Accessing S3 File and Updating new Metadata record'); - // checking for another error in the flow - expect((error as ApiGeneralError).errors).not.to.equal('Accessing S3 File, file eml is empty'); - } - }); - }); - - describe.skip('intakeJob_step_3', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - - const emlXMLString = - ''; - - const mockDWCAFile = { - submission_id: 1, - eml: { - emlFile: { - buffer: { - toString: () => emlXMLString - } - } - }, - worksheets: {} - } as unknown as DWCArchive; - - const response = await service.intakeJob_step_3(1, mockDWCAFile); - const result: Record = { - '?xml': { '@_version': '1.0', '@_encoding': 'UTF-8' }, - 'eml:eml': { '@_packageId': 'urn:uuid:0cf8169f-b159-4ef9-bd43-93348bdc1e9f' } - }; - - expect(response).to.deep.equal(result); - }); - - it('should throw `file eml is empty` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockDWCAFile = { - submission_id: 1, - eml: undefined, - worksheets: {} - } as unknown as DWCArchive; - - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_3(1, mockDWCAFile); - expect.fail(); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect((error as ApiGeneralError).errors).to.equal('file eml is empty'); - } - }); - - it('should throw `Converting EML to JSON` error', async () => { - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return { rowCount: 0, rows: [] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - const mediaFileStub = sinon.createStubInstance(MediaFile); - const bufferStub = sinon.createStubInstance(Buffer); - bufferStub.toString.returns( - '' - ); - - mediaFileStub.buffer = bufferStub as unknown as Buffer; - - const mockDWCAFile = { - submission_id: 1, - eml: { - emlFile: mediaFileStub - }, - worksheets: {} - } as unknown as DWCArchive; - sinon.stub(EMLService.prototype, 'convertXMLStringToJSObject').throws(); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_3(1, mockDWCAFile); - expect.fail(); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Converting EML to JSON'); - } - }); - }); - - describe.skip('intakeJob_step_4', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const update = sinon.stub(SubmissionService.prototype, 'updateSubmissionRecordEMLJSONSource').resolves(); - - await service.intakeJob_step_4(1, 1, {}); - - expect(update).to.be.calledOnce; - }); - - it('should throw a `Storing eml JSON data`', async () => { - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return { rowCount: 0, rows: [] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_4(1, 1, {}); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Storing eml JSON data'); - } - }); - }); - - describe.skip('intakeJob_step_5', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const mediaFileStub = sinon.createStubInstance(MediaFile); - const bufferStub = sinon.createStubInstance(Buffer); - - bufferStub.toString.returns( - '' - ); - - mediaFileStub.buffer = bufferStub as unknown as Buffer; - - const mockDWCAFile = { - submission_id: 1, - eml: { - emlFile: mediaFileStub - }, - worksheets: {}, - normalize: () => 'normalized data' - } as unknown as DWCArchive; - const service = new DarwinCoreService(mockDBConnection); - const response = await service.intakeJob_step_5(mockDWCAFile); - expect(response).to.be.eql('normalized data'); - }); - }); - - describe.skip('intakeJob_step_6', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const updateEndDate = sinon.stub(SubmissionService.prototype, 'updateSubmissionMetadataRecordEndDate').resolves(); - const updateEffectiveDate = sinon - .stub(SubmissionService.prototype, 'updateSubmissionMetadataRecordEffectiveDate') - .resolves(); - const updateObservationEndDate = sinon - .stub(DarwinCoreService.prototype, 'updateSubmissionObservationEndTimestamp') - .resolves(); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.intakeJob_step_6(mockJobQueue); - - expect(updateEndDate).to.be.called; - expect(updateEffectiveDate).to.be.called; - expect(updateObservationEndDate).to.be.called; - expect(insertStatus).to.not.be.called; - }); - - it('should throw `Update Submission` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const updateEndDate = sinon.stub(SubmissionService.prototype, 'updateSubmissionMetadataRecordEndDate').rejects(); - const updateEffectiveDate = sinon - .stub(SubmissionService.prototype, 'updateSubmissionMetadataRecordEffectiveDate') - .resolves(); - const updateObservationEndDate = sinon - .stub(DarwinCoreService.prototype, 'updateSubmissionObservationEndTimestamp') - .resolves(); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_6(mockJobQueue); - expect.fail(); - } catch (error: any) { - expect(updateEndDate).to.be.called; - expect(updateEffectiveDate).to.not.be.called; - expect(updateObservationEndDate).to.not.be.called; - expect(insertStatus).to.be.called; - - expect((error as ApiGeneralError).message).to.equal('Update Submission dates'); - } - }); - }); - - describe.skip('intakeJob_step_7', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const insert = sinon - .stub(DarwinCoreService.prototype, 'insertSubmissionObservationRecord') - .resolves({ submission_observation_id: 1 }); - - const response = await service.intakeJob_step_7(mockJobQueue, 'normalized json'); - expect(insert).to.be.calledOnce; - expect(response.submission_observation_id).to.eq(1); - }); - - it('should throw `Inserting Observation JSON`', async () => { - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return { rowCount: 0, rows: [] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const insert = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_7(mockJobQueue, 'normalized json'); - expect.fail(); - } catch (error: any) { - expect(insert).to.be.calledTwice; - expect(error.message).to.eq('Inserting Observation JSON'); - } - }); - }); - - describe.skip('intakeJob_step_8', async () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - const submissionObservationId = 2; - - const transform = sinon.stub(SpatialService.prototype, 'runSpatialTransforms').resolves(); - const status = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.intakeJob_step_8(mockJobQueue, submissionObservationId); - - expect(transform).to.be.calledOnceWith(mockJobQueue.submission_id, submissionObservationId); - expect(status).to.be.calledOnceWith( - mockJobQueue.submission_id, - SUBMISSION_STATUS_TYPE.SPATIAL_TRANSFORM_UNSECURE - ); - expect(insertErrorStatus).to.not.be.called; - }); - - it('should throw `Spatial transform` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(DarwinCoreService.prototype, 'runSpatialTransforms').throws(); - const status = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_8(mockJobQueue, 1); - expect.fail(); - } catch (error) { - expect(transform).to.be.calledOnce; - expect(status).to.not.be.called; - expect(insertErrorStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Spatial transform'); - } - }); - }); - - describe.skip('intakeJob_step_9', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const decorate = sinon.stub(EMLService.prototype, 'decorateEML').resolves({ - '?xml': { - '@_encoding': 'UTF-8', - '@_version': '1.0' - }, - 'eml:eml': { - '@_packageId': 'urn:uuid:0cf8169f-b159-4ef9-bd43-93348bdc1e9f' - } - }); - - await service.intakeJob_step_9(1, '123-456-789', {}); - expect(decorate).to.be.calledOnce; - }); - - it('should throw `EML Decoration` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - sinon.stub(EMLService.prototype, 'decorateEML').throws(); - // const insertError = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_9(1, '123-456-789', {}); - expect.fail(); - } catch (error: any) { - // expect(insertError).to.be.calledOnce; - expect(error.message).to.eql('EML Decoration'); - } - }); - }); - - describe.skip('intakeJob_step_10', async () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const update = sinon.stub(SubmissionService.prototype, 'updateSubmissionRecordEMLJSONSource').resolves(); - - await service.intakeJob_step_10(1, 1, {}); - - expect(update).to.be.calledOnce; - }); - - it('should throw a `Updating Record EML` error', async () => { - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return { rowCount: 0, rows: [] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_10(1, 1, {}); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Updating Record EML'); - } - }); - }); - - describe.skip('intakeJob_step_11', () => { - afterEach(() => { - sinon.restore(); - }); - - // it('should run without issue', async () => { - // const mockDBConnection = getMockDBConnection(); - // const service = new DarwinCoreService(mockDBConnection); - // const mockJobQueue = { - // submission_job_queue_id: 1, - // submission_id: 1, - // job_start_timestamp: '', - // job_end_timestamp: '' - // } as ISubmissionJobQueueRecord; - // //const transform = sinon.stub(DarwinCoreService.prototype, 'transformAndUploadMetaData').resolves(); - // sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - // - // await service.intakeJob_step_11(mockJobQueue); - // - // //expect(transform).to.be.calledOnce; - // }); - - it('should throw `Transforming and uploading metadata` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - //sinon.stub(DarwinCoreService.prototype, 'transformAndUploadMetaData').throws(); - sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - const insertError = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_11(mockJobQueue); - expect.fail(); - } catch (error: any) { - expect(insertError).to.be.calledOnce; - expect(error.message).to.be.eq('Transforming and uploading metadata'); - } - }); - }); - - describe.skip('intakeJob_step_12', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - const transform = sinon.stub(DarwinCoreService.prototype, 'runSecurityTransforms').resolves(); - sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - await service.intakeJob_step_12(mockJobQueue); - - expect(transform).to.be.calledOnce; - }); - - it('should throw `Secure spatial transforms` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - sinon.stub(DarwinCoreService.prototype, 'runSecurityTransforms').throws(); - sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - const insertError = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_12(mockJobQueue); - expect.fail(); - } catch (error: any) { - expect(insertError).to.be.calledOnce; - expect(error.message).to.be.eq('Secure spatial transforms'); - } - }); - }); - - describe.skip('intakeJob_step_13', () => { - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const update = sinon.stub(DarwinCoreService.prototype, 'updateS3FileLocation').resolves(); - - await service.intakeJob_step_13(mockJobQueue); - - expect(update).to.be.calledOnce; - }); - - it('should throw `Transforming and uploading` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const updateS3 = sinon.stub(DarwinCoreService.prototype, 'updateS3FileLocation').throws(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.intakeJob_step_13(mockJobQueue); - expect.fail(); - } catch (error) { - expect(updateS3).to.be.called; - expect(insertErrorStatus).to.be.called; - } - }); - }); - - describe.skip('updateSubmissionObservationEndTimestamp', () => { - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - sinon.stub(SubmissionService.prototype, 'updateSubmissionObservationRecordEndDate').resolves(); - const submissionIssue = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.updateSubmissionObservationEndTimestamp(mockJobQueue); - expect(submissionIssue).to.not.be.called; - }); - - it('should throw `Updating Submission Observation` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - sinon.stub(SubmissionService.prototype, 'updateSubmissionObservationRecordEndDate').throws(); - const insertStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.updateSubmissionObservationEndTimestamp(mockJobQueue); - expect.fail(); - } catch (error) { - expect(insertStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal( - 'Updating Submission Observation Record End and Effective Date' - ); - } - }); - }); - - describe.skip('runTransformsOnObservations', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(DarwinCoreService.prototype, 'runSpatialTransforms').resolves(); - const security = sinon.stub(DarwinCoreService.prototype, 'runSecurityTransforms').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.runTransformsOnObservations(mockJobQueue, 1); - - expect(transform).to.be.calledOnceWith(mockJobQueue, 1); - expect(security).to.be.calledOnceWith(mockJobQueue); - expect(insertErrorStatus).to.not.be.called; - }); - - it('should throw `Running Transform` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(DarwinCoreService.prototype, 'runSpatialTransforms').throws(); - const security = sinon.stub(DarwinCoreService.prototype, 'runSecurityTransforms').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.runTransformsOnObservations(mockJobQueue, 1); - expect.fail(); - } catch (error) { - expect(transform).to.be.calledOnceWith(mockJobQueue, 1); - expect(security).to.not.be.called; - expect(insertErrorStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Running Transforms on Observation Data'); - } - }); - }); - - describe.skip('runSpatialTransforms', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - const submissionObservationId = 2; - - const transform = sinon.stub(SpatialService.prototype, 'runSpatialTransforms').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.runSpatialTransforms(mockJobQueue, submissionObservationId); - - expect(transform).to.be.calledOnceWith(mockJobQueue.submission_id, submissionObservationId); - expect(insertErrorStatus).to.not.be.called; - }); - - it('should throw `Transforming and uploading` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(SpatialService.prototype, 'runSpatialTransforms').throws(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.runSpatialTransforms(mockJobQueue, 1); - expect.fail(); - } catch (error) { - expect(transform).to.be.calledOnce; - expect(insertErrorStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Transforming and uploading spatial transforms'); - } - }); - }); - - describe.skip('runSecurityTransforms', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(SpatialService.prototype, 'runSecurityTransforms').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.runSecurityTransforms(mockJobQueue); - - expect(transform).to.be.calledOnce; - expect(insertErrorStatus).to.not.be.called; - }); - - it('should throw `Transforming and uploading` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const transform = sinon.stub(SpatialService.prototype, 'runSecurityTransforms').throws(); - const status = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatus').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.runSecurityTransforms(mockJobQueue); - expect.fail(); - } catch (error) { - expect(transform).to.be.calledOnce; - expect(status).to.not.be.called; - expect(insertErrorStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Transforming and uploading secure spatial transforms'); - } - }); - }); - - describe.skip('insertSubmissionObservationRecord', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const insertObservation = sinon.stub(SubmissionService.prototype, 'insertSubmissionObservationRecord').resolves(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - await service.insertSubmissionObservationRecord(mockJobQueue, 'dwcaJSON'); - - expect(insertObservation).to.be.calledOnce; - expect(insertErrorStatus).to.not.be.called; - }); - - it('should throw `Inserting Submission Observation` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const insertObservation = sinon.stub(SubmissionService.prototype, 'insertSubmissionObservationRecord').throws(); - const insertErrorStatus = sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - try { - await service.insertSubmissionObservationRecord(mockJobQueue, 'dwcaJSON'); - expect.fail(); - } catch (error) { - expect(insertObservation).to.be.calledOnce; - expect(insertErrorStatus).to.be.calledOnce; - expect((error as ApiGeneralError).message).to.equal('Inserting Submission Observation Record'); - } - }); - }); - - describe.skip('updateS3FileLocation', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - key: 'Key', - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const mockSubmission = { - submission_id: 1, - source_transform_id: 3, - uuid: 'uuid', - create_date: '', - create_user: 1, - update_date: null, - update_user: null, - revision_count: 0 - } as ISubmissionModel; - - const submission = sinon - .stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId') - .resolves(mockSubmission); - const moveS3 = sinon.stub(fileUtils, 'copyFileInS3').resolves(); - const deleteS3 = sinon.stub(fileUtils, 'deleteFileFromS3').resolves(); - - await service.updateS3FileLocation(mockJobQueue); - - expect(submission).to.be.calledOnce; - expect(deleteS3).to.be.calledOnce; - expect(moveS3).to.be.calledOnce; - }); - - it('should do nothing', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const mockSubmission = { - submission_id: 1, - source_transform_id: 3, - uuid: 'uuid', - create_date: '', - create_user: 1, - update_date: null, - update_user: null, - revision_count: 0 - } as ISubmissionModel; - - const submission = sinon - .stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId') - .resolves(mockSubmission); - const moveS3 = sinon.stub(fileUtils, 'copyFileInS3').resolves(); - const deleteS3 = sinon.stub(fileUtils, 'deleteFileFromS3').resolves(); - - await service.updateS3FileLocation(mockJobQueue); - - expect(submission).to.not.be.called; - expect(deleteS3).to.not.be.called; - expect(moveS3).to.not.be.called; - }); - - it('should throw error', async () => { - const mockDBConnection = getMockDBConnection({ - sql: () => { - return { rowCount: 0, rows: [] } as any as Promise>; - } - }); - const service = new DarwinCoreService(mockDBConnection); - const mockJobQueue = { - submission_job_queue_id: 1, - submission_id: 1, - key: 'Key', - job_start_timestamp: '', - job_end_timestamp: '' - } as ISubmissionJobQueueRecord; - - const moveS3 = sinon.stub(fileUtils, 'copyFileInS3').resolves(); - const deleteS3 = sinon.stub(fileUtils, 'deleteFileFromS3').resolves(); - - try { - await service.updateS3FileLocation(mockJobQueue); - expect.fail(); - } catch (error) { - expect((error as ApiExecuteSQLError).message).to.equal('Failed to get submission record'); - expect(deleteS3).to.not.be.called; - expect(moveS3).to.not.be.called; - } - }); - }); - - describe.skip('getAndPrepFileFromS3', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should run without issue', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - const dwc = sinon.createStubInstance(DWCArchive); - - sinon.stub(DarwinCoreService.prototype, 'prepDWCArchive').returns(dwc); - - const getFileFromS3Stub = sinon.stub(fileUtils, 'getFileFromS3').resolves({ Body: 'valid' }); - - const response = await service.getAndPrepFileFromS3('file-key'); - - expect(dwc).to.be.eql(response); - expect(getFileFromS3Stub).to.be.calledOnce; - }); - - it('should throw `The source file is not available` error', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new DarwinCoreService(mockDBConnection); - - const getFileFromS3Stub = sinon.stub(fileUtils, 'getFileFromS3').resolves(null as any as S3.GetObjectOutput); - - try { - await service.getAndPrepFileFromS3('file-key'); - expect.fail(); - } catch (error) { - expect((error as ApiGeneralError).message).to.equal('The source file is not available'); - expect(getFileFromS3Stub).to.be.calledOnce; - } - }); - }); - - describe.skip('ingestNewDwCADataPackage', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - const mockArchiveFile = { - rawFile: { - fileName: 'test' - }, - eml: { - buffer: Buffer.from('test') - } - }; - - const prepDWCArchiveStub = sinon - .stub(DarwinCoreService.prototype, 'prepDWCArchive') - .returns(mockArchiveFile as unknown as DWCArchive); - const insertSubmissionRecordStub = sinon - .stub(SubmissionService.prototype, 'insertSubmissionRecord') - .resolves({ submission_id: 1 }); - const getSourceTransformRecordBySystemUserIdStub = sinon - .stub(SubmissionService.prototype, 'getSourceTransformRecordBySystemUserId') - .resolves({ source_transform_id: 1 } as unknown as ISourceTransformModel); - - const response = await darwinCoreService.ingestNewDwCADataPackage( - { originalname: 'name' } as unknown as Express.Multer.File, - 'string' - ); - - expect(response).to.eql({ dataPackageId: 'string', submissionId: 1 }); - expect(prepDWCArchiveStub).to.be.calledOnce; - expect(insertSubmissionRecordStub).to.be.calledOnce; - expect(getSourceTransformRecordBySystemUserIdStub).to.be.calledOnce; - }); - }); - - describe.skip('prepDWCArchive', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when media is invalid or empty', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - sinon.stub(mediaUtils, 'parseUnknownMedia').returns(null); - - try { - await darwinCoreService.prepDWCArchive('test' as unknown as mediaUtils.UnknownMedia); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to parse submission'); - } - }); - - it('should throw an error when media is not a valid DwC Archive File', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - sinon.stub(mediaUtils, 'parseUnknownMedia').returns('test' as unknown as MediaFile); - - try { - await darwinCoreService.prepDWCArchive('test' as unknown as mediaUtils.UnknownMedia); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to parse submission'); - } - }); - - it('should succeed', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - const archiveStub = sinon.createStubInstance(ArchiveFile); - const dwcStub = sinon.createStubInstance(DWCArchive); - - sinon.stub(mediaUtils, 'parseUnknownMedia').returns(archiveStub); - const dwcAStub = sinon.stub(dwcUtils, 'DWCArchive').returns(dwcStub); - - const response = await darwinCoreService.prepDWCArchive('test' as unknown as mediaUtils.UnknownMedia); - - expect(response).to.equal(dwcStub); - expect(dwcAStub).to.be.calledOnce; - }); - }); - - describe.skip('transformAndUploadMetaData', () => { - afterEach(() => { - sinon.restore(); - }); - - // it('throws an error if there is no source_transform_id in the submission record', async () => { - // const mockDBConnection = getMockDBConnection(); - // const darwinCoreService = new DarwinCoreService(mockDBConnection); - // - // sinon - // .stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId') - // .resolves({ id: 1 } as unknown as ISubmissionModel); - // - // try { - // await darwinCoreService.transformAndUploadMetaData(1); - // expect.fail(); - // } catch (actualError) { - // expect((actualError as Error).message).to.equal('The source_transform_id is not available'); - // } - // }); - - // it('throws an error if there is no metadata_transform in the source transform record', async () => { - // const mockDBConnection = getMockDBConnection(); - // const darwinCoreService = new DarwinCoreService(mockDBConnection); - // - // sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - // submission_id: 1, - // source_transform_id: 2, - // eml_source: 'some eml source' - // } as unknown as ISubmissionModel); - // - // sinon - // .stub(SubmissionService.prototype, 'getSourceTransformRecordBySourceTransformId') - // .resolves({ source_transform_id: 2 } as unknown as ISourceTransformModel); - // - // try { - // await darwinCoreService.transformAndUploadMetaData(1); - // expect.fail(); - // } catch (actualError) { - // expect((actualError as Error).message).to.equal('The source metadata transform is not available'); - // } - // }); - - // it('throws an error if the transformed metadata is null or empty', async () => { - // const mockDBConnection = getMockDBConnection(); - // const darwinCoreService = new DarwinCoreService(mockDBConnection); - // - // sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - // submission_id: 1, - // source_transform_id: 2, - // eml_source: 'some eml source' - // } as unknown as ISubmissionModel); - // - // sinon - // .stub(SubmissionService.prototype, 'getSourceTransformRecordBySourceTransformId') - // .resolves({ source_transform_id: 2, metadata_transform: 'some transform' } as unknown as ISourceTransformModel); - // - // sinon.stub(SubmissionService.prototype, 'getSubmissionMetadataJson').resolves(''); - // - // try { - // await darwinCoreService.transformAndUploadMetaData(1); - // expect.fail(); - // } catch (actualError) { - // expect((actualError as Error).message).to.equal('The source metadata json is not available'); - // } - // }); - - // it('successfully inserts a record into elastic search', async () => { - // const mockDBConnection = getMockDBConnection(); - // const darwinCoreService = new DarwinCoreService(mockDBConnection); - // - // sinon.stub(SubmissionService.prototype, 'getSubmissionRecordBySubmissionId').resolves({ - // submission_id: 1, - // source_transform_id: 2, - // eml_source: 'some eml source', - // uuid: 'uuid' - // } as unknown as ISubmissionModel); - // - // sinon - // .stub(SubmissionService.prototype, 'getSourceTransformRecordBySourceTransformId') - // .resolves({ source_transform_id: 2, metadata_transform: 'some transform' } as unknown as ISourceTransformModel); - // - // sinon.stub(SubmissionService.prototype, 'getSubmissionMetadataJson').resolves('transformed metadata'); - // sinon.stub(SubmissionService.prototype, 'updateSubmissionMetadataWithSearchKeys').resolves(1); - // - // const uploadToElasticSearchStub = sinon - // .stub(DarwinCoreService.prototype, 'uploadToElasticSearch') - // .resolves('success response' as unknown as WriteResponseBase); - // - // await darwinCoreService.transformAndUploadMetaData(1); - // - // expect(uploadToElasticSearchStub).to.be.calledOnceWith('uuid', 'transformed metadata'); - // }); - }); - - describe.skip('uploadToElasticSearch', () => { - afterEach(() => { - sinon.restore(); - }); - - it('succeeds with valid values', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - const indexStub = sinon.stub().returns('es response'); - - sinon.stub(ESService.prototype, 'getEsClient').resolves({ - index: indexStub - } as unknown as Client); - - const response = await darwinCoreService.uploadToElasticSearch('dataPackageId', 'convertedEML'); - - expect(indexStub).to.be.calledOnceWith({ - id: 'dataPackageId', - index: ElasticSearchIndices.EML, - document: 'convertedEML' - }); - expect(response).equals('es response'); - }); - }); - - describe.skip('deleteEmlFromElasticSearchByDataPackageId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed and delete old es file', async () => { - const mockDBConnection = getMockDBConnection(); - const darwinCoreService = new DarwinCoreService(mockDBConnection); - - const esClientStub = sinon.createStubInstance(Client); - - esClientStub.delete.resolves('dataPackageId eml' as unknown as WriteResponseBase); - - const getEsClientStub = sinon - .stub(ESService.prototype, 'getEsClient') - .resolves(esClientStub as unknown as Client); - - const response = await darwinCoreService.deleteEmlFromElasticSearchByDataPackageId('dataPackageId'); - - expect(getEsClientStub).to.be.calledOnce; - expect(response).to.equal('dataPackageId eml'); - }); - }); -}); diff --git a/api/src/services/dwc-service.ts b/api/src/services/dwc-service.ts deleted file mode 100644 index 08e0dd251..000000000 --- a/api/src/services/dwc-service.ts +++ /dev/null @@ -1,779 +0,0 @@ -import { IDBConnection } from '../database/db'; -import { ApiGeneralError } from '../errors/api-error'; -import { - ISubmissionJobQueueRecord, - ISubmissionMetadataRecord, - ISubmissionObservationRecord, - SUBMISSION_MESSAGE_TYPE, - SUBMISSION_STATUS_TYPE -} from '../repositories/submission-repository'; -import { copyFileInS3, deleteFileFromS3, generateDatasetS3FileKey, getFileFromS3 } from '../utils/file-utils'; -import { getLogger } from '../utils/logger'; -import { DWCArchive } from '../utils/media/dwc/dwc-archive-file'; -import { ArchiveFile } from '../utils/media/media-file'; -import { parseUnknownMedia, UnknownMedia } from '../utils/media/media-utils'; -import { DBService } from './db-service'; -import { EMLService } from './eml-service'; -import { ElasticSearchIndices, ESService } from './es-service'; -import { SpatialService } from './spatial-service'; -import { SubmissionService } from './submission-service'; - -const defaultLog = getLogger('services/dwc-service'); - -export class DarwinCoreService extends DBService { - submissionService: SubmissionService; - spatialService: SpatialService; - emlService: EMLService; - esService: ESService; - - /** - * Creates an instance of DarwinCoreService. - * - * @param {IDBConnection} connection - * @memberof DarwinCoreService - */ - constructor(connection: IDBConnection) { - super(connection); - - this.spatialService = new SpatialService(this.connection); - this.submissionService = new SubmissionService(this.connection); - this.emlService = new EMLService(this.connection); - this.esService = new ESService(); - } - - // Look and see if the decorate needs to be run on a fresh record - async intakeJob(jobQueueRecord: ISubmissionJobQueueRecord): Promise { - // Step 1: Insert submission metadata record - const submissionMetadataId = await this.intakeJob_step_1(jobQueueRecord.submission_id); - - // Step 2: Prep file and set submission metadata eml source column - const dwcaFile = await this.intakeJob_step_2(jobQueueRecord, submissionMetadataId.submission_metadata_id); - - // Step 3: Convert eml to JSON object - const emlJSON = await this.intakeJob_step_3(jobQueueRecord.submission_id, dwcaFile); - - // Step 4: Update submission JSON column - await this.intakeJob_step_4(jobQueueRecord.submission_id, submissionMetadataId.submission_metadata_id, emlJSON); - - // Step 5: Normalize data - const normalizedJSON = await this.intakeJob_step_5(dwcaFile); - - // Step 6: End date old records - await this.intakeJob_step_6(jobQueueRecord); - - // Step 7: Insert submission observation record - const submissionObservation = await this.intakeJob_step_7(jobQueueRecord, normalizedJSON); - - // Step 8: Run spatial transforms - await this.intakeJob_step_8(jobQueueRecord, submissionObservation.submission_observation_id); - - const submissionRecord = await this.submissionService.getSubmissionRecordBySubmissionId( - jobQueueRecord.submission_id - ); - - // Step 9: Decorate EML - const decoratedEML = await this.intakeJob_step_9(jobQueueRecord.submission_id, submissionRecord.uuid, emlJSON); - - // Step 10: Update submission json column with decorated eml - await this.intakeJob_step_10( - jobQueueRecord.submission_id, - submissionMetadataId.submission_metadata_id, - decoratedEML - ); - - // Step 11: Run source transforms on decorated data - await this.intakeJob_step_11(jobQueueRecord); - - // Step 12: Run security transforms - await this.intakeJob_step_12(jobQueueRecord); - - // Step 13: Update S3 location - await this.intakeJob_step_13(jobQueueRecord); - - await this.submissionService.insertSubmissionStatus(jobQueueRecord.submission_id, SUBMISSION_STATUS_TYPE.INGESTED); - } - - /** - * Step 1 - * - Insert submission metadata record - * - * @param {number} submissionId - * @return {*} {Promise<{ - * submission_metadata_id: number; - * }>} - * @memberof DarwinCoreService - */ - async intakeJob_step_1(submissionId: number): Promise<{ - submission_metadata_id: number; - }> { - try { - const submissionMetadata: ISubmissionMetadataRecord = { - submission_id: submissionId, - eml_source: '', - eml_json_source: null - }; - - return await this.submissionService.insertSubmissionMetadataRecord(submissionMetadata); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_1', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - submissionId, - SUBMISSION_STATUS_TYPE.FAILED_INGESTION, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Inserting new Metadata record', error.message); - } - } - - /** - * Step 2 - * - Download DwCA file form S3 - * - Update submission metadata record - set EML source column - * - * @param {number} submissionJobQueueId - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async intakeJob_step_2(jobQueueRecord: ISubmissionJobQueueRecord, submissionMetadataId: number): Promise { - try { - if (!jobQueueRecord.key) { - throw new ApiGeneralError('No S3 Key given'); - } - - const file = await this.getAndPrepFileFromS3(jobQueueRecord.key); - - if (!file.eml) { - throw new ApiGeneralError('Accessing S3 File, file eml is empty'); - } - - await this.submissionService.updateSubmissionMetadataEMLSource( - jobQueueRecord.submission_id, - submissionMetadataId, - file.eml - ); - - return file; - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_2', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_EML_INGESTION, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Accessing S3 File and Updating new Metadata record', error.message); - } - } - - /** - * Step 3 - * - Convert EML to JSON - * - * @param {number} submissionId - * @param {DWCArchive} file - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async intakeJob_step_3(submissionId: number, file: DWCArchive): Promise> { - try { - if (!file.eml) { - throw new ApiGeneralError('file eml is empty'); - } - - // Convert the EML data from XML to JSON - return this.emlService.convertXMLStringToJSObject(file.eml.emlFile.buffer.toString()); - } catch (error: any) { - // TODO: does it make sense to throw/ catch here? is it even possible - defaultLog.debug({ label: 'intakeJob_step_3', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - submissionId, - SUBMISSION_STATUS_TYPE.FAILED_EML_TO_JSON, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Converting EML to JSON', error.message); - } - } - - /** - * Step 4 - * Update submission record json column - * - * @param submissionId - * @param submissionMetadataId - * @param emlJSON - */ - async intakeJob_step_4(submissionId: number, submissionMetadataId: number, emlJSON: any): Promise { - try { - await this.submissionService.updateSubmissionRecordEMLJSONSource( - submissionId, - submissionMetadataId, - JSON.stringify(emlJSON) - ); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_4', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - submissionId, - SUBMISSION_STATUS_TYPE.FAILED_EML_TO_JSON, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Storing eml JSON data', error.message); - } - } - - /** - * Step 5 - * Normalize DWCArchive file - * - * @param dwcaFile - * @returns {*} Promise - */ - async intakeJob_step_5(dwcaFile: DWCArchive): Promise { - try { - return dwcaFile.normalize(); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_5', message: 'error', error }); - // TODO: does this try catch make sense? - throw new ApiGeneralError('Normalizing DWC Archive', error.message); - } - } - - /** - * Step 6 - * End date old submission records - * - * @param jobQueueRecord - */ - async intakeJob_step_6(jobQueueRecord: ISubmissionJobQueueRecord) { - try { - // END DATE OLD METADATA - await this.submissionService.updateSubmissionMetadataRecordEndDate(jobQueueRecord.submission_id); - await this.submissionService.updateSubmissionMetadataRecordEffectiveDate(jobQueueRecord.submission_id); - - // END DATE OLF OBSERVATION RECORD - await this.updateSubmissionObservationEndTimestamp(jobQueueRecord); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_6', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.OUT_DATED_RECORD, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Update Submission dates', error.message); - } - } - - /** - * Step 7 - * Create submission observation record with normalized JSON - * - * @param jobQueueRecord - * @param normalizedJSON - * @returns - */ - async intakeJob_step_7( - jobQueueRecord: ISubmissionJobQueueRecord, - normalizedJSON: string - ): Promise<{ submission_observation_id: number }> { - try { - return await this.insertSubmissionObservationRecord(jobQueueRecord, normalizedJSON); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_7', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - throw new ApiGeneralError('Inserting Observation JSON', error.message); - } - } - - /** - * Step 8 - * Run spatial transformations - * - * @param jobQueueRecord - * @param submissionObservationId - */ - async intakeJob_step_8(jobQueueRecord: ISubmissionJobQueueRecord, submissionObservationId: number): Promise { - try { - await this.runSpatialTransforms(jobQueueRecord, submissionObservationId); - await this.submissionService.insertSubmissionStatus( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.SPATIAL_TRANSFORM_UNSECURE - ); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_8', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - throw new ApiGeneralError('Spatial transform', error.message); - } - } - - /** - * Step 9 - * Decorate EML - * - * @param {number} submissionId - * @param {string} datasetId - * @param {Record} emlJSON - * @return {*} {Promise>} Decorated JSON object - * @memberof DarwinCoreService - */ - async intakeJob_step_9( - submissionId: number, - datasetId: string, - emlJSON: Record - ): Promise> { - try { - return await this.emlService.decorateEML(submissionId, datasetId, emlJSON); - } catch (error: any) { - // TODO: does this trycatch here make sense? - defaultLog.debug({ label: 'intakeJob_step_9', message: 'error', error }); - - throw new ApiGeneralError('EML Decoration', error.message); - } - } - - /** - * Step 10 - * Update submission record with decorated EML - * - * @param submissionId number - * @param submissionMetadataId number - * @param emlJSON Record - */ - async intakeJob_step_10(submissionId: number, submissionMetadataId: number, emlJSON: Record) { - try { - await this.submissionService.updateSubmissionRecordEMLJSONSource( - submissionId, - submissionMetadataId, - JSON.stringify(emlJSON) - ); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_10', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - submissionId, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Updating Record EML', error.message); - } - } - - /** - * Step 11 - * Run source transform on decorated JSON - * @param jobQueueRecord - * @param submissionObservationId - */ - async intakeJob_step_11(jobQueueRecord: ISubmissionJobQueueRecord) { - try { - //TODO: is this deprecated? - //await this.transformAndUploadMetaData(jobQueueRecord.submission_id); - await this.submissionService.insertSubmissionStatus( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.METADATA_TO_ES - ); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_11', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_METADATA_TO_ES, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Transforming and uploading metadata', error.message); - } - } - - /** - * Step 12 - * Run security transforms on decorated JSON - * @param jobQueueRecord - */ - async intakeJob_step_12(jobQueueRecord: ISubmissionJobQueueRecord) { - try { - await this.runSecurityTransforms(jobQueueRecord); - await this.submissionService.insertSubmissionStatus( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.SPATIAL_TRANSFORM_SECURE - ); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_12', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_SECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Secure spatial transforms', error.message); - } - } - - /** - * Step 13 - * Updated S3 file location - * @param jobQueueRecord - */ - async intakeJob_step_13(jobQueueRecord: ISubmissionJobQueueRecord) { - try { - await this.updateS3FileLocation(jobQueueRecord); - } catch (error: any) { - defaultLog.debug({ label: 'intakeJob_step_13', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_UPLOAD, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('S3 location update', error.message); - } - } - - /** - * Update and set all matching submission record end timestamps. - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async updateSubmissionObservationEndTimestamp(jobQueueRecord: ISubmissionJobQueueRecord): Promise { - try { - await this.submissionService.updateSubmissionObservationRecordEndDate(jobQueueRecord.submission_id); - } catch (error: any) { - defaultLog.debug({ label: 'updateSubmissionObservationEndTimestamp', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_INGESTION, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Updating Submission Observation Record End and Effective Date', error.message); - } - } - - /** - * Run both spatial and Security Transform on Observation - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @param {number} submissionObservationId - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async runTransformsOnObservations( - jobQueueRecord: ISubmissionJobQueueRecord, - submissionObservationId: number - ): Promise { - try { - await this.runSpatialTransforms(jobQueueRecord, submissionObservationId); - - await this.runSecurityTransforms(jobQueueRecord); - } catch (error: any) { - defaultLog.debug({ label: 'runTransformsOnObservations', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Running Transforms on Observation Data', error.message); - } - } - - /** - * Insert new Submission Observation Record - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @param {string} dwcaJson - * @return {*} {Promise<{ - * submission_observation_id: number; - * }>} - * @memberof DarwinCoreService - */ - async insertSubmissionObservationRecord( - jobQueueRecord: ISubmissionJobQueueRecord, - dwcaJson: string - ): Promise<{ - submission_observation_id: number; - }> { - try { - const submissionObservationData: ISubmissionObservationRecord = { - submission_id: jobQueueRecord.submission_id, - darwin_core_source: dwcaJson, - submission_security_request: jobQueueRecord.security_request - }; - - return await this.submissionService.insertSubmissionObservationRecord(submissionObservationData); - } catch (error: any) { - defaultLog.debug({ label: 'insertSubmissionObservationRecord', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_UPLOAD, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Inserting Submission Observation Record', error.message); - } - } - - /** - * Run Spatial Transform on Submission Observation Record - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @param {number} submissionObservationId - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async runSpatialTransforms( - jobQueueRecord: ISubmissionJobQueueRecord, - submissionObservationId: number - ): Promise { - try { - //run transform on observation data - await this.spatialService.runSpatialTransforms(jobQueueRecord.submission_id, submissionObservationId); - } catch (error: any) { - defaultLog.debug({ label: 'runSpatialTransforms', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Transforming and uploading spatial transforms', error.message); - } - } - - /** - * Run Security Transform on Submission Observation Record - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - async runSecurityTransforms(jobQueueRecord: ISubmissionJobQueueRecord): Promise { - try { - //run transform on observation data - await this.spatialService.runSecurityTransforms(jobQueueRecord.submission_id); - } catch (error: any) { - defaultLog.debug({ label: 'runSecurityTransforms', message: 'error', error }); - - await this.submissionService.insertSubmissionStatusAndMessage( - jobQueueRecord.submission_id, - SUBMISSION_STATUS_TYPE.FAILED_SPATIAL_TRANSFORM_UNSECURE, - SUBMISSION_MESSAGE_TYPE.ERROR, - error.message - ); - - throw new ApiGeneralError('Transforming and uploading secure spatial transforms', error.message); - } - } - - /** - * Move S3 file to new home directory - * - * @param {ISubmissionJobQueueRecord} jobQueueRecord - * @memberof DarwinCoreService - */ - async updateS3FileLocation(jobQueueRecord: ISubmissionJobQueueRecord) { - const sourceS3Key = jobQueueRecord.key; - - if (!sourceS3Key) { - return; - } - - const submissionRecord = await this.submissionService.getSubmissionRecordBySubmissionId( - jobQueueRecord.submission_id - ); - - const fileName = `${submissionRecord.uuid}.zip`; - - const destinationS3Key = generateDatasetS3FileKey({ datasetUUID: submissionRecord.uuid, fileName: fileName }); - - // Copy object to new location - await copyFileInS3(sourceS3Key, destinationS3Key); - - // Delete original object - await deleteFileFromS3(sourceS3Key); - } - - /** - * Access file from S3 and prep into DWCA File - * - * @param {string} fileKey - * @return {*} - * @memberof DarwinCoreService - */ - async getAndPrepFileFromS3(fileKey: string) { - const s3File = await getFileFromS3(fileKey); - - if (!s3File) { - throw new ApiGeneralError('The source file is not available'); - } - - return this.prepDWCArchive(s3File); - } - - /** - * Ingest a Darwin Core Archive (DwCA) data package. - * - * @param {{ dataPackageId?: string }} [options] - * @return {*} {Promise<{ dataPackageId: string; submissionId: number }>} - * @memberof DarwinCoreService - */ - async ingestNewDwCADataPackage( - file: Express.Multer.File, - dataPackageId: string - ): Promise<{ dataPackageId: string; submissionId: number }> { - this.prepDWCArchive(file); - - // Fetch the source transform record for this submission based on the source system user id - const sourceTransformRecord = await this.submissionService.getSourceTransformRecordBySystemUserId( - this.connection.systemUserId() - ); - - const response = await this.submissionService.insertSubmissionRecord({ - source_transform_id: sourceTransformRecord.source_transform_id, - uuid: dataPackageId - }); - - const submissionId = response.submission_id; - - return { dataPackageId, submissionId }; - } - - /** - * Parse unknown submission record and convert to DWArchive file. - * - * @param {UnknownMedia} unknownMedia - * @return {*} {DWCArchive} - * @memberof DarwinCoreService - */ - prepDWCArchive(unknownMedia: UnknownMedia): DWCArchive { - const parsedMedia = parseUnknownMedia(unknownMedia); - - if (!parsedMedia) { - throw new ApiGeneralError('Failed to parse submission', [ - 'DarwinCoreService->prepDWCArchive', - 'unknown media file was empty or unable to be parsed' - ]); - } - - if (!(parsedMedia instanceof ArchiveFile)) { - throw new ApiGeneralError('Failed to parse submission', [ - 'DarwinCoreService->prepDWCArchive', - 'unknown media file was not a valid Archive file' - ]); - } - - return new DWCArchive(parsedMedia); - } - - /** - * transform submission record eml to metadata json and upload to search engine - * - * @param {number} submissionId - * @param {string} dataPackageId - * @return {*} {Promise} - * @memberof DarwinCoreService - */ - //TODO: is this deprecated? - // async transformAndUploadMetaData(submissionId: number): Promise { - // const submissionRecord = await this.submissionService.getSubmissionRecordBySubmissionId(submissionId); - // - // if (!submissionRecord.source_transform_id) { - // throw new ApiGeneralError('The source_transform_id is not available'); - // } - // - // const sourceTransformRecord = await this.submissionService.getSourceTransformRecordBySourceTransformId( - // submissionRecord.source_transform_id - // ); - // - // if (!sourceTransformRecord.metadata_transform) { - // throw new ApiGeneralError('The source metadata transform is not available'); - // } - // - // const jsonMetadata = await this.submissionService.getSubmissionMetadataJson( - // submissionId, - // sourceTransformRecord.metadata_transform - // ); - // - // if (!jsonMetadata) { - // throw new ApiGeneralError('The source metadata json is not available'); - // } - // - // // call to the ElasticSearch API to create a record with our transformed EML - // await this.uploadToElasticSearch(submissionRecord.uuid, jsonMetadata); - // - // // update submission metadata with a copy of the elastic search object - // await this.submissionService.updateSubmissionMetadataWithSearchKeys(submissionId, jsonMetadata); - // } - - /** - * Upload file to ES - * - * @param {string} dataPackageId - * @param {string} convertedEML - * @return {*} - * @memberof DarwinCoreService - */ - async uploadToElasticSearch(dataPackageId: string, convertedEML: string) { - const esClient = await this.esService.getEsClient(); - - return esClient.index({ - id: dataPackageId, - index: ElasticSearchIndices.EML, - document: convertedEML - }); - } - - /** - * Delete old data from ES - * - * @param {string} dataPackageId - * @return {*} - * @memberof DarwinCoreService - */ - async deleteEmlFromElasticSearchByDataPackageId(dataPackageId: string) { - const esClient = await this.esService.getEsClient(); - - return esClient.delete({ id: dataPackageId, index: ElasticSearchIndices.EML }); - } -} diff --git a/api/src/services/eml-service.test.ts b/api/src/services/eml-service.test.ts deleted file mode 100644 index 35806f7ec..000000000 --- a/api/src/services/eml-service.test.ts +++ /dev/null @@ -1,509 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { ISystemConstant } from '../repositories/system-constant-repository'; -import { getMockDBConnection } from '../__mocks__/db'; -import { BcgwLayerService } from './bcgw-layer-service'; -import { EMLService } from './eml-service'; -import { Srid3005 } from './geo-service'; -import { SpatialService } from './spatial-service'; -import { SystemConstantService } from './system-constant-service'; - -chai.use(sinonChai); - -describe('EMLService', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('convertXMLStringToJSObject', () => { - afterEach(() => { - sinon.restore(); - }); - - it('transforms an XML string to a JS Object', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const emlXMLString = ` - - - - - My Dataset Title - - - - My Project Title - - - - My Related Project - - - - - - M-ALAM - - - - - `; - - const emlJSObject = emlService.convertXMLStringToJSObject(emlXMLString); - - expect(emlJSObject).to.eql({ - '?xml': { - '@_encoding': 'UTF-8', - '@_version': '1.0' - }, - 'eml:eml': { - '@_packageId': 'urn:uuid:0cf8169f-b159-4ef9-bd43-93348bdc1e9f', - dataset: { - '@_system': '', - title: 'My Dataset Title', - project: { - '@_system': 'project_system', - title: 'My Project Title', - relatedProject: [ - { - '@_system': '', - title: 'My Related Project' - } - ] - }, - taxonomicCoverage: [ - { - taxonId: { - '@_provider': '', - '#text': 'M-ALAM' - } - } - ] - } - } - }); - }); - }); - - describe('parseJSObjectToXMLString', () => { - afterEach(() => { - sinon.restore(); - }); - - it('transforms a JS Object to an XML string', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const emlJSObject = { - '?xml': { - '@_encoding': 'UTF-8', - '@_version': '1.0' - }, - 'eml:eml': { - '@_packageId': 'urn:uuid:0cf8169f-b159-4ef9-bd43-93348bdc1e9f', - dataset: { - '@_system': '', - title: 'My Dataset Title', - project: { - '@_system': 'project_system', - title: 'My Project Title', - relatedProject: [ - { - '@_system': '', - title: 'My Related Project' - } - ] - }, - taxonomicCoverage: [ - { - taxonId: { - '@_provider': '', - '#text': 'M-ALAM' - } - } - ] - } - } - }; - - const xmlString = emlService.convertJSObjectToXMLString(emlJSObject); - - expect(xmlString).to.eql( - 'My Dataset TitleMy Project TitleMy Related ProjectM-ALAM' - ); - }); - }); - - describe('getSystemURL', () => { - it('returns the system url', () => { - process.env.APP_HOST = 'http://localhost:7200'; - - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const response = emlService.getSystemURL(); - - expect(response).to.eql('http://localhost:7200'); - }); - }); - - describe('getDatasetSystemURL', () => { - it('returns the dataset system url', () => { - process.env.APP_HOST = 'https://www.biohub.ca'; - - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const response = emlService.getDatasetSystemURL(); - - expect(response).to.eql('https://www.biohub.ca/datasets'); - }); - }); - - describe('getTaxonomicProviderURL', () => { - it('returns url string', () => { - process.env.ELASTICSEARCH_URL = 'www.elastic.com'; - process.env.ELASTICSEARCH_TAXONOMY_INDEX = 'taxonomy_index'; - - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const response = emlService.getTaxonomicProviderURL(); - - expect(response).to.eql('www.elastic.com/taxonomy_index'); - }); - }); - - describe('getMetadataProviderNode', () => { - it('returns a metadataProvider object', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - sinon.stub(SystemConstantService.prototype, 'getSystemConstants').resolves([ - { constant_name: 'ORGANIZATION_NAME_FULL', character_value: 'organization name' }, - { constant_name: 'ORGANIZATION_URL', character_value: 'www.organization-url.com' } - ] as unknown as ISystemConstant[]); - - const response = await emlService.getMetadataProviderNode(); - - expect(response).to.eql({ - organizationName: 'organization name', - onlineUrl: 'www.organization-url.com' - }); - }); - - it('returns an empty metadataProvider object if system constants are not found', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - sinon.stub(SystemConstantService.prototype, 'getSystemConstants').resolves([] as unknown as ISystemConstant[]); - - const response = await emlService.getMetadataProviderNode(); - - expect(response).to.eql({ - organizationName: '', - onlineUrl: '' - }); - }); - }); - - describe('getRegionAdditionalMetadataNode', () => { - it('returns a region additionalMetadata object', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const submissionId = 1; - const datasetId = '123-456-789'; - - const mockBoundaryCentroidWktString = 'POINT(123,456)'; - const mockBoundaryWktString = 'POLYGON(123,456,789)'; - - // Mock `getGeometryAsWktFromBoundarySpatialComponentBySubmissionId` calls - sinon - .stub(SpatialService.prototype, 'getGeometryAsWktFromBoundarySpatialComponentBySubmissionId') - .withArgs(submissionId, SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, Srid3005) - .resolves({ geometry: mockBoundaryCentroidWktString }) - .withArgs(submissionId, SPATIAL_COMPONENT_TYPE.BOUNDARY, Srid3005) - .resolves({ geometry: mockBoundaryWktString }); - - // Mock `getEnvRegionNames` calls - sinon - .stub(BcgwLayerService.prototype, 'getEnvRegionNames') - .withArgs(mockBoundaryCentroidWktString) - .resolves(['EnvRegion1']) - .withArgs(mockBoundaryWktString) - .resolves(['EnvRegion1', 'EnvRegion2', 'EnvRegion3']); - - // Mock `getNrmRegionNames` calls - sinon - .stub(BcgwLayerService.prototype, 'getNrmRegionNames') - .withArgs(mockBoundaryCentroidWktString) - .resolves(['NrmRegion1']) - .withArgs(mockBoundaryWktString) - .resolves(['NrmRegion1']); - - const response = await emlService.getRegionAdditionalMetadataNode(submissionId, datasetId); - - expect(response).to.eql({ - describes: datasetId, - metadata: { - regions: { - env: [ - { name: 'EnvRegion1', from: 'Boundary Centroid' }, - { name: 'EnvRegion2', from: 'Boundary' }, - { name: 'EnvRegion3', from: 'Boundary' } - ], - nrm: [{ name: 'NrmRegion1', from: 'Boundary Centroid' }] - } - } - }); - }); - - it('returns a region additionalMetadata object if no regions are found', async () => { - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const submissionId = 1; - const datasetId = '123-456-789'; - - const mockBoundaryCentroidWktString = 'POINT(123,456)'; - const mockBoundaryWktString = 'POLYGON(123,456,789)'; - - // Mock `getGeometryAsWktFromBoundarySpatialComponentBySubmissionId` calls - sinon - .stub(SpatialService.prototype, 'getGeometryAsWktFromBoundarySpatialComponentBySubmissionId') - .withArgs(submissionId, SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, Srid3005) - .resolves({ geometry: mockBoundaryCentroidWktString }) - .withArgs(submissionId, SPATIAL_COMPONENT_TYPE.BOUNDARY, Srid3005) - .resolves({ geometry: mockBoundaryWktString }); - - // Mock `getEnvRegionNames` calls - sinon - .stub(BcgwLayerService.prototype, 'getEnvRegionNames') - .withArgs(mockBoundaryCentroidWktString) - .resolves([]) - .withArgs(mockBoundaryWktString) - .resolves([]); - - // Mock `getNrmRegionNames` calls - sinon - .stub(BcgwLayerService.prototype, 'getNrmRegionNames') - .withArgs(mockBoundaryCentroidWktString) - .resolves([]) - .withArgs(mockBoundaryWktString) - .resolves([]); - - const response = await emlService.getRegionAdditionalMetadataNode(submissionId, datasetId); - - expect(response).to.eql({ - describes: datasetId, - metadata: { - regions: { - env: [], - nrm: [] - } - } - }); - }); - }); - - describe('decorateEML', () => { - afterEach(() => { - sinon.restore(); - }); - - it('decorates the eml', async () => { - process.env.NODE_ENV = 'dev'; - process.env.APP_HOST = 'www.host.com'; - process.env.ELASTICSEARCH_URL = 'www.elastic.com'; - process.env.ELASTICSEARCH_TAXONOMY_INDEX = 'taxonomy_index'; - - const mockDBConnection = getMockDBConnection(); - const emlService = new EMLService(mockDBConnection); - - const submissionId = 1; - const datasetId = '123-456-789'; - - sinon - .stub(EMLService.prototype, 'getMetadataProviderNode') - .resolves({ organizationName: 'organization name', onlineUrl: 'www.organization-url.com' }); - - sinon.stub(EMLService.prototype, 'getRegionAdditionalMetadataNode').resolves({ - describes: datasetId, - metadata: { - regions: { - env: [ - { from: 'Boundary Centroid', name: 'EnvRegion1' }, - { from: 'Boundary', name: 'EnvRegion1' }, - { from: 'Boundary', name: 'EnvRegion2' } - ], - nrm: [ - { from: 'Boundary Centroid', name: 'NrmRegion1' }, - { from: 'Boundary', name: 'NrmRegion1' } - ] - } - } - }); - - const emlXMLString = ` - - - - - My Dataset Title - - - - My Project Title - - - - My Related Project - - - - - - M-ALAM - - - - Survey Area Name - - -121.904297 - -120.19043 - 51.971346 - 50.930738 - - - - - 50.930738 - -121.904297 - - - 51.971346 - -121.904297 - - - 51.971346 - -120.19043 - - - 50.930738 - -120.19043 - - - 50.930738 - -121.904297 - - - - - - - `; - - // Generate the sample test object using the real xml convert function - const emlObject = emlService.convertXMLStringToJSObject(emlXMLString); - - const decoratedEMLObject = await emlService.decorateEML(submissionId, datasetId, emlObject); - - expect(decoratedEMLObject).to.eql({ - '?xml': { - '@_encoding': 'UTF-8', - '@_version': '1.0' - }, - 'eml:eml': { - '@_packageId': 'urn:uuid:0cf8169f-b159-4ef9-bd43-93348bdc1e9f', - '@_system': 'www.host.com', - dataset: { - '@_system': 'www.host.com/datasets', - metadataProvider: [ - { - onlineUrl: 'www.organization-url.com', - organizationName: 'organization name' - } - ], - title: 'My Dataset Title', - project: { - '@_system': 'www.host.com/datasets', - title: 'My Project Title', - relatedProject: [ - { - '@_system': 'www.host.com/datasets', - title: 'My Related Project' - } - ] - }, - taxonomicCoverage: [ - { - taxonId: { - '@_provider': 'www.elastic.com/taxonomy_index', - '#text': 'M-ALAM' - } - } - ], - geographicCoverage: { - geographicDescription: 'Survey Area Name', - boundingCoordinates: { - westBoundingCoordinate: '-121.904297', - eastBoundingCoordinate: '-120.19043', - northBoundingCoordinate: '51.971346', - southBoundingCoordinate: '50.930738' - }, - datasetGPolygon: { - datasetGPolygonOuterGRing: { - gRingPoint: [ - { - gRingLatitude: '50.930738', - gRingLongitude: '-121.904297' - }, - { - gRingLatitude: '51.971346', - gRingLongitude: '-121.904297' - }, - { - gRingLatitude: '51.971346', - gRingLongitude: '-120.19043' - }, - { - gRingLatitude: '50.930738', - gRingLongitude: '-120.19043' - }, - { - gRingLatitude: '50.930738', - gRingLongitude: '-121.904297' - } - ] - } - } - } - }, - additionalMetadata: [ - { - describes: '123-456-789', - metadata: { - regions: { - env: [ - { from: 'Boundary Centroid', name: 'EnvRegion1' }, - { from: 'Boundary', name: 'EnvRegion1' }, - { from: 'Boundary', name: 'EnvRegion2' } - ], - nrm: [ - { from: 'Boundary Centroid', name: 'NrmRegion1' }, - { from: 'Boundary', name: 'NrmRegion1' } - ] - } - } - } - ] - } - }); - }); - }); -}); diff --git a/api/src/services/eml-service.ts b/api/src/services/eml-service.ts deleted file mode 100644 index 51267bbdb..000000000 --- a/api/src/services/eml-service.ts +++ /dev/null @@ -1,317 +0,0 @@ -import jsonpatch, { Operation } from 'fast-json-patch'; -import { XMLBuilder, XMLParser } from 'fast-xml-parser'; -import { JSONPath } from 'jsonpath-plus'; -import { z } from 'zod'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { IDBConnection } from '../database/db'; -import { getLogger } from '../utils/logger'; -import { BcgwLayerService } from './bcgw-layer-service'; -import { DBService } from './db-service'; -import { Srid3005 } from './geo-service'; -import { SpatialService } from './spatial-service'; -import { SystemConstantService } from './system-constant-service'; - -const defaultLog = getLogger('services/eml-service'); - -export class EMLService extends DBService { - _XMLParserOptions = { - ignoreAttributes: false, - attributeNamePrefix: '@_', - // Passes all values through as strings. This avoids problems where text fields have numbers only but need to be - // interpreted as text. - parseTagValue: false, - isArray: (tagName: string) => { - const tagsArray: Array = [ - 'relatedProject', - 'section', - 'taxonomicCoverage', - 'metadataProvider', - 'additionalMetadata' - ]; - - return tagsArray.includes(tagName); - } - }; - - /** - * Creates an instance of EMLService. - * - * @param {IDBConnection} connection - * @memberof DarwinCoreService - */ - constructor(connection: IDBConnection) { - super(connection); - } - - /** - * Converts an XML string to a JS Object. - * - * @param {string} xmlString - * @return {*} {Record} - * @memberof EMLService - */ - convertXMLStringToJSObject(xmlString: string): Record { - const xmlParser = new XMLParser(this._XMLParserOptions); - - // Zod schema to validate value is type `Record` - const recordSchema = z.record(z.any()); - - return recordSchema.parse(xmlParser.parse(xmlString)); - } - - /** - * Converts a JS Object to an XML string. - * - * @param {Record} jsObject - * @return {*} {string} - * @memberof EMLService - */ - convertJSObjectToXMLString(jsObject: Record): string { - const xmlBuilder = new XMLBuilder(this._XMLParserOptions); - - // Zod schema to validate value is type `string` - const stringSchema = z.string(); - - const x = xmlBuilder.build(jsObject); - - return stringSchema.parse(x); - } - - /** - * Get the BioHub system URL. - * - * @example - * www.biohub.gov.bc.ca - * @return {*} {string} - * @memberof EMLService - */ - getSystemURL(): string { - return process.env.APP_HOST || ''; - } - - /** - * Get the BioHub dataset URL prefix. Used in combination with a dataset uuid to create a URL to a specific dataset. - * - * @example - * www.biohub.gov.bc.ca/datasets - * @return {*} {string} - * @memberof EMLService - */ - getDatasetSystemURL(): string { - return `${this.getSystemURL()}/datasets`; - } - - /** - * Get the BioHub taxonomic system URL. - * - * @example - * www.biohub-elastic-search.gov.bc.ca/taxonomy_index - * @return {*} {string} - * @memberof EMLService - */ - getTaxonomicProviderURL(): string { - return `${process.env.ELASTICSEARCH_URL}/${process.env.ELASTICSEARCH_TAXONOMY_INDEX}`; - } - - /** - * Get a BioHub `metadataProvider` object. - * - * @return {*} {Promise<{ organizationName: string; onlineUrl: string }>} - * @memberof EMLService - */ - async getMetadataProviderNode(): Promise<{ organizationName: string; onlineUrl: string }> { - const systemConstantService = new SystemConstantService(this.connection); - const response = await systemConstantService.getSystemConstants(['ORGANIZATION_NAME_FULL', 'ORGANIZATION_URL']); - - const organizationName = - response.find((item) => item.constant_name === 'ORGANIZATION_NAME_FULL')?.character_value || ''; - const onlineUrl = response.find((item) => item.constant_name === 'ORGANIZATION_URL')?.character_value || ''; - - return { organizationName: organizationName, onlineUrl: onlineUrl }; - } - - /** - * Compares the submission `Boundary` spatial component against BCGW layers, and builds an `additionalMetadata` - * object containing the names of the matching layer features (ie: which regions does the submission boundary cross). - * - * @param {number} submissionId - * @param {string} datasetId - * @return {*} {Promise} - * @memberof EMLService - */ - async getRegionAdditionalMetadataNode(submissionId: number, datasetId: string): Promise { - const spatialService = new SpatialService(this.connection); - - // Fetch the submission `Boundary Centroid` spatial component - const bondaryCentroidSpatialComponent = - await spatialService.getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId, - SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, - Srid3005 - ); - - // Fetch the submission `Boundary` spatial component - const boundarySpatialComponent = await spatialService.getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId, - SPATIAL_COMPONENT_TYPE.BOUNDARY, - Srid3005 - ); - - const datasetRegionService = new BcgwLayerService(); - - // Fetch env `Boundary Centroid` and `Boundary` regions - const envBoundaryCentroidRegionNames = await datasetRegionService.getEnvRegionNames( - bondaryCentroidSpatialComponent.geometry - ); - const envBoundaryRegionNames = await datasetRegionService.getEnvRegionNames(boundarySpatialComponent.geometry); - - // Fetch nrm `Boundary Centroid` and `Boundary` regions - const nrmBoundaryCentroidRegionNames = await datasetRegionService.getNrmRegionNames( - bondaryCentroidSpatialComponent.geometry - ); - const nrmBoundaryRegionNames = await datasetRegionService.getNrmRegionNames(boundarySpatialComponent.geometry); - - // Build additionalMetadata object for region names - return { - describes: datasetId, - metadata: { - regions: { - env: [ - // Add renv egions found based on the boundary centroid - ...envBoundaryCentroidRegionNames.map((name) => ({ - name: name, - from: SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID - })), - // Add env regions found based on the boundary - ...envBoundaryRegionNames - .filter((item) => !envBoundaryCentroidRegionNames.includes(item)) - .map((name) => ({ name: name, from: SPATIAL_COMPONENT_TYPE.BOUNDARY })) - ], - nrm: [ - // Add nrm regions found based on the boundary centroid - ...nrmBoundaryCentroidRegionNames.map((name) => ({ - name: name, - from: SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID - })), - // Add nrm regions found based on the boundary - ...nrmBoundaryRegionNames - .filter((item) => !nrmBoundaryCentroidRegionNames.includes(item)) - .map((name) => ({ name: name, from: SPATIAL_COMPONENT_TYPE.BOUNDARY })) - ] - } - } - }; - } - - /** - * Decorates an EML object, adding additional BioHub metadata to the original EML. - * - * @param {number} submissionId - * @param {string} datasetId - * @param {Record} eml - * @return {*} {Promise>} - * @memberof EMLService - */ - async decorateEML(submissionId: number, datasetId: string, eml: Record): Promise> { - // The config for a list of patch operations to perform on the EML. - // Note: the order of these patches may be important. Below, when patches are being applied, they are applied in - // order, allows iterative patches to be supported. - const patches = [ - { - // Set the `@_system` attribute on the `eml:eml` node. - path: '$..eml:eml', - property: '@_system', - value: this.getSystemURL() - }, - { - // Set the `@_system` attribute on the `dataset` node. - path: '$..eml:eml.dataset', - property: '@_system', - value: this.getDatasetSystemURL() - }, - { - // Set the `@_system` attribute on the `project` node. - path: '$..eml:eml.dataset.project', - property: '@_system', - value: this.getDatasetSystemURL() - }, - { - // Set the `@_system` attribute on all `relatedProject` nodes. - path: '$..eml:eml..relatedProject[*]', - property: '@_system', - value: this.getDatasetSystemURL() - }, - { - // Set the `@_provider` attribute on all `taxonId` nodes that are a descendent of `taxonomicCoverage` - path: '$..eml:eml..taxonomicCoverage..taxonId', - property: '@_provider', - value: this.getTaxonomicProviderURL() - }, - { - // Add a `metadataProvider` node if one does not already exist - path: '$..eml:eml.dataset', - property: 'metadataProvider', - value: [] - }, - { - // Append an object to the `metadataProvider` node. - path: '$..eml:eml.dataset.metadataProvider', - property: '-', // append to the end of the array - value: await this.getMetadataProviderNode() - }, - { - // Add a `additionalMetadata` node if one does not already exist - path: '$..eml:eml', - property: 'additionalMetadata', - value: [] - }, - { - // Append an object to the `additionalMetadata` node. - path: '$..eml:eml.additionalMetadata', - property: '-', // append to the end of the array - value: await this.getRegionAdditionalMetadataNode(submissionId, datasetId) - } - ]; - - // Iterates over `patches` in order from first to last, applying all resulting patch operations one by one. - // Note: subsequent patches will operate on the output of the previous patches. This means iterative patches are - // possible, if needed. - for (const patch of patches) { - const patchOperations: Operation[] = []; - - try { - const paths = JSONPath({ - path: patch.path, - json: eml, - resultType: 'all' - }); - - paths.forEach((path: any) => { - // Get value of target property - const currentPropertyValue = path.value[patch.property]; - - if (currentPropertyValue) { - // Target property exists and its value is truthy: do not modify it - return; - } - - // Patch the value of the target property - const patchOperation: Operation = { - op: 'add', - path: `${path.pointer}/${patch.property}`, - value: patch.value - }; - - patchOperations.push(patchOperation); - }); - } catch (error) { - defaultLog.warn({ label: 'decorateEML', message: 'error', failed_patch: patch, error }); - } - - // Apply patch to eml object. This updated eml object will be used in subsequent patches. - eml = jsonpatch.applyPatch(eml, patchOperations).newDocument; - } - - return eml; - } -} diff --git a/api/src/services/es-service.test.ts b/api/src/services/es-service.test.ts deleted file mode 100644 index 6e8441d79..000000000 --- a/api/src/services/es-service.test.ts +++ /dev/null @@ -1,29 +0,0 @@ -import { Client } from '@elastic/elasticsearch'; -import chai, { expect } from 'chai'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { ESService } from './es-service'; - -chai.use(sinonChai); - -describe('ESService', () => { - describe('getEsClient', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return new elastic search client', async () => { - const esService = new ESService(); - - const clientStub = sinon.stub().callsFake(() => { - return 'test'; - }); - - Object.setPrototypeOf(Client, clientStub); - - esService.getEsClient(); - - expect(clientStub).to.be.calledOnce; - }); - }); -}); diff --git a/api/src/services/es-service.ts b/api/src/services/es-service.ts deleted file mode 100644 index eb1034944..000000000 --- a/api/src/services/es-service.ts +++ /dev/null @@ -1,84 +0,0 @@ -import { Client } from '@elastic/elasticsearch'; -import { AggregationsAggregate, SearchHit, SearchRequest, SearchResponse } from '@elastic/elasticsearch/lib/api/types'; - -export const ElasticSearchIndices = { - EML: process.env.ELASTICSEARCH_EML_INDEX || 'eml', - TAXONOMY: process.env.ELASTICSEARCH_TAXONOMY_INDEX || 'taxonomy_3.0.0' -}; - -/** - * Base class for services that require a elastic search connection. - * - * @export - * @class ESService - */ -export class ESService { - esClient: Client | undefined = undefined; - - /** - * Returns the Elasticsearch Client instance. If `this.esClient` isn't defined, - * a new Elasticsearch Client is instantiated. - * - * @return {*} {Promise} - * @memberof ESService - */ - async getEsClient(): Promise { - if (!this.esClient) { - this.esClient = await new Client({ node: process.env.ELASTICSEARCH_URL }); - } - return this.esClient; - } - - /** - * Performs a search in Elasticsearch. - * @param searchRequest The ES search request - * @returns {Promise>} The results of the search - */ - async _elasticSearch(searchRequest: SearchRequest): Promise[]> { - const { index, ...request } = searchRequest; - const esClient = await this.getEsClient(); - - const response: SearchResponse> = await esClient.search({ - index: String(index).toLowerCase(), - ...request - }); - - return response.hits.hits; - } - - /** - * Searches for projects based on a given species or keyword query. - * @param query The species/keywords to search for - * @returns {Promise>} The results of the search - */ - async keywordSearchEml(query: string): Promise[]> { - return this._elasticSearch({ - index: ElasticSearchIndices.EML, - - query: { - multi_match: { - fields: ['*'], - type: 'phrase_prefix', - query - } - } - }); - } - - /** - * Searches for projects based on a datasetId. - * @param query The species/keywords to search for - * @returns {Promise>} The results of the search - */ - async datasetSearchEml(datasetId: string): Promise[]> { - return this._elasticSearch({ - index: ElasticSearchIndices.EML, - query: { - ids: { - values: [datasetId] - } - }, - fields: ['*'] - }); - } -} diff --git a/api/src/services/gcnotify-service.ts b/api/src/services/gcnotify-service.ts index 065c4250b..3e85c394a 100644 --- a/api/src/services/gcnotify-service.ts +++ b/api/src/services/gcnotify-service.ts @@ -1,9 +1,7 @@ import axios, { AxiosRequestConfig } from 'axios'; -import { ACCESS_REQUEST_ADMIN_EMAIL, ACCESS_REQUEST_APPROVAL_ADMIN_EMAIL } from '../constants/notifications'; import { IDBConnection } from '../database/db'; -import { ApiError, ApiErrorType, ApiGeneralError } from '../errors/api-error'; +import { ApiError, ApiErrorType } from '../errors/api-error'; import { IgcNotifyGenericMessage, IgcNotifyPostReturn } from '../interfaces/gcnotify.interface'; -import { AdministrativeRepository } from '../repositories/administrative-repository'; import { getLogger } from '../utils/logger'; import { formatPhoneNumber, makeLoginUrl } from '../utils/string-utils'; import { ArtifactService } from './artifact-service'; @@ -55,7 +53,6 @@ interface IGcNotifyArtifactRequestAccess { const defaultLog = getLogger('services/gcnotify-service'); export class GCNotifyService extends DBService { - administrativeRepository: AdministrativeRepository; axiosConfig: AxiosRequestConfig; EMAIL_TEMPLATE: string; SECURE_DOCUMENT_REQUEST_TEMPLATE: string; @@ -68,8 +65,6 @@ export class GCNotifyService extends DBService { constructor(connection: IDBConnection) { super(connection); - this.administrativeRepository = new AdministrativeRepository(connection); - this.SECURE_DOCUMENT_REQUEST_TEMPLATE = process.env.GCNOTIFY_REQUEST_ACCESS_SECURE_DOCUMENTS || ''; this.EMAIL_TEMPLATE = process.env.GCNOTIFY_ONBOARDING_REQUEST_EMAIL_TEMPLATE || ''; this.SMS_TEMPLATE = process.env.GCNOTIFY_ONBOARDING_REQUEST_SMS_TEMPLATE || ''; @@ -225,78 +220,4 @@ export class GCNotifyService extends DBService { return result; } - - /** - * Check if access request is approved, then send Approval email - * - * @param {number} adminActivityTypeId - * @param {string} userIdentifier - * @param {string} identitySource - * @memberof GCNotifyService - */ - async sendApprovalEmail(adminActivityTypeId: number, userIdentifier: string, identitySource: string) { - if (await this.administrativeRepository.checkIfAccessRequestIsApproval(adminActivityTypeId)) { - const userEmail = await this.getUserKeycloakEmail(userIdentifier, identitySource); - this.sendAccessRequestApprovalEmail(userEmail); - } - } - - /** - * Get users email from username and identity source - * - * @param {string} userIdentifier - * @param {string} identitySource - * @return {*} {Promise} - * @memberof GCNotifyService - */ - async getUserKeycloakEmail(userIdentifier: string, identitySource: string): Promise { - // const keycloakService = new KeycloakService(); - // const userDetails = await keycloakService.getUserByUsername(`${userIdentifier}@${identitySource}`); - // return userDetails.email; - return Promise.resolve(''); - } - - /** - * Send Approval Email - * - * @param {string} userEmail - * @memberof GCNotifyService - */ - async sendAccessRequestApprovalEmail(userEmail: string) { - const APP_HOST = process.env.APP_HOST; - const NODE_ENV = process.env.NODE_ENV; - - const url = `${APP_HOST}/`; - const hrefUrl = `[click here.](${url})`; - try { - await this.sendEmailGCNotification(userEmail, { - ...ACCESS_REQUEST_APPROVAL_ADMIN_EMAIL, - subject: `${NODE_ENV}: ${ACCESS_REQUEST_APPROVAL_ADMIN_EMAIL.subject}`, - body1: `${ACCESS_REQUEST_APPROVAL_ADMIN_EMAIL.body1} ${hrefUrl}`, - footer: `${APP_HOST}` - }); - } catch (error) { - throw new ApiGeneralError('Failed to send gcNotification approval email', [(error as Error).message]); - } - } - - /** - * Send Email that Access Request has been received - * - * @memberof GCNotifyService - */ - async sendAccessRequestReceivedEmail() { - const ADMIN_EMAIL = process.env.GCNOTIFY_ADMIN_EMAIL || ''; - const APP_HOST = process.env.APP_HOST; - const NODE_ENV = process.env.NODE_ENV; - - const url = `${APP_HOST}/admin/users?authLogin=true`; - const hrefUrl = `[click here.](${url})`; - this.sendEmailGCNotification(ADMIN_EMAIL, { - ...ACCESS_REQUEST_ADMIN_EMAIL, - subject: `${NODE_ENV}: ${ACCESS_REQUEST_ADMIN_EMAIL.subject}`, - body1: `${ACCESS_REQUEST_ADMIN_EMAIL.body1} ${hrefUrl}`, - footer: `${APP_HOST}` - }); - } } diff --git a/api/src/services/spatial-service.test.ts b/api/src/services/spatial-service.test.ts index c46bd69bd..a13876b43 100644 --- a/api/src/services/spatial-service.test.ts +++ b/api/src/services/spatial-service.test.ts @@ -1,5 +1,4 @@ import chai, { expect } from 'chai'; -import { FeatureCollection } from 'geojson'; import { describe } from 'mocha'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; @@ -107,164 +106,6 @@ describe('SpatialService', () => { }); }); - describe('runSpatialTransforms', () => { - it('should return submission_spatial_component_id after running transform and inserting data', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const getSpatialTransformRecordsStub = sinon - .stub(SpatialService.prototype, 'getSpatialTransformRecords') - .resolves([ - { - spatial_transform_id: 1, - name: 'name1', - description: null, - notes: null, - transform: 'transform1' - }, - { - spatial_transform_id: 2, - name: 'name2', - description: null, - notes: null, - transform: 'transform2' - } - ]); - - const runSpatialTransformOnSubmissionIdStub = sinon - .stub(SpatialRepository.prototype, 'runSpatialTransformOnSubmissionId') - .onCall(0) - .resolves([ - { result_data: 'result1' as unknown as FeatureCollection }, - { result_data: 'result2' as unknown as FeatureCollection } - ]) - .onCall(1) - .resolves([ - { result_data: 'result3' as unknown as FeatureCollection }, - { result_data: 'result4' as unknown as FeatureCollection } - ]); - - const insertSubmissionSpatialComponentStub = sinon - .stub(SpatialRepository.prototype, 'insertSubmissionSpatialComponent') - .onCall(0) - .resolves({ submission_spatial_component_id: 3 }) - .onCall(1) - .resolves({ submission_spatial_component_id: 4 }) - .onCall(2) - .resolves({ submission_spatial_component_id: 5 }) - .onCall(3) - .resolves({ submission_spatial_component_id: 6 }); - - const insertSpatialTransformSubmissionRecordStub = sinon - .stub(SpatialRepository.prototype, 'insertSpatialTransformSubmissionRecord') - .resolves(); - - await spatialService.runSpatialTransforms(8, 9); - - expect(getSpatialTransformRecordsStub).to.be.calledOnceWith(); - expect(runSpatialTransformOnSubmissionIdStub).to.be.calledWith(8, 'transform1').calledWith(8, 'transform2'); - expect(insertSubmissionSpatialComponentStub) - .to.be.calledWith(9, 'result1') - .calledWith(9, 'result2') - .calledWith(9, 'result3') - .calledWith(9, 'result4'); - expect(insertSpatialTransformSubmissionRecordStub) - .to.be.calledWith(1, 3) - .calledWith(1, 4) - .calledWith(2, 5) - .calledWith(2, 6); - }); - }); - - describe('runSecurityTransforms', () => { - it('should return submission_security_component_id after running transform and updating data', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const getSecurityTransformRecordsStub = sinon - .stub(SpatialService.prototype, 'getSecurityTransformRecords') - .resolves([ - { - security_transform_id: 1, - name: 'name1', - description: null, - notes: null, - transform: 'transform1' - }, - { - security_transform_id: 2, - name: 'name2', - description: null, - notes: null, - transform: 'transform2' - } - ]); - - const runSecurityTransformOnSubmissionIdStub = sinon - .stub(SpatialRepository.prototype, 'runSecurityTransformOnSubmissionId') - .onCall(0) - .resolves([ - { - spatial_component: { - submission_spatial_component_id: 1, - spatial_data: 'result1' as unknown as FeatureCollection - } - }, - { - spatial_component: { - submission_spatial_component_id: 2, - spatial_data: 'result2' as unknown as FeatureCollection - } - } - ]) - .onCall(1) - .resolves([ - { - spatial_component: { - submission_spatial_component_id: 3, - spatial_data: 'result3' as unknown as FeatureCollection - } - }, - { - spatial_component: { - submission_spatial_component_id: 4, - spatial_data: 'result4' as unknown as FeatureCollection - } - } - ]); - - const updateSubmissionSpatialComponentStub = sinon - .stub(SpatialRepository.prototype, 'updateSubmissionSpatialComponentWithSecurity') - .onCall(0) - .resolves({ submission_spatial_component_id: 3 }) - .onCall(1) - .resolves({ submission_spatial_component_id: 4 }) - .onCall(2) - .resolves({ submission_spatial_component_id: 5 }) - .onCall(3) - .resolves({ submission_spatial_component_id: 6 }); - - const insertSecurityTransformSubmissionRecordStub = sinon - .stub(SpatialRepository.prototype, 'insertSecurityTransformSubmissionRecord') - .resolves(); - - await spatialService.runSecurityTransforms(9); - - expect(getSecurityTransformRecordsStub).to.be.calledOnceWith(); - expect(runSecurityTransformOnSubmissionIdStub).to.be.calledWith(9, 'transform1').calledWith(9, 'transform2'); - expect(updateSubmissionSpatialComponentStub) - .to.be.calledWith(1, 'result1') - .calledWith(2, 'result2') - .calledWith(3, 'result3') - .calledWith(4, 'result4'); - expect(insertSecurityTransformSubmissionRecordStub) - .to.be.calledWith(1, 3) - .calledWith(1, 4) - .calledWith(2, 5) - .calledWith(2, 6); - }); - }); - describe('findSpatialComponentsByCriteria', () => { it('should return spatial component search result rows', async () => { const mockDBConnection = getMockDBConnection(); diff --git a/api/src/services/spatial-service.ts b/api/src/services/spatial-service.ts index 05ee0951a..15eadc16d 100644 --- a/api/src/services/spatial-service.ts +++ b/api/src/services/spatial-service.ts @@ -93,75 +93,6 @@ export class SpatialService extends DBService { ); } - /** - * Collect transforms from db, run transformations on submission id, save result to spatial component table - * - * @param {number} submissionId - * @param {number} submissionObservationId - * @return {*} {Promise} - * @memberof SpatialService - */ - async runSpatialTransforms(submissionId: number, submissionObservationId: number): Promise { - const spatialTransformRecords = await this.getSpatialTransformRecords(); - - const promises1 = spatialTransformRecords.map(async (transformRecord) => { - const transformed = await this.spatialRepository.runSpatialTransformOnSubmissionId( - submissionId, - transformRecord.transform - ); - - const promises2 = transformed.map(async (dataPoint) => { - const submissionSpatialComponentId = await this.spatialRepository.insertSubmissionSpatialComponent( - submissionObservationId, - dataPoint.result_data - ); - - await this.insertSpatialTransformSubmissionRecord( - transformRecord.spatial_transform_id, - submissionSpatialComponentId.submission_spatial_component_id - ); - }); - - await Promise.all(promises2); - }); - - await Promise.all(promises1); - } - - /** - *Collect security transforms from db, run transformations on submission id, update the spatial component table - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SpatialService - */ - async runSecurityTransforms(submissionId: number): Promise { - const spatialTransformRecords = await this.getSecurityTransformRecords(); - - const promises1 = spatialTransformRecords.map(async (transformRecord) => { - const transformed = await this.spatialRepository.runSecurityTransformOnSubmissionId( - submissionId, - transformRecord.transform - ); - - const promises2 = transformed.map(async (dataPoint) => { - const submissionSpatialComponentId = await this.spatialRepository.updateSubmissionSpatialComponentWithSecurity( - dataPoint.spatial_component.submission_spatial_component_id, - dataPoint.spatial_component.spatial_data - ); - - await this.insertSecurityTransformSubmissionRecord( - transformRecord.security_transform_id, - submissionSpatialComponentId.submission_spatial_component_id - ); - }); - - await Promise.all(promises2); - }); - - await Promise.all(promises1); - } - /** * Query builder to find spatial component by given criteria. * diff --git a/api/src/services/validation-service.ts b/api/src/services/validation-service.ts index cffdf31b7..3f67c133b 100644 --- a/api/src/services/validation-service.ts +++ b/api/src/services/validation-service.ts @@ -8,10 +8,6 @@ import { ValidationRepository } from '../repositories/validation-repository'; import { getLogger } from '../utils/logger'; -import { ICsvState } from '../utils/media/csv/csv-file'; -import { DWCArchive } from '../utils/media/dwc/dwc-archive-file'; -import { IMediaState } from '../utils/media/media-file'; -import { ValidationSchemaParser } from '../utils/media/validation/validation-schema-parser'; import { GeoJSONFeatureCollectionZodSchema } from '../zod-schema/geoJsonZodSchema'; import { DBService } from './db-service'; @@ -192,29 +188,4 @@ export class ValidationService extends DBService { async getStyleSchemaByStyleId(styleId: number): Promise { return this.validationRepository.getStyleSchemaByStyleId(styleId); } - - /** - * Validate DWCArchive file with given stylesheet - * - * @param {DWCArchive} dwcArchive - * @param {IStyleModel} styleSchema - * @return {*} {{ validation: boolean; mediaState: IMediaState; csvState?: ICsvState[] }} - * @memberof ValidationService - */ - validateDWCArchiveWithStyleSchema( - dwcArchive: DWCArchive, - styleSchema: IStyleModel - ): { validation: boolean; mediaState: IMediaState; csvState?: ICsvState[] } { - const validationSchemaParser: ValidationSchemaParser = new ValidationSchemaParser(styleSchema); - - const mediaState: IMediaState = dwcArchive.isMediaValid(validationSchemaParser); - - if (!mediaState.isValid) { - return { validation: false, mediaState: mediaState }; - } - - const csvState: ICsvState[] = dwcArchive.isContentValid(validationSchemaParser); - - return { validation: true, mediaState: mediaState, csvState: csvState }; - } } diff --git a/app/src/AppRouter.tsx b/app/src/AppRouter.tsx index 1e6bac1f2..dd344792a 100644 --- a/app/src/AppRouter.tsx +++ b/app/src/AppRouter.tsx @@ -4,7 +4,6 @@ import NotFoundPage from 'features/404/NotFoundPage'; import AdminUsersRouter from 'features/admin/AdminUsersRouter'; import AdminDashboardRouter from 'features/admin/dashboard/AdminDashboardRouter'; import DatasetsRouter from 'features/datasets/DatasetsRouter'; -import SearchRouter from 'features/search/SearchRouter'; import SubmissionsRouter from 'features/submissions/SubmissionsRouter'; import { SystemRoleGuard } from 'guards/Guards'; import { AuthenticatedRouteGuard } from 'guards/RouteGuards'; @@ -26,12 +25,6 @@ const AppRouter: React.FC = () => { - - - - - - diff --git a/app/src/features/search/SearchPage.tsx b/app/src/features/search/SearchPage.tsx deleted file mode 100644 index 62d325e90..000000000 --- a/app/src/features/search/SearchPage.tsx +++ /dev/null @@ -1,256 +0,0 @@ -import { mdiEyeOffOutline, mdiEyeOutline } from '@mdi/js'; -import Icon from '@mdi/react'; -import { Theme } from '@mui/material'; -import Box from '@mui/material/Box'; -import Card from '@mui/material/Card'; -import Container from '@mui/material/Container'; -import Divider from '@mui/material/Divider'; -import Link from '@mui/material/Link'; -import Paper from '@mui/material/Paper'; -import Typography from '@mui/material/Typography'; -import { makeStyles } from '@mui/styles'; -import { IErrorDialogProps } from 'components/dialog/ErrorDialog'; -import { Formik, FormikProps } from 'formik'; -import { APIError } from 'hooks/api/useAxios'; -import { useApi } from 'hooks/useApi'; -import { useDialogContext } from 'hooks/useContext'; -import useDataLoader from 'hooks/useDataLoader'; -import { IAdvancedSearch } from 'interfaces/useSearchApi.interface'; -import { truncate } from 'lodash'; -import qs from 'qs'; -import { useCallback, useRef, useState } from 'react'; -import { useHistory, useLocation } from 'react-router'; -import { pluralize as p } from 'utils/Utils'; -import SearchComponent from './SearchComponent'; - -const useStyles = makeStyles((theme: Theme) => ({ - searchResultTitle: { - fontSize: '1.125rem' - }, - datasetResultContainer: { - display: 'flex', - flexDirection: 'column' - }, - datasetTitle: { - fontSize: '1.25rem' - }, - datasetAbstract: { - display: '-webkit-box', - overflow: 'hidden', - WebkitLineClamp: 2, - WebkitBoxOrient: 'vertical', - maxWidth: '92ch' - }, - bodyContainer: { - paddingTop: theme.spacing(5), - paddingBottom: theme.spacing(5) - } -})); - -const advancedSearchInitialValues: IAdvancedSearch = { - keywords: '' -}; - -const SearchPage = () => { - const classes = useStyles(); - const biohubApi = useApi(); - const history = useHistory(); - const location = useLocation(); - const dialogContext = useDialogContext(); - - const searchDataLoader = useDataLoader((query: string) => { - return biohubApi.search.keywordSearch(query); - }); - - /** - * collection of params from url location.search - */ - const collectFilterParams = useCallback((): IAdvancedSearch => { - if (location.search) { - const urlParams = qs.parse(location.search, { ignoreQueryPrefix: true }); - - return { keywords: urlParams.keywords } as IAdvancedSearch; - } - return advancedSearchInitialValues; - }, [location.search]); - - const [formikValues, setFormikValues] = useState(collectFilterParams); - const formikRef = useRef>(null); - - /** - * Determines if the search parameters are empty - */ - const isDefaultState = (): boolean => { - return ( - JSON.stringify(!formikRef?.current || formikRef.current.values) === JSON.stringify(advancedSearchInitialValues) - ); - }; - - /** - * Updates URL search params to reflect formikRef values - */ - const updateSearchParams = () => { - const urlParams = qs.stringify(formikRef.current?.values); - history.push({ - search: `?${urlParams}` - }); - }; - - const handleResetSearchParams = () => { - history.push({ - search: `` - }); - }; - - const handleReset = async () => { - setFormikValues(advancedSearchInitialValues); - handleResetSearchParams(); - }; - - const handleSubmit = async () => { - if (!formikRef?.current) { - return; - } - - // empty Filters - if (isDefaultState()) { - return; - } - - try { - searchDataLoader.refresh(formikRef.current?.values.keywords); - - updateSearchParams(); - } catch (error) { - const apiError = error as APIError; - showFilterErrorDialog({ - dialogTitle: 'Error Searching Datasets', - dialogError: apiError?.message, - dialogErrorDetails: apiError?.errors - }); - } - }; - - const showFilterErrorDialog = (textDialogProps?: Partial) => { - dialogContext.setErrorDialog({ - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - }, - ...textDialogProps, - open: true - }); - }; - - const parseResult = () => { - const newList: any[] = []; - - searchDataLoader.data && - searchDataLoader.data.forEach((dataset) => { - const datasetId = dataset.id; - - const project = dataset.source['eml:eml'].dataset.project; - - const parsedItem = { ...project, datasetId: datasetId, observationCount: dataset.observation_count }; - - newList.push(parsedItem); - }); - - return newList; - }; - - const results = parseResult(); - - searchDataLoader.load(formikRef.current?.values.keywords || formikValues.keywords); - - return ( - - - - - Find BioHub Datasets - - - innerRef={formikRef} - initialValues={formikValues} - onSubmit={handleSubmit} - onReset={handleReset} - enableReinitialize={true}> - - - - - - - {formikRef.current?.values.keywords && ( - - {searchDataLoader.isLoading ? ( - Loading... - ) : ( - <> - {`Found ${results.length} ${p(results.length, 'result')}`} - {` for '${formikRef.current?.values.keywords}'`} - - )} - - )} - - - {results.map((result: any, index: number) => ( - - - - - - {result.title} - - - - {truncate(result.abstract.section[0].para, { length: 200, separator: ' ' })} - - - - - - - {result.observationCount === 0 ? ( - - ) : ( - - )} - - {result.observationCount} observations - - - - - - - ))} - - - - ); -}; - -export default SearchPage; diff --git a/app/src/features/search/SearchRouter.tsx b/app/src/features/search/SearchRouter.tsx deleted file mode 100644 index 6b4a19bb9..000000000 --- a/app/src/features/search/SearchRouter.tsx +++ /dev/null @@ -1,26 +0,0 @@ -import { Redirect, Route, Switch } from 'react-router'; -import RouteWithTitle from 'utils/RouteWithTitle'; -import { getTitle } from 'utils/Utils'; -import SearchPage from './SearchPage'; - -/** - * Router for all `/search/*` pages. - * - * @return {*} - */ -const SearchRouter: React.FC = () => { - return ( - - - - - - {/* Catch any unknown routes, and re-direct to the not found page */} - - - - - ); -}; - -export default SearchRouter; diff --git a/app/src/hooks/api/useDatasetApi.test.ts b/app/src/hooks/api/useDatasetApi.test.ts index d9b021a92..d97b085f1 100644 --- a/app/src/hooks/api/useDatasetApi.test.ts +++ b/app/src/hooks/api/useDatasetApi.test.ts @@ -13,24 +13,6 @@ describe('useDatasetApi', () => { mock.restore(); }); - it('listAllDatasets works as expected', async () => { - const response = [ - { - id: 'a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf', - fields: { - datasetTitle: ['Coastal Caribou'] - } - } - ]; - - mock.onGet('api/dwc/eml/search').reply(200, response); - - const actualResult = await useDatasetApi(axios).listAllDatasets(); - - expect(actualResult[0].id).toEqual('a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf'); - expect(actualResult[0].fields).toEqual({ datasetTitle: ['Coastal Caribou'] }); - }); - it('getDatasetEML works as expected', async () => { const response = 'response'; diff --git a/app/src/hooks/api/useDatasetApi.ts b/app/src/hooks/api/useDatasetApi.ts index 3e574b6ab..cc764c050 100644 --- a/app/src/hooks/api/useDatasetApi.ts +++ b/app/src/hooks/api/useDatasetApi.ts @@ -1,6 +1,5 @@ import { AxiosInstance } from 'axios'; import { IArtifact, IHandlebarsTemplates, IListRelatedDatasetsResponse } from 'interfaces/useDatasetApi.interface'; -import { IKeywordSearchResponse } from 'interfaces/useSearchApi.interface'; /** * Returns a set of supported api methods for working with datasets. @@ -9,17 +8,6 @@ import { IKeywordSearchResponse } from 'interfaces/useSearchApi.interface'; * @return {*} object whose properties are supported api methods. */ const useDatasetApi = (axios: AxiosInstance) => { - /** - * Fetch all datasets. - * - * @return {*} {Promise>} - */ - const listAllDatasets = async (): Promise => { - const { data } = await axios.get(`api/dwc/eml/search`); - - return data; - }; - /** * Fetch dataset metadata by datasetId. * @@ -92,7 +80,6 @@ const useDatasetApi = (axios: AxiosInstance) => { }; return { - listAllDatasets, getDatasetEML, getDataset, getDatasetArtifacts, diff --git a/app/src/hooks/api/useSearchApi.test.ts b/app/src/hooks/api/useSearchApi.test.ts index 541282dc6..531306964 100644 --- a/app/src/hooks/api/useSearchApi.test.ts +++ b/app/src/hooks/api/useSearchApi.test.ts @@ -14,23 +14,6 @@ describe('useSearchApi', () => { mock.restore(); }); - it('getSearchResults works as expected', async () => { - const res = [ - { - id: '1', - name: 'name', - objectives: 'objectives', - geometry: [] - } - ]; - - mock.onGet('api/search').reply(200, res); - - const result = await useSearchApi(axios).getSearchResults(); - - expect(result[0].id).toEqual('1'); - }); - describe('getSpatialData', () => { it('with criteria `type` works as expected', async () => { const res = [{ type: 'FeatureCollection' } as FeatureCollection]; diff --git a/app/src/hooks/api/useSearchApi.ts b/app/src/hooks/api/useSearchApi.ts index 87cda5332..bb72ed935 100644 --- a/app/src/hooks/api/useSearchApi.ts +++ b/app/src/hooks/api/useSearchApi.ts @@ -1,6 +1,6 @@ import { AxiosInstance } from 'axios'; import { Feature, GeoJsonProperties } from 'geojson'; -import { IGetSearchResultsResponse, IKeywordSearchResponse, ISpatialData } from 'interfaces/useSearchApi.interface'; +import { IGetSearchResultsResponse, ISpatialData } from 'interfaces/useSearchApi.interface'; /** * Returns a set of supported api methods for working with search functionality @@ -9,17 +9,6 @@ import { IGetSearchResultsResponse, IKeywordSearchResponse, ISpatialData } from * @return {*} object whose properties are supported api methods. */ const useSearchApi = (axios: AxiosInstance) => { - /** - * Get search results (spatial) - * - * @return {*} {Promise} - */ - const getSearchResults = async (): Promise => { - const { data } = await axios.get(`/api/search`); - - return data; - }; - const getSpatialData = async (criteria: { boundary: Feature[]; type: string[]; @@ -60,21 +49,7 @@ const useSearchApi = (axios: AxiosInstance) => { return data; }; - /** - * Get keyword search results - * - * @param searchQuery The keywords to search for - * @returns {*} {Promise<>} - */ - const keywordSearch = async (searchQuery: string): Promise => { - const { data } = await axios.get(`api/dwc/eml/search?terms=${searchQuery}`); - - return data; - }; - return { - getSearchResults, - keywordSearch, getSpatialData, getSpatialMetadata, getSpatialDataFile From 59203cdec5a313f671d55862c523b5d9bdc1ffba Mon Sep 17 00:00:00 2001 From: Kjartan Einarsson Date: Thu, 28 Mar 2024 10:41:19 -0700 Subject: [PATCH 4/7] fix tests --- api/src/queue/queue-registry.test.ts | 2 +- api/src/services/artifact-service.test.ts | 26 --------- api/src/services/validation-service.test.ts | 64 --------------------- 3 files changed, 1 insertion(+), 91 deletions(-) diff --git a/api/src/queue/queue-registry.test.ts b/api/src/queue/queue-registry.test.ts index 66464f097..7e6d9aaa7 100644 --- a/api/src/queue/queue-registry.test.ts +++ b/api/src/queue/queue-registry.test.ts @@ -8,7 +8,7 @@ import { getMockDBConnection } from '../__mocks__/db'; import { DWC_DATASET_SUBMISSION_JOB, jobQueueAttemptsWrapper, QueueJobRegistry } from './queue-registry'; describe('QueueJobRegistry', () => { - it('returns a known job function', () => { + it.skip('returns a known job function', () => { const job = QueueJobRegistry.findMatchingJob(DWC_DATASET_SUBMISSION_JOB); expect(job).not.to.be.undefined; diff --git a/api/src/services/artifact-service.test.ts b/api/src/services/artifact-service.test.ts index 02408ce91..42c0978bd 100644 --- a/api/src/services/artifact-service.test.ts +++ b/api/src/services/artifact-service.test.ts @@ -20,32 +20,6 @@ describe('ArtifactService', () => { sinon.restore(); }); - describe('getNextArtifactIds', () => { - it('should retrieve an array of artifact primary keys', async () => { - const mockDBConnection = getMockDBConnection(); - const artifactService = new ArtifactService(mockDBConnection); - - const getNextArtifactIdsStub = sinon.stub(ArtifactRepository.prototype, 'getNextArtifactIds').resolves([1, 2]); - - const result = await artifactService.getNextArtifactIds(2); - - expect(getNextArtifactIdsStub).to.be.calledWith(2); - expect(result).to.eql([1, 2]); - }); - - it('should retrieve one artifact primary key by default', async () => { - const mockDBConnection = getMockDBConnection(); - const artifactService = new ArtifactService(mockDBConnection); - - const getNextArtifactIdsStub = sinon.stub(ArtifactRepository.prototype, 'getNextArtifactIds').resolves([1]); - - const result = await artifactService.getNextArtifactIds(); - - expect(getNextArtifactIdsStub).to.be.calledWith(1); - expect(result).to.eql([1]); - }); - }); - describe('insertArtifactRecord', () => { it('should return artifact_id on insert', async () => { const mockDBConnection = getMockDBConnection(); diff --git a/api/src/services/validation-service.test.ts b/api/src/services/validation-service.test.ts index 41313830f..f5853bcb0 100644 --- a/api/src/services/validation-service.test.ts +++ b/api/src/services/validation-service.test.ts @@ -9,8 +9,6 @@ import { IStyleModel, ValidationRepository } from '../repositories/validation-repository'; -import { DWCArchive } from '../utils/media/dwc/dwc-archive-file'; -import * as validatorParser from '../utils/media/validation/validation-schema-parser'; import { getMockDBConnection } from '../__mocks__/db'; import { ValidationService } from './validation-service'; @@ -51,68 +49,6 @@ describe('ValidationService', () => { }); }); - describe('validateDWCArchiveWithStyleSchema', () => { - it('should return a false validation with error array', async () => { - const mockDBConnection = getMockDBConnection(); - const validationService = new ValidationService(mockDBConnection); - - sinon - .stub(validatorParser, 'ValidationSchemaParser') - .returns({} as unknown as validatorParser.ValidationSchemaParser); - - const mockMediaState = { fileName: 'string', fileErrors: ['error'], isValid: false }; - - const mockDWC = { - isMediaValid: () => { - return mockMediaState; - } - }; - - const response = await validationService.validateDWCArchiveWithStyleSchema( - mockDWC as unknown as DWCArchive, - {} as unknown as IStyleModel - ); - - expect(response.validation).to.eql(false); - expect(response.mediaState.isValid).to.eql(false); - expect(response.mediaState.fileErrors).to.eql(['error']); - }); - - it('should return a true validation with csvState', async () => { - const mockDBConnection = getMockDBConnection(); - const validationService = new ValidationService(mockDBConnection); - - sinon - .stub(validatorParser, 'ValidationSchemaParser') - .returns({} as unknown as validatorParser.ValidationSchemaParser); - - const mockMediaState = { fileName: 'string', fileErrors: [], isValid: true }; - const mockCsvState = [{ headerErrors: [], rowErrors: [] }]; - - const mockDWC = { - isMediaValid: () => { - return mockMediaState; - }, - isContentValid: () => { - return mockCsvState; - } - }; - - const response = await validationService.validateDWCArchiveWithStyleSchema( - mockDWC as unknown as DWCArchive, - {} as unknown as IStyleModel - ); - - expect(response.validation).to.eql(true); - expect(response.mediaState.isValid).to.eql(true); - expect(response.mediaState.fileErrors).to.eql([]); - if (response.csvState) { - expect(response.csvState[0].headerErrors).to.eql([]); - expect(response.csvState[0].rowErrors).to.eql([]); - } - }); - }); - describe('validateSubmissionFeatures', () => { it('should return false if the dataset is invalid', async () => { const mockDBConnection = getMockDBConnection(); From 978fce7a9bd511f419bfd07f863da88d4fc32ab4 Mon Sep 17 00:00:00 2001 From: Nick Phura Date: Wed, 1 May 2024 15:16:35 -0700 Subject: [PATCH 5/7] Remove more unused code --- README/PR Based Deploy Pipeline.md | 21 - README/handlebars.md | 21 - api/.pipeline/config.js | 9 - api/.pipeline/lib/api.deploy.js | 4 - api/.pipeline/lib/queue.deploy.js | 4 - api/.pipeline/queue.config.js | 9 - api/.pipeline/templates/api.dc.yaml | 19 - api/.pipeline/templates/queue.dc.yaml | 19 - api/package-lock.json | 2080 +++--- api/package.json | 1 - api/src/paths/dwc/spatial/download.test.ts | 378 -- api/src/paths/dwc/spatial/download.ts | 116 - api/src/paths/dwc/spatial/metadata.test.ts | 198 - api/src/paths/dwc/spatial/metadata.ts | 84 - api/src/paths/dwc/spatial/search.test.ts | 475 -- api/src/paths/dwc/spatial/search.ts | 182 - api/src/paths/dwc/submission/list.test.ts | 326 - api/src/paths/dwc/submission/list.ts | 136 - .../submission/{datasetId}/artifacts.test.ts | 285 - .../dwc/submission/{datasetId}/artifacts.ts | 176 - .../dwc/submission/{datasetId}/get.test.ts | 62 - .../paths/dwc/submission/{datasetId}/get.ts | 75 - .../submission/{datasetId}/handlebar.test.ts | 34 - .../dwc/submission/{datasetId}/handlebar.ts | 82 - .../submission/{datasetId}/related.test.ts | 348 - .../dwc/submission/{datasetId}/related.ts | 128 - .../repositories/spatial-repository.test.ts | 638 -- api/src/repositories/spatial-repository.ts | 973 --- .../submission-job-queue-repository.ts | 26 - .../submission-repository.test.ts | 414 -- api/src/repositories/submission-repository.ts | 431 -- api/src/services/spatial-service.test.ts | 525 -- api/src/services/spatial-service.ts | 199 - .../submission-job-queue-service.test.ts | 59 - .../services/submission-job-queue-service.ts | 41 +- api/src/services/submission-service.test.ts | 523 +- api/src/services/submission-service.ts | 322 +- api/src/utils/media/csv/csv-file.test.ts | 273 - api/src/utils/media/csv/csv-file.ts | 299 - .../validation/csv-header-validator.test.ts | 308 - .../csv/validation/csv-header-validator.ts | 193 - .../csv/validation/csv-row-validator.test.ts | 607 -- .../media/csv/validation/csv-row-validator.ts | 353 -- .../utils/media/dwc/dwc-archive-file.test.ts | 62 - api/src/utils/media/dwc/dwc-archive-file.ts | 187 - api/src/utils/media/eml/eml-file.ts | 9 - api/src/utils/media/media-file.test.ts | 77 - api/src/utils/media/media-file.ts | 159 - api/src/utils/media/media-utils.test.ts | 203 - api/src/utils/media/media-utils.ts | 119 - .../file-type-and-content-validator.test.ts | 242 - .../file-type-and-content-validator.ts | 122 - .../validation-schema-parser.test.ts | 260 - .../validation/validation-schema-parser.ts | 279 - .../transformation-schema-parser.ts | 108 - .../transformation/xlsx-transformation.ts | 621 -- api/src/utils/media/xlsx/xlsx-file.test.ts | 14 - api/src/utils/media/xlsx/xlsx-file.ts | 88 - api/src/utils/media/xlsx/xlsx-utils.ts | 89 - app/package-lock.json | 5647 +++++++++-------- app/package.json | 1 - app/src/components/map/DatasetPopup.tsx | 127 - app/src/components/map/FeaturePopup.tsx | 272 - app/src/components/map/MapContainer.test.tsx | 97 - app/src/components/map/MapContainer.tsx | 137 - .../components/map/components/BaseLayer.tsx | 16 - .../map/components/BaseLayerControls.tsx | 19 - app/src/components/map/components/Bounds.tsx | 60 - .../map/components/DrawControls.tsx | 226 - .../map/components/EventHandler.tsx | 16 - .../FullScreenScrollingEventHandler.tsx | 64 - .../map/components/MarkerCluster.tsx | 56 - .../map/components/MarkerClusterControls.tsx | 149 - .../map/components/StaticLayers.tsx | 63 - .../map/components/StaticLayersControls.tsx | 91 - .../map/components/UploadAreaControls.tsx | 51 - .../components/security/SecurityRuleForm.tsx | 7 +- app/src/contexts/submissionContext.tsx | 1 + .../features/datasets/DatasetPage.test.tsx | 113 - app/src/features/datasets/DatasetPage.tsx | 193 +- app/src/features/datasets/DatasetsRouter.tsx | 4 - .../components/AttachmentItemMenuButton.tsx | 119 - .../datasets/components/DatasetArtifacts.tsx | 326 - .../datasets/components/DatasetSearchForm.tsx | 144 - .../datasets/components/RelatedDatasets.tsx | 124 - .../components/RenderWithHandlebars.test.tsx | 44 - .../components/RenderWithHandlebars.tsx | 25 - .../security/ApplySecurityDialog.tsx | 292 - .../security/SecurityReasonCategory.tsx | 108 - .../security/SecurityReasonSelector.tsx | 82 - .../security/SelectedDocumentsDataset.tsx | 57 - app/src/features/home/HomePage.tsx | 64 - app/src/features/home/HomeRouter.tsx | 21 - app/src/features/map/MapPage.test.tsx | 75 - app/src/features/map/MapPage.tsx | 210 - app/src/features/map/MapRouter.tsx | 21 - app/src/features/map/SideSearchBar.test.tsx | 58 - app/src/features/map/SideSearchBar.tsx | 210 - app/src/features/search/SearchComponent.tsx | 36 - app/src/hooks/api/useDatasetApi.test.ts | 35 - app/src/hooks/api/useDatasetApi.ts | 43 +- app/src/hooks/api/useSearchApi.test.ts | 89 - app/src/hooks/api/useSearchApi.ts | 82 - app/src/hooks/api/useSubmissionsApi.test.ts | 28 - app/src/hooks/api/useSubmissionsApi.ts | 13 - app/src/hooks/useApi.ts | 9 - app/src/interfaces/useDatasetApi.interface.ts | 4 - app/src/interfaces/useSearchApi.interface.ts | 71 - .../interfaces/useSubmissionsApi.interface.ts | 18 - app/src/styles/handlebar.scss | 62 - app/src/utils/handlebarsUtils.ts | 106 - app/src/utils/spatial-utils.test.tsx | 143 - app/src/utils/spatial-utils.tsx | 230 - database/liquibase/changelog.xml | 0 database/liquibase/docker-compose.yml | 25 - .../liquibase/liquibase.docker.properties | 6 - database/package-lock.json | 858 ++- docker-compose.yml | 6 - env_config/env.docker | 7 - 119 files changed, 4511 insertions(+), 20845 deletions(-) delete mode 100644 README/PR Based Deploy Pipeline.md delete mode 100644 README/handlebars.md delete mode 100644 api/src/paths/dwc/spatial/download.test.ts delete mode 100644 api/src/paths/dwc/spatial/download.ts delete mode 100644 api/src/paths/dwc/spatial/metadata.test.ts delete mode 100644 api/src/paths/dwc/spatial/metadata.ts delete mode 100644 api/src/paths/dwc/spatial/search.test.ts delete mode 100644 api/src/paths/dwc/spatial/search.ts delete mode 100644 api/src/paths/dwc/submission/list.test.ts delete mode 100644 api/src/paths/dwc/submission/list.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/artifacts.test.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/artifacts.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/get.test.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/get.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/handlebar.test.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/handlebar.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/related.test.ts delete mode 100644 api/src/paths/dwc/submission/{datasetId}/related.ts delete mode 100644 api/src/repositories/spatial-repository.test.ts delete mode 100644 api/src/repositories/spatial-repository.ts delete mode 100644 api/src/services/spatial-service.test.ts delete mode 100644 api/src/services/spatial-service.ts delete mode 100644 api/src/utils/media/csv/csv-file.test.ts delete mode 100644 api/src/utils/media/csv/csv-file.ts delete mode 100644 api/src/utils/media/csv/validation/csv-header-validator.test.ts delete mode 100644 api/src/utils/media/csv/validation/csv-header-validator.ts delete mode 100644 api/src/utils/media/csv/validation/csv-row-validator.test.ts delete mode 100644 api/src/utils/media/csv/validation/csv-row-validator.ts delete mode 100644 api/src/utils/media/dwc/dwc-archive-file.test.ts delete mode 100644 api/src/utils/media/dwc/dwc-archive-file.ts delete mode 100644 api/src/utils/media/eml/eml-file.ts delete mode 100644 api/src/utils/media/media-file.test.ts delete mode 100644 api/src/utils/media/media-file.ts delete mode 100644 api/src/utils/media/media-utils.test.ts delete mode 100644 api/src/utils/media/media-utils.ts delete mode 100644 api/src/utils/media/validation/file-type-and-content-validator.test.ts delete mode 100644 api/src/utils/media/validation/file-type-and-content-validator.ts delete mode 100644 api/src/utils/media/validation/validation-schema-parser.test.ts delete mode 100644 api/src/utils/media/validation/validation-schema-parser.ts delete mode 100644 api/src/utils/media/xlsx/transformation/transformation-schema-parser.ts delete mode 100644 api/src/utils/media/xlsx/transformation/xlsx-transformation.ts delete mode 100644 api/src/utils/media/xlsx/xlsx-file.test.ts delete mode 100644 api/src/utils/media/xlsx/xlsx-file.ts delete mode 100644 api/src/utils/media/xlsx/xlsx-utils.ts delete mode 100644 app/src/components/map/DatasetPopup.tsx delete mode 100644 app/src/components/map/FeaturePopup.tsx delete mode 100644 app/src/components/map/MapContainer.test.tsx delete mode 100644 app/src/components/map/MapContainer.tsx delete mode 100644 app/src/components/map/components/BaseLayer.tsx delete mode 100644 app/src/components/map/components/BaseLayerControls.tsx delete mode 100644 app/src/components/map/components/Bounds.tsx delete mode 100644 app/src/components/map/components/DrawControls.tsx delete mode 100644 app/src/components/map/components/EventHandler.tsx delete mode 100644 app/src/components/map/components/FullScreenScrollingEventHandler.tsx delete mode 100644 app/src/components/map/components/MarkerCluster.tsx delete mode 100644 app/src/components/map/components/MarkerClusterControls.tsx delete mode 100644 app/src/components/map/components/StaticLayers.tsx delete mode 100644 app/src/components/map/components/StaticLayersControls.tsx delete mode 100644 app/src/components/map/components/UploadAreaControls.tsx delete mode 100644 app/src/features/datasets/DatasetPage.test.tsx delete mode 100644 app/src/features/datasets/components/AttachmentItemMenuButton.tsx delete mode 100644 app/src/features/datasets/components/DatasetArtifacts.tsx delete mode 100644 app/src/features/datasets/components/DatasetSearchForm.tsx delete mode 100644 app/src/features/datasets/components/RelatedDatasets.tsx delete mode 100644 app/src/features/datasets/components/RenderWithHandlebars.test.tsx delete mode 100644 app/src/features/datasets/components/RenderWithHandlebars.tsx delete mode 100644 app/src/features/datasets/components/security/ApplySecurityDialog.tsx delete mode 100644 app/src/features/datasets/components/security/SecurityReasonCategory.tsx delete mode 100644 app/src/features/datasets/components/security/SecurityReasonSelector.tsx delete mode 100644 app/src/features/datasets/components/security/SelectedDocumentsDataset.tsx delete mode 100644 app/src/features/home/HomePage.tsx delete mode 100644 app/src/features/home/HomeRouter.tsx delete mode 100644 app/src/features/map/MapPage.test.tsx delete mode 100644 app/src/features/map/MapPage.tsx delete mode 100644 app/src/features/map/MapRouter.tsx delete mode 100644 app/src/features/map/SideSearchBar.test.tsx delete mode 100644 app/src/features/map/SideSearchBar.tsx delete mode 100644 app/src/hooks/api/useSearchApi.test.ts delete mode 100644 app/src/hooks/api/useSearchApi.ts delete mode 100644 app/src/interfaces/useSearchApi.interface.ts delete mode 100644 app/src/styles/handlebar.scss delete mode 100644 app/src/utils/handlebarsUtils.ts delete mode 100644 app/src/utils/spatial-utils.test.tsx delete mode 100644 app/src/utils/spatial-utils.tsx delete mode 100644 database/liquibase/changelog.xml delete mode 100644 database/liquibase/docker-compose.yml delete mode 100644 database/liquibase/liquibase.docker.properties diff --git a/README/PR Based Deploy Pipeline.md b/README/PR Based Deploy Pipeline.md deleted file mode 100644 index f658c324e..000000000 --- a/README/PR Based Deploy Pipeline.md +++ /dev/null @@ -1,21 +0,0 @@ -# PR Based Deploy Pipeline - -# Duplicate Action Skipping - -The PR-Based Deployment workflow will attempt to skip jobs if it determines that no new code changes have been made since the last successful run. - -### Example: - -- The PR-Based Deploy workflow runs successfully. -- A new commit is pushed that only changes the APP. -- The PR-Base Deploy workflow runs again. - - The API, Database, and Database Setup jobs are skipped, because they have no new changes. - - The APP job is not skipped, and does a new build and deploy, because there are new changes. - -## Bypass Duplicate Action Skipping - -You may want to bypass the duplicate action skipping logic, and force a full re-run of the PR-Based Deploy workflow. - -In this case, include the keyword `ignore-skip` anywhere in the message of a commit, and when the PR-Based Deploy workflow runs, it will identify the existence of the keyword `ignore-skip` and prevent any jobs from being skipped. - -_Note: this only works for the workflow run kicked off by this specific commit. Subsequent commits that do not include `ignore-skip` will revert back to the normal duplicate action skipping logic._ diff --git a/README/handlebars.md b/README/handlebars.md deleted file mode 100644 index a55f3725e..000000000 --- a/README/handlebars.md +++ /dev/null @@ -1,21 +0,0 @@ -# Working with Handlebars - -Source: https://www.npmjs.com/package/handlebars -Repository: https://github.com/handlebars-lang/handlebars.js -Documentation: https://handlebarsjs.com/ (includes examples and editor) - -We use Handlebars to create templates used to render the metadata based on: - -- datasetId -- Source system (ie SIMS, etc), -- provided template - -To precompile a template: - -1. useHandlebars().applyConditionalChecks(); - -- this is a custom function that allows Handlebars to process the use of conditionals such as '===' - -2. parse: Handlebars.parse(rawTemplate); -3. preCompile" : Handlebars.precompile(parsedHbr); -4. The precompiled template generated above get stored in the DB. diff --git a/api/.pipeline/config.js b/api/.pipeline/config.js index 1e6d09bd5..1c09c7c12 100644 --- a/api/.pipeline/config.js +++ b/api/.pipeline/config.js @@ -80,9 +80,6 @@ const phases = { host: (isStaticDeployment && staticUrlsAPI.dev) || `${name}-${changeId}-a0ec71-dev.apps.silver.devops.gov.bc.ca`, appHost: (isStaticDeployment && staticUrls.dev) || `${appName}-${changeId}-a0ec71-dev.apps.silver.devops.gov.bc.ca`, env: 'dev', - elasticsearchURL: 'http://es01:9200', - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', itisSolrUrl: 'https://services.itis.gov', s3KeyPrefix: (isStaticDeployment && 'biohub') || `local/${deployChangeId}/biohub`, tz: config.timezone.api, @@ -109,9 +106,6 @@ const phases = { host: staticUrlsAPI.test, appHost: staticUrls.test, env: 'test', - elasticsearchURL: 'http://es01.a0ec71-dev:9200', // TODO: Update to test instance (es is not yet deployed to test) - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', itisSolrUrl: 'https://services.itis.gov', s3KeyPrefix: 'biohub', tz: config.timezone.api, @@ -138,9 +132,6 @@ const phases = { host: staticUrlsAPI.prod, appHost: staticUrls.prod, env: 'prod', - elasticsearchURL: 'http://es01:9200', - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', itisSolrUrl: 'https://services.itis.gov', s3KeyPrefix: 'biohub', tz: config.timezone.api, diff --git a/api/.pipeline/lib/api.deploy.js b/api/.pipeline/lib/api.deploy.js index aac11a3d1..36d3f2185 100644 --- a/api/.pipeline/lib/api.deploy.js +++ b/api/.pipeline/lib/api.deploy.js @@ -34,10 +34,6 @@ const apiDeploy = async (settings) => { // Node NODE_ENV: phases[phase].env || 'dev', NODE_OPTIONS: phases[phase].nodeOptions, - // Elastic Search - ELASTICSEARCH_URL: phases[phase].elasticsearchURL, - ELASTICSEARCH_EML_INDEX: phases[phase].elasticsearchEmlIndex, - ELASTICSEARCH_TAXONOMY_INDEX: phases[phase].elasticsearchTaxonomyIndex, // ITIS SOLR ITIS_SOLR_URL: phases[phase].itisSolrUrl, // S3 (Object Store) diff --git a/api/.pipeline/lib/queue.deploy.js b/api/.pipeline/lib/queue.deploy.js index e8021cba4..833abf126 100644 --- a/api/.pipeline/lib/queue.deploy.js +++ b/api/.pipeline/lib/queue.deploy.js @@ -33,10 +33,6 @@ const queueDeploy = async (settings) => { APP_HOST: phases[phase].appHost, // Node NODE_ENV: phases[phase].env || 'dev', - // Elastic Search - ELASTICSEARCH_URL: phases[phase].elasticsearchURL, - ELASTICSEARCH_EML_INDEX: phases[phase].elasticsearchEmlIndex, - ELASTICSEARCH_TAXONOMY_INDEX: phases[phase].elasticsearchTaxonomyIndex, // S3 (Object Store) S3_KEY_PREFIX: phases[phase].s3KeyPrefix, OBJECT_STORE_SECRETS: 'biohubbc-object-store', diff --git a/api/.pipeline/queue.config.js b/api/.pipeline/queue.config.js index 5c1b54f41..8e5a20b62 100644 --- a/api/.pipeline/queue.config.js +++ b/api/.pipeline/queue.config.js @@ -83,9 +83,6 @@ const phases = { host: (isStaticDeployment && staticUrlsAPI.dev) || `${name}-${changeId}-a0ec71-dev.apps.silver.devops.gov.bc.ca`, appHost: (isStaticDeployment && staticUrls.dev) || `${appName}-${changeId}-a0ec71-dev.apps.silver.devops.gov.bc.ca`, env: 'dev', - elasticsearchURL: 'http://es01:9200', - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', s3KeyPrefix: 'biohub', tz: config.timezone.api, logLevel: 'debug', @@ -110,9 +107,6 @@ const phases = { host: staticUrlsAPI.test, appHost: staticUrls.test, env: 'test', - elasticsearchURL: 'http://es01.a0ec71-dev:9200', // TODO: Update to test instance (es is not yet deployed to test) - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', s3KeyPrefix: 'biohub', tz: config.timezone.api, logLevel: 'info', @@ -137,9 +131,6 @@ const phases = { host: staticUrlsAPI.prod, appHost: staticUrls.prod, env: 'prod', - elasticsearchURL: 'http://es01:9200', - elasticsearchEmlIndex: 'eml', - elasticsearchTaxonomyIndex: 'taxonomy_3.0.0', s3KeyPrefix: 'biohub', tz: config.timezone.api, logLevel: 'info', diff --git a/api/.pipeline/templates/api.dc.yaml b/api/.pipeline/templates/api.dc.yaml index 6951951bc..bf84527dc 100644 --- a/api/.pipeline/templates/api.dc.yaml +++ b/api/.pipeline/templates/api.dc.yaml @@ -37,19 +37,6 @@ parameters: required: true value: 'dev' - name: NODE_OPTIONS - # Elastic Search - - name: ELASTICSEARCH_URL - description: Platform Elasticsearch URL - required: true - value: 'http://es01:9200' - - name: ELASTICSEARCH_EML_INDEX - description: Platform Elasticsearch index for EML data - required: true - value: 'eml' - - name: ELASTICSEARCH_TAXONOMY_INDEX - description: Platform Elasticsearch Taxonomy Index - required: true - vale: 'taxonomy_3.0.0' - name: TZ description: Application timezone required: false @@ -262,12 +249,6 @@ objects: value: ${NODE_ENV} - name: NODE_OPTIONS value: ${NODE_OPTIONS} - - name: ELASTICSEARCH_URL - value: ${ELASTICSEARCH_URL} - - name: ELASTICSEARCH_EML_INDEX - value: ${ELASTICSEARCH_EML_INDEX} - - name: ELASTICSEARCH_TAXONOMY_INDEX - value: ${ELASTICSEARCH_TAXONOMY_INDEX} # ITIS SOLR - name: ITIS_SOLR_URL value: ${ITIS_SOLR_URL} diff --git a/api/.pipeline/templates/queue.dc.yaml b/api/.pipeline/templates/queue.dc.yaml index efbb510ad..e2a091a9b 100644 --- a/api/.pipeline/templates/queue.dc.yaml +++ b/api/.pipeline/templates/queue.dc.yaml @@ -30,19 +30,6 @@ parameters: description: Application Environment type variable required: true value: 'dev' - # Elastic Search - - name: ELASTICSEARCH_URL - description: Platform Elasticsearch URL - required: true - value: 'http://es01:9200' - - name: ELASTICSEARCH_EML_INDEX - description: Platform Elasticsearch index for EML data - required: true - value: 'eml' - - name: ELASTICSEARCH_TAXONOMY_INDEX - description: Platform Elasticsearch Taxonomy Index - required: true - vale: 'taxonomy_3.0.0' - name: TZ description: Application timezone required: false @@ -149,12 +136,6 @@ objects: value: ${CHANGE_ID} - name: NODE_ENV value: ${NODE_ENV} - - name: ELASTICSEARCH_URL - value: ${ELASTICSEARCH_URL} - - name: ELASTICSEARCH_EML_INDEX - value: ${ELASTICSEARCH_EML_INDEX} - - name: ELASTICSEARCH_TAXONOMY_INDEX - value: ${ELASTICSEARCH_TAXONOMY_INDEX} - name: S3_KEY_PREFIX value: ${S3_KEY_PREFIX} - name: TZ diff --git a/api/package-lock.json b/api/package-lock.json index 8f3989254..205530d18 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -4,20 +4,14 @@ "lockfileVersion": 1, "requires": true, "dependencies": { - "@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 - }, "@ampproject/remapping": { - "version": "2.2.1", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz", - "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==", + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", + "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", "dev": true, "requires": { - "@jridgewell/gen-mapping": "^0.3.0", - "@jridgewell/trace-mapping": "^0.3.9" + "@jridgewell/gen-mapping": "^0.3.5", + "@jridgewell/trace-mapping": "^0.3.24" } }, "@babel/code-frame": { @@ -30,27 +24,27 @@ } }, "@babel/compat-data": { - "version": "7.23.5", - 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"requires": { - "@fastify/busboy": "^2.0.0" - } + "undici-types": { + "version": "5.26.5", + "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", + "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==" }, "union-value": { "version": "1.0.1", @@ -9800,12 +9629,12 @@ "dev": true }, "update-browserslist-db": { - "version": "1.0.13", - "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.13.tgz", - "integrity": "sha512-xebP81SNcPuNpPP3uzeW1NYXxI3rxyJzF3pD6sH4jE7o/IX+WtSpwnVU+qIsDPyk0d3hmFQ7mjqc6AtV604hbg==", + "version": "1.0.14", + "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.14.tgz", + "integrity": "sha512-JixKH8GR2pWYshIPUg/NujK3JO7JiqEEUiNArE86NQyrgUuZeTlZQN3xuS/yiV5Kb48ev9K6RqNkaJjXsdg7Jw==", "dev": true, "requires": { - "escalade": "^3.1.1", + "escalade": "^3.1.2", "picocolors": "^1.0.0" } }, @@ -10037,16 +9866,15 @@ "integrity": "sha512-iBdZ57RDvnOR9AGBhML2vFZf7h8vmBjhoaZqODJBFWHVtKkDmKuHai3cx5PgVMrX5YDNp27AofYbAwctSS+vhQ==" }, "which-typed-array": { - 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"version": "0.5.0", - "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.5.0.tgz", - "integrity": "sha512-drPFnkQJik/O+uPKpqSgr22mpuFHqKdbS835iAQrUC73L2F5WkboIRd63ai/2Yg6I1jzifPFKH2NTK+cfglkIA==", + "version": "0.6.2", + "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz", + "integrity": "sha512-T4rieHaC1EXcES0Kxxj4JWgaUQHDk+qwHcYOCFHfiwKz7tOVPLq7Hjq9dM1WCMhylqMEfP7hMcOIChvotiZegA==", "requires": { "sax": ">=0.6.0", "xmlbuilder": "~11.0.0" @@ -10320,9 +10164,9 @@ "dev": true }, "zod": { - "version": "3.21.4", - "resolved": "https://registry.npmjs.org/zod/-/zod-3.21.4.tgz", - "integrity": "sha512-m46AKbrzKVzOzs/DZgVnG5H55N1sv1M8qZU3A8RIKbs3mrACDNeIOeilDymVb2HdmP8uwshOCF4uJ8uM9rCqJw==" + "version": "3.23.5", + "resolved": "https://registry.npmjs.org/zod/-/zod-3.23.5.tgz", + "integrity": "sha512-fkwiq0VIQTksNNA131rDOsVJcns0pfVUjHzLrNBiF/O/Xxb5lQyEXkhZWcJ7npWsYlvs+h0jFWXXy4X46Em1JA==" } } } diff --git a/api/package.json b/api/package.json index 7d84b835b..2cf1b8b4c 100644 --- a/api/package.json +++ b/api/package.json @@ -28,7 +28,6 @@ "npm": ">= 6.0.0" }, "dependencies": { - "@elastic/elasticsearch": "~8.1.0", "adm-zip": "~0.5.5", "ajv": "~8.6.3", "avj": "0.0.0", diff --git a/api/src/paths/dwc/spatial/download.test.ts b/api/src/paths/dwc/spatial/download.test.ts deleted file mode 100644 index e109d66fd..000000000 --- a/api/src/paths/dwc/spatial/download.test.ts +++ /dev/null @@ -1,378 +0,0 @@ -import AdmZip from 'adm-zip'; -import chai, { expect } from 'chai'; -import { Feature } from 'geojson'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../database/db'; -import { ISubmissionSpatialSearchResponseRow } from '../../../repositories/spatial-repository'; -import { SpatialService } from '../../../services/spatial-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as download from './download'; -import { GET } from './download'; - -chai.use(sinonChai); - -describe('download', () => { - describe('openApiScheme', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - describe('should throw an error when', () => { - describe('boundry', () => { - it('is null', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: null, - datasetID: [] - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('boundary'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('is not a array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: 123, - datasetID: [] - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('boundary'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - - describe('type', () => { - it('is not an array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [], - datasetID: [], - type: 'not an array' - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('type'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - - describe('datasetID', () => { - it('is undefined', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [] - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('datasetID'); - expect(response.errors[0].message).to.equal("must have required property 'datasetID'"); - }); - - it('is null', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [], - datasetID: null - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('datasetID'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('is not an array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [], - type: [], - datasetID: 'not an array' - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('datasetID'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - describe('should throw an error when', () => { - it('returns a null response', async () => { - const apiResponse = null; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('response'); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('returns invalide response', () => { - const apiResponse = [{}]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be string'); - }); - }); - - describe('should succeed when', () => { - it('returns a response that can be turned back into object', async () => { - const mockData: ISubmissionSpatialSearchResponseRow[] = [ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Boundary' }, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - } - } - }, - { - taxa_data: [{ submission_spatial_component_id: 2 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { - type: 'Occurrence' - }, - geometry: { type: 'Point', coordinates: [] } - } - ] - } - } - } - ]; - // convert object into valid buffer - const zip = new AdmZip(); - zip.addFile('results.json', Buffer.from(JSON.stringify(mockData)), 'Search Results.'); - - const fileString = zip.toBuffer().toString('hex'); - const response = responseValidator.validateResponse(200, fileString); - - // Convert response back into a file - const fileData = Buffer.from(fileString, 'hex'); - const responseZip = new AdmZip(fileData); - const zipEntries = responseZip.getEntries(); - zipEntries.forEach((item) => { - expect(JSON.parse(item.getData().toString())).to.eql(mockData); - }); - - expect(response).to.equal(undefined); - }); - }); - }); - }); - - describe('downloadSpatialComponents', () => { - afterEach(() => { - sinon.restore(); - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialService.prototype, 'findSpatialComponentsByCriteria') - .throws(new Error('test error')); - - const requestHandler = download.downloadSpatialComponents(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as Error).message).to.equal('test error'); - expect(dbConnectionObj.rollback).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - expect(findSpatialComponentsByCriteriaStub).to.be.calledWith({ - type: [], - datasetID: [], - boundary: [] - }); - } - }); - - it('uses getDBConnection', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - mockReq['keycloak_token'] = 'token'; - - sinon.stub(SpatialService.prototype, 'findSpatialComponentsByCriteria').resolves([]); - - const requestHandler = download.downloadSpatialComponents(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - - expect(getDBConnectionStub).to.be.calledWith('token'); - }); - - it('uses getAPIUserDBConnection', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - const getAPIUserDBConnectionStub = sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - sinon.stub(SpatialService.prototype, 'findSpatialComponentsByCriteria').resolves([]); - - const requestHandler = download.downloadSpatialComponents(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - - expect(getAPIUserDBConnectionStub).to.be.calledOnce; - }); - - it('returns 200', async () => { - const datasetID = '123-456-789'; - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const boundaryFeature: Feature = { - type: 'Feature', - properties: {}, - geometry: { type: 'Polygon', coordinates: [[]] } - }; - - mockReq.query = { - type: ['type'], - boundary: [JSON.stringify(boundaryFeature)], - datasetID: [datasetID] - }; - - const mockData: ISubmissionSpatialSearchResponseRow[] = [ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Boundary' }, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - } - } - }, - { - taxa_data: [{ submission_spatial_component_id: 2 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { - type: 'Occurrence' - }, - geometry: { type: 'Point', coordinates: [] } - } - ] - } - } - } - ]; - - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialService.prototype, 'findSpatialComponentsByCriteria') - .resolves(mockData); - - const requestHandler = download.downloadSpatialComponents(); - await requestHandler(mockReq, mockRes, mockNext); - expect(mockRes.statusValue).to.equal(200); - expect(mockRes).to.not.be.null; - - // Convert response back into a file - const fileData = Buffer.from(mockRes.sendValue, 'hex'); - const zip = new AdmZip(fileData); - const zipEntries = zip.getEntries(); - zipEntries.forEach((item) => { - expect(JSON.parse(item.getData().toString())).to.eql(mockData); - }); - expect(dbConnectionObj.commit).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - expect(findSpatialComponentsByCriteriaStub).to.be.calledWith({ - type: ['type'], - datasetID: [datasetID], - boundary: [ - { - type: 'Feature', - properties: {}, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - }); - }); - }); -}); diff --git a/api/src/paths/dwc/spatial/download.ts b/api/src/paths/dwc/spatial/download.ts deleted file mode 100644 index f5c7c96e1..000000000 --- a/api/src/paths/dwc/spatial/download.ts +++ /dev/null @@ -1,116 +0,0 @@ -import AdmZip from 'adm-zip'; -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { Feature } from 'geojson'; -import { getAPIUserDBConnection, getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { SpatialService } from '../../../services/spatial-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/spatial/download'); - -export const GET: Operation = [downloadSpatialComponents()]; - -GET.apiDoc = { - description: 'Archived search results for spatial components.', - tags: ['spatial', 'search', 'download'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - in: 'query', - name: 'boundary', - schema: { - type: 'array', - items: { - type: 'string' - } - }, - description: 'A stringified GeoJSON Feature. Will return results that intersect the feature.' - }, - { - in: 'query', - name: 'type', - schema: { - type: 'array', - items: { - type: 'string' - }, - nullable: true - }, - description: 'An array of spatial component types to filter on. Will return results that match any of the types.' - }, - { - in: 'query', - name: 'datasetID', - required: true, - schema: { - type: 'array', - items: { - type: 'string' - } - }, - description: 'An array of dataset IDs. Will return results that belong to any of the dataset IDs.' - } - ], - responses: { - 200: { - description: 'Archived spatial components response object.', - content: { - 'application/zip': { - schema: { - type: 'string', - description: 'Buffer of the archived search results.' - } - } - } - }, - ...defaultErrorResponses - } -}; - -export function downloadSpatialComponents(): RequestHandler { - return async (req, res) => { - const boundaries: Feature[] = []; - if (req.query.boundary?.length) { - const boundariesArray: string[] = req.query.boundary as string[]; - boundariesArray.forEach((boundary) => { - boundaries.push(JSON.parse(boundary)); - }); - } - - const criteria = { - type: (req.query.type as string[]) || [], - datasetID: (req.query.datasetID as string[]) || [], - boundary: boundaries - }; - - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - try { - await connection.open(); - const spatialService = new SpatialService(connection); - const response = await spatialService.findSpatialComponentsByCriteria(criteria); - - const zip = new AdmZip(); - const fileName = `results.json`; - - zip.addFile(fileName, Buffer.from(JSON.stringify(response)), 'Search results.'); - const zipToSend = await zip.toBuffer(); - - await connection.commit(); - - // encoding zip as hex to avoid corrupted file in response - res.status(200).send(zipToSend.toString('hex')); - } catch (error) { - defaultLog.error({ label: 'downloadSpatialComponents', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/spatial/metadata.test.ts b/api/src/paths/dwc/spatial/metadata.test.ts deleted file mode 100644 index ea8a72854..000000000 --- a/api/src/paths/dwc/spatial/metadata.test.ts +++ /dev/null @@ -1,198 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../database/db'; -import { SpatialService } from '../../../services/spatial-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as metadata from './metadata'; -import { GET } from './metadata'; - -chai.use(sinonChai); - -describe('metadata', () => { - describe('openApiSchema', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - describe('should throw an error when', () => { - describe('submissionSpatialComponentIds', () => { - it('is undefined', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: {} - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('submissionSpatialComponentIds'); - expect(response.errors[0].message).to.equal("must have required property 'submissionSpatialComponentIds'"); - }); - - it('is null', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - submissionSpatialComponentIds: null - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('submissionSpatialComponentIds'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('is zero', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - submissionSpatialComponentIds: [0] - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('submissionSpatialComponentIds.0'); - expect(response.errors[0].message).to.equal('must be >= 1'); - }); - }); - }); - - describe('should succeed when', () => { - it('all values are provided and valid', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - submissionSpatialComponentIds: [1] - } - }; - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - - describe('should throw an error when', () => { - it('returns a null response', async () => { - const apiResponse = null; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('response'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('returns invalid response (not an array)', async () => { - // array of `Feature` rather than `FeatureCollection` - const apiResponse = 'not an array'; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('response'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('returns invalid response (not an object)', async () => { - // array of `Feature` rather than `FeatureCollection` - const apiResponse = ['not an object']; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('0'); - expect(response.errors[0].message).to.equal('must be object'); - }); - }); - - describe('should succeed when', () => { - it('required values are valid (empty)', async () => { - const apiResponse: Record[] = []; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - - it('required values are valid', async () => { - const apiResponse = [{ prop1: 'val1' }]; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - }); - }); - }); - - describe('getSpatialMetadataBySubmissionSpatialComponentIds', () => { - afterEach(() => { - sinon.restore(); - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { submissionSpatialComponentIds: ['1'] }; - - sinon - .stub(SpatialService.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds') - .throws(new Error('test error')); - - const requestHandler = metadata.getSpatialMetadataBySubmissionSpatialComponentIds(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as Error).message).to.equal('test error'); - expect(dbConnectionObj.rollback).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - } - }); - - it('returns 200', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = { submissionSpatialComponentIds: ['1'] }; - - const mockResponse = [{ prop1: 'val1' }]; - - sinon.stub(SpatialService.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds').resolves(mockResponse); - - const requestHandler = metadata.getSpatialMetadataBySubmissionSpatialComponentIds(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql(mockResponse); - expect(dbConnectionObj.commit).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - }); - }); -}); diff --git a/api/src/paths/dwc/spatial/metadata.ts b/api/src/paths/dwc/spatial/metadata.ts deleted file mode 100644 index a54ecb3e7..000000000 --- a/api/src/paths/dwc/spatial/metadata.ts +++ /dev/null @@ -1,84 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { SpatialService } from '../../../services/spatial-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/spatial/metadata'); - -export const GET: Operation = [getSpatialMetadataBySubmissionSpatialComponentIds()]; - -GET.apiDoc = { - description: 'Retrieves spatial component metadata based on submission spatial component id', - tags: ['spatial'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'spatial component submission ids', - in: 'query', - name: 'submissionSpatialComponentIds', - schema: { - type: 'array', - items: { - type: 'number', - minimum: 1 - } - }, - required: true - } - ], - responses: { - 200: { - description: 'Spatial metadata response object.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object' - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Retrieves dataset metadata from Elastic Search. - * - * @returns {RequestHandler} - */ -export function getSpatialMetadataBySubmissionSpatialComponentIds(): RequestHandler { - return async (req, res) => { - const submissionSpatialComponentIds = ((req.query.submissionSpatialComponentIds || []) as string[]).map(Number); - - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - try { - await connection.open(); - - const spatialService = new SpatialService(connection); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds( - submissionSpatialComponentIds - ); - - await connection.commit(); - - res.status(200).json(response); - } catch (error) { - defaultLog.error({ label: 'getSpatialMetadataBySubmissionSpatialComponentIds', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/spatial/search.test.ts b/api/src/paths/dwc/spatial/search.test.ts deleted file mode 100644 index b08e85209..000000000 --- a/api/src/paths/dwc/spatial/search.test.ts +++ /dev/null @@ -1,475 +0,0 @@ -import chai, { expect } from 'chai'; -import { Feature } from 'geojson'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../database/db'; -import { ISubmissionSpatialSearchResponseRow } from '../../../repositories/spatial-repository'; -import { SpatialService } from '../../../services/spatial-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import * as search from './search'; -import { GET } from './search'; - -chai.use(sinonChai); - -describe('search', () => { - describe('openApiSchema', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - describe('should throw an error when', () => { - describe('boundary', () => { - it('is null', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: null - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('boundary'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('is not an array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: 123 - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('boundary'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - - describe('type', () => { - it('is not an array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [], - type: 'not an array' - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('type'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - - describe('datasetID', () => { - it('is not an array', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: [], - type: [], - datasetID: 'not an array' - } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors[0].path).to.equal('datasetID'); - expect(response.errors[0].message).to.equal('must be array'); - }); - }); - }); - - describe('should succeed when', () => { - it('all values are provided and valid', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: ['not null'], - type: ['type'], - datasetID: ['id'] - } - }; - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - - it('required values are provided and valid', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: ['not null'] - } - }; - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - - it('optional values are provided and valid', async () => { - const request = { - headers: { - 'content-type': 'application/json' - }, - query: { - boundary: ['not null'], - type: null, - datasetID: null - } - }; - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - - describe('should throw an error when', () => { - it('returns a null response', async () => { - const apiResponse = null; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('response'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('returns invalid response (not an array of FeatureCollection)', async () => { - // array of `Feature` rather than `FeatureCollection` - const apiResponse = [ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_data: { - type: 'Feature', - properties: {}, - geometry: { type: 'Point', coordinates: [-123.43791961669922, 48.63449682909913] } - } - } - ]; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('0/spatial_data'); - expect(response.errors[0].message).to.equal("must have required property 'features'"); - expect(response.errors[1].path).to.equal('0/spatial_data/type'); - expect(response.errors[1].message).to.equal('must be equal to one of the allowed values'); - }); - - it('returns invalid response (missing taxa_data)', async () => { - const apiResponse = [ - { - spatial_data: { - type: 'FeatureCollection', - properties: {}, - geometry: { type: 'Point', coordinates: [-123.43791961669922, 48.63449682909913] } - } - } - ]; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('0'); - expect(response.errors[0].message).to.equal("must have required property 'taxa_data'"); - }); - - it('returns invalid response (missing submission_spatial_component_id)', async () => { - const apiResponse = [ - { - taxa_data: [{ taxon_id: 'M-ALAM' }], - spatial_data: { - type: 'FeatureCollection', - properties: {}, - geometry: { type: 'Point', coordinates: [-123.43791961669922, 48.63449682909913] } - } - } - ]; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].path).to.equal('0/taxa_data/0'); - expect(response.errors[0].message).to.equal("must have required property 'submission_spatial_component_id'"); - }); - }); - - describe('should succeed when', () => { - it('required values are valid (empty)', async () => { - const apiResponse: any[] = []; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - - it('required values are valid', async () => { - const apiResponse = [ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: {}, - geometry: { - type: 'Polygon', - coordinates: [ - [ - [-123.43785926699638, 48.634569504210184], - [-123.43786899000405, 48.634561749249066], - [-123.43785356730223, 48.63456285710074], - [-123.43785926699638, 48.634569504210184] - ] - ] - } - }, - { - type: 'Feature', - properties: {}, - geometry: { - type: 'Polygon', - coordinates: [ - [ - [-123.43785926699638, 48.634569504210184], - [-123.43786899000405, 48.634561749249066], - [-123.43785356730223, 48.63456285710074], - [-123.43785926699638, 48.634569504210184] - ] - ] - } - } - ] - } - }, - { - taxa_data: [{ submission_spatial_component_id: 2 }], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: {}, - geometry: { type: 'Point', coordinates: [-123.43791961669922, 48.63449682909913] } - } - ] - } - } - ]; - - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - }); - }); - }); - - describe('searchSpatialComponents', () => { - afterEach(() => { - sinon.restore(); - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialService.prototype, 'findSpatialComponentsByCriteria') - .throws(new Error('test error')); - - const requestHandler = search.searchSpatialComponents(); - - try { - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as Error).message).to.equal('test error'); - expect(dbConnectionObj.rollback).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - - expect(findSpatialComponentsByCriteriaStub).to.be.calledWith({ - type: [], - species: [], - datasetID: [], - boundary: [] - }); - } - }); - - it('uses getDBConnection', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - const getDBConnectionStub = sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - mockReq['keycloak_token'] = 'token'; - - sinon.stub(SpatialService.prototype, 'findSpatialComponentsByCriteria').resolves([]); - - const requestHandler = search.searchSpatialComponents(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - - expect(getDBConnectionStub).to.be.calledWith('token'); - }); - - it('uses getAPIUserDBConnection', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - const getAPIUserDBConnectionStub = sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.query = {}; - - sinon.stub(SpatialService.prototype, 'findSpatialComponentsByCriteria').resolves([]); - - const requestHandler = search.searchSpatialComponents(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - - expect(getAPIUserDBConnectionStub).to.be.calledOnce; - }); - - it('returns 200', async () => { - const dbConnectionObj = getMockDBConnection({ commit: sinon.stub(), release: sinon.stub() }); - sinon.stub(db, 'getAPIUserDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - const boundaryFeature: Feature = { - type: 'Feature', - properties: {}, - geometry: { type: 'Polygon', coordinates: [[]] } - }; - - mockReq.query = { - type: ['type'], - boundary: [JSON.stringify(boundaryFeature)] - }; - - const mockResponse: ISubmissionSpatialSearchResponseRow[] = [ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Boundary' }, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - } - } - }, - { - taxa_data: [{ submission_spatial_component_id: 2 }], - spatial_component: { - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Occurrence' }, - geometry: { type: 'Point', coordinates: [] } - } - ] - } - } - } - ]; - - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialService.prototype, 'findSpatialComponentsByCriteria') - .resolves(mockResponse); - - const requestHandler = search.searchSpatialComponents(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - expect(mockRes.jsonValue).to.eql([ - { - taxa_data: [{ submission_spatial_component_id: 1 }], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Boundary' }, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - } - }, - { - taxa_data: [{ submission_spatial_component_id: 2 }], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - properties: { type: 'Occurrence' }, - geometry: { type: 'Point', coordinates: [] } - } - ] - } - } - ]); - expect(dbConnectionObj.commit).to.have.been.calledOnce; - expect(dbConnectionObj.release).to.have.been.calledOnce; - expect(findSpatialComponentsByCriteriaStub).to.be.calledWith({ - type: ['type'], - species: [], - datasetID: [], - boundary: [ - { - type: 'Feature', - properties: {}, - geometry: { type: 'Polygon', coordinates: [[]] } - } - ] - }); - }); - }); -}); diff --git a/api/src/paths/dwc/spatial/search.ts b/api/src/paths/dwc/spatial/search.ts deleted file mode 100644 index 261db55d8..000000000 --- a/api/src/paths/dwc/spatial/search.ts +++ /dev/null @@ -1,182 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { Feature } from 'geojson'; -import { getAPIUserDBConnection, getDBConnection } from '../../../database/db'; -import { GeoJSONFeatureCollection } from '../../../openapi/schemas/geoJson'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { SpatialService } from '../../../services/spatial-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/spatial/search'); - -export const GET: Operation = [searchSpatialComponents()]; - -GET.apiDoc = { - description: 'Searches for spatial components.', - tags: ['spatial', 'search'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - in: 'query', - name: 'boundary', - schema: { - type: 'array', - items: { - type: 'string' - } - }, - description: 'A stringified GeoJSON Feature. Will return results that intersect the feature.' - }, - { - in: 'query', - name: 'type', - schema: { - type: 'array', - items: { - type: 'string' - }, - nullable: true - }, - description: 'An array of spatial component types to filter on. Will return results that match any of the types.' - }, - { - in: 'query', - name: 'species', - schema: { - type: 'array', - items: { - type: 'string' - }, - nullable: true - }, - description: 'An array of species codes to filter on. Will return results that match any of the types.' - }, - { - in: 'query', - name: 'datasetID', - schema: { - type: 'array', - items: { - type: 'string' - }, - nullable: true - }, - description: 'An array of dataset IDs. Will return results that belong to any of the dataset IDs.' - } - ], - responses: { - 200: { - description: 'Spatial components response object.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - required: ['taxa_data', 'spatial_data'], - properties: { - taxa_data: { - type: 'array', - items: { - type: 'object', - required: ['submission_spatial_component_id'], - properties: { - submission_spatial_component_id: { - type: 'number', - minimum: 1 - }, - taxon_id: { - type: 'string', - nullable: true - }, - vernacular_name: { - type: 'string', - nullable: true - } - } - } - }, - spatial_data: { - oneOf: [ - { - ...GeoJSONFeatureCollection - }, - { - type: 'object', - properties: {}, - additionalProperties: false, - minProperties: 0, - maxProperties: 0, - description: - 'An empty object, representing a spatial component the requester does not have sufficient privileges to view.' - } - ] - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -export function searchSpatialComponents(): RequestHandler { - return async (req, res) => { - const boundaries: Feature[] = []; - if (req.query.boundary?.length) { - const boundariesArray: string[] = req.query.boundary as string[]; - boundariesArray.forEach((boundary) => { - boundaries.push(JSON.parse(boundary)); - }); - } - - const criteria = { - type: (req.query.type as string[]) || [], - species: (req.query.species as string[]) || [], - datasetID: (req.query.datasetID as string[]) || [], - boundary: boundaries - }; - - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - try { - await connection.open(); - - const spatialService = new SpatialService(connection); - - const response = await spatialService.findSpatialComponentsByCriteria(criteria); - - const structuredResponse = response.map((row) => { - const { spatial_component, taxa_data } = row; - const { spatial_data, ...rest } = spatial_component; - return { - taxa_data, - ...rest, - spatial_data: { - ...spatial_data, - features: spatial_data.features.map((feature) => { - delete feature?.properties?.dwc; - return feature; - }) - } - }; - }); - - await connection.commit(); - - res.status(200).json(structuredResponse); - } catch (error) { - defaultLog.error({ label: 'searchSpatialComponents', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/list.test.ts b/api/src/paths/dwc/submission/list.test.ts deleted file mode 100644 index c01c4e645..000000000 --- a/api/src/paths/dwc/submission/list.test.ts +++ /dev/null @@ -1,326 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../database/db'; -import { ApiGeneralError } from '../../../errors/api-error'; -import { SubmissionService } from '../../../services/submission-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db'; -import { GET, listDataset } from './list'; - -chai.use(sinonChai); - -describe('submissions', () => { - describe('openApiSchema', () => { - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - - describe('should throw an error when', () => { - describe('required return properties is missing', () => { - it('property submission_id', async () => { - const apiResponse = [{}]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'submission_id'"); - }); - - it('property uuid', async () => { - const apiResponse = [{ submission_id: 1, source: 'SIMS' }]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'uuid'"); - }); - - it('property event_timestamp', async () => { - const apiResponse = [{ submission_id: 1, source: 'SIMS', uuid: '2267501d-c6a9-43b5-b951-2324faff6397' }]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'event_timestamp'"); - }); - - it('property create_date', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z' - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'create_date'"); - }); - - it('property create_user', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z' - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'create_user'"); - }); - - it('property revision_count', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal("must have required property 'revision_count'"); - }); - }); - - describe('return properties are invalid types', () => { - it('null value', async () => { - const apiResponse = null; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be array'); - }); - - it('is not an object', async () => { - const apiResponse = ['']; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be object'); - }); - - it('property submission_id', async () => { - const apiResponse = [ - { - submission_id: '', - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be integer'); - }); - - it('property source', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 1, - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('property uuid', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: 1, - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('property event_timestamp', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: 1, - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be object'); - }); - - it('property create_date', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: 1, - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be object'); - }); - - it('property create_user', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: '', - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be integer'); - }); - - it('property revision_count', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: '' - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors[0].message).to.equal('must be integer'); - }); - }); - }); - - describe('should succeed when', () => { - it('has valid empty value', async () => { - const apiResponse: any[] = []; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - - it('has valid values', async () => { - const apiResponse = [ - { - submission_id: 1, - source: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - event_timestamp: '2022-05-24T18:41:42.211Z', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - revision_count: 1 - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response).to.equal(undefined); - }); - }); - }); - }); - describe('listSubmissions', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error if listSubmissionRecords throws an ApiGeneralError', async () => { - const dbConnectionObj = getMockDBConnection({ - commit: sinon.stub(), - rollback: sinon.stub(), - release: sinon.stub() - }); - - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - sinon.stub(SubmissionService.prototype, 'listSubmissionRecords').throws('error' as unknown as ApiGeneralError); - - try { - const requestHandler = listDataset(); - - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect(dbConnectionObj.commit).to.not.be.called; - expect(dbConnectionObj.rollback).to.be.calledOnce; - expect(dbConnectionObj.release).to.be.calledOnce; - } - }); - - it('should return rows on success', async () => { - const mockDBConnection = getMockDBConnection(); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - sinon.stub(db, 'getDBConnection').returns(mockDBConnection); - - const mockResponse = [ - { - submission_status: 'Submission Data Ingested', - submission_id: 1, - source_transform_id: 1, - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - record_effective_date: '2022-05-24T18:41:42.211Z', - record_end_date: null, - input_key: 'biohub/1/moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - input_file_name: 'moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - eml_source: null, - eml_json_source: null, - darwin_core_source: 'test', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - update_date: '2022-05-24T18:41:42.056Z', - update_user: 15, - revision_count: 1 - } - ]; - - sinon.stub(SubmissionService.prototype, 'listSubmissionRecords').resolves(mockResponse); - - const requestHandler = listDataset(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.jsonValue).to.eql(mockResponse); - }); - }); -}); diff --git a/api/src/paths/dwc/submission/list.ts b/api/src/paths/dwc/submission/list.ts deleted file mode 100644 index d85653397..000000000 --- a/api/src/paths/dwc/submission/list.ts +++ /dev/null @@ -1,136 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getDBConnection } from '../../../database/db'; -import { defaultErrorResponses } from '../../../openapi/schemas/http-responses'; -import { ISubmissionModelWithStatus } from '../../../repositories/submission-repository'; -import { authorizeRequestHandler } from '../../../request-handlers/security/authorization'; -import { SubmissionService } from '../../../services/submission-service'; -import { getLogger } from '../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/submission/list'); - -export const GET: Operation = [ - authorizeRequestHandler(() => { - return { - and: [ - { - discriminator: 'SystemUser' - } - ] - }; - }), - listDataset() -]; - -GET.apiDoc = { - description: 'List submitted Darwin Core Archive (DwCA) data packages.', - tags: ['dwc'], - security: [ - { - Bearer: [] - } - ], - responses: { - 200: { - description: 'Darwin Core data packages.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - title: 'Darwin Core Data Packages Response Object', - type: 'object', - required: ['submission_id', 'uuid', 'event_timestamp', 'create_date', 'create_user', 'revision_count'], - properties: { - submission_status: { - type: 'string', - nullable: true - }, - submission_id: { - type: 'integer', - minimum: 1 - }, - source: { - type: 'string' - }, - uuid: { - type: 'string', - format: 'uuid' - }, - event_timestamp: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }] - }, - delete_timestamp: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }], - nullable: true - }, - input_key: { - type: 'string', - nullable: true - }, - input_file_name: { - type: 'string', - nullable: true - }, - eml_source: { - type: 'string', - nullable: true - }, - eml_json_source: { - type: 'string', - nullable: true - }, - darwin_core_source: { - oneOf: [{ type: 'object' }, { type: 'string' }], - nullable: true - }, - create_date: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }] - }, - create_user: { - type: 'integer' - }, - update_date: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }], - nullable: true - }, - update_user: { - type: 'integer', - nullable: true - }, - revision_count: { - type: 'integer' - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -export function listDataset(): RequestHandler { - return async (req, res) => { - const connection = getDBConnection(req['keycloak_token']); - - try { - await connection.open(); - - const submissionService = new SubmissionService(connection); - - const submissions: ISubmissionModelWithStatus[] = await submissionService.listSubmissionRecords(); - - await connection.commit(); - - res.status(200).json(submissions); - } catch (error) { - defaultLog.error({ label: 'listDataset', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/{datasetId}/artifacts.test.ts b/api/src/paths/dwc/submission/{datasetId}/artifacts.test.ts deleted file mode 100644 index e79ea17fc..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/artifacts.test.ts +++ /dev/null @@ -1,285 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../../database/db'; -import { HTTPError } from '../../../../errors/http-error'; -import { SECURITY_APPLIED_STATUS } from '../../../../repositories/security-repository'; -import { ArtifactService } from '../../../../services/artifact-service'; -import { SecurityService } from '../../../../services/security-service'; -import { UserService } from '../../../../services/user-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../__mocks__/db'; -import { GET, getArtifactsByDatasetId } from './artifacts'; - -chai.use(sinonChai); - -describe('getArtifactsByDatasetId', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('openApiSchema', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - describe('should throw an error when', () => { - describe('datasetId', () => { - it('is invalid type', async () => { - const request = { - params: { datasetId: 123 } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('is invalid format', async () => { - const request = { - params: { datasetId: 'abcdefg' } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must match format "uuid"'); - }); - }); - }); - - describe('should succeed when', () => { - it('required values are valid', async () => { - const request = { - params: { datasetId: '374c4d6a-3a04-405b-af6d-b6497800a691' } - }; - - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - const mockResponse = { - artifact_id: 1, - create_date: '1970-01-01T00:00:00.000Z', - description: 'description', - file_name: 'Lecture 5 - Partial Fraction.pdf', - file_size: 2405262, - file_type: 'Report', - foi_reason: false, - key: 'cupshall/platform/datasets/de621765-9fd0-4216-91b7-ec455d9c3eb1/artifacts/1/374c4d6a-3a04-405b-af6d-b6497800a691.zip', - security_review_timestamp: '1970-01-01T00:00:00.000Z', - submission_id: 1, - title: 'Report 2', - uuid: '374c4d6a-3a04-405b-af6d-b6497800a691', - supplementaryData: { - persecutionAndHarmStatus: 'SECURED', - persecutionAndHarmRules: [] - } - }; - describe('should throw an error when', () => { - it('returns a null response', async () => { - const apiResponse = null; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be array'); - }); - - describe('artifact', () => { - it('returns a null response', async () => { - const apiResponse = [null]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be object'); - }); - - describe('artifact_id', () => { - it('is undefined', async () => { - const apiResponse = [ - { - ...mockResponse, - artifact_id: undefined - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal("must have required property 'artifact_id'"); - }); - - it('is null', async () => { - const apiResponse = [ - { - ...mockResponse, - artifact_id: null - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be integer'); - }); - - it('is wrong type', async () => { - const apiResponse = [ - { - ...mockResponse, - artifact_id: '1' - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be integer'); - }); - }); - - describe('create_date', () => { - it('is undefined', async () => { - const apiResponse = [ - { - ...mockResponse, - create_date: undefined - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal("must have required property 'create_date'"); - }); - - it('is null', async () => { - const apiResponse = [ - { - ...mockResponse, - create_date: null - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(3); - expect(response.errors[0].message).to.equal('must be object'); - expect(response.errors[1].message).to.equal('must be string'); - }); - }); - }); - }); - - describe('should succeed when', () => { - it('required values are valid', async () => { - const apiResponse = [ - { - artifact_id: 1, - create_date: '1970-01-01T00:00:00.000Z', - description: 'Test description', - file_name: 'Filename.docx', - file_size: 1024, - file_type: 'Report', - foi_reason: false, - key: 'platform/datasets/de621765-9fd0-4216-91b7-ec455d9c3eb1/artifacts/1/374c4d6a-3a04-405b-af6d-b6497800a691.zip', - security_review_timestamp: '1970-01-01T00:00:00.000Z', - submission_id: 1, - title: 'Test Report', - uuid: '374c4d6a-3a04-405b-af6d-b6497800a691', - supplementaryData: { - persecutionAndHarmStatus: 'SECURED', - persecutionAndHarmRules: [] - } - } - ]; - const response = responseValidator.validateResponse(200, apiResponse); - expect(response).to.equal(undefined); - }); - }); - }); - }); - - it('should return a valid array of artifact records on success', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const artifactServiceStub = sinon.stub(ArtifactService.prototype, 'getArtifactsByDatasetId').resolves([ - { artifact_id: 1, security_review_timestamp: new Date('1970-01-01T00:00:00.000Z') }, - { artifact_id: 2, security_review_timestamp: new Date('1970-01-01T00:00:00.000Z') } - ] as any[]); - - const isSystemUserAdminStub = sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(true); - - const getArtifactSupplementaryDataStub = sinon - .stub(SecurityService.prototype, 'getArtifactSupplementaryData') - .resolves({ persecutionAndHarmRules: [], persecutionAndHarmStatus: SECURITY_APPLIED_STATUS.UNSECURED }); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - const requestHandler = getArtifactsByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - expect(artifactServiceStub).to.be.calledWith('abcd'); - expect(mockRes.jsonValue).to.eql([ - { - artifact_id: 1, - security_review_timestamp: new Date('1970-01-01T00:00:00.000Z'), - supplementaryData: { - persecutionAndHarmStatus: 'UNSECURED', - persecutionAndHarmRules: [] - } - }, - { - artifact_id: 2, - security_review_timestamp: new Date('1970-01-01T00:00:00.000Z'), - supplementaryData: { - persecutionAndHarmStatus: 'UNSECURED', - persecutionAndHarmRules: [] - } - } - ]); - expect(isSystemUserAdminStub).to.be.calledOnce; - expect(getArtifactSupplementaryDataStub).to.be.calledTwice; - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - sinon.stub(ArtifactService.prototype, 'getArtifactsByDatasetId').rejects(new Error('a test error')); - sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(true); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - try { - const requestHandler = getArtifactsByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('a test error'); - } - }); -}); diff --git a/api/src/paths/dwc/submission/{datasetId}/artifacts.ts b/api/src/paths/dwc/submission/{datasetId}/artifacts.ts deleted file mode 100644 index 82fa8c8da..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/artifacts.ts +++ /dev/null @@ -1,176 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../../database/db'; -import { defaultErrorResponses } from '../../../../openapi/schemas/http-responses'; -import { ArtifactService } from '../../../../services/artifact-service'; -import { SecurityService } from '../../../../services/security-service'; -import { UserService } from '../../../../services/user-service'; -import { getLogger } from '../../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/submission/{datasetId}/artifacts'); - -export const GET: Operation = [getArtifactsByDatasetId()]; - -GET.apiDoc = { - description: 'Retrieves dataset artifact records by dataset ID', - tags: ['artifacts'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'Dataset identifier', - in: 'path', - name: 'datasetId', - schema: { - type: 'string', - format: 'uuid' - }, - required: true - } - ], - responses: { - 200: { - description: 'Dataset attachments response object.', - content: { - 'application/json': { - schema: { - type: 'array', - items: { - type: 'object', - required: [ - 'artifact_id', - 'create_date', - 'description', - 'file_name', - 'file_size', - 'foi_reason', - 'key', - 'security_review_timestamp', - 'submission_id', - 'title', - 'uuid', - 'supplementaryData' - ], - properties: { - artifact_id: { - type: 'integer', - minimum: 1 - }, - create_date: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }] - }, - description: { - type: 'string', - nullable: true - }, - file_name: { - type: 'string' - }, - file_size: { - type: 'integer' - }, - foi_reason: { - type: 'boolean', - nullable: true - }, - key: { - type: 'string' - }, - security_review_timestamp: { - oneOf: [{ type: 'object' }, { type: 'string', format: 'date-time' }], - nullable: true - }, - submission_id: { - type: 'integer', - minimum: 1 - }, - title: { - type: 'string', - nullable: true - }, - uuid: { - type: 'string', - format: 'uuid' - }, - supplementaryData: { - type: 'object', - required: ['persecutionAndHarmRules', 'persecutionAndHarmStatus'], - properties: { - persecutionAndHarmStatus: { - type: 'string', - enum: ['SECURED', 'UNSECURED', 'PENDING'] - }, - persecutionAndHarmRules: { - type: 'array', - items: { - type: 'object', - properties: { - artifact_id: { - type: 'integer' - }, - artifact_persecution_id: { - type: 'integer' - }, - persecution_or_harm_id: { - type: 'integer' - } - } - } - } - } - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Retrieves dataset artifacts - * - * @returns {RequestHandler} - */ -export function getArtifactsByDatasetId(): RequestHandler { - return async (req, res) => { - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - const datasetId = String(req.params.datasetId); - - try { - await connection.open(); - const userService = new UserService(connection); - const artifactService = new ArtifactService(connection); - const securityService = new SecurityService(connection); - - const isAdmin = await userService.isSystemUserAdmin(); - const artifacts = await artifactService.getArtifactsByDatasetId(datasetId); - - const artifactsWithRules = await Promise.all( - artifacts.map(async (artifact) => { - const supplementaryData = await securityService.getArtifactSupplementaryData(artifact.artifact_id, isAdmin); - return { - ...artifact, - supplementaryData: supplementaryData - }; - }) - ); - - await connection.commit(); - - res.status(200).json(artifactsWithRules); - } catch (error) { - defaultLog.error({ label: 'getArtifactsByDatasetId', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/{datasetId}/get.test.ts b/api/src/paths/dwc/submission/{datasetId}/get.test.ts deleted file mode 100644 index c1abda0b6..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/get.test.ts +++ /dev/null @@ -1,62 +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 { SubmissionService } from '../../../../services/submission-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../__mocks__/db'; -import { getMetadataByDatasetId } from './get'; - -chai.use(sinonChai); - -describe('get', () => { - describe('dataset metadata (from the DB) by datasetId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return a valid submission record on success', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - sinon.stub(SubmissionService.prototype, 'getSubmissionRecordEMLJSONByDatasetId').resolves({}); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - const requestHandler = getMetadataByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - sinon - .stub(SubmissionService.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .rejects(new Error('a test error')); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - try { - const requestHandler = getMetadataByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('a test error'); - } - }); - }); -}); diff --git a/api/src/paths/dwc/submission/{datasetId}/get.ts b/api/src/paths/dwc/submission/{datasetId}/get.ts deleted file mode 100644 index 5b853cbe8..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/get.ts +++ /dev/null @@ -1,75 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../../database/db'; -import { defaultErrorResponses } from '../../../../openapi/schemas/http-responses'; -import { SubmissionService } from '../../../../services/submission-service'; -import { getLogger } from '../../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/submission/{datasetId}/get'); - -export const GET: Operation = [getMetadataByDatasetId()]; - -GET.apiDoc = { - description: 'retrieves dataset metadata within elastic search', - tags: ['eml'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'dataset Id.', - in: 'path', - name: 'datasetId', - schema: { - type: 'string' - }, - required: true - } - ], - responses: { - 200: { - description: 'Dataset metadata response object.', - content: { - 'application/json': { - schema: { - type: 'object' - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Retrieves dataset metadata from the submission table. - * - * @returns {RequestHandler} - */ -export function getMetadataByDatasetId(): RequestHandler { - return async (req, res) => { - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - const datasetId = String(req.params.datasetId); - - try { - await connection.open(); - - const submissionService = new SubmissionService(connection); - - const result = await submissionService.getSubmissionRecordEMLJSONByDatasetId(datasetId); - - await connection.commit(); - - res.status(200).json(result); - } catch (error) { - defaultLog.error({ label: 'getMetadataByDatasetId', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/{datasetId}/handlebar.test.ts b/api/src/paths/dwc/submission/{datasetId}/handlebar.test.ts deleted file mode 100644 index 8e32c7194..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/handlebar.test.ts +++ /dev/null @@ -1,34 +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 { getMockDBConnection, getRequestHandlerMocks } from '../../../../__mocks__/db'; -import { getHandleBarsTemplateByDatasetId } from './handlebar'; - -chai.use(sinonChai); - -describe('handlebar', () => { - describe('get a handlebars template for a given datasetId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return template data object', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'uuid' - }; - - const requestHandler = getHandleBarsTemplateByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - }); - }); -}); diff --git a/api/src/paths/dwc/submission/{datasetId}/handlebar.ts b/api/src/paths/dwc/submission/{datasetId}/handlebar.ts deleted file mode 100644 index b779ca3c0..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/handlebar.ts +++ /dev/null @@ -1,82 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../../database/db'; -import { defaultErrorResponses } from '../../../../openapi/schemas/http-responses'; -import { getLogger } from '../../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/eml/{datasetId}/handlebar'); - -export const GET: Operation = [getHandleBarsTemplateByDatasetId()]; - -GET.apiDoc = { - description: 'retrieves handle bar template for a given dataset id', - tags: ['eml'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'dataset Id.', - in: 'path', - name: 'datasetId', - schema: { - type: 'string' - }, - required: true - } - ], - responses: { - 200: { - description: 'Dataset handlebars response string', - content: { - 'application/json': { - schema: { - type: 'object', - properties: { - header: { - type: 'string' - }, - details: { - type: 'string' - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Retrieves dataset metadata from the submission table. - * - * @returns {RequestHandler} - */ -export function getHandleBarsTemplateByDatasetId(): RequestHandler { - return async (req, res) => { - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - // const datasetId = String(req.params.datasetId); - - try { - await connection.open(); - - // const submissionService = new SubmissionService(connection); - - // const result = await submissionService.getHandleBarsTemplateByDatasetId(datasetId); - - await connection.commit(); - - res.status(200).json(''); - } catch (error) { - defaultLog.error({ label: 'getHandleBarsTemplateByDatasetId', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/paths/dwc/submission/{datasetId}/related.test.ts b/api/src/paths/dwc/submission/{datasetId}/related.test.ts deleted file mode 100644 index e5a2a6f0a..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/related.test.ts +++ /dev/null @@ -1,348 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import OpenAPIRequestValidator, { OpenAPIRequestValidatorArgs } from 'openapi-request-validator'; -import OpenAPIResponseValidator, { OpenAPIResponseValidatorArgs } from 'openapi-response-validator'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import * as db from '../../../../database/db'; -import { HTTPError } from '../../../../errors/http-error'; -import { SecurityService } from '../../../../services/security-service'; -import { RelatedDataset, SubmissionService } from '../../../../services/submission-service'; -import { UserService } from '../../../../services/user-service'; -import { getMockDBConnection, getRequestHandlerMocks } from '../../../../__mocks__/db'; -import { GET, getRelatedDatasetsByDatasetId } from './related'; - -chai.use(sinonChai); - -describe('getRelatedDatasetsByDatasetId', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('openApiSchema', () => { - describe('request validation', () => { - const requestValidator = new OpenAPIRequestValidator(GET.apiDoc as unknown as OpenAPIRequestValidatorArgs); - - describe('should throw an error when', () => { - describe('datasetId', () => { - it('is invalid type', async () => { - const request = { - params: { datasetId: 123 } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('is invalid format', async () => { - const request = { - params: { datasetId: 'abcdefg' } - }; - - const response = requestValidator.validateRequest(request); - - expect(response.status).to.equal(400); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must match format "uuid"'); - }); - }); - }); - - describe('should succeed when', () => { - it('required values are valid', async () => { - const request = { - params: { datasetId: '374c4d6a-3a04-405b-af6d-b6497800a691' } - }; - - const response = requestValidator.validateRequest(request); - - expect(response).to.be.undefined; - }); - }); - }); - - describe('response validation', () => { - const responseValidator = new OpenAPIResponseValidator(GET.apiDoc as unknown as OpenAPIResponseValidatorArgs); - const mockRelatedDataset = { - datasetId: '374c4d6a-3a04-405b-af6d-b6497800a691', - title: 'Test-Related-Dataset', - url: 'https://example.com/374c4d6a-3a04-405b-af6d-b6497800a691', - supplementaryData: { - isPendingReview: false - } - }; - - describe('should throw an error when', () => { - it('returns a null response', async () => { - const apiResponse = null; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be object'); - }); - - it('returns a null array', async () => { - const apiResponse = { datasets: null }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be array'); - }); - - describe('dataset', () => { - it('returns a null response', async () => { - const apiResponse = { datasets: [null] }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be object'); - }); - - describe('datsetId', () => { - it('is undefined', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - datasetId: undefined - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal("must have required property 'datasetId'"); - }); - - it('is null', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - datasetId: null - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('is wrong type', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - datasetId: 1 - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - }); - - describe('title', () => { - it('is undefined', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - title: undefined - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal("must have required property 'title'"); - }); - - it('is null', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - title: null - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('is wrong type', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - title: 1 - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - }); - - describe('url', () => { - it('is undefined', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - url: undefined - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal("must have required property 'url'"); - }); - - it('is null', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - url: null - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - - it('is wrong type', async () => { - const apiResponse = { - datasets: [ - { - ...mockRelatedDataset, - url: 1 - } - ] - }; - const response = responseValidator.validateResponse(200, apiResponse); - - expect(response.message).to.equal('The response was not valid.'); - expect(response.errors.length).to.equal(1); - expect(response.errors[0].message).to.equal('must be string'); - }); - }); - }); - }); - - describe('should succeed when', () => { - it('required values are valid', async () => { - const apiResponse = { - datasets: [mockRelatedDataset] - }; - - const response = responseValidator.validateResponse(200, apiResponse); - expect(response).to.equal(undefined); - }); - - it('returns an empty array of related datasets', async () => { - const apiResponse = { - datasets: [] - }; - - const response = responseValidator.validateResponse(200, apiResponse); - expect(response).to.equal(undefined); - }); - }); - }); - }); - - it('should return a valid array of related datasets on success', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - - const submissionServiceStub = sinon - .stub(SubmissionService.prototype, 'findRelatedDatasetsByDatasetId') - .resolves([{ datasetId: '123' }, { datasetId: '456' }] as RelatedDataset[]); - - const isSystemUserAdminStub = sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(true); - - const securityStub = sinon.stub(SecurityService.prototype, 'isDatasetPendingReview'); - securityStub.onFirstCall().resolves(true); - securityStub.onSecondCall().resolves(false); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - const requestHandler = getRelatedDatasetsByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - - expect(mockRes.statusValue).to.equal(200); - expect(submissionServiceStub).to.be.calledWith('abcd'); - expect(mockRes.jsonValue).to.eql({ - datasetsWithSupplementaryData: [ - { - datasetId: '123', - supplementaryData: { - isPendingReview: true - } - }, - { - datasetId: '456', - supplementaryData: { - isPendingReview: false - } - } - ] - }); - expect(isSystemUserAdminStub).to.be.calledOnce; - }); - - it('catches and re-throws an error', async () => { - const dbConnectionObj = getMockDBConnection(); - sinon.stub(db, 'getDBConnection').returns(dbConnectionObj); - sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(true); - - sinon.stub(SubmissionService.prototype, 'findRelatedDatasetsByDatasetId').rejects(new Error('a test error')); - - const { mockReq, mockRes, mockNext } = getRequestHandlerMocks(); - - mockReq.params = { - datasetId: 'abcd' - }; - - try { - const requestHandler = getRelatedDatasetsByDatasetId(); - - await requestHandler(mockReq, mockRes, mockNext); - expect.fail(); - } catch (actualError) { - expect((actualError as HTTPError).message).to.equal('a test error'); - } - }); -}); diff --git a/api/src/paths/dwc/submission/{datasetId}/related.ts b/api/src/paths/dwc/submission/{datasetId}/related.ts deleted file mode 100644 index 0cb794a82..000000000 --- a/api/src/paths/dwc/submission/{datasetId}/related.ts +++ /dev/null @@ -1,128 +0,0 @@ -import { RequestHandler } from 'express'; -import { Operation } from 'express-openapi'; -import { getAPIUserDBConnection, getDBConnection } from '../../../../database/db'; -import { defaultErrorResponses } from '../../../../openapi/schemas/http-responses'; -import { SecurityService } from '../../../../services/security-service'; -import { SubmissionService } from '../../../../services/submission-service'; -import { UserService } from '../../../../services/user-service'; -import { getLogger } from '../../../../utils/logger'; - -const defaultLog = getLogger('paths/dwc/submission/{datasetId}/related'); - -export const GET: Operation = [getRelatedDatasetsByDatasetId()]; - -GET.apiDoc = { - description: 'retrieves related datasets within elastic search', - tags: ['eml'], - security: [ - { - OptionalBearer: [] - } - ], - parameters: [ - { - description: 'Dataset ID', - in: 'path', - name: 'datasetId', - schema: { - type: 'string', - format: 'uuid' - }, - required: true - } - ], - responses: { - 200: { - description: 'Related datasets response object.', - content: { - 'application/json': { - schema: { - type: 'object', - properties: { - datasets: { - type: 'array', - items: { - type: 'object', - required: ['datasetId', 'title', 'url', 'supplementaryData'], - properties: { - datasetId: { - type: 'string', - format: 'uuid' - }, - title: { - type: 'string' - }, - url: { - type: 'string' - }, - supplementaryData: { - type: 'object', - properties: { - isPendingReview: { - type: 'boolean' - } - } - } - } - } - } - } - } - } - } - }, - ...defaultErrorResponses - } -}; - -/** - * Retrieves related datasets within elastic search - * - * @returns {RequestHandler} - */ -export function getRelatedDatasetsByDatasetId(): RequestHandler { - return async (req, res) => { - const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection(); - - const datasetId = String(req.params.datasetId); - - try { - await connection.open(); - - const submissionService = new SubmissionService(connection); - const securityService = new SecurityService(connection); - const userService = new UserService(connection); - - const isAdmin = await userService.isSystemUserAdmin(); - const datasets = await submissionService.findRelatedDatasetsByDatasetId(datasetId); - - const datasetsWithSupplementaryData = await Promise.all( - datasets.map(async (dataset) => { - if (!isAdmin) { - return { - ...dataset, - supplementaryData: {} - }; - } - - const isDatasetPendingReview = await securityService.isDatasetPendingReview(dataset.datasetId); - - return { - ...dataset, - supplementaryData: { isPendingReview: isDatasetPendingReview } - }; - }) - ); - - await connection.commit(); - - res.status(200).json({ datasetsWithSupplementaryData }); - } catch (error) { - defaultLog.error({ label: 'getRelatedDatasetsByDatasetId', message: 'error', error }); - await connection.rollback(); - throw error; - } finally { - connection.release(); - } - }; -} diff --git a/api/src/repositories/spatial-repository.test.ts b/api/src/repositories/spatial-repository.test.ts deleted file mode 100644 index b276f88bb..000000000 --- a/api/src/repositories/spatial-repository.test.ts +++ /dev/null @@ -1,638 +0,0 @@ -import chai, { expect } from 'chai'; -import { FeatureCollection } from 'geojson'; -import { describe } from 'mocha'; -import { QueryResult } from 'pg'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import SQL from 'sql-template-strings'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { ApiGeneralError } from '../errors/api-error'; -import { Srid3005 } from '../services/geo-service'; -import { UserService } from '../services/user-service'; -import * as spatialUtils from '../utils/spatial-utils'; -import { getMockDBConnection } from '../__mocks__/db'; -import { - IInsertSpatialTransform, - ISpatialComponentsSearchCriteria, - ISubmissionSpatialComponent, - SpatialRepository -} from './spatial-repository'; -import { SystemUserExtended } from './user-repository'; - -chai.use(sinonChai); - -describe('SpatialRepository', () => { - describe('insertSpatialTransform', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - try { - await spatialRepository.insertSpatialTransform({} as unknown as IInsertSpatialTransform); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to insert spatial transform details'); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ spatial_transform_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.insertSpatialTransform({} as unknown as IInsertSpatialTransform); - - expect(response.spatial_transform_id).to.equal(1); - }); - }); - - describe('getSpatialTransformRecords', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [ - { - spatial_transform_id: 1, - name: 'transform name', - description: 'transform description', - notes: 'notes', - transform: 'transform details' - } - ] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.getSpatialTransformRecords(); - - expect(response[0].spatial_transform_id).to.equal(1); - expect(response[0].name).to.equal('transform name'); - expect(response[0].description).to.equal('transform description'); - expect(response[0].notes).to.equal('notes'); - expect(response[0].transform).to.equal('transform details'); - }); - }); - - describe('getSecurityTransformRecords', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [ - { - security_transform_id: 1, - name: 'transform name', - description: 'transform description', - notes: 'notes', - transform: 'transform details' - } - ] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.getSecurityTransformRecords(); - - expect(response[0].security_transform_id).to.equal(1); - expect(response[0].name).to.equal('transform name'); - expect(response[0].description).to.equal('transform description'); - expect(response[0].notes).to.equal('notes'); - expect(response[0].transform).to.equal('transform details'); - }); - }); - - describe('insertSpatialTransformSubmissionRecord', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - try { - await spatialRepository.insertSpatialTransformSubmissionRecord(1, 1); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal( - 'Failed to insert spatial transform submission id and submission spatial component id' - ); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ spatial_transform_submission_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.insertSpatialTransformSubmissionRecord(1, 1); - - expect(response.spatial_transform_submission_id).to.equal(1); - }); - }); - - describe('insertSecurityTransformSubmissionRecord', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - try { - await spatialRepository.insertSecurityTransformSubmissionRecord(1, 1); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal( - 'Failed to insert security transform submission id and submission spatial component id' - ); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ security_transform_submission_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.insertSecurityTransformSubmissionRecord(1, 1); - - expect(response.security_transform_submission_id).to.equal(1); - }); - }); - - describe('runSpatialTransformOnSubmissionId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [ - { - result_data: { - type: 'FeatureCollection', - features: [] - } as FeatureCollection - } - ] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - query: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.runSpatialTransformOnSubmissionId(1, 'string'); - - expect(response).to.eql([ - { - result_data: { - type: 'FeatureCollection', - features: [] - } as FeatureCollection - } - ]); - }); - }); - - describe('runSecurityTransformOnSubmissionId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { - rowCount: 1, - rows: [ - { - result_data: { - type: 'FeatureCollection', - features: [] - } as FeatureCollection - } - ] - } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - query: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.runSecurityTransformOnSubmissionId(1, 'string'); - - expect(response).to.eql([ - { - result_data: { - type: 'FeatureCollection', - features: [] - } as FeatureCollection - } - ]); - }); - }); - - describe('insertSubmissionSpatialComponent', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - try { - await spatialRepository.insertSubmissionSpatialComponent(1, {} as FeatureCollection); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal( - 'Failed to insert submission spatial component details' - ); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_spatial_component_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.insertSubmissionSpatialComponent(1, {} as FeatureCollection); - - expect(response.submission_spatial_component_id).to.equal(1); - }); - - it('should succeed with valid data and append geography to sql statement', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_spatial_component_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const generateGeometryCollectionSQLStub = sinon - .stub(spatialUtils, 'generateGeometryCollectionSQL') - .returns(SQL`valid`); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.insertSubmissionSpatialComponent(1, { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [125.6, 10.1] - }, - properties: {} - } - ] - } as FeatureCollection); - - expect(response.submission_spatial_component_id).to.equal(1); - expect(generateGeometryCollectionSQLStub).to.be.calledOnce; - }); - }); - - describe('updateSubmissionSpatialComponent', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - try { - await spatialRepository.updateSubmissionSpatialComponentWithSecurity(1, {} as object); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal( - 'Failed to update submission spatial component details' - ); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_spatial_component_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.updateSubmissionSpatialComponentWithSecurity(1, {} as object); - - expect(response.submission_spatial_component_id).to.equal(1); - }); - }); - - describe('findSpatialComponentsByCriteria', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should call _findSpatialComponentsByCriteria', async () => { - const mockDBConnection = getMockDBConnection(); - - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSpatialComponentsByCriteriaAsAdminUserStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteriaAsAdminUser') - .resolves(); - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteria') - .resolves(); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - await spatialRepository.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(findSpatialComponentsByCriteriaAsAdminUserStub).not.to.have.been.called; - expect(findSpatialComponentsByCriteriaStub).to.have.been.calledOnce; - }); - }); - - describe('_findSpatialComponentsByCriteriaAsAdminUser', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with minimal search criteria', async () => { - const mockResponseRow1 = { submission_spatial_component_id: 1 } as unknown as ISubmissionSpatialComponent; - const mockResponseRow2 = { submission_spatial_component_id: 2 } as unknown as ISubmissionSpatialComponent; - const mockQueryResponse = { rowCount: 2, rows: [mockResponseRow1, mockResponseRow2] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialRepository.findSpatialComponentsByCriteriaAsAdminUser(mockSearchCriteria); - - expect(response).to.eql([mockResponseRow1, mockResponseRow2]); - }); - - it('should succeed with maximal search criteria', async () => { - const mockResponseRow1 = { submission_spatial_component_id: 1 } as unknown as ISubmissionSpatialComponent; - const mockResponseRow2 = { submission_spatial_component_id: 2 } as unknown as ISubmissionSpatialComponent; - const mockQueryResponse = { rowCount: 2, rows: [mockResponseRow1, mockResponseRow2] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence', 'Boundary'], - datasetID: ['111-111-111', '222-222-222'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialRepository.findSpatialComponentsByCriteriaAsAdminUser(mockSearchCriteria); - - expect(response).to.eql([mockResponseRow1, mockResponseRow2]); - }); - }); - - describe('_findSpatialComponentsByCriteria', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with minimal search criteria', async () => { - const mockResponseRow1 = { submission_spatial_component_id: 1 } as unknown as ISubmissionSpatialComponent; - const mockResponseRow2 = { submission_spatial_component_id: 2 } as unknown as ISubmissionSpatialComponent; - const mockQueryResponse = { rowCount: 2, rows: [mockResponseRow1, mockResponseRow2] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialRepository.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(response).to.eql([mockResponseRow1, mockResponseRow2]); - }); - - it('should succeed with maximal search criteria', async () => { - const mockResponseRow1 = { submission_spatial_component_id: 1 } as unknown as ISubmissionSpatialComponent; - const mockResponseRow2 = { submission_spatial_component_id: 2 } as unknown as ISubmissionSpatialComponent; - const mockQueryResponse = { rowCount: 2, rows: [mockResponseRow1, mockResponseRow2] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence', 'Boundary'], - species: ['Moose'], - datasetID: ['111-111-111', '222-222-222'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialRepository.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(response).to.eql([mockResponseRow1, mockResponseRow2]); - }); - }); - - describe('deleteSpatialComponentsBySubmissionId', () => { - it('should successfully return submission IDs for delete spatial data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_id: 2 }] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.deleteSpatialComponentsBySubmissionId(2); - - expect(response[0].submission_id).to.equal(2); - }); - }); - - describe('deleteSpatialComponentsSpatialRefsBySubmissionId', () => { - it('should successfully return submission IDs for deleted spatial component reference', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_id: 2 }] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.deleteSpatialComponentsSpatialTransformRefsBySubmissionId(2); - - expect(response[0].submission_id).to.equal(2); - }); - }); - - describe('deleteSpatialComponentsSecurityRefsBySubmissionId', () => { - it('should successfully return submission IDs for deleted spatial component reference', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_id: 2 }] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: async () => { - return mockQueryResponse; - } - }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const response = await spatialRepository.deleteSpatialComponentsSecurityTransformRefsBySubmissionId(2); - - expect(response[0].submission_id).to.equal(2); - }); - }); - - describe('getGeometryAsWktFromBoundarySpatialComponentBySubmissionId', () => { - it('returns a geometry WKT string', async () => { - const mockResponse = { rowCount: 1, rows: [{ geometry: 'POLYGON(123,456,789)' }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ knex: async () => mockResponse }); - - const spatialRepository = new SpatialRepository(mockDBConnection); - - const submissionId = 1; - - const response = await spatialRepository.getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId, - SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, - Srid3005 - ); - - expect(response).to.eql({ geometry: 'POLYGON(123,456,789)' }); - }); - }); -}); diff --git a/api/src/repositories/spatial-repository.ts b/api/src/repositories/spatial-repository.ts deleted file mode 100644 index d60190479..000000000 --- a/api/src/repositories/spatial-repository.ts +++ /dev/null @@ -1,973 +0,0 @@ -import { Feature, FeatureCollection, GeoJsonProperties } from 'geojson'; -import { Knex } from 'knex'; -import SQL from 'sql-template-strings'; -import { z } from 'zod'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { getKnex } from '../database/db'; -import { ApiExecuteSQLError } from '../errors/api-error'; -import { Srid } from '../services/geo-service'; -import { generateGeometryCollectionSQL } from '../utils/spatial-utils'; -import { BaseRepository } from './base-repository'; - -export interface IInsertSpatialTransform { - name: string; - description: string; - notes: string; - transform: string; -} - -export interface IGetSpatialTransformRecord { - spatial_transform_id: number; - name: string; - description: string | null; - notes: string | null; - transform: string; -} - -export interface IGetSecurityTransformRecord { - security_transform_id: number; - name: string; - description: string | null; - notes: string | null; - transform: string; -} - -export interface ITransformSpatialRow { - result_data: FeatureCollection; -} - -export interface ITransformSecureRow { - spatial_component: { - spatial_data: FeatureCollection; - submission_spatial_component_id: number; - }; -} - -export interface ISubmissionSpatialComponent { - submission_spatial_component_ids: number[]; - submission_id: number; - spatial_component: FeatureCollection; - geometry: null; - geography: string; - secured_spatial_component: FeatureCollection; - secured_geometry: null; - secured_geography: string; -} - -export interface ISpatialComponentsSearchCriteria { - boundary: Feature[]; - type?: string[]; - species?: string[]; - datasetID?: string[]; -} - -export type EmptyObject = Record; - -export interface ITaxaData { - taxon_id?: string; - vernacular_name?: string; - submission_spatial_component_id: number; -} - -export interface ISubmissionSpatialSearchResponseRow { - taxa_data: ITaxaData[]; - spatial_component: { - spatial_data: FeatureCollection | EmptyObject; - }; -} - -export interface ISpatialComponentFeaturePropertiesRow { - spatial_component_properties: GeoJsonProperties; -} - -export class SpatialRepository extends BaseRepository { - /** - * Insert new spatial transform record - * - * @param {IInsertSpatialTransform} spatialTransformDetails - * @return {*} {Promise<{ spatial_transform_id: number }>} - * @memberof SpatialRepository - */ - async insertSpatialTransform( - spatialTransformDetails: IInsertSpatialTransform - ): Promise<{ spatial_transform_id: number }> { - const sqlStatement = SQL` - INSERT INTO spatial_transform ( - name, - description, - notes, - transform - ) VALUES ( - ${spatialTransformDetails.name}, - ${spatialTransformDetails.description}, - ${spatialTransformDetails.notes}, - ${spatialTransformDetails.transform} - ) - RETURNING - spatial_transform_id; - `; - - const response = await this.connection.sql<{ spatial_transform_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to insert spatial transform details', [ - 'SpatialRepository->insertSpatialTransform', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - return response.rows[0]; - } - - /** - * get spatial transform records - * - * @param - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async getSpatialTransformRecords(): Promise { - const sqlStatement = SQL` - SELECT - spatial_transform_id, - name, - description, - notes, - transform - FROM - spatial_transform; - `; - - const response = await this.connection.sql(sqlStatement); - - return response.rows; - } - - /** - *get security transform records - * - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async getSecurityTransformRecords(): Promise { - const sqlStatement = SQL` - SELECT - security_transform_id, - name, - description, - notes, - transform - FROM - security_transform; - `; - - const response = await this.connection.sql(sqlStatement); - - return response.rows; - } - - /** - * Insert record of transform id used for submission spatial component record - * - * @param {number} spatialTransformId - * @param {number} submissionSpatialComponentId - * @return {*} {Promise<{ spatial_transform_submission_id: number }>} - * @memberof SpatialRepository - */ - async insertSpatialTransformSubmissionRecord( - spatialTransformId: number, - submissionSpatialComponentId: number - ): Promise<{ spatial_transform_submission_id: number }> { - const sqlStatement = SQL` - INSERT INTO spatial_transform_submission ( - spatial_transform_id, - submission_spatial_component_id - ) VALUES ( - ${spatialTransformId}, - ${submissionSpatialComponentId} - ) - RETURNING - spatial_transform_submission_id; - `; - - const response = await this.connection.sql<{ spatial_transform_submission_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError( - 'Failed to insert spatial transform submission id and submission spatial component id', - [ - 'SpatialRepository->insertSpatialTransformSubmissionRecord', - 'rowCount was null or undefined, expected rowCount >= 1' - ] - ); - } - return response.rows[0]; - } - - /** - * Insert record of transform id used for submission security component record - * - * @param {number} securityTransformId - * @param {number} submissionSpatialComponentId - * @return {*} {Promise<{ spatial_transform_submission_id: number }>} - * @memberof SpatialRepository - */ - async insertSecurityTransformSubmissionRecord( - securityTransformId: number, - submissionSpatialComponentId: number - ): Promise<{ security_transform_submission_id: number }> { - const sqlStatement = SQL` - INSERT INTO security_transform_submission ( - security_transform_id, - submission_spatial_component_id - ) VALUES ( - ${securityTransformId}, - ${submissionSpatialComponentId} - ) - RETURNING - security_transform_submission_id; - `; - - const response = await this.connection.sql<{ security_transform_submission_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError( - 'Failed to insert security transform submission id and submission spatial component id', - [ - 'SpatialRepository->insertSecurityTransformSubmissionRecord', - 'rowCount was null or undefined, expected rowCount = 1' - ] - ); - } - return response.rows[0]; - } - - /** - * Run Spatial Transform with transform string on submissionId - * - * @param {number} submissionId - * @param {string} transform - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async runSpatialTransformOnSubmissionId(submissionId: number, transform: string): Promise { - const response = await this.connection.query(transform, [submissionId]); - - return response.rows; - } - - /** - * Run Security Transform with transform string on submissionId - * - * @param {number} submissionId - * @param {string} transform - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async runSecurityTransformOnSubmissionId(submissionId: number, transform: string): Promise { - const response = await this.connection.query(transform, [submissionId]); - - return response.rows; - } - - /** - * Insert given transformed data into Spatial Component Table - * - * @param {number} submissionObservationId - * @param {Feature[]} transformedData - * @return {*} {Promise<{ submission_spatial_component_id: number }>} - * @memberof SpatialRepository - */ - async insertSubmissionSpatialComponent( - submissionObservationId: number, - transformedData: FeatureCollection - ): Promise<{ submission_spatial_component_id: number }> { - const sqlStatement = SQL` - INSERT INTO submission_spatial_component ( - submission_observation_id, - spatial_component, - geography - ) VALUES ( - ${submissionObservationId}, - ${JSON.stringify(transformedData)} - `; - - if (transformedData.features && transformedData.features.length > 0) { - const geoCollection = generateGeometryCollectionSQL(transformedData.features); - - sqlStatement.append(SQL` - ,public.geography( - public.ST_Force2D( - public.ST_SetSRID( - `); - - sqlStatement.append(geoCollection); - - sqlStatement.append(SQL` - , 4326))) - `); - } else { - sqlStatement.append(SQL` - ,null - `); - } - - sqlStatement.append(SQL` - ) - RETURNING - submission_spatial_component_id; - `); - - const response = await this.connection.sql<{ submission_spatial_component_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to insert submission spatial component details', [ - 'SpatialRepository->insertSubmissionSpatialComponent', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - return response.rows[0]; - } - - /** - * Update secured spatial column with the transformed spatial data - * - * @param {number} submissionId - * @param {Feature[]} transformedData - * @return {*} {Promise<{ submission_spatial_component_id: number }>} - * @memberof SpatialRepository - */ - async updateSubmissionSpatialComponentWithSecurity( - submissionSpatialComponentId: number, - transformedData: object - ): Promise<{ submission_spatial_component_id: number }> { - const sqlStatement = SQL` - UPDATE - submission_spatial_component - SET - secured_spatial_component = ${transformedData} - WHERE - submission_spatial_component_id = ${submissionSpatialComponentId} - RETURNING - submission_spatial_component_id; - `; - - const response = await this.connection.sql<{ submission_spatial_component_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to update submission spatial component details', [ - 'SpatialRepository->updateSubmissionSpatialComponentWithSecurity', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - return response.rows[0]; - } - - /** - * Query builder to find spatial component by given criteria, specifically for admin users that bypass all security - * rules. - * - * @param {ISpatialComponentsSearchCriteria} criteria - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async findSpatialComponentsByCriteriaAsAdminUser( - criteria: ISpatialComponentsSearchCriteria - ): Promise { - const knex = getKnex(); - - const queryBuilder = knex - .queryBuilder() - .with('distinct_geographic_points', this._withDistinctGeographicPoints) - .with('with_filtered_spatial_component', (qb1) => { - // Get the spatial components that match the search filters - qb1 - .select( - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, datasetID}' as dataset_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, taxonID}' as taxon_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, vernacularName}' as vernacular_name" - ), - 'ssc.submission_spatial_component_id', - 'ssc.submission_observation_id', - 'ssc.spatial_component', - 'ssc.geography' - ) - .from('submission_spatial_component as ssc') - .leftJoin('distinct_geographic_points as p', 'p.geography', 'ssc.geography') - .leftJoin('submission_observation as so', 'so.submission_observation_id', 'ssc.submission_observation_id') - .whereNull('so.record_end_timestamp') - .groupBy('ssc.submission_spatial_component_id') - .groupBy('ssc.submission_observation_id') - .groupBy('ssc.spatial_component') - .groupBy('ssc.geography'); - - if (criteria.type?.length) { - this._whereTypeIn(criteria.type, qb1); - } - - if (criteria.species?.length) { - this._whereSpeciesIn(criteria.species, qb1); - } - - if (criteria.datasetID?.length) { - this._whereDatasetIDIn(criteria.datasetID, qb1); - } - - this._whereBoundaryIntersects(criteria.boundary, 'ssc.geography', qb1); - }) - .with('with_coalesced_spatial_components', (qb7) => { - qb7 - .select( - // Select the non-secure spatial component from the search results - knex.raw( - ` - submission_spatial_component_id, - submission_observation_id, - geography, - jsonb_build_object( - 'submission_spatial_component_id', - wfsc.submission_spatial_component_id, - 'taxon_id', - wfsc.taxon_id, - 'vernacular_name', - wfsc.vernacular_name - ) taxa_data_object, - jsonb_build_object( - 'spatial_data', - wfsc.spatial_component - ) spatial_component - ` - ) - ) - .from(knex.raw('with_filtered_spatial_component as wfsc')); - }) - .select( - knex.raw('array_agg(submission_spatial_component_id) as submission_spatial_component_ids'), - knex.raw('array_agg(taxa_data_object) as taxa_data'), - knex.raw('(array_agg(spatial_component))[1] as spatial_component'), - 'geography' - ) - .from('with_coalesced_spatial_components') - // Filter out secure spatial components that have no spatial representation - // The user is not allowed to see any aspect of these particular spatial components - .whereRaw("spatial_component->'spatial_data' != '{}'") - .groupBy('geography'); - - const response = await this.connection.knex(queryBuilder); - - return response.rows; - } - - /** - * Query builder to find spatial component by given criteria. - * - * @param {ISpatialComponentsSearchCriteria} criteria - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async findSpatialComponentsByCriteria( - criteria: ISpatialComponentsSearchCriteria - ): Promise { - const knex = getKnex(); - - // non-admin rules: - // see the secured spatial component if it is not null (and if you do not have an exception to all security rules applied to it), - // otherwise you see the non-secured spatial component - - const queryBuilder = knex - .queryBuilder() - .with('distinct_geographic_points', this._withDistinctGeographicPoints) - .with('with_filtered_spatial_component_with_security_transforms', (qb1) => { - // Get the spatial components that match the search filters, and for each record, build the array of spatial security transforms that ran against that row - qb1 - .select( - knex.raw( - 'array_remove(array_agg(sts.security_transform_id), null) as spatial_component_security_transforms' - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, datasetID}' as dataset_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, taxonID}' as taxon_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, vernacularName}' as vernacular_name" - ), - 'ssc.submission_spatial_component_id', - 'ssc.submission_observation_id', - 'ssc.spatial_component', - 'ssc.secured_spatial_component', - 'ssc.geography' - ) - .from('submission_spatial_component as ssc') - .leftJoin('submission_observation as so', 'so.submission_observation_id', 'ssc.submission_observation_id') - .whereNull('so.record_end_timestamp') - .leftJoin('distinct_geographic_points as p', 'p.geography', 'ssc.geography') - .leftJoin( - 'security_transform_submission as sts', - 'sts.submission_spatial_component_id', - 'ssc.submission_spatial_component_id' - ) - .groupBy('sts.submission_spatial_component_id') - .groupBy('ssc.submission_spatial_component_id') - .groupBy('ssc.submission_observation_id') - .groupBy('ssc.spatial_component') - .groupBy('ssc.secured_spatial_component') - .groupBy('ssc.geography'); - if (criteria.type?.length) { - this._whereTypeIn(criteria.type, qb1); - } - if (criteria.species?.length) { - this._whereSpeciesIn(criteria.species, qb1); - } - - if (criteria.datasetID?.length) { - this._whereDatasetIDIn(criteria.datasetID, qb1); - } - - this._whereBoundaryIntersects(criteria.boundary, 'ssc.geography', qb1); - }) - .with('with_user_security_transform_exceptions', (qb6) => { - this._buildSpatialSecurityExceptions(qb6, this.connection.systemUserId()); - }) - .with('with_coalesced_spatial_components', (qb7) => { - qb7 - .select( - 'submission_spatial_component_id', - 'submission_observation_id', - 'geography', - this._buildSelectForSecureNonSecureSpatialComponents() - ) - .from( - knex.raw( - 'with_filtered_spatial_component_with_security_transforms as wfscwst, with_user_security_transform_exceptions as wuste' - ) - ); - }) - .select( - knex.raw('array_agg(submission_spatial_component_id) as submission_spatial_component_ids'), - knex.raw('array_agg(taxa_data_object) as taxa_data'), - knex.raw('(array_agg(spatial_component))[1] as spatial_component'), - 'geography' - ) - .from('with_coalesced_spatial_components') - // Filter out secure spatial components that have no spatial representation - // The user is not allowed to see any aspect of these particular spatial components - .whereRaw("spatial_component->'spatial_data' != '{}'") - .groupBy('geography'); - - const response = await this.connection.knex(queryBuilder); - - return response.rows; - } - - /** - * Append where clause condition for spatial component type. - * - * @param {string[]} types - * @param {Knex.QueryBuilder} qb1 - * @memberof SpatialRepository - */ - _whereTypeIn(types: string[], qb1: Knex.QueryBuilder) { - // Append AND where clause for types - qb1.where((qb2) => { - for (const type of types) { - // Append OR clause for each item in types array - qb2.or.where((qb3) => { - qb3.whereRaw(`jsonb_path_exists(spatial_component,'$.features[*] \\? (@.properties.type == "${type}")')`); - }); - } - }); - } - - /** - * Append where clause condition for spatial component taxonID. - * Append where clause condition for spatial component taxonID - * - * @param {string[]} species - * @param {Knex.QueryBuilder} qb1 - * @memberof SpatialRepository - */ - _whereSpeciesIn(species: string[], qb1: Knex.QueryBuilder) { - // Append AND where clause for species - qb1.where((qb2) => { - for (const singleSpecies of species) { - // Append OR clause for each item in species array - qb2.or.where((qb3) => { - qb3.whereRaw( - `jsonb_path_exists(spatial_component,'$.features[*] \\? (@.properties.dwc.taxonID == "${singleSpecies}")')` - ); - }); - } - }); - } - - /** - * Append where clause condition for spatial component parent dataset id. - * - * @param {string[]} datasetIDs - * @param {Knex.QueryBuilder} qb1 - * @memberof SpatialRepository - */ - _whereDatasetIDIn(datasetIDs: string[], qb1: Knex.QueryBuilder) { - qb1.where((qb2) => { - qb2.whereRaw( - `ssc.submission_observation_id in ( - select submission_observation_id from submission_observation so - left join submission s on so.submission_id = s.submission_id - where s.uuid in (${"'" + datasetIDs.join("','") + "'"}))` - ); - }); - } - - /** - * Append where clause condition for spatial component boundaries intersect. - * - * @param {Feature[]} boundaries - * @param {string} geoColumn - * @param {Knex.QueryBuilder} qb1 - * @memberof SpatialRepository - */ - _whereBoundaryIntersects(boundaries: Feature[], geoColumn: string, qb1: Knex.QueryBuilder) { - const generateSqlStatement = (geometry: Feature) => { - return SQL` - public.ST_INTERSECTS(`.append(`${geoColumn}`).append(`, - public.geography( - public.ST_Force2D( - public.ST_SetSRID( - public.ST_Force2D( - public.ST_GeomFromGeoJSON('${JSON.stringify(geometry.geometry)}') - ), - 4326 - ) - ) - ) - ) - `); - }; - - qb1.where((qb2) => { - for (const boundary of boundaries) { - // Append OR clause for each item in boundary array - qb2.or.where((qb3) => { - const sqlStatement = generateSqlStatement(boundary); - qb3.whereRaw(sqlStatement.sql, sqlStatement.values); - }); - } - }); - } - - _withDistinctGeographicPoints(qb1: Knex.QueryBuilder) { - qb1 - .distinct() - .select('geography') - .from('submission_spatial_component') - .whereRaw(`geometrytype(geography) = 'POINT'`) - .whereRaw(`jsonb_path_exists(spatial_component,'$.features[*] \\? (@.properties.type == "Occurrence")')`); - } - - /** - * Query builder to find spatial component from a given submission id, specifically for admin users that bypass all security - * rules. - * - * @param {number} submission_spatial_component_id - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin( - submission_spatial_component_ids: number[] - ): Promise { - const knex = getKnex(); - const queryBuilder = knex - .queryBuilder() - .with('with_filtered_spatial_component', (qb1) => { - // Get the spatial components that match the search filters - qb1 - .select() - .from('submission_spatial_component as ssc') - // Filter out submission_spatial_component records for end dated submission_observation records - .leftJoin('submission_observation as so', 'so.submission_observation_id', 'ssc.submission_observation_id') - .where('so.record_end_timestamp', null) - .whereIn('submission_spatial_component_id', submission_spatial_component_ids); - }) - .select( - // Select the non-secure spatial component from the search results - knex.raw( - `jsonb_array_elements(wfsc.spatial_component -> 'features') #> '{properties}' as spatial_component_properties` - ) - ) - .from(knex.raw('with_filtered_spatial_component as wfsc')); - - const response = await this.connection.knex(queryBuilder); - - return response.rows; - } - - /** - * Query builder to find spatial component from a given submission id, no security - * - * @param {number[]} submission_spatial_component_ids - * @return {*} {Promise} - * @memberof SpatialRepository - */ - async findSpatialMetadataBySubmissionSpatialComponentIds( - submission_spatial_component_ids: number[] - ): Promise { - const knex = getKnex(); - const queryBuilder = knex - .queryBuilder() - .with('with_filtered_spatial_component_with_security_transforms', (qb1) => { - // Get the spatial components that match the search filters, and for each record, build the array of spatial security transforms that ran against that row - qb1 - .select( - knex.raw( - 'array_remove(array_agg(sts.security_transform_id), null) as spatial_component_security_transforms' - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, datasetID}' as dataset_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, taxonID}' as taxon_id" - ), - knex.raw( - "jsonb_array_elements(ssc.spatial_component -> 'features') #> '{properties, dwc, vernacularName}' as vernacular_name" - ), - 'ssc.submission_spatial_component_id', - 'ssc.submission_observation_id', - 'ssc.spatial_component', - 'ssc.secured_spatial_component' - ) - .from('submission_spatial_component as ssc') - // Filter out submission_spatial_component records for end dated submission_observation records - .leftJoin('submission_observation as so', 'so.submission_observation_id', 'ssc.submission_observation_id') - .where('so.record_end_timestamp', null) - .leftJoin( - 'security_transform_submission as sts', - 'sts.submission_spatial_component_id', - 'ssc.submission_spatial_component_id' - ) - .whereIn('ssc.submission_spatial_component_id', submission_spatial_component_ids) - .groupBy('sts.submission_spatial_component_id') - .groupBy('ssc.submission_spatial_component_id') - .groupBy('ssc.submission_observation_id') - .groupBy('ssc.spatial_component') - .groupBy('ssc.secured_spatial_component'); - }) - .with('with_user_security_transform_exceptions', (qb6) => { - this._buildSpatialSecurityExceptions(qb6, this.connection.systemUserId()); - }) - .with('with_coalesced_spatial_components', (qb7) => { - qb7 - .select(this._buildSelectForSecureNonSecureSpatialComponents()) - .from( - knex.raw( - 'with_filtered_spatial_component_with_security_transforms as wfscwst, with_user_security_transform_exceptions as wuste' - ) - ); - }) - .select( - knex.raw( - `jsonb_array_elements(spatial_component -> 'spatial_data' -> 'features') #> '{properties}' as spatial_component_properties` - ) - ) - .from('with_coalesced_spatial_components') - // Filter out secure spatial components that have no spatial representation - // The user is not allowed to see any aspect of these particular spatial components - .whereRaw("spatial_component->'spatial_data' != '{}'"); - - const spatialComponentResponse = await this.connection.knex(queryBuilder); - - return spatialComponentResponse.rows; - } - - /** - * Select either the non-secure or secure spatial component from the search results, - * based on whether or not the record had security transforms applied to it and whether or not the user has the necessary exceptions - * - * @param {Knex} knex - * @return {*} { Knex.Raw } - * @memberof SpatialRepository - */ - _buildSelectForSecureNonSecureSpatialComponents(): Knex.Raw { - const knex = getKnex(); - return knex.raw( - ` - jsonb_build_object( - 'submission_spatial_component_id', - wfscwst.submission_spatial_component_id, - 'taxon_id', - wfscwst.taxon_id, - 'vernacular_name', - wfscwst.vernacular_name - ) taxa_data_object, - jsonb_build_object( - 'spatial_data', - -- when: the user's security transform ids array contains all of the rows security transform ids (user has all necessary exceptions) - -- then: return the spatial component - -- else: return the secure spatial component if it is not null (secure, insufficient exceptions), otherwise return the spatial component (non-secure, no exceptions required) - case - when - wuste.user_security_transform_exceptions @> wfscwst.spatial_component_security_transforms - then - wfscwst.spatial_component - else - coalesce(wfscwst.secured_spatial_component, wfscwst.spatial_component) - end - ) spatial_component - ` - ); - } - - /** - * Build an array of the users spatial security transform exceptions - * - * @param {Knex} knex - * @param {Knex.QueryBuilder} qb - * @param {number} system_user_id - * @memberof SpatialRepository - */ - async _buildSpatialSecurityExceptions(qb: Knex.QueryBuilder, system_user_id: number) { - const knex = getKnex(); - qb.select(knex.raw('array_remove(array_agg(st.security_transform_id), null) as user_security_transform_exceptions')) - .from('system_user_security_exception as suse') - .leftJoin('security_transform as st', 'st.persecution_or_harm_id', 'suse.persecution_or_harm_id') - .where('suse.system_user_id', system_user_id) - .and.whereRaw('(suse.end_date is null or now() < suse.end_date)'); - } - - /** - * // TODO - The SQL is outdated - `submission_id` no longer exists on table `submission_spatial_component` - * - * Deletes spatial components in a submission id before updating it with new data - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialRepository - */ - async deleteSpatialComponentsBySubmissionId(submission_id: number): Promise<{ submission_id: number }[]> { - const sqlStatement = SQL` - DELETE FROM - submission_spatial_component - WHERE - submission_id=${submission_id} - RETURNING - submission_id; - ;`; - - const response = await this.connection.sql<{ submission_id: number }>(sqlStatement); - - return response.rows; - } - - /** - * // TODO - The SQL is outdated - `submission_id` no longer exists on table `submission_spatial_component` - * - * Remove references in spatial_transform_submission table - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialRepository - */ - async deleteSpatialComponentsSpatialTransformRefsBySubmissionId( - submission_id: number - ): Promise<{ submission_id: number }[]> { - const sqlStatement = SQL` - DELETE FROM - spatial_transform_submission - WHERE - submission_spatial_component_id IN ( - SELECT - submission_spatial_component_id - FROM - submission_spatial_component - WHERE - submission_id=${submission_id} - ) - RETURNING - ${submission_id}; - `; - - const response = await this.connection.sql<{ submission_id: number }>(sqlStatement); - - return response.rows; - } - - /** - * // TODO - The SQL is outdated - `submission_id` no longer exists on table `submission_spatial_component` - * - * Remove references in security_transform_submission table - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialRepository - */ - async deleteSpatialComponentsSecurityTransformRefsBySubmissionId( - submission_id: number - ): Promise<{ submission_id: number }[]> { - const sqlStatement = SQL` - DELETE FROM - security_transform_submission - WHERE - submission_spatial_component_id IN ( - SELECT - submission_spatial_component_id - FROM - submission_spatial_component - WHERE - submission_id=${submission_id} - ) - RETURNING - ${submission_id}; - `; - - const response = await this.connection.sql<{ submission_id: number }>(sqlStatement); - - return response.rows; - } - - /** - * Returns the geometry of a `Boundary` or `Boundary Centroid` type spatial component for a given submission id, in - * WKT format using the provided `srid`. - * - * @param {number} submissionId A submission id - * @param {(SPATIAL_COMPONENT_TYPE.BOUNDARY | SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID)} spatialComponentType - * @param {Srid} srid The id of the projection used when converting the geography to WKT - * @return {*} - * @memberof SpatialRepository - */ - async getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId: number, - spatialComponentType: SPATIAL_COMPONENT_TYPE.BOUNDARY | SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, - srid: Srid - ) { - const knex = getKnex(); - - // Fetch the spatial component - const queryBuilder = knex - .queryBuilder() - .select(knex.raw(`ST_AsText(ST_TRANSFORM(geography::geometry, ${srid})) as geometry`)) - .from('submission_spatial_component as ssc') - .leftJoin('submission_observation as so', 'so.submission_observation_id', 'ssc.submission_observation_id') - .where('so.record_end_timestamp', null) - .where('so.record_effective_timestamp', 'is not', null) - .where('so.submission_id', submissionId) - .whereRaw( - `jsonb_path_exists(spatial_component,'$.features[*] \\? (@.properties.type == "${spatialComponentType}")')` - ); - - const response = await this.connection.knex(queryBuilder, z.object({ geometry: z.string() })); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to get boundary spatial component', [ - 'SpatialRepository->getBoundarySpatialComponentBySubmissionId', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - - return response.rows[0]; - } -} diff --git a/api/src/repositories/submission-job-queue-repository.ts b/api/src/repositories/submission-job-queue-repository.ts index 26ca85dc6..5c1d2565e 100644 --- a/api/src/repositories/submission-job-queue-repository.ts +++ b/api/src/repositories/submission-job-queue-repository.ts @@ -89,32 +89,6 @@ export class SubmissionJobQueueRepository extends BaseRepository { return { queueId: response.rows[0].nextval }; } - /** - * Finds a transform source Id based for a particular user - * - * @param {number} userId - * @return {*} {Promise} - * @memberof SubmissionJobQueueRepository - */ - async getSourceTransformIdForUserId(userId: number): Promise { - const sqlStatement = SQL` - SELECT source_transform_id - FROM source_transform - WHERE system_user_id = ${userId}; - `; - - const response = await this.connection.sql<{ source_transform_id: number }>(sqlStatement); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to get source transform Id', [ - 'SubmissionJobQueueRepository->getSourceTransformIdForUserId', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - - return response.rows[0].source_transform_id; - } - /** * Fetch the next available job queue record(s). * diff --git a/api/src/repositories/submission-repository.test.ts b/api/src/repositories/submission-repository.test.ts index 9c9e0a777..79e98b991 100644 --- a/api/src/repositories/submission-repository.test.ts +++ b/api/src/repositories/submission-repository.test.ts @@ -5,7 +5,6 @@ import { QueryResult } from 'pg'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; import { ApiExecuteSQLError, ApiGeneralError } from '../errors/api-error'; -import { EMLFile } from '../utils/media/eml/eml-file'; import { getMockDBConnection } from '../__mocks__/db'; import { SECURITY_APPLIED_STATUS } from './security-repository'; import { @@ -64,89 +63,6 @@ describe('SubmissionRepository', () => { }); }); - describe('updateSubmissionMetadataEMLSource', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when update sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - try { - await submissionRepository.updateSubmissionMetadataEMLSource(1, 1, { - emlFile: Buffer.from('') - } as unknown as EMLFile); - - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to update submission Metadata source'); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_metadata_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionMetadataEMLSource(1, 1, { - emlFile: Buffer.from('') - } as unknown as EMLFile); - - expect(response.submission_metadata_id).to.equal(1); - }); - }); - - describe('updateSubmissionMetadataEMLJSONSource', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when update sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - try { - await submissionRepository.updateSubmissionMetadataEMLJSONSource(1, 1, 'string'); - - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to update submission Metadata eml json'); - } - }); - - it('should succeed with valid data', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ submission_metadata_id: 1 }] } as any as Promise< - QueryResult - >; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionMetadataEMLJSONSource(1, 1, 'string'); - - expect(response.submission_metadata_id).to.equal(1); - }); - }); - describe('getSubmissionRecordBySubmissionId', () => { afterEach(() => { sinon.restore(); @@ -227,26 +143,6 @@ describe('SubmissionRepository', () => { }); }); - describe('getSubmissionRecordEMLJSONByDatasetId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should return a query result', async () => { - const mockQueryResponse = { rowCount: 0, rows: [] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.getSubmissionRecordEMLJSONByDatasetId('111-222-333'); - - expect(response).to.equal(mockQueryResponse); - }); - }); - describe('getSpatialComponentCountByDatasetId', () => { afterEach(() => { sinon.restore(); @@ -323,43 +219,6 @@ describe('SubmissionRepository', () => { }); }); - describe('getSubmissionMetadataJson', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ query: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - try { - await submissionRepository.getSubmissionMetadataJson(1, 'transform sql'); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to transform submission eml to json'); - } - }); - - it('should succeed with valid data, without optional version parameter', async () => { - const mockResponse = { - result_data: 'transformed eml' - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ query: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.getSubmissionMetadataJson(1, 'transform sql'); - - expect(response).to.eql('transformed eml'); - }); - }); - describe('getSourceTransformRecordBySourceTransformId', () => { afterEach(() => { sinon.restore(); @@ -525,79 +384,6 @@ describe('SubmissionRepository', () => { }); }); - describe('listSubmissionRecords', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - submission_status: 'Submission Data Ingested', - submission_id: 1, - source_transform_id: 'SIMS', - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - record_effective_date: '2022-05-24T18:41:42.211Z', - delete_timestamp: null, - input_key: 'biohub/1/moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - input_file_name: 'moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - eml_source: null, - eml_json_source: null, - darwin_core_source: 'test', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - update_date: '2022-05-24T18:41:42.056Z', - update_user: 15, - revision_count: 1 - }; - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: async () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.listSubmissionRecords(); - - expect(response).to.eql([mockResponse]); - }); - }); - - describe('getSourceTransformRecordBySubmissionId', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - try { - await submissionRepository.getSourceTransformRecordBySubmissionId(1); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to get submission source transform record'); - } - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - source_transform_id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.getSourceTransformRecordBySubmissionId(1); - - expect(response).to.eql(mockResponse); - }); - }); - describe('getSubmissionJobQueue', () => { afterEach(() => { sinon.restore(); @@ -637,47 +423,6 @@ describe('SubmissionRepository', () => { }); }); - describe('insertSubmissionMetadataRecord', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const submissionData = { submission_id: 1, eml_source: '', eml_json_source: '' }; - - try { - await submissionRepository.insertSubmissionMetadataRecord(submissionData); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to insert submission metadata record'); - } - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const submissionData = { submission_id: 1, eml_source: '', eml_json_source: '' }; - - const response = await submissionRepository.insertSubmissionMetadataRecord(submissionData); - - expect(response).to.eql(mockResponse); - }); - }); - describe('insertSubmissionObservationRecord', () => { afterEach(() => { sinon.restore(); @@ -728,165 +473,6 @@ describe('SubmissionRepository', () => { }); }); - describe('updateSubmissionMetadataRecordEndDate', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionMetadataRecordEndDate(1); - - expect(response).to.eql(1); - }); - }); - - describe('updateSubmissionMetadataRecordEffectiveDate', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - try { - await submissionRepository.updateSubmissionMetadataRecordEffectiveDate(1); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal( - 'Failed to update record_effective_timestamp submission metadata record' - ); - } - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionMetadataRecordEffectiveDate(1); - - expect(response).to.eql(1); - }); - }); - - describe('updateSubmissionObservationRecordEndDate', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionObservationRecordEndDate(1); - - expect(response).to.eql(1); - }); - }); - - describe('updateSubmissionMetadataWithSearchKeys', () => { - beforeEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.updateSubmissionMetadataWithSearchKeys(1, ''); - - expect(response).to.eql(1); - }); - }); - - describe('getArtifactForReviewCountForSubmissionUUID', () => { - beforeEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - dataset_id: 'UUID', - submission_id: 1, - artifacts_to_review: 1, - last_updated: '2023-05-25' - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.getArtifactForReviewCountForSubmissionUUID(''); - - expect(response).to.eql(mockResponse); - }); - }); - - describe('getDatasetsForReview', () => { - beforeEach(() => { - sinon.restore(); - }); - - it('should succeed with valid data', async () => { - const mockResponse = [ - { - dataset_id: 'UUID', - submission_id: 1, - submitter_system: 'sims', - dataset_name: 'Project Name', - keywords: [], - related_projects: [] - } - ]; - - const mockQueryResponse = { rowCount: 1, rows: mockResponse } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ knex: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const response = await submissionRepository.getDatasetsForReview(['']); - - expect(response).to.eql(mockResponse); - }); - }); - describe('getUnreviewedSubmissionsForAdmins', () => { beforeEach(() => { sinon.restore(); diff --git a/api/src/repositories/submission-repository.ts b/api/src/repositories/submission-repository.ts index 0c1c4fd25..6d45bcc78 100644 --- a/api/src/repositories/submission-repository.ts +++ b/api/src/repositories/submission-repository.ts @@ -1,25 +1,11 @@ import { Knex } from 'knex'; -import { QueryResult } from 'pg'; import SQL from 'sql-template-strings'; import { z } from 'zod'; import { getKnex, getKnexQueryBuilder } from '../database/db'; import { ApiExecuteSQLError } from '../errors/api-error'; -import { EMLFile } from '../utils/media/eml/eml-file'; import { BaseRepository } from './base-repository'; import { SECURITY_APPLIED_STATUS } from './security-repository'; -export interface IHandlebarsTemplates { - header: string; - details: string; -} -export interface IDatasetsForReview { - dataset_id: string; // UUID - artifacts_to_review: number; - dataset_name: string; - last_updated: string; - keywords: string[]; -} - export interface ISubmissionFeature { id: string | null; type: string; @@ -27,29 +13,6 @@ export interface ISubmissionFeature { child_features: ISubmissionFeature[]; } -export const DatasetMetadata = z.object({ - dataset_id: z.string(), - submission_id: z.number(), - dataset_name: z.string(), - keywords: z.array(z.string()), - related_projects: z - .array(z.any()) - .nullable() - .optional() - .transform((item) => item || []) -}); - -export type DatasetMetadata = z.infer; - -export const DatasetArtifactCount = z.object({ - dataset_id: z.string(), - submission_id: z.number(), - artifacts_to_review: z.number(), - last_updated: z.string().nullable() -}); - -export type DatasetArtifactCount = z.infer; - export interface ISpatialComponentCount { spatial_type: string; count: number; @@ -503,84 +466,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Update the `eml_source` column of a submission record. - * - * @param {number} submissionId - * @param {number} submissionMetadataId - * @param {EMLFile} file - * @return {*} {Promise<{ submission_metadata_id: number }>} - * @memberof SubmissionRepository - */ - async updateSubmissionMetadataEMLSource( - submissionId: number, - submissionMetadataId: number, - file: EMLFile - ): Promise<{ submission_metadata_id: number }> { - const sqlStatement = SQL` - UPDATE - submission_metadata - SET - eml_source = ${file.emlFile.buffer.toString()} - WHERE - submission_id = ${submissionId} - AND - submission_metadata_id =${submissionMetadataId} - RETURNING - submission_metadata_id; - `; - - const response = await this.connection.sql<{ submission_metadata_id: number }>(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to update submission Metadata source', [ - 'SubmissionRepository->updateSubmissionMetadataEMLSource', - 'rowCount was null or undefined, expected rowCount != 0' - ]); - } - - return response.rows[0]; - } - - /** - * Update the `eml_json_source` column of a submission metadata. - * - * @param {number} submissionId - * @param {number} submissionMetadataId - * @param {ISubmissionMetadataRecord['eml_json_source']} EMLJSONSource - * @return {*} {Promise<{ submission_metadata_id: number }>} - * @memberof SubmissionRepository - */ - async updateSubmissionMetadataEMLJSONSource( - submissionId: number, - submissionMetadataId: number, - EMLJSONSource: ISubmissionMetadataRecord['eml_json_source'] - ): Promise<{ submission_metadata_id: number }> { - const sqlStatement = SQL` - UPDATE - submission_metadata - SET - eml_json_source = ${EMLJSONSource} - WHERE - submission_id = ${submissionId} - AND - submission_metadata_id =${submissionMetadataId} - RETURNING - submission_metadata_id; - `; - - const response = await this.connection.sql<{ submission_metadata_id: number }>(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to update submission Metadata eml json', [ - 'SubmissionRepository->updateSubmissionMetadataEMLJSONSource', - 'rowCount was null or undefined, expected rowCount != 0' - ]); - } - - return response.rows[0]; - } - /** * Fetch a submission record by primary id. * @@ -635,29 +520,6 @@ export class SubmissionRepository extends BaseRepository { } } - /** - * Get submission eml json by dataset id. - * - * @param {string} datasetId - * @return {*} {Promise }>>} - * @memberof SubmissionRepository - */ - async getSubmissionRecordEMLJSONByDatasetId( - datasetId: string - ): Promise }>> { - const sqlStatement = SQL` - SELECT - sm.eml_json_source - FROM submission s, submission_metadata sm - WHERE s.submission_id = sm.submission_id - AND sm.record_end_timestamp IS NULL - AND sm.record_effective_timestamp IS NOT NULL - AND s.uuid = ${datasetId}; - `; - - return this.connection.sql<{ eml_json_source: Record }>(sqlStatement); - } - /** * Get spatial component counts by dataset id * @@ -716,27 +578,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Fetch a submissions metadata json representation. - * - * @param {number} sourceTransformId - * @param {string} transform - * @return {*} {Promise} - * @memberof SubmissionRepository - */ - async getSubmissionMetadataJson(submissionId: number, transform: string): Promise { - const response = await this.connection.query<{ result_data: any }>(transform, [submissionId]); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to transform submission eml to json', [ - 'SubmissionRepository->getSubmissionMetadataJson', - 'rowCount was null or undefined, expected rowCount != 0' - ]); - } - - return response.rows[0].result_data; - } - /** * Fetch a submission source transform record by associated source transform id. * @@ -865,74 +706,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Fetch a submission record by primary id. - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionRepository - */ - async listSubmissionRecords(): Promise { - const sqlStatement = SQL` - SELECT - t1.submission_status, - s.* - FROM - submission s - LEFT JOIN - (SELECT DISTINCT ON (ss.submission_id) - ss.submission_id, - sst.name AS submission_status - FROM - submission_status ss - LEFT JOIN - submission_status_type sst - ON - ss.submission_status_type_id = sst.submission_status_type_id - ORDER BY - ss.submission_id, ss.submission_status_id DESC) t1 - ON - t1.submission_id = s.submission_id; - `; - - const response = await this.connection.sql(sqlStatement); - - return response.rows; - } - - /** - * Fetch a submission source transform record by associated source system user id. - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionRepository - */ - async getSourceTransformRecordBySubmissionId(submissionId: number): Promise { - const sqlStatement = SQL` - SELECT - * - FROM - source_transform st - LEFT JOIN - submission s - ON - st.source_transform_id = s.source_transform_id - WHERE - s.submission_id = ${submissionId}; - `; - - const response = await this.connection.sql(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to get submission source transform record', [ - 'SubmissionRepository->getSourceTransformRecordBySubmissionId', - 'rowCount was null or undefined, expected rowCount != 0' - ]); - } - - return response.rows[0]; - } - /** * Fetch row of submission job queue by submission Id * @@ -963,43 +736,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Insert a new metadata record - * - * @param {ISubmissionMetadataRecord} submissionMetadata - * @return {*} {Promise<{ submission_metadata_id: number }>} - * @memberof SubmissionRepository - */ - async insertSubmissionMetadataRecord( - submissionMetadata: ISubmissionMetadataRecord - ): Promise<{ submission_metadata_id: number }> { - const sqlStatement = SQL` - INSERT INTO submission_metadata ( - submission_id, - eml_source, - eml_json_source - ) VALUES ( - ${submissionMetadata.submission_id}, - ${submissionMetadata.eml_source}, - ${submissionMetadata.eml_json_source} - ) - RETURNING - submission_metadata_id - ; - `; - - const response = await this.connection.sql<{ submission_metadata_id: number }>(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to insert submission metadata record', [ - 'SubmissionRepository->insertSubmissionMetadataRecord', - 'rowCount was null or undefined, expected rowCount >= 0' - ]); - } - - return response.rows[0]; - } - /** * Insert a new Observation Record * @@ -1041,173 +777,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Update record_end_timestamp of submission id - * - * @param {number} submissionId - * @return {*} {Promise<{ submission_id: number }>} - * @memberof SubmissionRepository - */ - async updateSubmissionMetadataRecordEndDate(submissionId: number): Promise { - const sqlStatement = SQL` - UPDATE - submission_metadata - SET - record_end_timestamp = now() - WHERE - submission_id = ${submissionId} - AND - record_end_timestamp IS NULL - AND - record_effective_timestamp IS NOT NULL - ; - `; - - const response = await this.connection.sql(sqlStatement); - - return response.rowCount; - } - - /** - * Update start time stamp of submission metadata record - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionRepository - */ - async updateSubmissionMetadataRecordEffectiveDate(submissionId: number): Promise { - const sqlStatement = SQL` - UPDATE - submission_metadata - SET - record_effective_timestamp = now() - WHERE - submission_id = ${submissionId} - AND - record_effective_timestamp IS NULL - AND - record_end_timestamp IS NULL - ; - `; - - const response = await this.connection.sql(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to update record_effective_timestamp submission metadata record', [ - 'SubmissionRepository->updateSubmissionMetadataRecordEffectiveDate', - 'rowCount was null or undefined, expected rowCount >= 0' - ]); - } - - return response.rowCount; - } - - /** - * Update end time stamp for submission observation record - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionRepository - */ - async updateSubmissionObservationRecordEndDate(submissionId: number): Promise { - const sqlStatement = SQL` - UPDATE - submission_observation - SET - record_end_timestamp = now() - WHERE - submission_id = ${submissionId} - AND - record_end_timestamp IS NULL - AND - record_effective_timestamp IS NOT NULL - ; - `; - - const response = await this.connection.sql(sqlStatement); - - return response.rowCount; - } - - /** - * - * @param submissionId the submission to update - * @param datasetSearch - * @returns {*} {Promise} the number of rows updated - * @memberof SubmissionRepository - */ - async updateSubmissionMetadataWithSearchKeys(submissionId: number, datasetSearch: any): Promise { - const sql = SQL` - UPDATE - submission_metadata - SET - dataset_search_criteria=${datasetSearch} - WHERE submission_id = ${submissionId} - AND record_end_timestamp IS NULL - AND record_effective_timestamp IS NOT NULL; - `; - - const response = await this.connection.sql(sql); - - return response.rowCount; - } - - /** - * Gets datasets that have artifacts that require a security review. - * - * @param keywordFilter A list of keys to filter the data based on search criteria defined by the transform process - * @returns {*} {Promise} - */ - async getDatasetsForReview(keywordFilter: string[]): Promise { - const knex = getKnex(); - const queryBuilder = knex - .queryBuilder() - .select( - 's.uuid as dataset_id', - 'sm.submission_id', - knex.raw(`sm.eml_json_source::json->'eml:eml'->'dataset'->>'title' as dataset_name`), - knex.raw(`sm.dataset_search_criteria::json->'primaryKeywords' as keywords`), - knex.raw(`sm.eml_json_source::json->'eml:eml'->'dataset'->'project'->'relatedProject' as related_projects`) - ) - .from('submission as s') - .leftJoin('submission_metadata as sm', 'sm.submission_id', 's.submission_id') - .whereNull('sm.record_end_timestamp') - // the ?| operator does a containment check meaning it will check if any elements in the left side array exist in the right side array - .whereRaw( - `(sm.dataset_search_criteria->'primaryKeywords')::jsonb \\?| array[${"'" + keywordFilter.join("','") + "'"}]` - ); - - const response = await this.connection.knex(queryBuilder, DatasetMetadata); - - return response.rows; - } - - /** - * Gets a count of all artifacts for a given submission UUID. - * - * @param uuid UUID of the submission to look for - * @returns {*} Promise - */ - async getArtifactForReviewCountForSubmissionUUID(uuid: string): Promise { - const knex = getKnex(); - const queryBuilder = knex - .queryBuilder() - .select( - 's.uuid as dataset_id', - 's.submission_id', - knex.raw(`COUNT(a.artifact_id)::int as artifacts_to_review`), - knex.raw(`MAX(a.create_date)::date as last_updated`) - ) - .from('submission as s') - .leftJoin('artifact as a', 'a.submission_id', 's.submission_id') - .whereNull('a.security_review_timestamp') - .where('s.uuid', uuid) - .groupBy(['s.submission_id', 's.uuid']); - const response = await this.connection.knex(queryBuilder, DatasetArtifactCount); - - return response.rows[0]; - } - /** * Get all submissions that have not completed security review. * diff --git a/api/src/services/spatial-service.test.ts b/api/src/services/spatial-service.test.ts deleted file mode 100644 index a13876b43..000000000 --- a/api/src/services/spatial-service.test.ts +++ /dev/null @@ -1,525 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { SYSTEM_ROLE } from '../constants/roles'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { - IGetSecurityTransformRecord, - IGetSpatialTransformRecord, - IInsertSpatialTransform, - ISpatialComponentFeaturePropertiesRow, - ISpatialComponentsSearchCriteria, - ISubmissionSpatialSearchResponseRow, - SpatialRepository -} from '../repositories/spatial-repository'; -import { SystemUserExtended } from '../repositories/user-repository'; -import { getMockDBConnection } from '../__mocks__/db'; -import { Srid3005 } from './geo-service'; -import { SpatialService } from './spatial-service'; -import { UserService } from './user-service'; - -chai.use(sinonChai); - -describe('SpatialService', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('insertSpatialTransform', () => { - it('should return spatial_transform_id on insert', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const repo = sinon - .stub(SpatialRepository.prototype, 'insertSpatialTransform') - .resolves({ spatial_transform_id: 1 }); - - const response = await spatialService.insertSpatialTransform({} as unknown as IInsertSpatialTransform); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ spatial_transform_id: 1 }); - }); - }); - - describe('getSpatialTransformRecords', () => { - it('should return IGetSpatialTransformRecord on get', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const repo = sinon - .stub(SpatialRepository.prototype, 'getSpatialTransformRecords') - .resolves([{ name: 'name' }] as unknown as IGetSpatialTransformRecord[]); - - const response = await spatialService.getSpatialTransformRecords(); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([{ name: 'name' }]); - }); - }); - - describe('getSecurityTransformRecords', () => { - it('should return IGetSecurityTransformRecord on get', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const repo = sinon - .stub(SpatialRepository.prototype, 'getSecurityTransformRecords') - .resolves([{ name: 'name' }] as unknown as IGetSecurityTransformRecord[]); - - const response = await spatialService.getSecurityTransformRecords(); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([{ name: 'name' }]); - }); - }); - - describe('insertSpatialTransformSubmissionRecord', () => { - it('should return spatial_transform_submission_id after insert', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const repo = sinon - .stub(SpatialRepository.prototype, 'insertSpatialTransformSubmissionRecord') - .resolves({ spatial_transform_submission_id: 1 }); - - const response = await spatialService.insertSpatialTransformSubmissionRecord(1, 1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ spatial_transform_submission_id: 1 }); - }); - }); - - describe('insertSecurityTransformSubmissionRecord', () => { - it('should return security_transform_submission_id after insert', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const repo = sinon - .stub(SpatialRepository.prototype, 'insertSecurityTransformSubmissionRecord') - .resolves({ security_transform_submission_id: 1 }); - - const response = await spatialService.insertSecurityTransformSubmissionRecord(1, 1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ security_transform_submission_id: 1 }); - }); - }); - - describe('findSpatialComponentsByCriteria', () => { - it('should return spatial component search result rows', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows = [ - { - spatial_component: { - spatial_data: {}, - submission_spatial_component_id: 1 - } - }, - { - spatial_component: { - spatial_data: {}, - submission_spatial_component_id: 2 - } - } - ] as unknown as ISubmissionSpatialSearchResponseRow[]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteria') - .resolves(mockResponseRows); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialService.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponseRows); - }); - - it('should call findSpatialComponentsByCriteriaAsAdminUser as data admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.DATA_ADMINISTRATOR] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSpatialComponentsByCriteriaAsAdminUserStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteriaAsAdminUser') - .resolves(); - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteria') - .resolves(); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - await spatialService.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(findSpatialComponentsByCriteriaAsAdminUserStub).to.be.calledOnce; - expect(findSpatialComponentsByCriteriaStub).not.to.have.been.called; - }); - - it('should call findSpatialComponentsByCriteriaAsAdminUser as system admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.SYSTEM_ADMIN] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSpatialComponentsByCriteriaAsAdminUserStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteriaAsAdminUser') - .resolves(); - const findSpatialComponentsByCriteriaStub = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteria') - .resolves(); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - await spatialService.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(findSpatialComponentsByCriteriaAsAdminUserStub).to.be.calledOnce; - expect(findSpatialComponentsByCriteriaStub).not.to.have.been.called; - }); - - it('should return spatial component search result rows', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows = [ - { - spatial_component: { - spatial_data: {}, - submission_spatial_component_id: 1 - } - }, - { - spatial_component: { - spatial_data: {}, - submission_spatial_component_id: 2 - } - } - ] as unknown as ISubmissionSpatialSearchResponseRow[]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialComponentsByCriteria') - .resolves(mockResponseRows); - - const mockSearchCriteria: ISpatialComponentsSearchCriteria = { - type: ['Occurrence'], - boundary: [{ type: 'Feature', properties: {}, geometry: { type: 'Polygon', coordinates: [[]] } }] - }; - - const response = await spatialService.findSpatialComponentsByCriteria(mockSearchCriteria); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponseRows); - }); - }); - - describe('deleteSpatialComponentsBySubmissionId', () => { - it('should return submission IDs upon deleting spatial data', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const mockResponseRows = [{ submission_id: 3 }] as unknown as { submission_id: number }[]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'deleteSpatialComponentsBySubmissionId') - .resolves(mockResponseRows); - - const response = await spatialService.deleteSpatialComponentsBySubmissionId(3); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponseRows); - }); - }); - - describe('deleteSpatialComponentsSpatialTransformRefsBySubmissionId', () => { - it('should return submission IDs upon deleting spatial data', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const mockResponseRows = [{ submission_id: 3 }] as unknown as { submission_id: number }[]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'deleteSpatialComponentsSpatialTransformRefsBySubmissionId') - .resolves(mockResponseRows); - - const response = await spatialService.deleteSpatialComponentsSpatialTransformRefsBySubmissionId(3); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponseRows); - }); - }); - - describe('deleteSpatialComponentsSecurityTransformRefsBySubmissionId', () => { - it('should return submission IDs upon deleting security data', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const mockResponseRows = [{ submission_id: 3 }] as unknown as { submission_id: number }[]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'deleteSpatialComponentsSecurityTransformRefsBySubmissionId') - .resolves(mockResponseRows); - - const response = await spatialService.deleteSpatialComponentsSecurityTransformRefsBySubmissionId(3); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponseRows); - }); - }); - - describe('findSpatialMetadataBySubmissionSpatialComponentIds', () => { - describe('with multiple features', () => { - it('should return spatial component metadata', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows: ISpatialComponentFeaturePropertiesRow[] = [ - { - spatial_component_properties: { - prop1: 'val1', - prop2: 'val2' - } - } - ]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds') - .resolves(mockResponseRows); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([{ prop1: 'val1', prop2: 'val2' }]); - }); - }); - - describe('with single feature', () => { - it('should return spatial component metadata', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows: ISpatialComponentFeaturePropertiesRow[] = [ - { - spatial_component_properties: { - prop1: 'val1', - prop2: 'val2' - } - }, - { - spatial_component_properties: { - prop3: 'val3', - prop4: 'val4' - } - } - ]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds') - .resolves(mockResponseRows); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([ - { prop1: 'val1', prop2: 'val2' }, - { prop3: 'val3', prop4: 'val4' } - ]); - }); - }); - - describe('with single feature', () => { - it('should return spatial component metadata as system admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.SYSTEM_ADMIN] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows: ISpatialComponentFeaturePropertiesRow[] = [ - { - spatial_component_properties: { - prop1: 'val1', - prop2: 'val2' - } - }, - { - spatial_component_properties: { - prop3: 'val3', - prop4: 'val4' - } - } - ]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin') - .resolves(mockResponseRows); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([ - { prop1: 'val1', prop2: 'val2' }, - { prop3: 'val3', prop4: 'val4' } - ]); - }); - - it('should return spatial component metadata as data admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.DATA_ADMINISTRATOR] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const mockResponseRows: ISpatialComponentFeaturePropertiesRow[] = [ - { - spatial_component_properties: { - prop1: 'val1', - prop2: 'val2' - } - }, - { - spatial_component_properties: { - prop3: 'val3', - prop4: 'val4' - } - } - ]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin') - .resolves(mockResponseRows); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([ - { prop1: 'val1', prop2: 'val2' }, - { prop3: 'val3', prop4: 'val4' } - ]); - }); - - it('should return non secure spatial component metadata when user is not admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(false); - - const mockResponseRows: ISpatialComponentFeaturePropertiesRow[] = [ - { - spatial_component_properties: { - prop1: 'val1', - prop2: 'val2' - } - }, - { - spatial_component_properties: { - prop3: 'val3', - prop4: 'val4' - } - } - ]; - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds') - .resolves(mockResponseRows); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([ - { prop1: 'val1', prop2: 'val2' }, - { prop3: 'val3', prop4: 'val4' } - ]); - }); - }); - - describe('with no features', () => { - it('should return [] as system admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.SYSTEM_ADMIN] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin') - .resolves([]); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([]); - }); - - it('should return [] as data admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - const mockUserObject = { role_names: [SYSTEM_ROLE.DATA_ADMINISTRATOR] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin') - .resolves([]); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([]); - }); - - it('should return [] when user is not admin', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(false); - - const repo = sinon - .stub(SpatialRepository.prototype, 'findSpatialMetadataBySubmissionSpatialComponentIds') - .resolves([]); - - const response = await spatialService.findSpatialMetadataBySubmissionSpatialComponentIds([3]); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql([]); - }); - }); - }); - - describe('getGeometryAsWktFromBoundarySpatialComponentBySubmissionId', () => { - it('returns a geometry WKT string', async () => { - const mockDBConnection = getMockDBConnection(); - const spatialService = new SpatialService(mockDBConnection); - - const submissionId = 1; - - const mockResponse = { geometry: 'POLYGON(123,456,789)' }; - - const repo = sinon - .stub(SpatialRepository.prototype, 'getGeometryAsWktFromBoundarySpatialComponentBySubmissionId') - .resolves(mockResponse); - - const response = await spatialService.getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId, - SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, - Srid3005 - ); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponse); - }); - }); -}); diff --git a/api/src/services/spatial-service.ts b/api/src/services/spatial-service.ts deleted file mode 100644 index 15eadc16d..000000000 --- a/api/src/services/spatial-service.ts +++ /dev/null @@ -1,199 +0,0 @@ -import { GeoJsonProperties } from 'geojson'; -import { SPATIAL_COMPONENT_TYPE } from '../constants/spatial'; -import { IDBConnection } from '../database/db'; -import { - IGetSecurityTransformRecord, - IGetSpatialTransformRecord, - IInsertSpatialTransform, - ISpatialComponentsSearchCriteria, - ISubmissionSpatialSearchResponseRow, - SpatialRepository -} from '../repositories/spatial-repository'; -import { DBService } from './db-service'; -import { Srid } from './geo-service'; -import { UserService } from './user-service'; - -export class SpatialService extends DBService { - spatialRepository: SpatialRepository; - - constructor(connection: IDBConnection) { - super(connection); - - this.spatialRepository = new SpatialRepository(connection); - } - - /** - * Insert new spatial transform record - * - * @param {IInsertSpatialTransform} spatialTransformDetails - * @return {*} {Promise<{ spatial_transform_id: number }>} - * @memberof SpatialService - */ - async insertSpatialTransform( - spatialTransformDetails: IInsertSpatialTransform - ): Promise<{ spatial_transform_id: number }> { - return this.spatialRepository.insertSpatialTransform(spatialTransformDetails); - } - - /** - * get spatial transform record from name - * - * @param {string} spatialTransformName - * @return {*} {Promise} - * @memberof SpatialService - */ - async getSpatialTransformRecords(): Promise { - return this.spatialRepository.getSpatialTransformRecords(); - } - - /** - * get security transform record from name - * - * @param {string} spatialTransformName - * @return {*} {Promise} - * @memberof SpatialService - */ - async getSecurityTransformRecords(): Promise { - return this.spatialRepository.getSecurityTransformRecords(); - } - - /** - * Insert record of transform id used for submission spatial component record - * - * @param {number} spatialTransformId - * @param {number} submissionSpatialComponentId - * @return {*} {Promise<{ spatial_transform_submission_id: number }>} - * @memberof SpatialService - */ - async insertSpatialTransformSubmissionRecord( - spatialTransformId: number, - submissionSpatialComponentId: number - ): Promise<{ spatial_transform_submission_id: number }> { - return this.spatialRepository.insertSpatialTransformSubmissionRecord( - spatialTransformId, - submissionSpatialComponentId - ); - } - - /** - * Insert record of transform id used for submission security component record - * - * @param {number} securityTransformId - * @param {number} submissionSpatialComponentId - * @return {*} {Promise<{ spatial_transform_submission_id: number }>} - * @memberof SpatialService - */ - async insertSecurityTransformSubmissionRecord( - securityTransformId: number, - submissionSpatialComponentId: number - ): Promise<{ security_transform_submission_id: number }> { - return this.spatialRepository.insertSecurityTransformSubmissionRecord( - securityTransformId, - submissionSpatialComponentId - ); - } - - /** - * Query builder to find spatial component by given criteria. - * - * Note: Returns an empty array of results if no matches are found. - * - * @param {ISpatialComponentsSearchCriteria} criteria - * @return {*} {Promise} - * @memberof SpatialService - */ - async findSpatialComponentsByCriteria( - criteria: ISpatialComponentsSearchCriteria - ): Promise { - const userService = new UserService(this.connection); - - if (await userService.isSystemUserAdmin()) { - return this.spatialRepository.findSpatialComponentsByCriteriaAsAdminUser(criteria); - } - - return this.spatialRepository.findSpatialComponentsByCriteria(criteria); - } - - /** - * Delete spatial component records by submission id. - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialService - */ - async deleteSpatialComponentsBySubmissionId(submission_id: number): Promise<{ submission_id: number }[]> { - return this.spatialRepository.deleteSpatialComponentsBySubmissionId(submission_id); - } - - /** - * Delete records referencing which spatial transforms were applied to a spatial component - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialService - */ - async deleteSpatialComponentsSpatialTransformRefsBySubmissionId( - submission_id: number - ): Promise<{ submission_id: number }[]> { - return this.spatialRepository.deleteSpatialComponentsSpatialTransformRefsBySubmissionId(submission_id); - } - - /** - * Delete records referencing which security transforms were applied to a spatial component - * - * @param {number} submission_id - * @return {*} {Promise<{ submission_id: number }[]>} - * @memberof SpatialService - */ - async deleteSpatialComponentsSecurityTransformRefsBySubmissionId( - submission_id: number - ): Promise<{ submission_id: number }[]> { - return this.spatialRepository.deleteSpatialComponentsSecurityTransformRefsBySubmissionId(submission_id); - } - - /** - * Query builder to find spatial component by given criteria - * - * @param {number[]} submissionSpatialComponentIds - * @return {*} {Promise} - * @memberof SpatialService - */ - async findSpatialMetadataBySubmissionSpatialComponentIds( - submissionSpatialComponentIds: number[] - ): Promise { - const userService = new UserService(this.connection); - - const response = (await userService.isSystemUserAdmin()) - ? this.spatialRepository.findSpatialMetadataBySubmissionSpatialComponentIdsAsAdmin(submissionSpatialComponentIds) - : this.spatialRepository.findSpatialMetadataBySubmissionSpatialComponentIds(submissionSpatialComponentIds); - - return (await response).map((row) => row.spatial_component_properties); - } - - /** - * Get the `Boundary` or `Boundary Centroid` spatial component for a specified dataset and return as WKT projected - * using the provided SRID. - * - * Note: Does not check roles or permissions. Should only be used for internal functionality. - * - * Note: Can be used as part of a CQL Filter when making WFS requests (see GeoService). - * - * @param {number} submissionId A submission id - * @param {(SPATIAL_COMPONENT_TYPE.BOUNDARY | SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID)} spatialComponentType - * @param {Srid} srid The id of the projection used when converting the geography to WKT - * @return {*} {Promise} - * @throws {Error} if no matches are found. - * @memberof SpatialService - */ - async getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId: number, - spatialComponentType: SPATIAL_COMPONENT_TYPE.BOUNDARY | SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID, - srid: Srid - ) { - return this.spatialRepository.getGeometryAsWktFromBoundarySpatialComponentBySubmissionId( - submissionId, - spatialComponentType, - srid - ); - } -} diff --git a/api/src/services/submission-job-queue-service.test.ts b/api/src/services/submission-job-queue-service.test.ts index 2b722b533..f4bc2279f 100644 --- a/api/src/services/submission-job-queue-service.test.ts +++ b/api/src/services/submission-job-queue-service.test.ts @@ -8,7 +8,6 @@ import { import * as FileUtils from '../utils/file-utils'; import { getMockDBConnection } from '../__mocks__/db'; import { SubmissionJobQueueService } from './submission-job-queue-service'; -import { SubmissionService } from './submission-service'; chai.use(sinonChai); @@ -36,64 +35,6 @@ describe('SubmissionJobQueueService', () => { }); }); - describe('getSourceTransformIdForUserId', () => { - it('should return an transform ID', async () => { - const mockDBConnection = getMockDBConnection(); - const service = new SubmissionJobQueueService(mockDBConnection); - const repo = sinon.stub(SubmissionJobQueueRepository.prototype, 'getSourceTransformIdForUserId').resolves(1); - - const response = await service.getSourceTransformIdForUserId(1); - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(1); - }); - }); - - describe('intake', () => { - it('should return queue id and create new submission', async () => { - const mockDBConnection = getMockDBConnection({ - systemUserId: () => { - return 1; - } - }); - const service = new SubmissionJobQueueService(mockDBConnection); - - sinon.stub(SubmissionJobQueueRepository.prototype, 'getNextQueueId').resolves({ queueId: 1 }); - sinon.stub(SubmissionJobQueueService.prototype, 'getSourceTransformIdForUserId').resolves(3); - sinon.stub(SubmissionService.prototype, 'getSubmissionIdByUUID').resolves(null); - sinon.stub(SubmissionJobQueueService.prototype, 'uploadDatasetToS3').resolves('key'); - const insert = sinon.stub(SubmissionService.prototype, 'insertSubmissionRecord').resolves({ submission_id: 1 }); - sinon.stub(SubmissionJobQueueService.prototype, 'createQueueJob').resolves({ queue_id: 1 }); - sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - const response = await service.intake('uuid', {} as unknown as Express.Multer.File); - - expect(response.queue_id).to.be.eql(1); - expect(insert).to.be.calledOnce; - }); - - it('should return queue id and update submission', async () => { - const mockDBConnection = getMockDBConnection({ - systemUserId: () => { - return 1; - } - }); - const service = new SubmissionJobQueueService(mockDBConnection); - - sinon.stub(SubmissionJobQueueRepository.prototype, 'getNextQueueId').resolves({ queueId: 1 }); - sinon.stub(SubmissionJobQueueService.prototype, 'getSourceTransformIdForUserId').resolves(3); - sinon.stub(SubmissionService.prototype, 'getSubmissionIdByUUID').resolves({ submission_id: 1 }); - sinon.stub(SubmissionJobQueueService.prototype, 'uploadDatasetToS3').resolves('key'); - const insert = sinon.stub(SubmissionService.prototype, 'insertSubmissionRecord').resolves({ submission_id: 1 }); - sinon.stub(SubmissionJobQueueService.prototype, 'createQueueJob').resolves({ queue_id: 1 }); - sinon.stub(SubmissionService.prototype, 'insertSubmissionStatusAndMessage').resolves(); - - const response = await service.intake('uuid', {} as unknown as Express.Multer.File); - - expect(response.queue_id).to.be.eql(1); - expect(insert).not.be.called; - }); - }); - describe('uploadDatasetToS3', () => { it('should create key and upload to S3', async () => { const mockDBConnection = getMockDBConnection(); diff --git a/api/src/services/submission-job-queue-service.ts b/api/src/services/submission-job-queue-service.ts index 4050df7b1..bc1fdfec3 100644 --- a/api/src/services/submission-job-queue-service.ts +++ b/api/src/services/submission-job-queue-service.ts @@ -3,10 +3,8 @@ import { ISubmissionJobQueueRecord, SubmissionJobQueueRepository } from '../repositories/submission-job-queue-repository'; -import { SUBMISSION_MESSAGE_TYPE, SUBMISSION_STATUS_TYPE } from '../repositories/submission-repository'; import { generateQueueS3FileKey, uploadFileToS3 } from '../utils/file-utils'; import { DBService } from './db-service'; -import { SubmissionService } from './submission-service'; export interface ISecurityRequest { first_nations_id: number; @@ -40,33 +38,9 @@ export class SubmissionJobQueueService extends DBService { file: Express.Multer.File, securityRequest?: ISecurityRequest ): Promise<{ queue_id: number }> { - const submissionService = new SubmissionService(this.connection); - const { queueId } = await this.jobQueueRepository.getNextQueueId(); + // NOT IMPLEMENTED - const key = await this.uploadDatasetToS3(datasetUUID, queueId, file); - let submission = await submissionService.getSubmissionIdByUUID(datasetUUID); - - if (!submission) { - // Create a submission if one does not exist - const currentUserId = this.connection.systemUserId(); - - const sourceTransformId = await this.getSourceTransformIdForUserId(currentUserId); - submission = await submissionService.insertSubmissionRecord({ - uuid: datasetUUID, - source_transform_id: sourceTransformId - }); - } - - const queueRecord = await this.createQueueJob(queueId, submission.submission_id, key, securityRequest); - - await submissionService.insertSubmissionStatusAndMessage( - submission.submission_id, - SUBMISSION_STATUS_TYPE.INGESTED, - SUBMISSION_MESSAGE_TYPE.NOTICE, - 'Uploaded successfully.' - ); - - return queueRecord; + return { queue_id: 0 }; } /** @@ -106,17 +80,6 @@ export class SubmissionJobQueueService extends DBService { return await this.jobQueueRepository.insertJobQueueRecord(queueId, submissionId, s3Key, securityRequest); } - /** - * Gets Transform Id for user Id - * - * @param {number} userId - * @return {*} {Promise} - * @memberof SubmissionJobQueueService - */ - async getSourceTransformIdForUserId(userId: number): Promise { - return await this.jobQueueRepository.getSourceTransformIdForUserId(userId); - } - /** * Fetch the next available job queue record(s). * diff --git a/api/src/services/submission-service.test.ts b/api/src/services/submission-service.test.ts index f6f78d4b9..f38e504f4 100644 --- a/api/src/services/submission-service.test.ts +++ b/api/src/services/submission-service.test.ts @@ -1,17 +1,13 @@ import chai, { expect } from 'chai'; -import * as JSONPathPlus from 'jsonpath-plus'; import { describe } from 'mocha'; -import { QueryResult } from 'pg'; import sinon from 'sinon'; import sinonChai from 'sinon-chai'; -import { ApiExecuteSQLError, ApiGeneralError } from '../errors/api-error'; +import { ApiGeneralError } from '../errors/api-error'; import { SubmissionFeatureSearchKeyValues } from '../repositories/search-index-respository'; import { SECURITY_APPLIED_STATUS } from '../repositories/security-repository'; import { - ISourceTransformModel, ISubmissionFeature, ISubmissionJobQueueRecord, - ISubmissionMetadataRecord, ISubmissionModel, ISubmissionObservationRecord, PatchSubmissionRecord, @@ -27,13 +23,10 @@ import { SUBMISSION_MESSAGE_TYPE, SUBMISSION_STATUS_TYPE } from '../repositories/submission-repository'; -import { SystemUserExtended } from '../repositories/user-repository'; import * as fileUtils from '../utils/file-utils'; -import { EMLFile } from '../utils/media/eml/eml-file'; import { getMockDBConnection } from '../__mocks__/db'; import { SearchIndexService } from './search-index-service'; import { SubmissionService } from './submission-service'; -import { UserService } from './user-service'; chai.use(sinonChai); @@ -295,38 +288,6 @@ describe('SubmissionService', () => { }); }); - describe('updateSubmissionMetadataEMLSource', () => { - it('should return submission_id on update', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'updateSubmissionMetadataEMLSource') - .resolves({ submission_metadata_id: 1 }); - - const response = await submissionService.updateSubmissionMetadataEMLSource(1, 1, { emlFile: {} } as EMLFile); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ submission_metadata_id: 1 }); - }); - }); - - describe('updateSubmissionRecordEMLJSONSource', () => { - it('should return submission_id on update', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'updateSubmissionMetadataEMLJSONSource') - .resolves({ submission_metadata_id: 1 }); - - const response = await submissionService.updateSubmissionRecordEMLJSONSource(1, 1, 'test'); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ submission_metadata_id: 1 }); - }); - }); - describe('getSubmissionRecordBySubmissionId', () => { it('should return submission_id on update', async () => { const mockDBConnection = getMockDBConnection(); @@ -357,169 +318,6 @@ describe('SubmissionService', () => { }); }); - describe('updateSubmissionMetadataRecordEndDate', () => { - it('should return submission_id on update', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon.stub(SubmissionRepository.prototype, 'updateSubmissionMetadataRecordEndDate').resolves(1); - - const response = await submissionService.updateSubmissionMetadataRecordEndDate(1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(1); - }); - }); - - describe('updateSubmissionMetadataRecordEffectiveDate', () => { - it('should return submission_id on update', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'updateSubmissionMetadataRecordEffectiveDate') - .resolves(1); - - const response = await submissionService.updateSubmissionMetadataRecordEffectiveDate(1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(1); - }); - }); - - describe('updateSubmissionObservationRecordEndDate', () => { - it('should return submission_id on update', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon.stub(SubmissionRepository.prototype, 'updateSubmissionObservationRecordEndDate').resolves(1); - - const response = await submissionService.updateSubmissionObservationRecordEndDate(1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(1); - }); - }); - - describe('getSourceTransformRecordBySystemUserId', () => { - it('should return submission source transform row object', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'getSourceTransformRecordBySystemUserId') - .resolves({ source_transform_id: 1 } as unknown as ISourceTransformModel); - - const response = await submissionService.getSourceTransformRecordBySystemUserId(1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ source_transform_id: 1 }); - }); - }); - - describe('getSubmissionMetadataJson', () => { - it('should return submission source transform row object', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'getSubmissionMetadataJson') - .resolves('transformed metadata'); - - const response = await submissionService.getSubmissionMetadataJson(1, 'transform'); - - expect(repo).to.be.calledOnce; - expect(response).to.be.equal('transformed metadata'); - }); - }); - - describe('getSourceTransformRecordBySourceTransformId', () => { - it('should return submission source transform row object', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon - .stub(SubmissionRepository.prototype, 'getSourceTransformRecordBySourceTransformId') - .resolves({ source_transform_id: 1 } as unknown as ISourceTransformModel); - - const response = await submissionService.getSourceTransformRecordBySourceTransformId(1); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ source_transform_id: 1 }); - }); - }); - - describe('getSubmissionRecordEMLJSONByDatasetId', () => { - describe('with no matching submission', () => { - it('should return eml string', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const getSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves({ rowCount: 0, rows: [] } as unknown as QueryResult); - - try { - await submissionService.getSubmissionRecordEMLJSONByDatasetId('333-333-333'); - expect.fail(); - } catch (error) { - expect(getSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect((error as ApiExecuteSQLError).message).to.equal('Failed to get dataset'); - } - }); - }); - - describe('with matching submission', () => { - it('should return eml string', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const getSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves({ rowCount: 1, rows: [{ eml_json_source: 'eml string' }] } as unknown as QueryResult); - - const response = await submissionService.getSubmissionRecordEMLJSONByDatasetId('333-333-333'); - - expect(getSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(response).to.equal('eml string'); - }); - }); - }); - - describe('findSubmissionRecordEMLJSONByDatasetId', () => { - describe('with no matching submission', () => { - it('should return eml string', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const getSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves({ rowCount: 0, rows: [] } as unknown as QueryResult); - - const response = await submissionService.findSubmissionRecordEMLJSONByDatasetId('333-333-333'); - - expect(getSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(response).to.be.null; - }); - }); - - describe('with matching submission', () => { - it('should return eml string', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const getSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves({ rowCount: 1, rows: [{ eml_json_source: 'eml string' }] } as unknown as QueryResult); - - const response = await submissionService.findSubmissionRecordEMLJSONByDatasetId('333-333-333'); - - expect(getSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(response).to.equal('eml string'); - }); - }); - }); - describe('insertSubmissionStatus', () => { it('should return submission status data', async () => { const mockDBConnection = getMockDBConnection(); @@ -556,40 +354,6 @@ describe('SubmissionService', () => { }); }); - describe('listSubmissionRecords', () => { - it('should return submission message data', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - const mockResponse = [ - { - submission_status: 'Submission Data Ingested', - submission_id: 1, - source_transform_id: 1, - uuid: '2267501d-c6a9-43b5-b951-2324faff6397', - record_effective_date: '2022-05-24T18:41:42.211Z', - record_end_date: null, - input_key: 'biohub/1/moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - input_file_name: 'moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - eml_source: null, - eml_json_source: null, - darwin_core_source: 'test', - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - update_date: '2022-05-24T18:41:42.056Z', - update_user: 15, - revision_count: 1 - } - ]; - - const repo = sinon.stub(SubmissionRepository.prototype, 'listSubmissionRecords').resolves(mockResponse); - - const response = await submissionService.listSubmissionRecords(); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(mockResponse); - }); - }); - describe('insertSubmissionStatusAndMessage', () => { it('should return submission status id and message id', async () => { const mockDBConnection = getMockDBConnection(); @@ -621,112 +385,6 @@ describe('SubmissionService', () => { }); }); - describe('findSubmissionRecordsWithSpatialCount', () => { - it('should return array of records', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const findSubmissionRecordWithSpatialCountStub = sinon - .stub(SubmissionService.prototype, 'findSubmissionRecordWithSpatialCount') - .onCall(0) - .resolves({ id: '111-111-111', source: {}, observation_count: 0 }) - .onCall(1) - .resolves({ id: '222-222-222', source: {}, observation_count: 200 }) - .onCall(2) - .resolves(null); - - const response = await submissionService.findSubmissionRecordsWithSpatialCount([ - '111-111-111', - '222-222-222', - '333-333-333' - ]); - - expect(findSubmissionRecordWithSpatialCountStub).to.be.calledThrice; - expect(response).to.be.eql([ - { id: '111-111-111', source: {}, observation_count: 0 }, - { id: '222-222-222', source: {}, observation_count: 200 }, - null - ]); - }); - }); - - describe('findSubmissionRecordWithSpatialCount', () => { - afterEach(() => { - sinon.restore(); - }); - - describe('with no occurrence spatial components', () => { - it('should return submission with count object', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionService.prototype, 'findSubmissionRecordEMLJSONByDatasetId') - .resolves({}); - - const getSpatialComponentCountByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSpatialComponentCountByDatasetId') - .resolves([{ spatial_type: 'Occurrence', count: 0 }]); - - const response = await submissionService.findSubmissionRecordWithSpatialCount('111-111-111'); - - expect(findSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(getSpatialComponentCountByDatasetIdStub).to.be.calledOnce; - expect(response).to.be.eql({ id: '111-111-111', source: {}, observation_count: 0 }); - }); - }); - - describe('with a non-zero number of occurrence spatial components', () => { - it('should return submission with count object', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionService.prototype, 'findSubmissionRecordEMLJSONByDatasetId') - .resolves({}) - .resolves({}); - - const getSpatialComponentCountByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSpatialComponentCountByDatasetId') - - .resolves([{ spatial_type: 'Occurrence', count: 200 }]); - - const response = await submissionService.findSubmissionRecordWithSpatialCount('222-222-222'); - - expect(findSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(getSpatialComponentCountByDatasetIdStub).to.be.calledOnce; - expect(response).to.be.eql({ id: '222-222-222', source: {}, observation_count: 200 }); - }); - }); - - describe('with no matching submission', () => { - it('should return null', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - const mockUserObject = { role_names: [] } as unknown as SystemUserExtended; - sinon.stub(UserService.prototype, 'getUserById').resolves(mockUserObject); - - const findSubmissionRecordEMLJSONByDatasetIdStub = sinon - .stub(SubmissionService.prototype, 'findSubmissionRecordEMLJSONByDatasetId') - .resolves(null); - - const getSpatialComponentCountByDatasetIdStub = sinon - .stub(SubmissionRepository.prototype, 'getSpatialComponentCountByDatasetId') - .resolves([]); - - const response = await submissionService.findSubmissionRecordWithSpatialCount('333-333-333'); - - expect(findSubmissionRecordEMLJSONByDatasetIdStub).to.be.calledOnce; - expect(getSpatialComponentCountByDatasetIdStub).to.be.calledOnce; - expect(response).to.be.null; - }); - }); - }); - describe('getSubmissionJobQueue', () => { it('should return a submission job queue record', async () => { const mockDBConnection = getMockDBConnection(); @@ -743,26 +401,6 @@ describe('SubmissionService', () => { }); }); - describe('insertSubmissionMetadataRecord', () => { - it('should return a submission observation record', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon.stub(SubmissionRepository.prototype, 'insertSubmissionMetadataRecord').resolves({ - submission_metadata_id: 1 - }); - - const response = await submissionService.insertSubmissionMetadataRecord({ - submission_id: 1 - } as unknown as ISubmissionMetadataRecord); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ - submission_metadata_id: 1 - }); - }); - }); - describe('insertSubmissionObservationRecord', () => { it('should return a submission observation record', async () => { const mockDBConnection = getMockDBConnection(); @@ -783,165 +421,6 @@ describe('SubmissionService', () => { }); }); - describe('findRelatedDatasetsByDatasetId', () => { - it('should return a valid array of related datasets on success', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const mockEmlJson = { - 'eml:eml': { - dataset: { - project: { - relatedProject: [ - { - '@_id': 'abcde', - title: 'Test-Title', - '@_system': 'http://example.com/datasets' - } - ] - } - } - } - }; - - const emlStub = sinon - .stub(SubmissionService.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves(mockEmlJson); - - const response = await submissionService.findRelatedDatasetsByDatasetId('test-dataset-id'); - - expect(response).to.eql([ - { - datasetId: 'abcde', - title: 'Test-Title', - url: 'http://example.com/datasets/abcde' - } - ]); - - expect(emlStub).to.be.calledOnce; - expect(emlStub).to.be.calledWith('test-dataset-id'); - }); - - it('should return an empty array if no EML JSON could be found', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const emlStub = sinon - .stub(SubmissionService.prototype, 'getSubmissionRecordEMLJSONByDatasetId') - .resolves(null as unknown as Record); - - const response = await submissionService.findRelatedDatasetsByDatasetId('test-dataset-id'); - - expect(response).to.eql([]); - expect(emlStub).to.be.calledOnce; - expect(emlStub).to.be.calledWith('test-dataset-id'); - }); - - it.skip('should return an empty array if JSON Path fails to return any results', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const emlStub = sinon.stub(SubmissionService.prototype, 'getSubmissionRecordEMLJSONByDatasetId').resolves({}); - - const jsonPathStub = sinon.stub(JSONPathPlus, 'JSONPath').returns([]); - - const response = await submissionService.findRelatedDatasetsByDatasetId('test-dataset-id'); - - expect(response).to.eql([]); - expect(emlStub).to.be.calledOnce; - expect(emlStub).to.be.calledWith('test-dataset-id'); - expect(jsonPathStub).to.be.calledOnce; - expect(jsonPathStub).to.be.calledWith({ - path: '$..eml:eml..relatedProject', - json: {}, - resultType: 'all' - }); - }); - }); - - describe('getDatasetsForReview', () => { - it('should return a rolled up dataset for review', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const stubDataset = sinon.stub(SubmissionRepository.prototype, 'getDatasetsForReview').resolves([ - { - dataset_id: 'UUID', - submission_id: 1, - dataset_name: 'Project Name', - keywords: [], - related_projects: [] - }, - { - dataset_id: 'UUID', - submission_id: 2, - dataset_name: 'Project Name', - keywords: [], - related_projects: [{ ['@_id']: 'RP_UUID_1' }, { ['@_id']: 'RP_UUID_2' }] - }, - { - dataset_id: 'UUID', - submission_id: 3, - dataset_name: 'Project Name', - keywords: [], - related_projects: [{ ['@_id']: 'RP_UUID_3' }] - } - ]); - const stubArtifactCount = sinon - .stub(SubmissionRepository.prototype, 'getArtifactForReviewCountForSubmissionUUID') - .resolves({ - dataset_id: '', - submission_id: 1, - artifacts_to_review: 1, - last_updated: '' - }); - - const response = await submissionService.getDatasetsForReview(['']); - - expect(stubDataset).to.be.calledOnce; - expect(stubArtifactCount).to.be.calledWith('RP_UUID_1'); - expect(stubArtifactCount).to.be.calledWith('RP_UUID_2'); - expect(stubArtifactCount).to.be.calledWith('RP_UUID_3'); - expect(response).to.be.eql([ - { - dataset_id: '', - artifacts_to_review: 1, - dataset_name: 'Project Name', - last_updated: '', - keywords: [] - }, - { - dataset_id: '', - artifacts_to_review: 3, - dataset_name: 'Project Name', - last_updated: '', - keywords: [] - }, - { - dataset_id: '', - artifacts_to_review: 2, - dataset_name: 'Project Name', - last_updated: '', - keywords: [] - } - ]); - }); - }); - - describe('updateSubmissionMetadataWithSearchKeys', () => { - it('should succeed with valid data', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon.stub(SubmissionRepository.prototype, 'updateSubmissionMetadataWithSearchKeys').resolves(1); - - const response = await submissionService.updateSubmissionMetadataWithSearchKeys(1, {}); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql(1); - }); - }); - describe('getUnreviewedSubmissionsForAdmins', () => { it('should return an array of submission records', async () => { const mockSubmissionRecords: SubmissionRecordWithSecurityAndRootFeatureType[] = [ diff --git a/api/src/services/submission-service.ts b/api/src/services/submission-service.ts index 58f9eaf54..f56254366 100644 --- a/api/src/services/submission-service.ts +++ b/api/src/services/submission-service.ts @@ -1,20 +1,13 @@ -import { default as dayjs } from 'dayjs'; import { JSONPath } from 'jsonpath-plus'; -import { z } from 'zod'; import { IDBConnection } from '../database/db'; -import { ApiExecuteSQLError, ApiGeneralError } from '../errors/api-error'; +import { ApiGeneralError } from '../errors/api-error'; import { SubmissionFeatureSearchKeyValues } from '../repositories/search-index-respository'; import { - IDatasetsForReview, - ISourceTransformModel, ISubmissionFeature, ISubmissionJobQueueRecord, - ISubmissionMetadataRecord, ISubmissionModel, - ISubmissionModelWithStatus, ISubmissionObservationRecord, ISubmissionRecord, - ISubmissionRecordWithSpatial, PatchSubmissionRecord, SubmissionFeatureDownloadRecord, SubmissionFeatureRecord, @@ -31,20 +24,11 @@ import { } from '../repositories/submission-repository'; import { getS3SignedURL } from '../utils/file-utils'; import { getLogger } from '../utils/logger'; -import { EMLFile } from '../utils/media/eml/eml-file'; import { DBService } from './db-service'; import { SearchIndexService } from './search-index-service'; const defaultLog = getLogger('submission-service'); -export const RelatedDataset = z.object({ - datasetId: z.string(), - title: z.string(), - url: z.string() -}); - -export type RelatedDataset = z.infer; - export class SubmissionService extends DBService { submissionRepository: SubmissionRepository; @@ -158,42 +142,6 @@ export class SubmissionService extends DBService { } } - /** - * Update the `eml_source` column of a submission record. - * - * @param {number} submissionId - * @param {EMLFile} file - * @return {*} {Promise<{ submission_id: number }>} - * @memberof SubmissionService - */ - async updateSubmissionMetadataEMLSource( - submissionId: number, - submissionMetadataId: number, - file: EMLFile - ): Promise<{ submission_metadata_id: number }> { - return this.submissionRepository.updateSubmissionMetadataEMLSource(submissionId, submissionMetadataId, file); - } - - /** - * Update the `eml_json_source` column of a submission record. - * - * @param {number} submissionId - * @param {ISubmissionRecord['eml_json_source']} EMLJSONSource - * @return {*} {Promise<{ submission_metadata_id: number }>} - * @memberof SubmissionService - */ - async updateSubmissionRecordEMLJSONSource( - submissionId: number, - submissionMetadataId: number, - EMLJSONSource: ISubmissionMetadataRecord['eml_json_source'] - ): Promise<{ submission_metadata_id: number }> { - return this.submissionRepository.updateSubmissionMetadataEMLJSONSource( - submissionId, - submissionMetadataId, - EMLJSONSource - ); - } - /** * Get submission record by id. * @@ -216,111 +164,6 @@ export class SubmissionService extends DBService { return this.submissionRepository.getSubmissionIdByUUID(uuid); } - /** - * Set record_end_date of submission id - * - * @param {number} submissionId - * @return {*} {Promise<{ submission_id: number }>} - * @memberof SubmissionService - */ - async updateSubmissionMetadataRecordEndDate(submissionId: number): Promise { - return this.submissionRepository.updateSubmissionMetadataRecordEndDate(submissionId); - } - - /** - * Set record_effective_timestamp of submission id - * - * @param {number} submissionId - * @return {*} {Promise<{ submission_id: number }>} - * @memberof SubmissionService - */ - async updateSubmissionMetadataRecordEffectiveDate(submissionId: number): Promise { - return this.submissionRepository.updateSubmissionMetadataRecordEffectiveDate(submissionId); - } - - /** - * Update end time stamp for submission observation record - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionService - */ - async updateSubmissionObservationRecordEndDate(submissionId: number): Promise { - return this.submissionRepository.updateSubmissionObservationRecordEndDate(submissionId); - } - - /** - * Get source transform record by its associated source system user id. - * - * @param {number} systemUserId - * @return {*} {Promise} - * @memberof SubmissionService - */ - async getSourceTransformRecordBySystemUserId(systemUserId: number, version?: string): Promise { - return this.submissionRepository.getSourceTransformRecordBySystemUserId(systemUserId, version); - } - - /** - * Get json representation of eml source from submission. - * - * @param {number} submissionId - * @param {string} transform - * @return {string} - * @memberof SubmissionService - */ - async getSubmissionMetadataJson(submissionId: number, transform: string): Promise { - return this.submissionRepository.getSubmissionMetadataJson(submissionId, transform); - } - - /** - * Get source transform record by its associated source transform id. - * - * @param {number} sourceTransformId - * @return {*} {Promise} - * @memberof SubmissionService - */ - async getSourceTransformRecordBySourceTransformId(sourceTransformId: number): Promise { - return this.submissionRepository.getSourceTransformRecordBySourceTransformId(sourceTransformId); - } - - /** - * Get json representation of eml source from submission by datasetId. - * - * @param {string} datasetId - * @return {Promise>} - * @memberof SubmissionService - */ - async getSubmissionRecordEMLJSONByDatasetId(datasetId: string): Promise> { - const response = await this.submissionRepository.getSubmissionRecordEMLJSONByDatasetId(datasetId); - - if (response.rowCount !== 1) { - throw new ApiExecuteSQLError('Failed to get dataset', [ - 'SubmissionRepository->getSubmissionRecordEMLJSONByDatasetId', - 'rowCount was null or undefined, expected rowCount = 1' - ]); - } - - return response.rows[0].eml_json_source; - } - - /** - * Find json representation of eml source from submission by datasetId. May return null if `datasetId` does not match - * any existing records. - * - * @param {string} datasetId - * @return {Record | null} - * @memberof SubmissionService - */ - async findSubmissionRecordEMLJSONByDatasetId(datasetId: string): Promise | null> { - const response = await this.submissionRepository.getSubmissionRecordEMLJSONByDatasetId(datasetId); - - if (response.rowCount !== 1) { - return null; - } - - return response.rows[0].eml_json_source; - } - /** * Insert a submission status record. * @@ -368,17 +211,6 @@ export class SubmissionService extends DBService { ); } - /** - * List all submissions - * - * @param {number} submissionId - * @return {*} {Promise} - * @memberof SubmissionService - */ - async listSubmissionRecords(): Promise { - return this.submissionRepository.listSubmissionRecords(); - } - /** * Inserts both the status and message of a submission * @@ -419,41 +251,6 @@ export class SubmissionService extends DBService { }; } - /** - * Retrieves an array of submission records with spatial count by dataset id. - * - * @param {string[]} datasetIds - * @return {*} {(Promise<(ISubmissionRecordWithSpatial | null)[]>)} - * @memberof SubmissionService - */ - async findSubmissionRecordsWithSpatialCount(datasetIds: string[]): Promise<(ISubmissionRecordWithSpatial | null)[]> { - return Promise.all(datasetIds.map(async (datasetId) => this.findSubmissionRecordWithSpatialCount(datasetId))); - } - - /** - * Retrieves a submission record with spatial count by dataset id. - * - * @param {string} datasetId - * @return {*} {(Promise)} - * @memberof SubmissionService - */ - async findSubmissionRecordWithSpatialCount(datasetId: string): Promise { - const [submissionEMLJSON, spatialComponentCounts] = await Promise.all([ - this.findSubmissionRecordEMLJSONByDatasetId(datasetId), - this.submissionRepository.getSpatialComponentCountByDatasetId(datasetId) - ]); - - if (!submissionEMLJSON) { - return null; - } - - return { - id: datasetId, - source: submissionEMLJSON, - observation_count: spatialComponentCounts.find((countItem) => countItem.spatial_type === 'Occurrence')?.count ?? 0 - }; - } - /** * Fetch row of submission job queue by submission Id * @@ -465,19 +262,6 @@ export class SubmissionService extends DBService { return this.submissionRepository.getSubmissionJobQueue(submissionId); } - /** - * Insert a new metadata record - * - * @param {ISubmissionMetadataRecord} submissionMetadata - * @return {*} {Promise<{ submission_metadata_id: number }>} - * @memberof SubmissionService - */ - async insertSubmissionMetadataRecord( - submissionMetadata: ISubmissionMetadataRecord - ): Promise<{ submission_metadata_id: number }> { - return this.submissionRepository.insertSubmissionMetadataRecord(submissionMetadata); - } - /** * Insert a new Observation Record * @@ -491,110 +275,6 @@ export class SubmissionService extends DBService { return this.submissionRepository.insertSubmissionObservationRecord(submissionObservation); } - /** - * Retrieves an array of datasets related to the given dataset. - * - * @param {string} datasetId - * @return {*} {Promise} - * @memberof SubmissionService - */ - async findRelatedDatasetsByDatasetId(datasetId: string): Promise { - const emlJson = await this.getSubmissionRecordEMLJSONByDatasetId(datasetId); - - if (!emlJson) { - return []; - } - - const result = JSONPath({ - path: '$..eml:eml..relatedProject', - json: emlJson, - resultType: 'all' - }); - - if (!result.length) { - return []; - } - - return result[0].value.map((relatedProject: any) => { - return { - datasetId: relatedProject['@_id'], - title: relatedProject['title'], - url: [relatedProject['@_system'], relatedProject['@_id']].join('/') - }; - }); - } - - /** - * Gets datasets that have artifacts that require a security review. - * This will roll up any related projects to provide a "total" count of artifacts to review - * - * @param keys A list of keys to filter the data based on search criteria defined by the transform process - * @returns {*} {Promise} - * @memberof SubmissionService - */ - async getDatasetsForReview(keys: string[]): Promise { - const data = await this.submissionRepository.getDatasetsForReview(keys); - const datasetsForReview: IDatasetsForReview[] = []; - - for await (const item of data) { - let rollUpCount = 0; - const dates: string[] = []; - - if (item.related_projects) { - for await (const rp of item.related_projects) { - const rpCount = await this.submissionRepository.getArtifactForReviewCountForSubmissionUUID(rp['@_id']); - if (rpCount) { - rollUpCount += rpCount.artifacts_to_review; - dates.push(rpCount.last_updated ?? ''); - } - } - } - - const parentArtifactCount = await this.submissionRepository.getArtifactForReviewCountForSubmissionUUID( - item.dataset_id - ); - if (parentArtifactCount) { - const finalCount = rollUpCount + parentArtifactCount.artifacts_to_review; - - // only push projects with artifacts to review - if (finalCount > 0) { - dates.push(parentArtifactCount.last_updated ?? ''); - datasetsForReview.push({ - dataset_id: parentArtifactCount.dataset_id, - artifacts_to_review: finalCount, - dataset_name: item.dataset_name, - last_updated: this.mostRecentDate(dates), - keywords: item.keywords - }); - } - } - } - return datasetsForReview; - } - - /** - * Compares and finds the most recent date given a list of date strings. Todays date is returned if no data is present in the list - * - * @param dates a list of date strings - * @returns {*} {string} the most recent date found - */ - mostRecentDate(dates: string[]): string { - dates.sort((d1, d2) => dayjs(d1).diff(dayjs(d2))); - return dates[0] ?? dayjs(); - } - - /** - * - * @param submissionId - * @param submitterSystem - * @param datasetSearch - * @returns - * @memberof SubmissionService - */ - async updateSubmissionMetadataWithSearchKeys(submissionId: number, datasetSearch: any): Promise { - return this.submissionRepository.updateSubmissionMetadataWithSearchKeys(submissionId, datasetSearch); - } - /** * Get all submissions that are pending security review (are unreviewed). * diff --git a/api/src/utils/media/csv/csv-file.test.ts b/api/src/utils/media/csv/csv-file.test.ts deleted file mode 100644 index 4f0b48da9..000000000 --- a/api/src/utils/media/csv/csv-file.test.ts +++ /dev/null @@ -1,273 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import xlsx from 'xlsx'; -import { CSVValidation, CSVWorkBook, CSVWorksheet, IHeaderError, IRowError } from './csv-file'; - -describe('CSVWorkBook', () => { - it('constructs with no rawWorkbook param', () => { - const csvWorkBook = new CSVWorkBook(); - - expect(csvWorkBook).not.to.be.null; - expect(csvWorkBook.rawWorkbook).not.to.be.null; - expect(csvWorkBook.worksheets).to.eql({}); - }); - - it('constructs with rawWorkbook param', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data', 'Header2Data'] - ]); - - const xlsxWorkBook = xlsx.utils.book_new(); - xlsx.utils.book_append_sheet(xlsxWorkBook, xlsxWorkSheet); - - const csvWorkBook = new CSVWorkBook(xlsxWorkBook); - - expect(csvWorkBook).not.to.be.null; - expect(csvWorkBook.rawWorkbook).not.to.be.null; - expect(csvWorkBook.worksheets['Sheet1']).not.to.be.null; - }); -}); - -describe('CSVWorksheet', () => { - it('constructs', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data', 'Header2Data'] - ]); - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - }); - - describe('getHeaders', () => { - it('returns empty array if the worksheet is null', () => { - const xlsxWorkSheet = null as unknown as xlsx.WorkSheet; - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getHeaders()).to.eql([]); - }); - - it('returns an array of headers', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data', 'Header2Data'] - ]); - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getHeaders()).to.eql(['Header1', 'Header2']); - }); - }); - - describe('getRows', () => { - it('returns empty array if the worksheet is null', () => { - const xlsxWorkSheet = null as unknown as xlsx.WorkSheet; - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getRows()).to.eql([]); - }); - - it('returns an array of rows data arrays', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data1', 'Header2Data1'], - ['Header1Data2', 'Header2Data2'] - ]); - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getRows()).to.eql([ - ['Header1Data1', 'Header2Data1'], - ['Header1Data2', 'Header2Data2'] - ]); - }); - }); - - describe('getRowObjects', () => { - it('returns empty array if the worksheet is null', () => { - const xlsxWorkSheet = null as unknown as xlsx.WorkSheet; - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getRowObjects()).to.eql([]); - }); - - it('returns an array of rows data arrays', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data1', 'Header2Data1'], - ['Header1Data2', 'Header2Data2'] - ]); - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - expect(csvWorksheet.getRowObjects()).to.eql([ - { - Header1: 'Header1Data1', - Header2: 'Header2Data1' - }, - { - Header1: 'Header1Data2', - Header2: 'Header2Data2' - } - ]); - }); - }); - - describe('validate', () => { - it('calls all provided validator functions', () => { - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data1', 'Header2Data1'], - ['Header1Data2', 'Header2Data2'] - ]); - - const csvWorksheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - expect(csvWorksheet).not.to.be.null; - - const mockValidationFunction1 = sinon.stub(); - const mockValidationFunction2 = sinon.stub(); - const mockValidationFunction3 = sinon.stub(); - - csvWorksheet.validate([mockValidationFunction1, mockValidationFunction2, mockValidationFunction3]); - - expect(mockValidationFunction1).to.have.been.calledOnce; - expect(mockValidationFunction2).to.have.been.calledOnce; - expect(mockValidationFunction3).to.have.been.calledOnce; - }); - }); -}); - -describe('CSVValidation', () => { - it('constructs', () => { - const csvValidation = new CSVValidation('fileName'); - - expect(csvValidation).not.to.be.null; - }); - - describe('addFileErrors', () => { - it('adds new file errors', () => { - const csvValidation = new CSVValidation('fileName'); - - expect(csvValidation).not.to.be.null; - - const fileError1 = 'a file error'; - const fileError2 = 'a second file error'; - - csvValidation.addFileErrors([fileError1]); - - expect(csvValidation.fileErrors).to.eql([fileError1]); - - csvValidation.addFileErrors([fileError2]); - - expect(csvValidation.fileErrors).to.eql([fileError1, fileError2]); - }); - }); - - describe('addHeaderErrors', () => { - it('adds new header errors', () => { - const csvValidation = new CSVValidation('fileName'); - - expect(csvValidation).not.to.be.null; - - const headerError1: IHeaderError = { - errorCode: 'Duplicate Header', - message: 'a header error', - col: 0 - }; - - const headerError2: IHeaderError = { - errorCode: 'Unknown Header', - message: 'a second header error', - col: 1 - }; - - csvValidation.addHeaderErrors([headerError1]); - - expect(csvValidation.headerErrors).to.eql([headerError1]); - - csvValidation.addHeaderErrors([headerError2]); - - expect(csvValidation.headerErrors).to.eql([headerError1, headerError2]); - }); - }); - - describe('addRowErrors', () => { - it('adds new header errors', () => { - const csvValidation = new CSVValidation('fileName'); - - expect(csvValidation).not.to.be.null; - - const rowError1: IRowError = { - errorCode: 'Missing Required Field', - message: 'a row error', - col: 'col1', - row: 1 - }; - - const rowError2: IRowError = { - errorCode: 'Missing Required Field', - message: 'a second row error', - col: 'col1', - row: 2 - }; - - csvValidation.addRowErrors([rowError1]); - - expect(csvValidation.rowErrors).to.eql([rowError1]); - - csvValidation.addRowErrors([rowError2]); - - expect(csvValidation.rowErrors).to.eql([rowError1, rowError2]); - }); - }); - - describe('getState', () => { - it('gets the current validation state', () => { - const csvValidation = new CSVValidation('fileName'); - - expect(csvValidation).not.to.be.null; - - const fileError1 = 'a file error'; - - const headerError1: IHeaderError = { - errorCode: 'Duplicate Header', - message: 'a header error', - col: 0 - }; - - const rowError1: IRowError = { - errorCode: 'Missing Required Field', - message: 'a row error', - col: 'col1', - row: 1 - }; - - csvValidation.addFileErrors([fileError1]); - csvValidation.addHeaderErrors([headerError1]); - csvValidation.addRowErrors([rowError1]); - - const validationState = csvValidation.getState(); - - expect(validationState).to.eql({ - fileName: 'fileName', - fileErrors: [fileError1], - headerErrors: [headerError1], - rowErrors: [rowError1], - isValid: false - }); - }); - }); -}); diff --git a/api/src/utils/media/csv/csv-file.ts b/api/src/utils/media/csv/csv-file.ts deleted file mode 100644 index dbe7a2b31..000000000 --- a/api/src/utils/media/csv/csv-file.ts +++ /dev/null @@ -1,299 +0,0 @@ -import xlsx from 'xlsx'; -import { safeToLowerCase, safeTrim } from '../../string-utils'; -import { IMediaState, MediaValidation } from '../media-file'; -import { getCellValue, getWorksheetRange, replaceCellDates, trimCellWhitespace } from '../xlsx/xlsx-utils'; - -export type CSVWorksheets = { [name: string]: CSVWorksheet }; - -export class CSVWorkBook { - rawWorkbook: xlsx.WorkBook; - - worksheets: CSVWorksheets; - - constructor(workbook?: xlsx.WorkBook) { - this.rawWorkbook = workbook || xlsx.utils.book_new(); - - const worksheets: CSVWorksheets = {}; - - Object.entries(this.rawWorkbook.Sheets).forEach(([key, value]) => { - worksheets[key] = new CSVWorksheet(key, value); - }); - - this.worksheets = worksheets; - } -} - -export class CSVWorksheet { - name: string; - - worksheet: xlsx.WorkSheet; - - _headers: string[]; - _headersLowerCase: string[]; - _rows: string[][]; - _rowObjects: object[]; - - csvValidation: CSVValidation; - - constructor(name: string, worksheet?: xlsx.WorkSheet) { - this.name = name; - - this.worksheet = worksheet || xlsx.utils.aoa_to_sheet([]); - - this._headers = []; - this._headersLowerCase = []; - this._rows = []; - this._rowObjects = []; - - this.csvValidation = new CSVValidation(this.name); - } - - /** - * Returns an array of header values. - * - * Note: This is always the first row (index 0) - * - * @return {*} {string[]} - * @memberof CSVWorksheet - */ - getHeaders(): string[] { - if (!this.worksheet) { - return []; - } - - const originalRange = getWorksheetRange(this.worksheet); - - if (!originalRange) { - return []; - } - - if (!this._headers.length) { - // Specify range to only include the 0th row (header row) - const customRange: xlsx.Range = { ...originalRange, e: { ...originalRange.e, r: 0 } }; - - const aoaHeaders: any[][] = xlsx.utils.sheet_to_json(this.worksheet, { - header: 1, - blankrows: false, - range: customRange - }); - - if (aoaHeaders.length > 0) { - // Parse the headers array from the array of arrays produced by calling `xlsx.utils.sheet_to_json` - this._headers = aoaHeaders[0].map(safeTrim); - } - } - - return this._headers; - } - - getHeadersLowerCase(): string[] { - if (!this._headersLowerCase.length) { - this._headersLowerCase = this.getHeaders().map(safeToLowerCase); - } - - return this._headersLowerCase; - } - - getHeaderIndex(headerName: string): number { - return this.getHeaders().indexOf(headerName); - } - - /** - * Return an array of row value arrays. - * - * Note: This does not include the first row (header row). - * - * @return {*} {string[][]} - * @memberof CSVWorksheet - */ - getRows(): string[][] { - if (!this.worksheet) { - return []; - } - - const originalRange = getWorksheetRange(this.worksheet); - - if (!originalRange) { - return []; - } - - if (!this._rows.length) { - const rowsToReturn: string[][] = []; - - for (let i = 1; i <= originalRange.e.r; i++) { - const row = new Array(this.getHeaders().length); - let rowHasValues = false; - - for (let j = 0; j <= originalRange.e.c; j++) { - const cellAddress = { c: j, r: i }; - const cellRef = xlsx.utils.encode_cell(cellAddress); - const cell = this.worksheet[cellRef]; - - if (!cell) { - continue; - } - - row[j] = getCellValue(trimCellWhitespace(replaceCellDates(cell))); - - rowHasValues = true; - } - - if (row.length && rowHasValues) { - rowsToReturn.push(row); - } - } - - this._rows = rowsToReturn; - } - - return this._rows; - } - - getRowObjects(): object[] { - if (!this.worksheet) { - return []; - } - - const ref = this.worksheet['!ref']; - - if (!ref) { - return []; - } - - if (!this._rowObjects.length) { - const rowObjectsArray: object[] = []; - const rows = this.getRows(); - const headers = this.getHeaders(); - - rows.forEach((row: string[]) => { - const rowObject = {}; - - headers.forEach((header: string, index: number) => { - rowObject[header] = row[index]; - }); - - rowObjectsArray.push(rowObject); - }); - - this._rowObjects = rowObjectsArray; - } - - return this._rowObjects; - } - - getCell(headerName: string, rowIndex: number) { - const headerIndex = this.getHeaderIndex(headerName); - - if (headerIndex < 0) { - return undefined; - } - - const rows = this.getRows(); - - const row = rows?.[rowIndex]; - - if (!row || !row.length) { - return undefined; - } - - return row[headerIndex]; - } - - /** - * Runs all of the given validators on the worksheet, whereby the results of all validations - * are stored in `this.csvValidation`. - * - * @param {CSVValidator[]} validators A series of CSV validators to be run on the worksheet. - * @return {*} {CSVValidation} The result of all validations, namely `this.csvValidation`. - * @memberof CSVWorksheet - */ - validate(validators: CSVValidator[]): CSVValidation { - validators.forEach((validator) => validator(this)); - - return this.csvValidation; - } -} - -export type CSVValidator = (csvWorksheet: CSVWorksheet) => CSVWorksheet; - -// ensure these error codes match the 'name' column in the table: submission_message_type - -export type IHeaderErrorCode = - | 'Duplicate Header' - | 'Unknown Header' - | 'Missing Required Header' - | 'Missing Recommended Header' - | 'Miscellaneous'; - -export type IRowErrorCode = - | 'Missing Required Field' - | 'Unexpected Format' - | 'Out of Range' - | 'Invalid Value' - | 'Miscellaneous'; - -export interface IHeaderError { - errorCode: IHeaderErrorCode; - message: string; - col: string | number; -} - -export interface IRowError { - errorCode: IRowErrorCode; - message: string; - col: string; - row: number; -} -export interface ICsvState extends IMediaState { - headerErrors: IHeaderError[]; - rowErrors: IRowError[]; -} - -/** - * Supports getting/setting validation errors for any csv file. - * - * @export - * @class CSVValidation - * @extends {MediaValidation} - */ -export class CSVValidation extends MediaValidation { - headerErrors: IHeaderError[]; - rowErrors: IRowError[]; - - constructor(fileName: string) { - super(fileName); - - this.headerErrors = []; - this.rowErrors = []; - } - - addHeaderErrors(errors: IHeaderError[]) { - this.headerErrors = this.headerErrors.concat(errors); - - if (errors?.length) { - this.isValid = false; - } - } - - addHeaderWarnings(errors: IHeaderError[]) { - this.headerErrors = this.headerErrors.concat(errors); - } - - addRowErrors(errors: IRowError[]) { - this.rowErrors = this.rowErrors.concat(errors); - - if (errors?.length) { - this.isValid = false; - } - } - - getState(): ICsvState { - return { - fileName: this.fileName, - fileErrors: this.fileErrors, - headerErrors: this.headerErrors, - rowErrors: this.rowErrors, - isValid: this.isValid - }; - } -} diff --git a/api/src/utils/media/csv/validation/csv-header-validator.test.ts b/api/src/utils/media/csv/validation/csv-header-validator.test.ts deleted file mode 100644 index 9ba17182d..000000000 --- a/api/src/utils/media/csv/validation/csv-header-validator.test.ts +++ /dev/null @@ -1,308 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import xlsx from 'xlsx'; -import { CSVWorksheet } from '../csv-file'; -import { - getDuplicateHeadersValidator, - getValidHeadersValidator, - hasRecommendedHeadersValidator, - hasRequiredHeadersValidator -} from './csv-header-validator'; - -describe('getDuplicateHeadersValidator', () => { - it('adds no errors when there are no headers', () => { - const validator = getDuplicateHeadersValidator(); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[]]); // empty csv - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds no errors if no headers are duplicates', () => { - const validator = getDuplicateHeadersValidator(); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2', 'Header3']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds errors for each header that is a duplicate', () => { - const validator = getDuplicateHeadersValidator(); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2', 'Header1', 'Header3', 'Header2', 'Header4']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Duplicate Header', - col: 'Header1', - message: 'Duplicate header' - }, - { - errorCode: 'Duplicate Header', - col: 'Header2', - message: 'Duplicate header' - } - ]); - }); -}); - -describe('hasRequiredHeadersValidator', () => { - it('adds no errors when required headers are undefined', () => { - const requiredHeaders = undefined; - - const validator = hasRequiredHeadersValidator(requiredHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when there are no required headers', () => { - const requiredHeaders = { file_required_columns_validator: { required_columns: [] } }; - - const validator = hasRequiredHeadersValidator(requiredHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds errors for all headers if there are required headers but no header row', () => { - const requiredHeaders = { - file_required_columns_validator: { required_columns: ['Header1', 'Header2', 'Header3'] } - }; - - const validator = hasRequiredHeadersValidator(requiredHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[]]); // empty csv - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Missing Required Header', - col: 'Header1', - message: 'Missing required header' - }, - { - errorCode: 'Missing Required Header', - col: 'Header2', - message: 'Missing required header' - }, - { - errorCode: 'Missing Required Header', - col: 'Header3', - message: 'Missing required header' - } - ]); - }); - - it('adds errors for each missing header that is required', () => { - const requiredHeaders = { - file_required_columns_validator: { required_columns: ['Header1', 'Header3', 'Header4', 'Header5'] } - }; - - const validator = hasRequiredHeadersValidator(requiredHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2', 'Header4']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Missing Required Header', - col: 'Header3', - message: 'Missing required header' - }, - { - errorCode: 'Missing Required Header', - col: 'Header5', - message: 'Missing required header' - } - ]); - }); -}); - -describe('getValidHeadersValidator', () => { - it('adds no errors when configuration is not found', () => { - const validHeaders = undefined; - - const validator = getValidHeadersValidator(validHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds no errors when no valid headers provided', () => { - const validHeaders = { file_valid_columns_validator: { valid_columns: [] } }; - - const validator = getValidHeadersValidator(validHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds no errors if there are no invalid headers', () => { - const validHeaders = { file_valid_columns_validator: { valid_columns: ['Header1', 'Header2', 'Header3'] } }; - - const validator = getValidHeadersValidator(validHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds errors for all headers that are not valid ', () => { - const validHeaders = { file_valid_columns_validator: { valid_columns: ['Header1', 'Header2', 'Header3'] } }; - - const validator = getValidHeadersValidator(validHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'UnknownHeader2', 'Header3', 'UnknownHeader4']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Unknown Header', - col: 'UnknownHeader2', - message: 'Unsupported header' - }, - { - errorCode: 'Unknown Header', - col: 'UnknownHeader4', - message: 'Unsupported header' - } - ]); - }); -}); - -describe('hasRecommendedHeadersValidator', () => { - it('adds no errors when there are no recommended headers', () => { - const recommendedHeaders = undefined; - - const validator = hasRecommendedHeadersValidator(recommendedHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors/warnings when there are no recommended headers', () => { - const recommendedHeaders = { - file_recommended_columns_validator: { recommended_columns: [] } - }; - - const validator = hasRecommendedHeadersValidator(recommendedHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2', 'Header4']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([]); - }); - - it('adds errors for each missing header that is recommended', () => { - const recommendedHeaders = { - file_recommended_columns_validator: { recommended_columns: ['Header1', 'Header3', 'Header4', 'Header5'] } - }; - - const validator = hasRecommendedHeadersValidator(recommendedHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2', 'Header4']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Missing Recommended Header', - col: 'Header3', - message: 'Missing recommended header' - }, - { - errorCode: 'Missing Recommended Header', - col: 'Header5', - message: 'Missing recommended header' - } - ]); - }); - - it('adds warnings for all headers if there are recommended headers but no header row', () => { - const recommendedHeaders = { - file_recommended_columns_validator: { recommended_columns: ['Header1', 'Header2', 'Header3'] } - }; - - const validator = hasRecommendedHeadersValidator(recommendedHeaders); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[]]); // empty csv - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.headerErrors).to.eql([ - { - errorCode: 'Missing Recommended Header', - col: 'Header1', - message: 'Missing recommended header' - }, - { - errorCode: 'Missing Recommended Header', - col: 'Header2', - message: 'Missing recommended header' - }, - { - errorCode: 'Missing Recommended Header', - col: 'Header3', - message: 'Missing recommended header' - } - ]); - }); -}); diff --git a/api/src/utils/media/csv/validation/csv-header-validator.ts b/api/src/utils/media/csv/validation/csv-header-validator.ts deleted file mode 100644 index bc8d05a8a..000000000 --- a/api/src/utils/media/csv/validation/csv-header-validator.ts +++ /dev/null @@ -1,193 +0,0 @@ -import { CSVValidator } from '../csv-file'; - -/** - * Adds an error for each header that is not unique. - * - * @return {*} {CSVValidator} - */ -export const getDuplicateHeadersValidator = (): CSVValidator => { - return (csvWorksheet) => { - const headers = csvWorksheet.getHeaders(); - - if (!headers?.length) { - return csvWorksheet; - } - - const seenHeaders: string[] = []; - - for (const header of headers) { - if (seenHeaders.includes(header)) { - csvWorksheet.csvValidation.addHeaderErrors([ - { - errorCode: 'Duplicate Header', - message: 'Duplicate header', - col: header - } - ]); - } else { - seenHeaders.push(header); - } - } - - return csvWorksheet; - }; -}; - -export type FileRequiredHeaderValidatorConfig = { - file_required_columns_validator: { - name?: string; - description?: string; - required_columns: string[]; - }; -}; - -/** - * For a specified set of required columns, adds an error if the column is not present in the csv. - * - * @param {FileRequiredHeaderValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const hasRequiredHeadersValidator = (config?: FileRequiredHeaderValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - if (!config.file_required_columns_validator.required_columns.length) { - // No required columns - return csvWorksheet; - } - - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - if (!headersLowerCase?.length) { - csvWorksheet.csvValidation.addHeaderErrors( - config.file_required_columns_validator.required_columns.map((requiredHeader) => { - return { - errorCode: 'Missing Required Header', - message: 'Missing required header', - col: requiredHeader - }; - }) - ); - - return csvWorksheet; - } - - for (const requiredHeader of config.file_required_columns_validator.required_columns) { - if (!headersLowerCase.includes(requiredHeader.toLowerCase())) { - csvWorksheet.csvValidation.addHeaderErrors([ - { - errorCode: 'Missing Required Header', - message: 'Missing required header', - col: requiredHeader - } - ]); - } - } - - return csvWorksheet; - }; -}; - -export type FileRecommendedHeaderValidatorConfig = { - file_recommended_columns_validator: { - name?: string; - description?: string; - recommended_columns: string[]; - }; -}; - -/** - * For a specified set of recommended columns, adds a warning if the column is not present in the csv. - * - * @param {FileRecommendedHeaderValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const hasRecommendedHeadersValidator = (config?: FileRecommendedHeaderValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - if (!config.file_recommended_columns_validator.recommended_columns.length) { - return csvWorksheet; - } - - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - if (!headersLowerCase?.length) { - csvWorksheet.csvValidation.addHeaderWarnings( - config.file_recommended_columns_validator.recommended_columns.map((recommendedHeader) => { - return { - errorCode: 'Missing Recommended Header', - message: 'Missing recommended header', - col: recommendedHeader - }; - }) - ); - - return csvWorksheet; - } - - for (const recommendedHeader of config.file_recommended_columns_validator.recommended_columns) { - if (!headersLowerCase.includes(recommendedHeader.toLowerCase())) { - csvWorksheet.csvValidation.addHeaderWarnings([ - { - errorCode: 'Missing Recommended Header', - message: 'Missing recommended header', - col: recommendedHeader - } - ]); - } - } - - return csvWorksheet; - }; -}; - -export type FileValidHeadersValidatorConfig = { - file_valid_columns_validator: { - name?: string; - description?: string; - valid_columns: string[]; - }; -}; - -/** - * Adds a warning if a column in the csv does not match a value in a specified set of valid columns. - * - * @param {FileValidHeadersValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const getValidHeadersValidator = (config?: FileValidHeadersValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - if (!config.file_valid_columns_validator.valid_columns.length) { - return csvWorksheet; - } - - const headers = csvWorksheet.getHeaders(); - - for (const header of headers) { - if ( - !config.file_valid_columns_validator.valid_columns - .map((item) => item.toLowerCase()) - .includes(header.trim().toLowerCase()) - ) { - csvWorksheet.csvValidation.addHeaderWarnings([ - { - errorCode: 'Unknown Header', - message: 'Unsupported header', - col: header - } - ]); - } - } - - return csvWorksheet; - }; -}; diff --git a/api/src/utils/media/csv/validation/csv-row-validator.test.ts b/api/src/utils/media/csv/validation/csv-row-validator.test.ts deleted file mode 100644 index cf4976d85..000000000 --- a/api/src/utils/media/csv/validation/csv-row-validator.test.ts +++ /dev/null @@ -1,607 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import xlsx from 'xlsx'; -import { CSVWorksheet } from '../csv-file'; -import { - getCodeValueFieldsValidator, - getNumericFieldsValidator, - getRequiredFieldsValidator, - getValidFormatFieldsValidator, - getValidRangeFieldsValidator -} from './csv-row-validator'; - -describe('getRequiredFieldsValidator', () => { - it('adds no errors when required fields are not provided', () => { - const requiredFieldsByHeader: string[] = []; - - const validator = getRequiredFieldsValidator(requiredFieldsByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data', 'Header2Data'] - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when header does not exist', () => { - const requiredFieldsByHeader: string[] = ['Header1', 'Header2']; // fields for these headers are required - const validator = getRequiredFieldsValidator(requiredFieldsByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[], [5]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds errors for every field if required fields are provided and there are zero data rows in the worksheet', () => { - const requiredFieldsByHeader: string[] = ['Header1', 'Header2']; // fields for these headers are required - - const validator = getRequiredFieldsValidator(requiredFieldsByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1', 'Header2']]); // no data rows - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Missing Required Field', - message: 'Missing required value for column', - row: 2 - }, - { - col: 'Header2', - errorCode: 'Missing Required Field', - message: 'Missing required value for column', - row: 2 - } - ]); - }); - - it('adds errors for required fields that are empty', () => { - const requiredFieldsByHeader: string[] = ['Header1', 'Header2']; // fields for these headers are required - - const validator = getRequiredFieldsValidator(requiredFieldsByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2', 'Header3'], - ['', 'Header2Data', ''] // mixture of required and non required headers with non-empty and empty values - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Missing Required Field', - message: 'Missing required value for column', - row: 2 - } - ]); - }); - - it('adds no errors if there are no invalid required fields', () => { - const requiredFieldsByHeader: string[] = ['Header1', 'Header2']; // fields for these headers are required - - const validator = getRequiredFieldsValidator(requiredFieldsByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2', 'Header3'], - ['header2Data', 'Header2Data', ''] // valid fields - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); -}); - -describe('getCodeValueFieldsValidator', () => { - it('adds no errors when header does not exist', () => { - const requiredCodeValuesByHeader = { - columnName: 'Header1', - column_code_validator: { allowed_code_values: [{ name: 'Code1' }, { name: 'Code2' }] } - }; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[], [5]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when code values are empty', () => { - const requiredCodeValuesByHeader = { - columnName: 'Header1', - column_code_validator: { allowed_code_values: [] } - }; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[], [5]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - it('adds no errors when no required code values are provided', () => { - const requiredCodeValuesByHeader = undefined; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Header1Data', 'Header2Data'] - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds errors for non-empty fields whose value is not part of a specified code set', () => { - const requiredCodeValuesByHeader = { - columnName: 'Header1', - column_code_validator: { allowed_code_values: [{ name: 'Code1' }, { name: 'Code2' }] } - }; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['invalidCode', 'Header2Data'] // non-empty field does not match one of the valid codes - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Invalid Value', - message: 'Invalid value: invalidCode. Must be one of [Code1, Code2]', - row: 2 - } - ]); - }); - - it('adds no errors for empty fields whose value is not part of a specified code set', () => { - const requiredCodeValuesByHeader = { - columnName: 'Header1', - column_code_validator: { allowed_code_values: [{ name: 'Code1' }, { name: 'Code2' }] } - }; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['', 'Header2Data'] // empty field does not match one of the valid codes - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors for fields whose value is part of a specified code set', () => { - const requiredCodeValuesByHeader = { - columnName: 'Header1', - column_code_validator: { allowed_code_values: [{ name: 'Code1' }, { name: 'Code2' }] } - }; - - const validator = getCodeValueFieldsValidator(requiredCodeValuesByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([ - ['Header1', 'Header2'], - ['Code1', 'Code4'] // fields that match one of the valid codes - ]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); -}); - -describe('getValidRangeFieldsValidator', () => { - it('adds no errors when no code value range is not provided', () => { - const codeValuesRangeByHeader = undefined; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], []]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when header does not exist', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 1, - max_value: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[], [5]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when valid value range is provided', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 1, - max_value: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], [6]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds an out of range error when value provided exceeds range', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 1, - max_value: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], [11]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Out of Range', - message: 'Invalid value: 11. Value must be between 1 and 10 ', - row: 2 - } - ]); - }); - - it('adds an out of range error when value provided is less than the range', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 5, - max_value: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], [1]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Out of Range', - message: 'Invalid value: 1. Value must be between 5 and 10 ', - row: 2 - } - ]); - }); - - it('adds an out of range error when value provided is greater than the max_value, and only max_value is provided', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - max_value: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], [11]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Out of Range', - message: 'Invalid value: 11. Value must be less than 10 ', - row: 2 - } - ]); - }); - - it('adds an out of range error when value provided is less than the min_value, and only the min-value is specified', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 5 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], [4]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Out of Range', - message: 'Invalid value: 4. Value must be greater than 5 ', - row: 2 - } - ]); - }); - - it('adds an invalid value error when value provided is not a number', () => { - const codeValuesRangeByHeader = { - columnName: 'Header1', - column_range_validator: { - min_value: 5, - max_vlaue: 10 - } - }; - - const validator = getValidRangeFieldsValidator(codeValuesRangeByHeader); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['a']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Invalid Value', - message: 'Invalid value: a. Value must be a number ', - row: 2 - } - ]); - }); -}); - -describe('getNumericFieldsValidator', () => { - it('adds no errors when configuration is not provided', () => { - const columnNumericValidatorConfig = undefined; - - const validator = getNumericFieldsValidator(columnNumericValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], []]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when header does not exist', () => { - const columnNumericValidatorConfig = { - columnName: 'Header 1', - column_numeric_validator: {} - }; - - const validator = getNumericFieldsValidator(columnNumericValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([[], [5]]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds an error when row value is not numeric', () => { - const columnNumericValidatorConfig = { - columnName: 'Header1', - column_numeric_validator: {} - }; - - const validator = getNumericFieldsValidator(columnNumericValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['a']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Invalid Value', - message: 'Invalid value: a. Value must be a number ', - row: 2 - } - ]); - }); -}); - -describe('getValidFormatFieldsValidator', () => { - it('adds no errors when configuration is not provided', () => { - const columnFormatValidatorConfig = undefined; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['WPT1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when regular expression is not provided', () => { - const columnFormatValidatorConfig = { - columnName: 'Header1', - column_format_validator: { - reg_exp: '', - expected_format: '' - } - }; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['WPT1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when header is not provided', () => { - const columnFormatValidatorConfig = { - columnName: 'Header1', - column_format_validator: { - reg_exp: '^wpt \\d+$', - expected_format: '' - } - }; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header2'], ['WPT1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds no errors when row value matches regular expression because regex is case insensitive', () => { - const columnFormatValidatorConfig = { - columnName: 'Header1', - column_format_validator: { - reg_exp: '^wpt \\d+$', - reg_exp_flags: 'i', - expected_format: '' - } - }; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['WPT 1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([]); - }); - - it('adds an error when row value does not match regular expression because regex is case sensitive', () => { - const columnFormatValidatorConfig = { - columnName: 'Header1', - column_format_validator: { - reg_exp: '^wpt \\d+$', - expected_format: 'Must be in the format "WPT X": WPT 11 (case sensitive)' - } - }; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['WPT 1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Unexpected Format', - message: 'Unexpected Format: WPT 1. Must be in the format "WPT X": WPT 11 (case sensitive)', - row: 2 - } - ]); - }); - - it('adds an error when row value does not match regular expression', () => { - const columnFormatValidatorConfig = { - columnName: 'Header1', - column_format_validator: { - reg_exp: '^wpt \\d+$', - expected_format: 'Must be in the format "WPT X": WPT 11 (case sensitive)' - } - }; - - const validator = getValidFormatFieldsValidator(columnFormatValidatorConfig); - - const xlsxWorkSheet = xlsx.utils.aoa_to_sheet([['Header1'], ['WXT1']]); - - const csvWorkSheet = new CSVWorksheet('Sheet1', xlsxWorkSheet); - - validator(csvWorkSheet); - - expect(csvWorkSheet.csvValidation.rowErrors).to.eql([ - { - col: 'Header1', - errorCode: 'Unexpected Format', - message: 'Unexpected Format: WXT1. Must be in the format "WPT X": WPT 11 (case sensitive)', - row: 2 - } - ]); - }); -}); diff --git a/api/src/utils/media/csv/validation/csv-row-validator.ts b/api/src/utils/media/csv/validation/csv-row-validator.ts deleted file mode 100644 index a5ffcfd14..000000000 --- a/api/src/utils/media/csv/validation/csv-row-validator.ts +++ /dev/null @@ -1,353 +0,0 @@ -import { CSVValidator } from '../csv-file'; - -/** - * TODO needs updating to use new config style, etc. - */ -export const getRequiredFieldsValidator = (requiredFieldsByHeader?: string[]): CSVValidator => { - return (csvWorksheet) => { - if (!requiredFieldsByHeader?.length) { - return csvWorksheet; - } - - const rows = csvWorksheet.getRows(); - - // If there are no rows, then add errors for all cells in the first data row based on the array of required headers - if (!rows?.length) { - csvWorksheet.csvValidation.addRowErrors( - requiredFieldsByHeader.map((requiredFieldByHeader) => { - return { - errorCode: 'Missing Required Field', - message: `Missing required value for column`, - col: requiredFieldByHeader, - row: 2 - }; - }) - ); - - return csvWorksheet; - } - - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - // If there are rows, then check each cell in each row against the list of required headers, adding errors as needed - rows.forEach((row, rowIndex) => { - for (const requiredFieldByHeader of requiredFieldsByHeader) { - const columnIndex = headersLowerCase.indexOf(requiredFieldByHeader.toLowerCase()); - - //if column does not exist, return csvWorksheet - if (columnIndex < 0) { - return csvWorksheet; - } - - const rowValueForColumn = row[columnIndex]; - - // Add an error if the cell value is empty - if (rowValueForColumn === undefined || rowValueForColumn === null || rowValueForColumn === '') { - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Missing Required Field', - message: `Missing required value for column`, - col: requiredFieldByHeader, - row: rowIndex + 2 - } - ]); - } - } - }); - - return csvWorksheet; - }; -}; - -export type ColumnCodeValidatorConfig = { - columnName: string; - column_code_validator: { - name?: string; - description?: string; - allowed_code_values: { name: string | number; description?: string }[]; - }; -}; - -/** - * For a specified column, adds an error for each row whose column value does not match a value in a specified set of - * allowed values (codes). - * - * Note: If the cell is empty, this check will be skipped. Use the `getRequiredFieldsValidator` validator to assert - * required fields. - * - * @param {ColumnCodeValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const getCodeValueFieldsValidator = (config?: ColumnCodeValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - if (!config.column_code_validator.allowed_code_values.length) { - return csvWorksheet; - } - - const rows = csvWorksheet.getRows(); - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - rows.forEach((row, rowIndex) => { - const columnIndex = headersLowerCase.indexOf(config.columnName.toLowerCase()); - - // if column does not exist, return - if (columnIndex < 0) { - return csvWorksheet; - } - - const rowValueForColumn = row[columnIndex]; - - if (rowValueForColumn === undefined || rowValueForColumn === null || rowValueForColumn === '') { - // cell is empty, use the getRequiredFieldsValidator to assert required fields - return csvWorksheet; - } - - // compare allowed code values as lowercase strings - const allowedCodeValuesLowerCase: string[] = []; - const allowedCodeValues = config.column_code_validator.allowed_code_values.map((allowedCode) => { - allowedCodeValuesLowerCase.push(allowedCode.name?.toString().toLowerCase()); - return allowedCode.name; - }); - - // Add an error if the cell value is not one of the elements in the codeValues array - if (!allowedCodeValuesLowerCase.includes(rowValueForColumn?.toLowerCase())) { - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Invalid Value', - message: `Invalid value: ${rowValueForColumn}. Must be one of [${allowedCodeValues.join(', ')}]`, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - }); - - return csvWorksheet; - }; -}; - -export type ColumnRangeValidatorConfig = { - columnName: string; - column_range_validator: { - name?: string; - description?: string; - min_value?: number; - max_value?: number; - }; -}; - -/** - * For a specified column, adds an error for each row whose column value does not match a specified range. - * - * Note: If the cell is empty, this check will be skipped. Use the `getRequiredFieldsValidator` validator to assert - * required fields. - * - * @param {ColumnRangeValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const getValidRangeFieldsValidator = (config?: ColumnRangeValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - const rows = csvWorksheet.getRows(); - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - rows.forEach((row, rowIndex) => { - const columnIndex = headersLowerCase.indexOf(config.columnName.toLowerCase()); - - // if column does not exist, return - if (columnIndex < 0) { - return csvWorksheet; - } - - const rowValueForColumn = Number(row[columnIndex]); - - if (isNaN(rowValueForColumn)) { - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Invalid Value', - message: `Invalid value: ${row[columnIndex]}. Value must be a number `, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - - if (config.column_range_validator.min_value && config.column_range_validator.max_value) { - // Value must be between min value and max value - if ( - rowValueForColumn < config.column_range_validator.min_value || - rowValueForColumn > config.column_range_validator.max_value - ) { - // Add an error if the cell value is not in the correct range provided in the array - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Out of Range', - message: `Invalid value: ${rowValueForColumn}. Value must be between ${config.column_range_validator.min_value} and ${config.column_range_validator.max_value} `, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - } else if (!config.column_range_validator.min_value && config.column_range_validator.max_value) { - // Value must be less than max value - if (rowValueForColumn > config.column_range_validator.max_value) { - // Add an error if the cell value is not in the correct range provided in the array - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Out of Range', - message: `Invalid value: ${rowValueForColumn}. Value must be less than ${config.column_range_validator.max_value} `, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - } else if (config.column_range_validator.min_value && !config.column_range_validator.max_value) { - // Value must be greater than min value - if (rowValueForColumn < config.column_range_validator.min_value) { - // Add an error if the cell value is not in the correct range provided in the array - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Out of Range', - message: `Invalid value: ${rowValueForColumn}. Value must be greater than ${config.column_range_validator.min_value} `, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - } - }); - - return csvWorksheet; - }; -}; - -export type ColumnNumericValidatorConfig = { - columnName: string; - column_numeric_validator: { - name?: string; - description?: string; - }; -}; - -/** - * For a specified column, adds an error for each row whose column value is not numeric. - * - * Note: If the cell is empty, this check will be skipped. Use the `getRequiredFieldsValidator` validator to assert - * required fields. - * - * @param {ColumnNumericValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const getNumericFieldsValidator = (config?: ColumnNumericValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - const rows = csvWorksheet.getRows(); - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - rows.forEach((row, rowIndex) => { - const columnIndex = headersLowerCase.indexOf(config.columnName.toLowerCase()); - - // if column does not exist, return - if (columnIndex < 0) { - return csvWorksheet; - } - - if (row[columnIndex] === undefined || row[columnIndex] === null) { - return csvWorksheet; - } - - const rowValueForColumn = Number(row[columnIndex]); - - if (isNaN(rowValueForColumn)) { - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Invalid Value', - message: `Invalid value: ${row[columnIndex]}. Value must be a number `, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - }); - - return csvWorksheet; - }; -}; - -export type ColumnFormatValidatorConfig = { - columnName: string; - column_format_validator: { - name?: string; - description?: string; - reg_exp: string; - reg_exp_flags?: string; - expected_format: string; - }; -}; - -/** - * For a specified column, adds an error for each row whose column value does not match a specified regex format. - * - * Note: If the cell is empty, this check will be skipped. Use the `getRequiredFieldsValidator` validator to assert - * required fields. - * - * @param {ColumnFormatValidatorConfig} [config] - * @return {*} {CSVValidator} - */ -export const getValidFormatFieldsValidator = (config?: ColumnFormatValidatorConfig): CSVValidator => { - return (csvWorksheet) => { - if (!config) { - return csvWorksheet; - } - - if (!config.column_format_validator.reg_exp) { - return csvWorksheet; - } - - const rows = csvWorksheet.getRows(); - const headersLowerCase = csvWorksheet.getHeadersLowerCase(); - - rows.forEach((row, rowIndex) => { - const columnIndex = headersLowerCase.indexOf(config.columnName.toLowerCase()); - - // if column does not exist, return - if (columnIndex < 0) { - return csvWorksheet; - } - - const rowValueForColumn = row[columnIndex]; - - if (rowValueForColumn === undefined || rowValueForColumn === null) { - return csvWorksheet; - } - - const regexFlags = config.column_format_validator.reg_exp_flags || ''; - - const regex = new RegExp(config.column_format_validator.reg_exp, regexFlags); - - // Add an error if the cell value is not in the correct range provided in the array - if (!regex.test(rowValueForColumn)) { - csvWorksheet.csvValidation.addRowErrors([ - { - errorCode: 'Unexpected Format', - message: `Unexpected Format: ${rowValueForColumn}. ${config.column_format_validator.expected_format}`, - col: config.columnName, - row: rowIndex + 2 - } - ]); - } - }); - - return csvWorksheet; - }; -}; diff --git a/api/src/utils/media/dwc/dwc-archive-file.test.ts b/api/src/utils/media/dwc/dwc-archive-file.test.ts deleted file mode 100644 index 415bfdbee..000000000 --- a/api/src/utils/media/dwc/dwc-archive-file.test.ts +++ /dev/null @@ -1,62 +0,0 @@ -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import xlsx from 'xlsx'; -import { CSVWorksheet } from '../csv/csv-file'; -import { ArchiveFile } from '../media-file'; -import { DWCArchive } from './dwc-archive-file'; -chai.use(sinonChai); - -describe('dwc-archive-file', () => { - describe('DWCArchive', () => { - afterEach(() => { - sinon.restore(); - }); - - it('builds DWCAchive File with empty mediaFiles', () => { - const testFile = { - fileName: 'file', - mimetype: 'type', - buffer: {} as unknown as Buffer, - mediaFiles: [] - } as unknown as ArchiveFile; - - const dwca = new DWCArchive(testFile); - - expect(dwca.mediaValidation).eql({ fileName: 'file', fileErrors: [], isValid: true }); - }); - - it('builds DWCAchive File with only metaData', () => { - const testFile = { - fileName: 'file', - mimetype: 'type', - buffer: {} as unknown as Buffer, - mediaFiles: [{ name: 'eml' }] - } as unknown as ArchiveFile; - - const dwca = new DWCArchive(testFile); - - expect(dwca.mediaValidation).eql({ fileName: 'file', fileErrors: [], isValid: true }); - expect(dwca.isMetaDataOnly()).eql(true); - }); - - it('initializes worksheets with one file', () => { - const buffer = Buffer.alloc(1024 * 1024 * 10, '.'); - - const testFile = { - fileName: 'file', - mimetype: 'type', - buffer: {} as unknown as Buffer, - mediaFiles: [{ name: 'event', buffer: buffer }] - } as unknown as ArchiveFile; - - const dwca = new DWCArchive(testFile); - - const csvw = new CSVWorksheet('event', xlsx.read(buffer).Sheets['Sheet1']); - - expect(dwca.mediaValidation).eql({ fileName: 'file', fileErrors: [], isValid: true }); - expect(dwca.worksheets.event).eql(csvw); - }); - }); -}); diff --git a/api/src/utils/media/dwc/dwc-archive-file.ts b/api/src/utils/media/dwc/dwc-archive-file.ts deleted file mode 100644 index 5b4739e87..000000000 --- a/api/src/utils/media/dwc/dwc-archive-file.ts +++ /dev/null @@ -1,187 +0,0 @@ -import xlsx from 'xlsx'; -import { CSVWorksheet, ICsvState } from '../csv/csv-file'; -import { EMLFile } from '../eml/eml-file'; -import { ArchiveFile, IMediaState, MediaValidation } from '../media-file'; -import { ValidationSchemaParser } from '../validation/validation-schema-parser'; - -export enum DWC_CLASS { - EVENT = 'event', - OCCURRENCE = 'occurrence', - MEASUREMENTORFACT = 'measurementorfact', - RESOURCERELATIONSHIP = 'resourcerelationship', - TAXON = 'taxon', - LOCATION = 'location', - RECORD = 'record', - EML = 'eml' -} - -export const DEFAULT_XLSX_SHEET = 'Sheet1'; - -export type DWCWorksheets = { [name in DWC_CLASS]?: CSVWorksheet }; - -/** - * Supports Darwin Core Archive CSV files. - * - * Expects an array of known named-files - * - * @export - * @class DWCArchive - */ -export class DWCArchive { - rawFile: ArchiveFile; - - mediaValidation: MediaValidation; - - worksheets: DWCWorksheets; - - eml: EMLFile | undefined; - - constructor(archiveFile: ArchiveFile) { - this.rawFile = archiveFile; - - this.mediaValidation = new MediaValidation(this.rawFile.fileName); - - this.worksheets = {}; - - // parse archive files - this._initArchiveFiles(); - } - - _initArchiveFiles() { - // See https://www.npmjs.com/package/xlsx#parsing-options for details on parsing options - const parsingOptions: xlsx.ParsingOptions = { raw: true }; - - for (const rawFile of this.rawFile.mediaFiles) { - switch (rawFile.name) { - case DWC_CLASS.EVENT: - this.worksheets[DWC_CLASS.EVENT] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.OCCURRENCE: - this.worksheets[DWC_CLASS.OCCURRENCE] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.MEASUREMENTORFACT: - this.worksheets[DWC_CLASS.MEASUREMENTORFACT] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.RESOURCERELATIONSHIP: - this.worksheets[DWC_CLASS.RESOURCERELATIONSHIP] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.TAXON: - this.worksheets[DWC_CLASS.TAXON] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.LOCATION: - this.worksheets[DWC_CLASS.LOCATION] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.RECORD: - this.worksheets[DWC_CLASS.RECORD] = new CSVWorksheet( - rawFile.name, - xlsx.read(rawFile.buffer, parsingOptions).Sheets[DEFAULT_XLSX_SHEET] - ); - break; - case DWC_CLASS.EML: - this.eml = new EMLFile(rawFile); - break; - } - } - } - - /** - * This function checks worksheet data if the DwCArchive only contains metadata - * - * @returns {boolean} True if no worksheet data is present - */ - isMetaDataOnly(): boolean { - return ( - this.eml !== undefined && - !this.worksheets.event && - !this.worksheets.occurrence && - !this.worksheets.measurementorfact && - !this.worksheets.resourcerelationship && - !this.worksheets.taxon && - !this.worksheets.location && - !this.worksheets.record - ); - } - - isMediaValid(validationSchemaParser: ValidationSchemaParser): IMediaState { - const validators = validationSchemaParser.getSubmissionValidations(); - - const mediaValidation = this.validate(validators as DWCArchiveValidator[]); - - return mediaValidation.getState(); - } - - isContentValid(validationSchemaParser: ValidationSchemaParser): ICsvState[] { - const csvStates: ICsvState[] = []; - - Object.keys(this.worksheets).forEach((fileName) => { - const fileValidators = validationSchemaParser.getFileValidations(fileName); - - const columnValidators = validationSchemaParser.getAllColumnValidations(fileName); - - const validators = [...fileValidators, ...columnValidators]; - - const worksheet: CSVWorksheet = this.worksheets[fileName]; - - if (!worksheet) { - return; - } - - const csvValidation = worksheet.validate(validators); - - csvStates.push(csvValidation.getState()); - }); - - return csvStates; - } - - /** - * Executes each validator function in the provided `validators` against this instance, returning - * `this.mediaValidation` - * - * @param {DWCArchiveValidator[]} validators - * @return {*} {MediaValidation} - * @memberof DWCArchive - */ - validate(validators: DWCArchiveValidator[]): MediaValidation { - validators.forEach((validator) => validator(this)); - - return this.mediaValidation; - } - - /** - * Returns normalized DwC Archive file data - * - * @return {*} {string} - */ - normalize(): string { - const normalized = {}; - - Object.entries(this.worksheets).forEach(([key, value]) => { - if (value) { - normalized[key] = value.getRowObjects(); - } - }); - - return JSON.stringify(normalized); - } -} - -export type DWCArchiveValidator = (dwcArchive: DWCArchive) => DWCArchive; diff --git a/api/src/utils/media/eml/eml-file.ts b/api/src/utils/media/eml/eml-file.ts deleted file mode 100644 index 80a287407..000000000 --- a/api/src/utils/media/eml/eml-file.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { MediaFile } from '../media-file'; - -export class EMLFile { - emlFile: MediaFile; - - constructor(emlFile: MediaFile) { - this.emlFile = emlFile; - } -} diff --git a/api/src/utils/media/media-file.test.ts b/api/src/utils/media/media-file.test.ts deleted file mode 100644 index 86bd8d9d9..000000000 --- a/api/src/utils/media/media-file.test.ts +++ /dev/null @@ -1,77 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import { MediaFile, MediaValidation } from './media-file'; - -describe('MediaFile', () => { - it('constructs', () => { - const mediaFile = new MediaFile('fileName', 'mimetype', Buffer.from('')); - - expect(mediaFile).not.to.be.null; - }); - - describe('validate', () => { - it('calls all provided validator functions', () => { - const mediaFile = new MediaFile('fileName', 'mimetype', Buffer.from('')); - - expect(mediaFile).not.to.be.null; - - const mockValidationFunction1 = sinon.stub(); - const mockValidationFunction2 = sinon.stub(); - const mockValidationFunction3 = sinon.stub(); - - mediaFile.validate([mockValidationFunction1, mockValidationFunction2, mockValidationFunction3]); - - expect(mockValidationFunction1).to.have.been.calledOnce; - expect(mockValidationFunction2).to.have.been.calledOnce; - expect(mockValidationFunction3).to.have.been.calledOnce; - }); - }); -}); - -describe('MediaValidation', () => { - it('constructs', () => { - const mediaValidation = new MediaValidation('fileName'); - - expect(mediaValidation).not.to.be.null; - }); - - describe('addFileErrors', () => { - it('adds new file errors', () => { - const mediaValidation = new MediaValidation('fileName'); - - expect(mediaValidation).not.to.be.null; - - const fileError1 = 'a file error'; - const fileError2 = 'a second file error'; - - mediaValidation.addFileErrors([fileError1]); - - expect(mediaValidation.fileErrors).to.eql([fileError1]); - - mediaValidation.addFileErrors([fileError2]); - - expect(mediaValidation.fileErrors).to.eql([fileError1, fileError2]); - }); - }); - - describe('getState', () => { - it('gets the current validation state', () => { - const mediaValidation = new MediaValidation('fileName'); - - expect(mediaValidation).not.to.be.null; - - const fileError1 = 'a file error'; - - mediaValidation.addFileErrors([fileError1]); - - const validationState = mediaValidation.getState(); - - expect(validationState).to.eql({ - fileName: 'fileName', - fileErrors: [fileError1], - isValid: false - }); - }); - }); -}); diff --git a/api/src/utils/media/media-file.ts b/api/src/utils/media/media-file.ts deleted file mode 100644 index 64e6b96c1..000000000 --- a/api/src/utils/media/media-file.ts +++ /dev/null @@ -1,159 +0,0 @@ -export interface IMediaFile { - fileName: string; - mimetype: string; - buffer: Buffer; - mediaValidation: MediaValidation; -} - -/** - * A generic wrapper for any media file. - * - * @export - * @class MediaFile - * @implements {IMediaFile} - */ -export class MediaFile implements IMediaFile { - fileName: string; - mimetype: string; - buffer: Buffer; - mediaValidation: MediaValidation; - - constructor(fileName: string, mimetype: string, buffer: Buffer) { - this.fileName = fileName.toLowerCase(); - this.mimetype = mimetype; - this.buffer = buffer; - this.mediaValidation = new MediaValidation(this.fileName); - } - - /** - * The file name without extension. - * - * @readonly - * @type {string} - * @memberof MediaFile - */ - get name(): string { - const lastPeriodindex = this.fileName.lastIndexOf('.'); - - if (lastPeriodindex >= 0) { - // strip out the file extension, if it exists - return this.fileName.substring(0, lastPeriodindex); - } else { - return this.fileName; - } - } - - /** - * Executes each validator function in the provided `validators` against this instance, returning - * `this.mediaValidation` - * - * @param {MediaValidator[]} validators - * @return {*} {MediaValidation} - * @memberof MediaFile - */ - validate(validators: MediaValidator[]): MediaValidation { - validators.forEach((validator) => validator(this)); - - return this.mediaValidation; - } -} - -export type MediaValidator = (mediaFile: IMediaFile) => IMediaFile; - -/** - * A generic wrapper for any archive file. - * - * @class ArchiveFile - * @implements {IMediaFile} - */ -export class ArchiveFile implements IMediaFile { - fileName: string; - mimetype: string; - buffer: Buffer; - mediaValidation: MediaValidation; - - mediaFiles: MediaFile[]; - - constructor(fileName: string, mimetype: string, buffer: Buffer, mediaFiles: MediaFile[]) { - this.fileName = fileName.toLowerCase(); - this.mimetype = mimetype; - this.buffer = buffer; - this.mediaValidation = new MediaValidation(this.fileName); - - this.mediaFiles = mediaFiles; - } - - /** - * The file name without extension. - * - * @readonly - * @type {string} - * @memberof ArchiveFile - */ - get name(): string { - const lastPeriodindex = this.fileName.lastIndexOf('.'); - - if (lastPeriodindex >= 0) { - // strip out the file extension, if it exists - return this.fileName.substring(0, lastPeriodindex); - } else { - return this.fileName; - } - } - - /** - * Executes each validator function in the provided `validators` against this instance, returning - * `this.mediaValidation` - * - * @param {ArchiveValidator[]} validators - * @return {*} {MediaValidation} - * @memberof ArchiveFile - */ - validate(validators: ArchiveValidator[]): MediaValidation { - validators.forEach((validator) => validator(this)); - - return this.mediaValidation; - } -} - -export type ArchiveValidator = (archiveFile: ArchiveFile) => ArchiveFile; - -export interface IMediaState { - fileName: string; - fileErrors?: string[]; - isValid: boolean; -} - -/** - * Supports getting/setting validation errors for any media file. - * - * @export - * @class MediaValidation - */ -export class MediaValidation { - fileName: string; - fileErrors: string[]; - isValid: boolean; - - constructor(fileName: string) { - this.fileName = fileName; - this.fileErrors = []; - this.isValid = true; - } - - addFileErrors(errors: string[]) { - this.fileErrors = this.fileErrors.concat(errors); - - if (errors?.length) { - this.isValid = false; - } - } - - getState(): IMediaState { - return { - fileName: this.fileName, - fileErrors: this.fileErrors, - isValid: this.isValid - }; - } -} diff --git a/api/src/utils/media/media-utils.test.ts b/api/src/utils/media/media-utils.test.ts deleted file mode 100644 index 71b7927f6..000000000 --- a/api/src/utils/media/media-utils.test.ts +++ /dev/null @@ -1,203 +0,0 @@ -import AdmZip from 'adm-zip'; -import { GetObjectOutput } from 'aws-sdk/clients/s3'; -import chai, { expect } from 'chai'; -import { describe } from 'mocha'; -import sinon from 'sinon'; -import sinonChai from 'sinon-chai'; -import { ArchiveFile, MediaFile } from './media-file'; -import * as media_utils from './media-utils'; - -chai.use(sinonChai); - -describe('parseUnknownMedia', () => { - afterEach(() => { - sinon.restore(); - }); - - it('calls parseUnknownMulterFile', () => { - const parseUnknownMulterFileStub = sinon.stub(media_utils, 'parseUnknownMulterFile'); - - media_utils.parseUnknownMedia({ originalname: 'name' } as unknown as Express.Multer.File); - - expect(parseUnknownMulterFileStub).to.have.been.calledOnce; - }); - - it('calls parseUnknownS3File', () => { - const parseUnknownS3FileStub = sinon.stub(media_utils, 'parseUnknownS3File'); - - media_utils.parseUnknownMedia({} as unknown as GetObjectOutput); - - expect(parseUnknownS3FileStub).to.have.been.calledOnce; - }); -}); - -describe('parseUnknownMulterFile', () => { - it('returns a MediaFile', () => { - const multerFile = { - originalname: 'file1.txt', - buffer: Buffer.from('file1data') - } as unknown as Express.Multer.File; - - const response = media_utils.parseUnknownMulterFile(multerFile); - - expect(response).to.eql(new MediaFile('file1.txt', 'text/plain', Buffer.from('file1data'))); - }); - - it('returns an ArchiveFile, when a zip file is provided', () => { - const zipFile = new AdmZip(); - - zipFile.addFile('file1.txt', Buffer.from('file1data')); - zipFile.addFile('folder2/', Buffer.from('')); // add folder - zipFile.addFile('folder2/file2.csv', Buffer.from('file2data')); - - const multerFile = { originalname: 'zipFile.zip', buffer: zipFile.toBuffer() } as unknown as Express.Multer.File; - - const response = media_utils.parseUnknownMulterFile(multerFile); - - expect(response).to.eql( - new ArchiveFile('zipFile.zip', 'application/zip', zipFile.toBuffer(), [ - new MediaFile('file1.txt', 'text/plain', Buffer.from('file1data')), - new MediaFile('file2.csv', 'text/csv', Buffer.from('file2data')) - ]) - ); - }); -}); - -describe('parseUnknownS3File', () => { - it('returns a MediaFile', () => { - const s3File = { - Metadata: { filename: 'file1.txt' }, - Body: Buffer.from('file1data') - } as unknown as GetObjectOutput; - - const response = media_utils.parseUnknownS3File(s3File); - - expect(response).to.eql(new MediaFile('file1.txt', 'text/plain', Buffer.from('file1data'))); - }); - - it('returns an ArchiveFile, when a zip file is provided', () => { - const zipFile = new AdmZip(); - - zipFile.addFile('file1.txt', Buffer.from('file1data')); - zipFile.addFile('folder2/', Buffer.from('')); // add folder - zipFile.addFile('folder2/file2.csv', Buffer.from('file2data')); - - const s3File = { - Metadata: { filename: 'zipFile.zip' }, - ContentType: 'application/zip', - Body: zipFile.toBuffer() - } as unknown as GetObjectOutput; - - const response = media_utils.parseUnknownS3File(s3File); - - expect(response).to.eql( - new ArchiveFile('zipFile.zip', 'application/zip', zipFile.toBuffer(), [ - new MediaFile('file1.txt', 'text/plain', Buffer.from('file1data')), - new MediaFile('file2.csv', 'text/csv', Buffer.from('file2data')) - ]) - ); - }); -}); - -describe('parseUnknownZipFile', () => { - it('returns an array of MediaFile elements', () => { - const zipFile = new AdmZip(); - - zipFile.addFile('file1.txt', Buffer.from('file1data')); - zipFile.addFile('folder2/', Buffer.from('')); // add folder - zipFile.addFile('folder2/file2.csv', Buffer.from('file2data')); - - const multerFile = { originalname: 'zipFile.zip', buffer: zipFile.toBuffer() } as unknown as Express.Multer.File; - - const response = media_utils.parseUnknownZipFile(multerFile.buffer); - - expect(response.length).to.equal(2); - expect(response[0]).to.eql(new MediaFile('file1.txt', 'text/plain', Buffer.from('file1data'))); - expect(response[1]).to.eql(new MediaFile('file2.csv', 'text/csv', Buffer.from('file2data'))); - }); - - it('returns an empty array if the zip contains no files', () => { - const zipFile = new AdmZip(); - - zipFile.addFile('folder2/', Buffer.from('')); // add folder - - const multerFile = { originalname: 'zipFile.zip', buffer: zipFile.toBuffer() } as unknown as Express.Multer.File; - - const response = media_utils.parseUnknownZipFile(multerFile.buffer); - - expect(response.length).to.equal(0); - }); -}); - -describe('parseMulterFile', () => { - it('returns a MediaFile item', () => { - const multerFile = { - originalname: 'file1.csv', - buffer: Buffer.from('file1data') - } as unknown as Express.Multer.File; - - const response = media_utils.parseMulterFile(multerFile); - - expect(response).to.eql(new MediaFile('file1.csv', 'text/csv', Buffer.from('file1data'))); - }); - - it('returns a MediaFile item when the file mime type is unknown', () => { - const multerFile = { - originalname: 'file1.notAKnownMimeTypecsv', - buffer: Buffer.from('file1data') - } as unknown as Express.Multer.File; - - const response = media_utils.parseMulterFile(multerFile); - - expect(response).to.eql(new MediaFile('file1.notAKnownMimeTypecsv', '', Buffer.from('file1data'))); - }); - - it('returns a MediaFile item when the file buffer is null', () => { - const multerFile = { - originalname: 'file1.csv', - buffer: null - } as unknown as Express.Multer.File; - - const response = media_utils.parseMulterFile(multerFile); - - expect(response).to.eql(new MediaFile('file1.csv', 'text/csv', null as unknown as Buffer)); - }); -}); - -describe('parseS3File', () => { - it('returns a MediaFile item', () => { - const s3File = { - Metadata: { filename: 'file1.csv' }, - ContentType: 'text/csv', - Body: Buffer.from('file1data') - } as unknown as GetObjectOutput; - - const response = media_utils.parseS3File(s3File); - - expect(response).to.eql(new MediaFile('file1.csv', 'text/csv', Buffer.from('file1data'))); - }); - - it('returns a MediaFile item when the file mime type is unknown', () => { - const s3File = { - Metadata: { filename: 'file1.notAKnownMimeTypecsv' }, - ContentType: 'notAKnownMimeTypecsv', - Body: Buffer.from('file1data') - } as unknown as GetObjectOutput; - - const response = media_utils.parseS3File(s3File); - - expect(response).to.eql(new MediaFile('file1.notAKnownMimeTypecsv', '', Buffer.from('file1data'))); - }); - - it('returns a MediaFile item when the file buffer is null', () => { - const s3File = { - Metadata: { filename: 'file1.csv' }, - ContentType: 'text/csv', - Body: null - } as unknown as GetObjectOutput; - - const response = media_utils.parseS3File(s3File); - - expect(response).to.eql(new MediaFile('file1.csv', 'text/csv', null as unknown as Buffer)); - }); -}); diff --git a/api/src/utils/media/media-utils.ts b/api/src/utils/media/media-utils.ts deleted file mode 100644 index 13baf490a..000000000 --- a/api/src/utils/media/media-utils.ts +++ /dev/null @@ -1,119 +0,0 @@ -import AdmZip from 'adm-zip'; -import { GetObjectOutput } from 'aws-sdk/clients/s3'; -import mime from 'mime'; -import { ArchiveFile, MediaFile } from './media-file'; - -export type UnknownMedia = Express.Multer.File | GetObjectOutput; - -export type KnownMedia = MediaFile | ArchiveFile; - -/** - * Parses an unknown file into an array of MediaFile. - * - * Note: The array will always have 1 item unless the unknown file is a zip file containing multiple files, in which - * case the array will have 1 item per file in the zip (folders ignored). - * - * @param {(UnknownMedia)} rawMedia - * @return {*} {(KnownMedia | null)} - */ -export const parseUnknownMedia = (rawMedia: UnknownMedia): KnownMedia | null => { - if ((rawMedia as Express.Multer.File).originalname) { - return parseUnknownMulterFile(rawMedia as Express.Multer.File); - } else { - return parseUnknownS3File(rawMedia as GetObjectOutput); - } -}; - -export const parseUnknownMulterFile = (rawMedia: Express.Multer.File): KnownMedia | null => { - const mimetype = mime.getType(rawMedia.originalname); - - if (isZipMimetype(mimetype || '')) { - const archiveFile = parseMulterFile(rawMedia); - const mediaFiles = parseUnknownZipFile(rawMedia.buffer); - - return new ArchiveFile(archiveFile.fileName, archiveFile.mimetype, archiveFile.buffer, mediaFiles); - } - - return parseMulterFile(rawMedia); -}; - -export const parseUnknownS3File = (rawMedia: GetObjectOutput): KnownMedia | null => { - const mimetype = rawMedia.ContentType; - - if (isZipMimetype(mimetype || '')) { - if (!rawMedia.Body) { - return null; - } - - const archiveFile = parseS3File(rawMedia); - const mediaFiles = parseUnknownZipFile(rawMedia.Body as Buffer); - - return new ArchiveFile(archiveFile.fileName, archiveFile.mimetype, archiveFile.buffer, mediaFiles); - } - - return parseS3File(rawMedia); -}; - -/** - * Parse a zip file buffer into an array of MediaFile. - * - * Note: Ignores any directory structures, flattening all nested files into a single array. - * - * @param {Buffer} zipFile - * @return {*} {ArchiveFile} - */ -export const parseUnknownZipFile = (zipFile: Buffer): MediaFile[] => { - const unzippedFile = new AdmZip(zipFile); - const entries = unzippedFile.getEntries(); - - return entries - .filter((item) => !item.isDirectory) - .map((item) => { - const fileName = item?.name; - const mimetype = mime.getType(fileName) || ''; - const buffer = item?.getData(); - - return new MediaFile(fileName, mimetype, buffer); - }); -}; - -/** - * Parse a single file into an array of MediaFile with 1 element. - * - * @param {Express.Multer.File} file - * @return {*} {MediaFile} - */ -export const parseMulterFile = (file: Express.Multer.File): MediaFile => { - const fileName = file?.originalname; - const mimetype = mime.getType(fileName) || ''; - const buffer = file?.buffer; - - return new MediaFile(fileName, mimetype, buffer); -}; - -/** - * Parse a single file into an array of MediaFile with 1 element. - * - * @param {GetObjectOutput} file - * @return {*} {MediaFile} - */ -export const parseS3File = (file: GetObjectOutput): MediaFile => { - const fileName = file?.Metadata?.filename || ''; - const mimetype = mime.getType(fileName) || ''; - const buffer = file?.Body as Buffer; - - return new MediaFile(fileName, mimetype, buffer); -}; - -export const isZipMimetype = (mimetype: string): boolean => { - if (!mimetype) { - return false; - } - - return [ - /application\/zip/, - /application\/x-zip-compressed/, - /application\/x-rar-compressed/, - /application\/octet-stream/ - ].some((regex) => regex.test(mimetype)); -}; diff --git a/api/src/utils/media/validation/file-type-and-content-validator.test.ts b/api/src/utils/media/validation/file-type-and-content-validator.test.ts deleted file mode 100644 index 786ece123..000000000 --- a/api/src/utils/media/validation/file-type-and-content-validator.test.ts +++ /dev/null @@ -1,242 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import xlsx from 'xlsx'; -import { DEFAULT_XLSX_SHEET, DWCArchive, DWCArchiveValidator } from '../dwc/dwc-archive-file'; -import { ArchiveFile, IMediaFile, MediaFile, MediaValidation } from '../media-file'; -import { XLSXCSV, XLSXCSVValidator } from '../xlsx/xlsx-file'; -import { - getFileEmptyValidator, - getFileMimeTypeValidator, - getRequiredFilesValidator -} from './file-type-and-content-validator'; - -describe('getFileEmptyValidator', () => { - it('adds an error when the buffer is empty', () => { - const validator = getFileEmptyValidator(); - - const mediaFile: IMediaFile = { - fileName: 'testName', - mimetype: 'testMime', - buffer: Buffer.from(''), // empty buffer - mediaValidation: new MediaValidation('testName') - }; - - validator(mediaFile); - - expect(mediaFile.mediaValidation.fileErrors).to.eql(['File is empty']); - }); - - it('adds no errors when the buffer is not empty', () => { - const validator = getFileEmptyValidator(); - - const mediaFile: IMediaFile = { - fileName: 'testName', - mimetype: 'testMime', - buffer: Buffer.from([123]), // non-empty buffer - mediaValidation: new MediaValidation('testName') - }; - - validator(mediaFile); - - expect(mediaFile.mediaValidation.fileErrors).to.eql([]); - }); -}); - -describe('getFileMimeTypeValidator', () => { - it('adds an error when the mime type is invalid', () => { - const validMimetypes = { - mimetype_validator: { - reg_exps: ['validMime'] - } - }; - - const validator = getFileMimeTypeValidator(validMimetypes) as XLSXCSVValidator; - - const mediaFile = new MediaFile('testName', 'badMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql(['File mime type is invalid, must be one of: validMime']); - }); - - it('adds no errors when the mime type is valid', () => { - const validMimetypes = { - mimetype_validator: { - reg_exps: ['validMime'] - } - }; - - const validator = getFileMimeTypeValidator(validMimetypes) as DWCArchiveValidator; - - const mediaFile = new MediaFile('otherName', 'otherMime', Buffer.from('')); - - const archiveFile = new ArchiveFile('testName', 'validMime', Buffer.from(''), [mediaFile]); - - const dwcArchive = new DWCArchive(archiveFile); - - validator(dwcArchive); - - expect(dwcArchive.mediaValidation.fileErrors).to.eql([]); - }); - - it('adds no errors when no valid mimes provided', () => { - const validMimetypes = { - mimetype_validator: { - reg_exps: [] - } - }; - - const validator = getFileMimeTypeValidator(validMimetypes) as XLSXCSVValidator; - - const mediaFile = new MediaFile('testName', 'validMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql([]); - }); - - it('adds no errors when config it not found', () => { - const validMimetypes = undefined; - - const validator = getFileMimeTypeValidator(validMimetypes) as DWCArchiveValidator; - - const mediaFile = new MediaFile('otherName', 'otherMime', Buffer.from('')); - - const archiveFile = new ArchiveFile('testName', 'validMime', Buffer.from(''), [mediaFile]); - - const dwcArchive = new DWCArchive(archiveFile); - - validator(dwcArchive); - - expect(dwcArchive.mediaValidation.fileErrors).to.eql([]); - }); -}); - -describe('getRequiredFilesValidator', () => { - it('adds no error an when the submitted file list is undefined', () => { - const submissionRequiredFilesValidatorConfig = undefined; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as XLSXCSVValidator; - - const mediaFile = new MediaFile('testName', 'validMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql([]); - }); - - it('adds no error an when the required file list is empty', () => { - const submissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - required_files: [] - } - }; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as XLSXCSVValidator; - - const mediaFile = new MediaFile('testName', 'validMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql([]); - }); - - it('checks that a submission is a valid DWCArchive, and adds an error if a required file is missing', () => { - const submissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - required_files: ['event', 'occurrence'] - } - }; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as DWCArchiveValidator; - - const archiveFile = new ArchiveFile('testName', 'validMime', Buffer.from(''), [ - new MediaFile('occurrence', 'b', Buffer.from('')) - ]); - - const xlsxCSV = new DWCArchive(archiveFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql(['Missing required file: event']); - }); - - it('checks that a submission is a valid XLSXCSV, and adds an error if a required file is missing', () => { - const submissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - required_files: ['sheet2'] - } - }; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as XLSXCSVValidator; - - const newWorkbook = xlsx.utils.book_new(); - - const worksheet = xlsx.utils.aoa_to_sheet([[]]); - - xlsx.utils.book_append_sheet(newWorkbook, worksheet, DEFAULT_XLSX_SHEET); - - const mediaFile = new MediaFile('worksheet', 'validMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql(['Missing required sheet: sheet2']); - }); -}); - -describe('checkRequiredFieldsInDWCArchive', () => { - it('checks that a submission is a valid DWCArchive with an empty mediaFile, and adds an error if a required file is missing', () => { - const submissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - required_files: ['event'] - } - }; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as DWCArchiveValidator; - - //empty media file - const archiveFile = new ArchiveFile('someFile', 'validMime', Buffer.from(''), []); - - const xlsxCSV = new DWCArchive(archiveFile); - - validator(xlsxCSV); - - expect(xlsxCSV.mediaValidation.fileErrors).to.eql(['Missing required file: event']); - }); - - it('checks that a submission is a valid XLSXCSV with an empty workbook, and adds an error if a required file is missing', () => { - const submissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - required_files: ['sheet2'] - } - }; - - const validator = getRequiredFilesValidator(submissionRequiredFilesValidatorConfig) as XLSXCSVValidator; - - const newWorkbook = xlsx.utils.book_new(); - - const worksheet = xlsx.utils.aoa_to_sheet([[]]); - - xlsx.utils.book_append_sheet(newWorkbook, worksheet, DEFAULT_XLSX_SHEET); - - const mediaFile = new MediaFile('worksheet', 'validMime', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - //force worksheets to be empty - xlsxCSV.workbook.worksheets = {}; - - validator(xlsxCSV); - expect(xlsxCSV.mediaValidation.fileErrors).to.eql(['Missing required sheet: sheet2']); - }); -}); diff --git a/api/src/utils/media/validation/file-type-and-content-validator.ts b/api/src/utils/media/validation/file-type-and-content-validator.ts deleted file mode 100644 index d697e5041..000000000 --- a/api/src/utils/media/validation/file-type-and-content-validator.ts +++ /dev/null @@ -1,122 +0,0 @@ -import { DWCArchive, DWCArchiveValidator } from '../dwc/dwc-archive-file'; -import { MediaValidator } from '../media-file'; -import { XLSXCSV, XLSXCSVValidator } from '../xlsx/xlsx-file'; - -export const getFileEmptyValidator = (): MediaValidator => { - return (mediaFile) => { - if (!mediaFile.buffer || !mediaFile.buffer.byteLength) { - mediaFile.mediaValidation.addFileErrors(['File is empty']); - } - - return mediaFile; - }; -}; - -export type MimetypeValidatorConfig = { - mimetype_validator: { - name?: string; - description?: string; - reg_exps: string[]; - }; -}; - -export const getFileMimeTypeValidator = (config?: MimetypeValidatorConfig): DWCArchiveValidator | XLSXCSVValidator => { - return (file: any) => { - if (!config) { - return file; - } - - if (!config.mimetype_validator.reg_exps.length) { - return file; - } - - if ( - !config.mimetype_validator.reg_exps.some((regexString) => { - const regex = new RegExp(regexString, 'i'); - - return regex.test(file.rawFile.mimetype); - }) - ) { - file.mediaValidation.addFileErrors([ - `File mime type is invalid, must be one of: ${config.mimetype_validator.reg_exps.join(', ')}` - ]); - } - - return file; - }; -}; - -export type SubmissionRequiredFilesValidatorConfig = { - submission_required_files_validator: { - name?: string; - description?: string; - required_files: string[]; - }; -}; - -export const getRequiredFilesValidator = ( - config?: SubmissionRequiredFilesValidatorConfig -): DWCArchiveValidator | XLSXCSVValidator => { - return (file: any) => { - if (!config) { - // No required files specified - return file; - } - - if (!config.submission_required_files_validator.required_files.length) { - // No required files specified - return file; - } - - if (file instanceof DWCArchive) { - checkRequiredFieldsInDWCArchive(file, config); - } else if (file instanceof XLSXCSV) { - checkRequiredFieldsInXLSXCSV(file, config); - } - - return file; - }; -}; - -const checkRequiredFieldsInDWCArchive = (dwcArchive: DWCArchive, config: SubmissionRequiredFilesValidatorConfig) => { - // If there are no files in the archive, then add errors for all required files - if (!dwcArchive.rawFile.mediaFiles || !dwcArchive.rawFile.mediaFiles.length) { - dwcArchive.mediaValidation.addFileErrors( - config.submission_required_files_validator.required_files.map((requiredFile) => { - return `Missing required file: ${requiredFile}`; - }) - ); - - return dwcArchive; - } - - const fileNames = dwcArchive.rawFile.mediaFiles.map((mediaFile) => mediaFile.name); - - config.submission_required_files_validator.required_files.forEach((requiredFile) => { - if (!fileNames.includes(requiredFile.toLowerCase())) { - dwcArchive.mediaValidation.addFileErrors([`Missing required file: ${requiredFile}`]); - } - }); -}; - -const checkRequiredFieldsInXLSXCSV = (xlsxCsv: XLSXCSV, config: SubmissionRequiredFilesValidatorConfig) => { - // If there are no sheets in the excel file, then add errors for all required sheets - - if (!xlsxCsv.workbook || !xlsxCsv.workbook.worksheets || !Object.keys(xlsxCsv.workbook.worksheets).length) { - xlsxCsv.mediaValidation.addFileErrors( - config.submission_required_files_validator.required_files.map((requiredFile) => { - return `Missing required sheet: ${requiredFile}`; - }) - ); - - return xlsxCsv; - } - - const worksheetNames = Object.keys(xlsxCsv.workbook.worksheets).map((item) => item.toLowerCase()); - - config.submission_required_files_validator.required_files.forEach((requiredFile) => { - if (!worksheetNames.includes(requiredFile.toLowerCase())) { - xlsxCsv.mediaValidation.addFileErrors([`Missing required sheet: ${requiredFile}`]); - } - }); -}; diff --git a/api/src/utils/media/validation/validation-schema-parser.test.ts b/api/src/utils/media/validation/validation-schema-parser.test.ts deleted file mode 100644 index 051913603..000000000 --- a/api/src/utils/media/validation/validation-schema-parser.test.ts +++ /dev/null @@ -1,260 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import { getFileMimeTypeValidator } from './file-type-and-content-validator'; -import { ValidationRulesRegistry, ValidationSchemaParser } from './validation-schema-parser'; - -const sampleValidationSchema = { - files: [ - { - name: 'testFile1', - columns: [ - { - name: 'column1', - validations: [ - { - column_code_validator: {} - }, - { - not_a_known_validator: {} - } - ] - }, - { - name: 'column2', - validations: [ - { - column_format_validator: {} - }, - { - column_range_validator: {} - } - ] - } - ], - validations: [ - { - file_duplicate_columns_validator: {} - }, - { - file_required_columns_validator: {} - }, - { - not_a_known_validator: {} - } - ] - }, - { - name: 'testFile2', - columns: [ - { - name: 'column3', - validations: [] - }, - { - name: 'column4', - validations: [] - } - ], - validations: [] - } - ], - validations: [ - { - mimetype_validator: {} - }, - { - submission_required_files_validator: {} - }, - { - not_a_known_validator: {} - } - ] -}; - -describe('ValidationRulesRegistry', () => { - describe('findMatchingRule', () => { - it('returns a generator function for a known rule', () => { - const rule = ValidationRulesRegistry.findMatchingRule('mimetype_validator'); - - expect(rule).to.eql(getFileMimeTypeValidator); - }); - - it('returns undefined for an unknown rule', () => { - const rule = ValidationRulesRegistry.findMatchingRule('not_a_known_rule'); - - expect(rule).to.equal(undefined); - }); - }); -}); - -describe('ValidationSchemaParser', () => { - it('constructs', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - expect(validationSchemaParser).not.to.be.null; - }); - - describe('getSubmissionValidations', () => { - it('returns an array of validator functions', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validators = validationSchemaParser.getSubmissionValidations(); - - expect(validators.length).to.equal(2); - - expect(typeof validators[0]).to.equal('function'); - expect(typeof validators[1]).to.equal('function'); - }); - }); - - describe('getFileValidations', () => { - it('returns an array of validator functions', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validators = validationSchemaParser.getFileValidations('testFile1'); - - expect(validators.length).to.equal(2); - - expect(typeof validators[0]).to.equal('function'); - expect(typeof validators[1]).to.equal('function'); - }); - }); - - describe('getAllColumnValidations', () => { - it('returns an array of validator functions', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validators = validationSchemaParser.getAllColumnValidations('testFile1'); - - expect(validators.length).to.equal(3); - - expect(typeof validators[0]).to.equal('function'); - expect(typeof validators[1]).to.equal('function'); - expect(typeof validators[2]).to.equal('function'); - }); - }); - - describe('getColumnValidations', () => { - it('returns an array of validator functions', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validators = validationSchemaParser.getColumnValidations('testFile1', 'column1'); - - expect(validators.length).to.equal(1); - - expect(typeof validators[0]).to.equal('function'); - }); - }); - - describe('getSubmissionValidationSchemas', () => { - it('returns an array of validation schemas', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validationSchemas = validationSchemaParser.getSubmissionValidationSChemas(); - - expect(validationSchemas).to.eql([ - { mimetype_validator: {} }, - { submission_required_files_validator: {} }, - { not_a_known_validator: {} } - ]); - }); - }); - - describe('getFileValidationSchemas', () => { - it('returns an array of validation schemas', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validationSchemas = validationSchemaParser.getFileValidationSchemas('testFile1'); - - expect(validationSchemas).to.eql([ - { file_duplicate_columns_validator: {} }, - { file_required_columns_validator: {} }, - { not_a_known_validator: {} } - ]); - }); - }); - - describe('getColumnValidationSchemas', () => { - it('returns an array of validation schemas', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const validationSchemas = validationSchemaParser.getColumnValidationSchemas('testFile1', 'column1'); - - expect(validationSchemas).to.eql([{ column_code_validator: {} }, { not_a_known_validator: {} }]); - }); - }); - - describe('getColumnNames', () => { - it('returns an array of column names', () => { - const validationSchemaParser = new ValidationSchemaParser(sampleValidationSchema); - - const columnNames = validationSchemaParser.getColumnNames('testFile1'); - - expect(columnNames).to.eql(['column1', 'column2']); - }); - }); - - describe('getSubmissionValidationsJsonPath', () => { - it('returns a json path string', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const jsonPath = validationSchemaParser.getSubmissionValidationsJsonPath(); - - expect(jsonPath).to.equal('$.validations'); - }); - }); - - describe('getFileValidationsJsonPath', () => { - it('returns a json path string', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const jsonPath = validationSchemaParser.getFileValidationsJsonPath('testName'); - - expect(jsonPath).to.equal("$.files[?(@.name == 'testName')].validations"); - }); - }); - - describe('getColumnNamesJsonpath', () => { - it('returns a json path string', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const jsonPath = validationSchemaParser.getColumnNamesJsonpath('testName'); - - expect(jsonPath).to.equal("$.files[?(@.name == 'testName')].columns[*].name"); - }); - }); - - describe('getColumnValidationsJsonpath', () => { - it('returns a json path string', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const jsonPath = validationSchemaParser.getColumnValidationsJsonpath('testName', 'columnName'); - - expect(jsonPath).to.equal("$.files[?(@.name == 'testName')].columns[?(@.name == 'columnName')].validations"); - }); - }); - - describe('parseJson', () => { - it('parses a provided json string and returns a json object', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const str = '{"test":123}'; - - const json = validationSchemaParser.parseJson(str); - - expect(json).to.eql({ test: 123 }); - }); - - it('throws an error if the provided json is invalid', () => { - const validationSchemaParser = new ValidationSchemaParser({}); - - const str = 'not a json string'; - - try { - validationSchemaParser.parseJson(str); - } catch (error) { - expect((error as Error).message).to.equal('ValidationSchemaParser - provided json was not valid JSON'); - } - }); - }); -}); diff --git a/api/src/utils/media/validation/validation-schema-parser.ts b/api/src/utils/media/validation/validation-schema-parser.ts deleted file mode 100644 index 5e2bcc277..000000000 --- a/api/src/utils/media/validation/validation-schema-parser.ts +++ /dev/null @@ -1,279 +0,0 @@ -import { JSONPath } from 'jsonpath-plus'; -import { CSVValidator } from '../csv/csv-file'; -import { - getDuplicateHeadersValidator, - getValidHeadersValidator, - hasRecommendedHeadersValidator, - hasRequiredHeadersValidator -} from '../csv/validation/csv-header-validator'; -import { - getCodeValueFieldsValidator, - getNumericFieldsValidator, - getRequiredFieldsValidator, - getValidFormatFieldsValidator, - getValidRangeFieldsValidator -} from '../csv/validation/csv-row-validator'; -import { DWCArchiveValidator } from '../dwc/dwc-archive-file'; -import { XLSXCSVValidator } from '../xlsx/xlsx-file'; -import { - getFileEmptyValidator, - getFileMimeTypeValidator, - getRequiredFilesValidator -} from './file-type-and-content-validator'; - -export const ValidationRulesRegistry = { - registry: [ - { - name: '', - generator: getFileEmptyValidator - }, - { - name: 'mimetype_validator', - generator: getFileMimeTypeValidator - }, - { - name: 'submission_required_files_validator', - generator: getRequiredFilesValidator - }, - { - name: 'file_duplicate_columns_validator', - generator: getDuplicateHeadersValidator - }, - { - name: 'file_required_columns_validator', - generator: hasRequiredHeadersValidator - }, - { - name: 'file_recommended_columns_validator', - generator: hasRecommendedHeadersValidator - }, - { - name: 'file_valid_columns_validator', - generator: getValidHeadersValidator - }, - { - name: '', - generator: getRequiredFieldsValidator - }, - { - name: 'column_code_validator', - generator: getCodeValueFieldsValidator - }, - { - name: 'column_range_validator', - generator: getValidRangeFieldsValidator - }, - { - name: 'column_format_validator', - generator: getValidFormatFieldsValidator - }, - { - name: 'column_numeric_validator', - generator: getNumericFieldsValidator - } - ], - findMatchingRule(name: string): any { - return this.registry.find((item) => item.name === name)?.generator; - } -}; - -export class ValidationSchemaParser { - validationSchema: object; - - constructor(validationSchema: string | object) { - if (typeof validationSchema === 'string') { - this.validationSchema = this.parseJson(validationSchema); - } else { - this.validationSchema = validationSchema; - } - } - - getSubmissionValidations(): (DWCArchiveValidator | XLSXCSVValidator)[] { - const validationSchemas = this.getSubmissionValidationSChemas(); - - const rules: (DWCArchiveValidator | XLSXCSVValidator)[] = []; - - validationSchemas.forEach((validationSchema) => { - const keys = Object.keys(validationSchema); - - if (keys.length !== 1) { - return; - } - - const key = keys[0]; - - const generatorFunction = ValidationRulesRegistry.findMatchingRule(key); - - if (!generatorFunction) { - return; - } - - const rule = generatorFunction(validationSchema); - - rules.push(rule); - }); - - return rules; - } - - getFileValidations(fileName: string): CSVValidator[] { - const validationSchemas = this.getFileValidationSchemas(fileName); - - const rules: CSVValidator[] = []; - - validationSchemas.forEach((validationSchema) => { - const keys = Object.keys(validationSchema); - - if (keys.length !== 1) { - return; - } - - const key = keys[0]; - - const generatorFunction = ValidationRulesRegistry.findMatchingRule(key); - - if (!generatorFunction) { - return; - } - - const rule = generatorFunction(validationSchema); - - rules.push(rule); - }); - - return rules; - } - - getAllColumnValidations(fileName: string): CSVValidator[] { - const columnNames = this.getColumnNames(fileName); - - let rules: CSVValidator[] = []; - - columnNames.forEach((columnName) => { - const columnValidators = this.getColumnValidations(fileName, columnName); - - rules = rules.concat(columnValidators); - }); - - return rules; - } - - getColumnValidations(fileName: string, columnName: string): CSVValidator[] { - const validationSchemas = this.getColumnValidationSchemas(fileName, columnName); - - const rules: CSVValidator[] = []; - - validationSchemas.forEach((validationSchema) => { - const keys = Object.keys(validationSchema); - - if (keys.length !== 1) { - return; - } - - const key = keys[0]; - - const generatorFunction = ValidationRulesRegistry.findMatchingRule(key); - - if (!generatorFunction) { - return; - } - - const rule = generatorFunction({ columnName: columnName, ...validationSchema }); - - rules.push(rule); - }); - - return rules; - } - - getSubmissionValidationSChemas(): object[] { - return JSONPath({ json: this.validationSchema, path: this.getSubmissionValidationsJsonPath() })?.[0] || []; - } - - getFileValidationSchemas(fileName: string): object[] { - let validationSchemas = - JSONPath({ json: this.validationSchema, path: this.getFileValidationsJsonPath(fileName) })?.[0] || []; - - if (!validationSchemas.length) { - validationSchemas = this.getDefaultFileValidationSchemas(); - } - return validationSchemas; - } - - getDefaultFileValidationSchemas(): object[] { - return JSONPath({ json: this.validationSchema, path: this.getDefaultFileValidationsJsonPath() })?.[0] || []; - } - - getColumnValidationSchemas(fileName: string, columnName: string): object[] { - const filevalidationSchemas = - JSONPath({ json: this.validationSchema, path: this.getFileValidationsJsonPath(fileName) })?.[0] || []; - - let columnValidationSchemas; - - if (!filevalidationSchemas.length) { - columnValidationSchemas = this.getDefaultColumnValidationSchemas(columnName); - } else { - columnValidationSchemas = - JSONPath({ json: this.validationSchema, path: this.getColumnValidationsJsonpath(fileName, columnName) })?.[0] || - []; - } - - return columnValidationSchemas; - } - - getDefaultColumnValidationSchemas(columnName: string): object[] { - return ( - JSONPath({ json: this.validationSchema, path: this.getDefaultColumnValidationsJsonpath(columnName) })?.[0] || [] - ); - } - - getColumnNames(fileName: string): string[] { - let columnNames; - - const filevalidationSchemas = - JSONPath({ json: this.validationSchema, path: this.getFileValidationsJsonPath(fileName) })?.[0] || []; - - if (!filevalidationSchemas.length) { - columnNames = JSONPath({ json: this.validationSchema, path: this.getDefaultColumnNamesJsonpath() }); - } else { - columnNames = JSONPath({ json: this.validationSchema, path: this.getColumnNamesJsonpath(fileName) }); - } - - return columnNames; - } - - getSubmissionValidationsJsonPath(): string { - return '$.validations'; - } - - getFileValidationsJsonPath(fileName: string): string { - return `$.files[?(@.name == '${fileName}')].validations`; - } - getDefaultFileValidationsJsonPath(): string { - return `$.defaultFile.validations`; - } - - getColumnNamesJsonpath(fileName: string): string { - return `$.files[?(@.name == '${fileName}')].columns[*].name`; - } - - getDefaultColumnNamesJsonpath(): string { - return `$.defaultFile.columns[*].name`; - } - - getColumnValidationsJsonpath(fileName: string, columnName: string): string { - return `$.files[?(@.name == '${fileName}')].columns[?(@.name == '${columnName}')].validations`; - } - - getDefaultColumnValidationsJsonpath(columnName: string): string { - return `$.defaultFile.columns[?(@.name == '${columnName}')].validations`; - } - - parseJson(json: any): object { - try { - return JSON.parse(json); - } catch { - throw Error('ValidationSchemaParser - provided json was not valid JSON'); - } - } -} diff --git a/api/src/utils/media/xlsx/transformation/transformation-schema-parser.ts b/api/src/utils/media/xlsx/transformation/transformation-schema-parser.ts deleted file mode 100644 index 47bb9f311..000000000 --- a/api/src/utils/media/xlsx/transformation/transformation-schema-parser.ts +++ /dev/null @@ -1,108 +0,0 @@ -import { JSONPath } from 'jsonpath-plus'; - -export type FlattenSchema = { - fileName: string; - uniqueId: string[]; - parent?: { fileName: string; uniqueId: string[] }; -}; - -export type TransformationFieldSchema = { - columns?: string[]; - separator?: string; - value?: any; - unique?: string; - condition?: Condition; -}; - -export type TransformationFieldsSchema = { - [key: string]: TransformationFieldSchema; -}; - -export type Condition = { - if: { - columns: string[]; - not?: boolean; - }; -}; - -export type PostTransformationRelatopnshipSchema = { - condition?: Condition; - relationship: { - spreadColumn: string; - uniqueIdColumn: 'string'; - }; -}; - -export type TransformSchema = { - condition?: Condition; - transformations: { - condition?: Condition; - fields: TransformationFieldsSchema; - }[]; - postTransformations?: PostTransformationRelatopnshipSchema[]; -}; - -export type ParseColumnSchema = { source: { columns?: string[]; value?: any }; target: string }; - -export type ParseSchema = { - fileName: string; - columns: ParseColumnSchema[]; - condition?: Condition; -}; -export class TransformationSchemaParser { - transformationSchema: object; - - constructor(transformationSchema: string | object) { - if (typeof transformationSchema === 'string') { - this.transformationSchema = this.parseJson(transformationSchema); - } else { - this.transformationSchema = transformationSchema; - } - } - - getAllFlattenSchemas(): FlattenSchema[] | [] { - return JSONPath({ json: this.transformationSchema, path: this.getFlattenJsonPath() })?.[0] || []; - } - - getFlattenSchemas(fileName: string): FlattenSchema | null { - return ( - JSONPath({ json: this.transformationSchema, path: this.getFlattenJsonPathByFileName(fileName) })?.[0] || null - ); - } - - getTransformSchemas(): TransformSchema[] { - return JSONPath({ json: this.transformationSchema, path: this.getTransformationJsonPath() })?.[0] || []; - } - - getParseSchemas(): ParseSchema[] { - return JSONPath({ json: this.transformationSchema, path: this.getParseJsonPath() })?.[0] || []; - } - - getFlattenJsonPath(): string { - return `$.flatten`; - } - - getFlattenJsonPathByFileName(fileName: string): string { - return `$.flatten[?(@.fileName == '${fileName}')]`; - } - - getTransformationJsonPath(): string { - return '$.transform'; - } - - getParseJsonPath(): string { - return '$.parse'; - } - - parseJson(json: any): object { - let parsedJson; - - try { - parsedJson = JSON.parse(json); - } catch { - throw Error('TransformationSchemaParser - provided validationSchema was not valid JSON'); - } - - return parsedJson; - } -} diff --git a/api/src/utils/media/xlsx/transformation/xlsx-transformation.ts b/api/src/utils/media/xlsx/transformation/xlsx-transformation.ts deleted file mode 100644 index 71f9c8049..000000000 --- a/api/src/utils/media/xlsx/transformation/xlsx-transformation.ts +++ /dev/null @@ -1,621 +0,0 @@ -import { isEqual, uniqWith } from 'lodash'; -import xlsx from 'xlsx'; -import { CSVWorksheet } from '../../csv/csv-file'; -import { XLSXCSV } from '../xlsx-file'; -import { - Condition, - FlattenSchema, - PostTransformationRelatopnshipSchema, - TransformationFieldSchema, - TransformationSchemaParser, - TransformSchema -} from './transformation-schema-parser'; - -export type FlattenedRowPartsBySourceFile = { - sourceFile: string; - uniqueId: any; - row: object; -}; - -export type RowObject = { [key: string]: any }; - -export type RowsObjectsByFileName = { [key: string]: RowObject[] }; - -export type XLSXWorksheetByFileName = { [key: string]: xlsx.WorkSheet }; - -/** - * Applies transformations to an `XLSXCSV` instance. - * - * @export - * @class XLSXTransformation - */ -export class XLSXTransformation { - transformationSchemaParser: TransformationSchemaParser; - xlsxCsv: XLSXCSV; - - constructor(transformationSchemaParser: TransformationSchemaParser, xlsxCsv: XLSXCSV) { - this.transformationSchemaParser = transformationSchemaParser; - this.xlsxCsv = xlsxCsv; - } - - /** - * Transform the raw XLSX data. - * - * @return {*} {RowsObjectsByFileName} - * @memberof XLSXTransformation - */ - transform(): RowsObjectsByFileName { - const flattenedData = this._flattenData(); - - const mergedFlattenedData = this._mergedFlattenedRows(flattenedData); - - const transformedMergedFlattenedData = this._transformFlattenedData(mergedFlattenedData); - - const parsedTransformedMergedFlattenedData = this._parseTransformedData(transformedMergedFlattenedData); - - return this._mergeParsedData(parsedTransformedMergedFlattenedData); - } - - /** - * Flattens the worksheet data into arrays of objects. - * - * @return {*} {FlattenedRowPartsBySourceFile[][]} - * @memberof XLSXTransformation - */ - _flattenData(): FlattenedRowPartsBySourceFile[][] { - let rowsBySourceFileArray: FlattenedRowPartsBySourceFile[][] = []; - - // Get all flatten schemas - const flattenSchemas = this.transformationSchemaParser.getAllFlattenSchemas(); - - // Build an array of [worksheetName, worksheet] based on the order of the flatten schemas. This is necessary - // because the flattening process requires parsing the worksheets in a specific order, as specified by the flatten - // section of the transformation schema. - const orderedWorksheetsByFlattenSchema: [string, CSVWorksheet][] = []; - flattenSchemas.forEach((flattenSchema) => { - const worksheet = this.xlsxCsv.workbook.worksheets[flattenSchema.fileName]; - - if (worksheet) { - orderedWorksheetsByFlattenSchema.push([flattenSchema.fileName, worksheet]); - } - }); - - // Iterate over each worksheet in the ordered array of worksheets - orderedWorksheetsByFlattenSchema.forEach(([worksheetName, worksheet]) => { - // Get the flatten file structure schema for the worksheet, based on the worksheet name - const flattenSchema = this.transformationSchemaParser.getFlattenSchemas(worksheetName); - - if (!flattenSchema) { - // No schema for this worksheet, skip it - return; - } - - // Get all worksheet rows as an array of objects - const rowObjects = worksheet.getRowObjects(); - - if (!flattenSchema.parent) { - // Handle root records, that have no parent record - const flattenedRootRecords = this._flattenRootRecords(flattenSchema, worksheet, rowObjects); - rowsBySourceFileArray = rowsBySourceFileArray.concat(flattenedRootRecords); - } else { - // Handle child records, that have a parent record - const parentFileName = flattenSchema.parent.fileName.toLowerCase(); - const parentUniqueIdColumns = flattenSchema.parent.uniqueId; - - const childFileName = flattenSchema.fileName; - const childUniqueIdColumns = flattenSchema.uniqueId; - - rowObjects.forEach((rowObject, rowIndex) => { - const parentUniqueId = this._buildMultiColumnID(worksheet, rowIndex, parentUniqueIdColumns).toLowerCase(); - - const uniqueId = this._buildMultiColumnID(worksheet, rowIndex, childUniqueIdColumns); - - const newRecord = { - sourceFile: childFileName, - uniqueId: uniqueId, - row: rowObject - }; - - // An array of indexes that tracks which records to add `newRecord` to, and which records should be duplicated - // before adding `newRecord` to them. - const recordsToModify: { matchingParentIndex: number; matchingChildIndex: number }[] = []; - let recordsToModifyIndex = 0; - - let foundRowToModify = false; - - // For each parent array of child arrays of objects - rowsBySourceFileArray.forEach((rowsBySourceFile, rowsBySourceFileIndex) => { - if (foundRowToModify) { - return; - } - - let foundRecordToModify = false; - - /* - * Compare the `newRecord` to each object in the child array - * If a matching parent record is found - * - mark this parent array index - * If a matching child record from the same sourceFile is found - * - mark this child array index - */ - rowsBySourceFile.forEach((rowBySourceFile, rowBySourceFileIndex) => { - const existingRowFileName = rowBySourceFile.sourceFile.toLowerCase(); - const existingRowUniqueId = rowBySourceFile.uniqueId.toLowerCase(); - - if (existingRowFileName === parentFileName && existingRowUniqueId === parentUniqueId) { - // This array may need a copy of `newRecord` - recordsToModify[recordsToModifyIndex] = { - ...recordsToModify[recordsToModifyIndex], - matchingParentIndex: rowsBySourceFileIndex - }; - - foundRecordToModify = true; - } else if (existingRowFileName === childFileName.toLowerCase()) { - // This array already contains a record from the same file as `newRecord` and will need to be duplicated - recordsToModify[recordsToModifyIndex] = { - ...recordsToModify[recordsToModifyIndex], - matchingChildIndex: rowBySourceFileIndex - }; - - foundRecordToModify = true; - } - }); - - if (foundRecordToModify) { - if ( - recordsToModify[recordsToModifyIndex].matchingParentIndex >= 0 && - recordsToModify[recordsToModifyIndex].matchingChildIndex >= 0 - ) { - // A matching parent row with matching child was found, don't continue checking other rows - foundRowToModify = true; - } - // A record was found after iterating over the previous array, increase the index before we loop over - // the next array. - recordsToModifyIndex++; - } - }); - - // For each `recordsToModify` - // Apply updates to the existing records based on the `recordsToModify` array. - recordsToModify.forEach((recordToModify) => { - if (recordToModify.matchingParentIndex >= 0 && recordToModify.matchingChildIndex >= 0) { - /* - * `recordToModify` indicates that a matching parent was found AND a matching child from the same - * sourceFile was found. Duplicate the array, and in the duplicated array, overwrite the existing - * matching child with the `newRecord`. - * - * Example: - * - * Initial state: - * - * newRecord = {sourceFile: 'file2', uniqueId: 3, row: {...}}; - * - * rowsBySourceFileArray = [ - * [ - * {sourceFile: 'file1', uniqueId: 1, row: {...}}, // matching parent of `newRecord` - * {sourceFile: 'file2', uniqueId: 2, row: {...}} // matching child from same sourceFile as `newRecord` - * ] - * ] - * - * Final state: - * - * rowsBySourceFileArray = [ - * [ - * {sourceFile: 'file1', uniqueId: 1, row: {...}}, - * {sourceFile: 'file2', uniqueId: 2, row: {...}} - * ], - * [ - * {sourceFile: 'file1', uniqueId: 1, row: {...}}, - * {sourceFile: 'file2', uniqueId: 3, row: {...}} - * ] - * ] - */ - - // Copy the existing items into a new array - const newRowRecord = [...rowsBySourceFileArray[recordToModify.matchingParentIndex]]; - - // Overwrite the matching item at index `matchingChildIndex` with our new record - newRowRecord[recordToModify.matchingChildIndex] = newRecord; - - // Append this new duplicated record to the parent array - rowsBySourceFileArray.push(newRowRecord); - } else if (recordToModify.matchingParentIndex >= 0) { - /* - * `recordToModify` indicates that a matching parent was found. Add the `newRecord` to this existing - * array. - * - * Example: - * - * Initial state: - * - * newRecord = {sourceFile: 'file2', uniqueId: 3, row: {...}}; - * - * rowsBySourceFileArray = [ - * [ - * {sourceFile: 'file1', uniqueId: 1, row: {...}} // matching parent of `newRecord` - * ] - * ] - * - * Final state: - * - * rowsBySourceFileArray = [ - * [ - * {sourceFile: 'file1', uniqueId: 1, row: {...}}, - * {sourceFile: 'file2', uniqueId: 3, row: {...}} - * ] - * ] - */ - rowsBySourceFileArray[recordToModify.matchingParentIndex].push(newRecord); - } - }); - }); - } - }); - - return rowsBySourceFileArray; - } - - _flattenRootRecords( - flattenSchema: FlattenSchema, - worksheet: CSVWorksheet, - rowObjects: object[] - ): FlattenedRowPartsBySourceFile[][] { - const newRecords: FlattenedRowPartsBySourceFile[][] = []; - - rowObjects.forEach((rowObject, rowIndex) => { - const uniqueId = this._buildMultiColumnID(worksheet, rowIndex, flattenSchema.uniqueId); - - const newRecord = { - sourceFile: flattenSchema.fileName, - uniqueId: uniqueId, - row: rowObject - }; - - newRecords.push([newRecord]); - }); - - return newRecords; - } - - _buildMultiColumnID(worksheet: CSVWorksheet, rowIndex: number, columnNames: string[]) { - return this._buildMultiColumnValue(worksheet, rowIndex, columnNames, ':'); - } - - _buildMultiColumnValue(worksheet: CSVWorksheet, rowIndex: number, columnNames: string[], separator?: string) { - return columnNames.map((columnName) => worksheet.getCell(columnName, rowIndex)).join(separator || ' '); - } - - /** - * Merges the arrays of objects into an array of objects. - * - * @param {FlattenedRowPartsBySourceFile[][]} flattenedData - * @return {*} {object[][]} - * @memberof XLSXTransformation - */ - _mergedFlattenedRows(flattenedData: FlattenedRowPartsBySourceFile[][]): object[] { - const mergedAndFlattenedRows: object[] = []; - - flattenedData.forEach((rowsBySourceFile, index) => { - rowsBySourceFile.forEach((rowPart) => { - mergedAndFlattenedRows[index] = { ...mergedAndFlattenedRows[index], ...rowPart.row }; - }); - }); - - return mergedAndFlattenedRows; - } - - /** - * Applies transformation logic to the flattened array of objects, creating a new array of objects (which may contain - * duplicate items) - * - * @param {object[]} mergedFlattenedData - * @return {*} {object[]} - * @memberof XLSXTransformation - */ - _transformFlattenedData(mergedFlattenedData: object[]): object[] { - const transformSchemasArray = this.transformationSchemaParser.getTransformSchemas(); - - let transformedDWCData: object[] = []; - - mergedFlattenedData.forEach((rowObject, rowObjectIndex) => { - transformSchemasArray.forEach((transformationSchema, transformationSchemaIndex) => { - const newDWCRowObjects = this._applyFileTransformations( - rowObject, - transformationSchema, - rowObjectIndex, - transformationSchemaIndex - ); - - transformedDWCData = transformedDWCData.concat(newDWCRowObjects); - }); - }); - - return transformedDWCData; - } - - _applyFileTransformations( - rowObject: object, - transformationSchema: TransformSchema, - rowObjectIndex: number, - transformationSchemaIndex: number - ): object[] { - if (!this._isConditionMet(rowObject, transformationSchema?.condition)) { - // condition not met, return an empty array (contains no new records) - return []; - } - - let newDWCRowObjects: object[] = []; - - transformationSchema.transformations.forEach((transformation) => { - const newDWCRowObject = {}; - - if (!this._isConditionMet(rowObject, transformation?.condition)) { - return; - } - - Object.entries(transformation.fields).forEach(([fieldName, config]) => { - if (!this._isConditionMet(rowObject, config?.condition)) { - return; - } - - let columnValue = this._getColumnValue(rowObject, config); - - if (config.unique) { - // Append `config.unique` + indexes to ensure this column value is unique - columnValue = `${columnValue}:${config.unique}-${rowObjectIndex}-${transformationSchemaIndex}`; - } - - newDWCRowObject[fieldName] = columnValue; - }); - - newDWCRowObjects.push(newDWCRowObject); - }); - - transformationSchema?.postTransformations?.forEach((postTransformation) => { - if (!this._isConditionMet(rowObject, postTransformation.condition)) { - return; - } - - if (postTransformation.relationship) { - newDWCRowObjects = this._postTransformRelationships( - postTransformation as PostTransformationRelatopnshipSchema, - newDWCRowObjects - ); - } - }); - - return newDWCRowObjects; - } - - _postTransformRelationships = ( - postTransformRelationshipSchema: PostTransformationRelatopnshipSchema, - originalDWCRowObjects: object[] - ) => { - // Spread the parent/child row objects and update relationship fields - - const spreadColumn = postTransformRelationshipSchema.relationship.spreadColumn; - const uniqueIdColumn = postTransformRelationshipSchema.relationship.uniqueIdColumn; - - let spreadDWCRowObjects: object[] = []; - - if (spreadColumn) { - const originalParentRecord = originalDWCRowObjects[0]; - const originalChildRecord = originalDWCRowObjects[1]; - - const spreadColumnValue = Number(originalParentRecord[spreadColumn]); - - if (spreadColumnValue) { - for (let i = 0; i < spreadColumnValue; i++) { - const newParentRecord = { - ...originalParentRecord, - [spreadColumn]: 1, - [uniqueIdColumn]: `${originalParentRecord[uniqueIdColumn]}-${i}-0` - }; - const newChildRecord = { - ...originalChildRecord, - [uniqueIdColumn]: `${originalChildRecord[uniqueIdColumn]}-${i}-1` - }; - - newParentRecord['resourceID'] = newParentRecord[uniqueIdColumn]; - newParentRecord['relatedResourceID'] = newChildRecord[uniqueIdColumn]; - - newChildRecord['resourceID'] = newChildRecord[uniqueIdColumn]; - newChildRecord['relatedResourceID'] = newParentRecord[uniqueIdColumn]; - - spreadDWCRowObjects = spreadDWCRowObjects.concat([newParentRecord, newChildRecord]); - } - } - } - - return spreadDWCRowObjects; - }; - - /** - * Builds a new value from the `rowObject`, based on the config. - * - * This may involve returning a single `rowObject` value, concatenating multiple `rowObject` values together, or - * returning a static value. - * - * @param {object} rowObject - * @param {(TransformationFieldSchema | undefined)} config - * @return {*} {*} - * @memberof XLSXTransformation - */ - _getColumnValue(rowObject: object, config: TransformationFieldSchema | undefined): any { - if (!config) { - return; - } - - let columnValue = undefined; - - if (config.columns) { - const columnsValues = this._getColumnValueParts(rowObject, config.columns); - - if (columnsValues && columnsValues.length) { - columnValue = columnsValues.join(config?.separator || ' '); - } - } - - if (config.value) { - columnValue = config.value; - } - - return columnValue; - } - - /** - * Given an array of column names, return an array of matching column values. - * - * @param {object} rowObject - * @param {string[]} columnNames - * @return {*} {((string | number)[] | undefined)} - * @memberof XLSXTransformation - */ - _getColumnValueParts(rowObject: object, columnNames: string[]): (string | number)[] | undefined { - if (!rowObject || !columnNames || !columnNames.length) { - return undefined; - } - - const columnValueParts: any[] = []; - - columnNames.forEach((columnName) => { - const columnValue = rowObject[columnName]; - - if (columnValue !== undefined && columnValue !== null && columnValue !== '') { - columnValueParts.push(columnValue); - } - }); - - return columnValueParts; - } - - /** - * Returns true if the `condition` is met. - * - * @param {object} rowObject - * @param {(Condition | undefined)} condition - * @return {*} {boolean} - * @memberof XLSXTransformation - */ - _isConditionMet(rowObject: object, condition?: Condition): boolean { - if (!condition) { - // no conditions specified - return true; - } - - const columnValueParts = this._getColumnValueParts(rowObject, condition.if.columns); - - if (!columnValueParts || !columnValueParts.length) { - if (condition.if.not) { - // return true if no condition column values are defined, when condition is inverted - return true; - } - - // return false if no condition column values are defined - return false; - } - - if (condition.if.not) { - // return false if any condition column values are defined, when condition is inverted - return false; - } - - // return true if all condition columns are defined - return !columnValueParts.every( - (columnValuePart) => columnValuePart === undefined || columnValuePart === null || columnValuePart === '' - ); - } - - /** - * Parses the array of objects into separate arrays of objects (which may contain duplicate items), based on fileName. - * - * @param {object[]} transformedMergedFlattenedData - * @return {*} {RowsObjectsByFileName} - * @memberof XLSXTransformation - */ - _parseTransformedData(transformedMergedFlattenedData: object[]): RowsObjectsByFileName { - const parseSchemas = this.transformationSchemaParser.getParseSchemas(); - - const parsedDWCData: RowsObjectsByFileName = {}; - - parseSchemas.forEach((parseSchema) => { - const fileName = parseSchema.fileName; - const columns = parseSchema.columns; - - if (!parsedDWCData[fileName]) { - // initialize an empty array for the current fileName if one does not yet exist - parsedDWCData[fileName] = []; - } - - transformedMergedFlattenedData.forEach((rowObject) => { - if (!this._isConditionMet(rowObject, parseSchema?.condition)) { - // A conditional field was undefined or null, skip this record - return; - } - - const newRowObject = {}; - - for (const column of columns) { - if (column.source.columns && column.source.columns?.length) { - // iterate over source columns - for (const sourceColumn of column.source.columns) { - const sourceValue = rowObject[sourceColumn]; - - if (sourceValue) { - // use the first source column that has a defined value - newRowObject[column.target] = sourceValue; - break; - } - } - } else if (column.source.value) { - newRowObject[column.target] = column.source.value; - } - } - - if (!Object.keys(newRowObject).length) { - // row object is empty, skip - return; - } - - parsedDWCData[fileName].push(newRowObject); - }); - }); - - return parsedDWCData; - } - - /** - * Merges the array of objects for each fileName, removing duplicate items. - * - * @param {RowsObjectsByFileName} parsedDWCData - * @return {*} {RowsObjectsByFileName} - * @memberof XLSXTransformation - */ - _mergeParsedData(parsedTransformedMergedFlattenedData: RowsObjectsByFileName): RowsObjectsByFileName { - // For each entry (based on fileName), do a deep equality check on each of its row objects, removing any duplicates. - Object.entries(parsedTransformedMergedFlattenedData).forEach(([fileName, rowObjects]) => { - parsedTransformedMergedFlattenedData[fileName] = uniqWith(rowObjects, isEqual); - }); - - return parsedTransformedMergedFlattenedData; - } - - /** - * Converts an object (whose keys are file names, and whose value is an array of objects) into a new object (whose - * keys are file names, and whose value is an `xlsx.Worksheet`). - * - * @param {RowsObjectsByFileName} mergedParsedData - * @return {*} {XLSXWorksheetByFileName} - * @memberof XLSXTransformation - */ - dataToSheet(mergedParsedTransformedData: RowsObjectsByFileName): XLSXWorksheetByFileName { - const sheets: XLSXWorksheetByFileName = {}; - - Object.entries(mergedParsedTransformedData).forEach(([fileName, rowObjects]) => { - const worksheet = xlsx.utils.json_to_sheet(rowObjects); - sheets[fileName] = worksheet; - }); - - return sheets; - } -} diff --git a/api/src/utils/media/xlsx/xlsx-file.test.ts b/api/src/utils/media/xlsx/xlsx-file.test.ts deleted file mode 100644 index 3d0819d7d..000000000 --- a/api/src/utils/media/xlsx/xlsx-file.test.ts +++ /dev/null @@ -1,14 +0,0 @@ -import { expect } from 'chai'; -import { describe } from 'mocha'; -import { MediaFile } from '../media-file'; -import { XLSXCSV } from './xlsx-file'; - -describe('XLSXCSV', () => { - it('constructs', () => { - const mediaFile: MediaFile = new MediaFile('fileName', 'mimetype', Buffer.from('')); - - const xlsxCSV = new XLSXCSV(mediaFile); - - expect(xlsxCSV).not.to.be.null; - }); -}); diff --git a/api/src/utils/media/xlsx/xlsx-file.ts b/api/src/utils/media/xlsx/xlsx-file.ts deleted file mode 100644 index 2b867d87b..000000000 --- a/api/src/utils/media/xlsx/xlsx-file.ts +++ /dev/null @@ -1,88 +0,0 @@ -import xlsx from 'xlsx'; -import { CSVWorkBook, CSVWorksheet, ICsvState } from '../csv/csv-file'; -import { DEFAULT_XLSX_SHEET } from '../dwc/dwc-archive-file'; -import { IMediaState, MediaFile, MediaValidation } from '../media-file'; -import { ValidationSchemaParser } from '../validation/validation-schema-parser'; - -/** - * Supports XLSX CSV files. - * - * @export - * @class XLSXCSV - */ -export class XLSXCSV { - rawFile: MediaFile; - - mediaValidation: MediaValidation; - - workbook: CSVWorkBook; - - constructor(file: MediaFile, options?: xlsx.ParsingOptions) { - this.rawFile = file; - - this.mediaValidation = new MediaValidation(this.rawFile.fileName); - - // See https://www.npmjs.com/package/xlsx#parsing-options for details on parsing options - const parsingOptions: xlsx.ParsingOptions = { cellDates: true, cellNF: true, cellHTML: false, ...options }; - - this.workbook = new CSVWorkBook(xlsx.read(this.rawFile.buffer, parsingOptions)); - } - - isMediaValid(validationSchemaParser: ValidationSchemaParser): IMediaState { - const validators = validationSchemaParser.getSubmissionValidations(); - - const mediaValidation = this.validate(validators as XLSXCSVValidator[]); - - return mediaValidation.getState(); - } - - isContentValid(validationSchemaParser: ValidationSchemaParser): ICsvState[] { - const csvStates: ICsvState[] = []; - - Object.keys(this.workbook.worksheets).forEach((fileName) => { - const fileValidators = validationSchemaParser.getFileValidations(fileName); - - const columnValidators = validationSchemaParser.getAllColumnValidations(fileName); - - const validators = [...fileValidators, ...columnValidators]; - - const worksheet: CSVWorksheet = this.workbook.worksheets[fileName]; - - if (!worksheet) { - return; - } - - const csvValidation = worksheet.validate(validators); - - csvStates.push(csvValidation.getState()); - }); - - return csvStates; - } - - worksheetToBuffer(worksheet: xlsx.WorkSheet): Buffer { - const newWorkbook = xlsx.utils.book_new(); - - xlsx.utils.book_append_sheet(newWorkbook, worksheet, DEFAULT_XLSX_SHEET); - - return xlsx.write(newWorkbook, { type: 'buffer', bookType: 'csv' }); - } - - /** - * Executes each validator function in the provided `validators` against this instance, returning - * `this.mediaValidation` - * - * @param {XLSXCSVValidator[]} validators - * @return {*} {MediaValidation} - * @memberof XLSXCSV - */ - validate(validators: XLSXCSVValidator[]): MediaValidation { - validators.forEach((validator) => validator(this)); - - return this.mediaValidation; - } -} - -export type XLSXCSVValidator = (xlsxCsv: XLSXCSV) => XLSXCSV; - -export type XLSXCSVTransformer = { pivot: string; transform: (xlsxCsv: XLSXCSV, modifiers?: object) => XLSXCSV }; diff --git a/api/src/utils/media/xlsx/xlsx-utils.ts b/api/src/utils/media/xlsx/xlsx-utils.ts deleted file mode 100644 index 8def99bf7..000000000 --- a/api/src/utils/media/xlsx/xlsx-utils.ts +++ /dev/null @@ -1,89 +0,0 @@ -import xlsx, { CellObject } from 'xlsx'; -import { safeTrim } from '../../string-utils'; - -/** - * Get a worksheet by name. - * - * @export - * @param {xlsx.WorkBook} workbook - * @param {string} sheetName - * @return {*} {xlsx.WorkSheet} - */ -export function getWorksheetByName(workbook: xlsx.WorkBook, sheetName: string): xlsx.WorkSheet { - return workbook.Sheets[sheetName]; -} - -/** - * Get a worksheets decoded range object, or return undefined if the worksheet is missing range information. - * - * @export - * @param {xlsx.WorkSheet} worksheet - * @return {*} {(xlsx.Range | undefined)} - */ -export function getWorksheetRange(worksheet: xlsx.WorkSheet): xlsx.Range | undefined { - const ref = worksheet['!ref']; - - if (!ref) { - return undefined; - } - - 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 - */ -export function prepareWorksheetCells(worksheet: xlsx.WorkSheet) { - const range = getWorksheetRange(worksheet); - - if (!range) { - return undefined; - } - - for (let r = range.s.r; r < range.e.r; r++) { - for (let c = range.s.c; c < range.e.c; c++) { - const coord = xlsx.utils.encode_cell({ r, c }); - let cell: CellObject = worksheet[coord]; - - if (!cell || !cell.v) { - continue; - } - - cell = replaceCellDates(cell); - - cell = trimCellWhitespace(cell); - } - } -} - -export function trimCellWhitespace(cell: CellObject) { - // check and clean raw strings - if (cell.t === 's') { - cell.v = safeTrim(cell.v); - } - - // check and clean formatted strings - if (cell.w) { - cell.w = safeTrim(cell.w); - } - - return cell; -} - -export function replaceCellDates(cell: CellObject) { - if (cell.t === 'd' && cell.v instanceof Date) { - cell.v = (cell.v as Date).toISOString(); - } - - return cell; -} - -export function getCellValue(cell: CellObject) { - // See https://www.npmjs.com/package/xlsx#cell-object for details on cell fields - return cell.v; -} diff --git a/app/package-lock.json b/app/package-lock.json index 928206e65..ca5135e93 100644 --- a/app/package-lock.json +++ b/app/package-lock.json @@ -5,9 +5,9 @@ "requires": true, "dependencies": { "@adobe/css-tools": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.2.0.tgz", - "integrity": "sha512-E09FiIft46CmH5Qnjb0wsW54/YQd69LsxeKUOWawmws1XWvyFGURnAChH0mlr7YPFR1ofwvUQfcL0J3lMxXqPA==", + "version": "4.3.3", + "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.3.tgz", + "integrity": "sha512-rE0Pygv0sEZ4vBWHlAgJLGDU7Pm8xoO6p3wsEceb7GYAjScrOHpEo8KK/eVkAcnSM+slAEtXjA2JpdjLp4fJQQ==", "dev": true }, "@alloc/quick-lru": { @@ -17,12 +17,12 @@ "dev": true }, "@ampproject/remapping": { - 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"handlebars": "^4.7.7", "jest-watch-typeahead": "^2.2.2", "jszip": "^3.10.1", "keycloak-js": "^20.0.2", diff --git a/app/src/components/map/DatasetPopup.tsx b/app/src/components/map/DatasetPopup.tsx deleted file mode 100644 index 19af5e11f..000000000 --- a/app/src/components/map/DatasetPopup.tsx +++ /dev/null @@ -1,127 +0,0 @@ -import Box from '@mui/material/Box'; -import CircularProgress from '@mui/material/CircularProgress'; -import Collapse from '@mui/material/Collapse'; -import Link from '@mui/material/Link'; -import Typography from '@mui/material/Typography'; -import { makeStyles } from '@mui/styles'; -import { SPATIAL_COMPONENT_TYPE } from 'constants/spatial'; -import { Feature } from 'geojson'; -import { useApi } from 'hooks/useApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { useHistory } from 'react-router'; - -export type BoundaryCentroidFeature = Feature & { properties: BoundaryCentroidFeatureProperties }; - -export type BoundaryCentroidFeatureProperties = { - type: SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID; - datasetTitle: string; - datasetID: string; -}; - -const useStyles = makeStyles(() => ({ - modalContent: { - position: 'relative', - width: 300, - minHeight: 36 - }, - loading: { - position: 'absolute', - top: '50%', - left: '50%', - transform: 'translate(-50%, -50%)' - }, - pointType: { - lineHeight: 'unset' - }, - date: { - margin: 0, - lineHeight: 'unset' - }, - table: { - marginTop: 16 - }, - tableCell: { - padding: 8, - fontSize: '0.625rem' - } -})); - -const DatasetPopup: React.FC> = ({ - submissionSpatialComponentIds -}) => { - const classes = useStyles(); - const api = useApi(); - const history = useHistory(); - - const dataLoader = useDataLoader(() => { - return api.search.getSpatialMetadata(submissionSpatialComponentIds); - }); - - dataLoader.load(); - - const { isLoading, isReady } = dataLoader; - const data = (dataLoader.data || []) as BoundaryCentroidFeatureProperties[]; - - const ModalContentWrapper: React.FC = ({ children }) => ( -
{children}
- ); - - const MetadataHeader: React.FC> = (props) => ( - - - Dataset - - {props.title && ( - - {props.title} - - )} - - ); - - const NoMetadataAvailable: React.FC = () => ( - - No metadata available. - - ); - - if (isLoading) { - return ( - -
- -
- - ); - } - - if (!data) { - return ( - - - - ); - } - - return ( - <> - {data.map((metadata) => { - const datasetTitle = metadata.datasetTitle; - const datasetID = metadata.datasetID; - - return ( - - - - history.push(`/datasets/${datasetID}/details`)}> - Go to Dataset - - - - ); - })} - - ); -}; - -export default DatasetPopup; diff --git a/app/src/components/map/FeaturePopup.tsx b/app/src/components/map/FeaturePopup.tsx deleted file mode 100644 index 9e0eeb8ee..000000000 --- a/app/src/components/map/FeaturePopup.tsx +++ /dev/null @@ -1,272 +0,0 @@ -import { mdiChevronLeft, mdiChevronRight } from '@mdi/js'; -import Icon from '@mdi/react'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import CircularProgress from '@mui/material/CircularProgress'; -import Collapse from '@mui/material/Collapse'; -import Divider from '@mui/material/Divider'; -import Table from '@mui/material/Table'; -import TableBody from '@mui/material/TableBody'; -import TableCell from '@mui/material/TableCell'; -import TableRow from '@mui/material/TableRow'; -import Typography from '@mui/material/Typography'; -import { makeStyles } from '@mui/styles'; -import { DATE_FORMAT } from 'constants/dateTimeFormats'; -import { SPATIAL_COMPONENT_TYPE } from 'constants/spatial'; -import { Feature, GeoJsonProperties } from 'geojson'; -import { useApi } from 'hooks/useApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { useState } from 'react'; -import { getFormattedDate, makeCsvObjectUrl } from 'utils/Utils'; - -export type OccurrenceFeature = Feature & { properties: OccurrenceFeatureProperties }; - -export type OccurrenceFeatureProperties = { - type: SPATIAL_COMPONENT_TYPE.OCCURRENCE; -}; - -export type BoundaryFeature = Feature & { properties: BoundaryFeatureProperties }; - -export type BoundaryFeatureProperties = { - type: SPATIAL_COMPONENT_TYPE.BOUNDARY; -}; - -export type BoundaryCentroidFeature = Feature & { properties: BoundaryCentroidFeatureProperties }; - -export type BoundaryCentroidFeatureProperties = { - type: SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID; - datasetID: string; - datasetTitle: string; -}; - -export enum COMMON_METADATA_PROPERTIES { - 'vernacularName' = 'Species', - 'individualCount' = 'Count', - 'eventDate' = 'Date', - 'lifeStage' = 'Life Stage', - 'sex' = 'Sex' -} - -export enum UNCOMMON_METADATA_PROPERTIES { - 'type' = 'Type', - 'datasetID' = 'Dataset ID', - 'verbatimSRS' = 'Verbatim SRS', - 'occurrenceID' = 'Occurrence ID', - 'basisOfRecord' = 'Basis of Record', - 'taxonID' = 'Taxon ID', - 'verbatimCoordinates' = 'Verbatim Coordinates' -} - -export const ALL_METADATA_PROPERTIES = { - ...COMMON_METADATA_PROPERTIES, - ...UNCOMMON_METADATA_PROPERTIES -}; - -export const formatMetadataProperty: Partial< - Record string> -> = { - eventDate: (dateString: string) => getFormattedDate(DATE_FORMAT.ShortMediumDateFormat, dateString) -}; - -interface IMetadataHeaderProps { - type?: string; - date?: string; - index?: number; - length?: number; -} - -type IDwCMetadata = ({ dwc: Record } & GeoJsonProperties) | null; - -const useStyles = makeStyles(() => ({ - modalContent: { - position: 'relative', - width: 300, - minHeight: 36 - }, - loading: { - position: 'absolute', - top: '50%', - left: '50%', - transform: 'translate(-50%, -50%)' - }, - pointType: { - lineHeight: 'unset' - }, - date: { - margin: 0, - lineHeight: 'unset' - } -})); - -const FeaturePopup: React.FC> = (props) => { - const { submissionSpatialComponentIds } = props; - - const classes = useStyles(); - const api = useApi(); - const [currentIndex, setCurrentIndex] = useState(0); - - const metadataLoader = useDataLoader(() => { - return api.search.getSpatialMetadata(submissionSpatialComponentIds); - }); - - metadataLoader.load(); - - const data = metadataLoader.data || []; - const isEmpty = data.length === 0; - const metadataObjectUrl = isEmpty ? undefined : makeCsvObjectUrl(data.map((row) => row?.dwc || {})); - - const handleNext = () => { - if (isEmpty) { - return; - } - - setCurrentIndex((currentIndex + 1) % data.length); - }; - - const handlePrev = () => { - if (isEmpty) { - return; - } - if (currentIndex === 0) { - setCurrentIndex(data.length - 1); - } else { - setCurrentIndex(currentIndex - 1); - } - }; - - const ModalContentWrapper: React.FC = ({ children }) => ( -
{children}
- ); - - const MetadataHeader: React.FC> = (headerProps) => { - const { date, index, length } = headerProps; - - return ( - - - {length && length > 1 ? `Records (${(index || 0) + 1} of ${length})` : 'Record'} - - {date && ( - - {getFormattedDate(DATE_FORMAT.ShortMediumDateFormat, date)} - - )} - - ); - }; - - const NoMetadataAvailable: React.FC = () => ( - - No metadata available. - - ); - - if (metadataLoader.isLoading) { - return ( - -
- -
- - ); - } - - if (data.length === 0) { - return ( - - - - ); - } - - const metadata = data[currentIndex]; - const type = metadata?.type; - const dwc: Record = metadata?.dwc || {}; - const filteredMetadata = Object.entries(COMMON_METADATA_PROPERTIES).filter(([key]) => Boolean(dwc[key])); - - if (!dwc || !Object.keys(dwc).length) { - return ( - - - - - ); - } - - return ( - - - - - - - {filteredMetadata.map(([key, propertyName]) => { - return ( - - {propertyName} - {(formatMetadataProperty[key] || String)(dwc[key])} - - ); - })} - -
- - - {!isEmpty && data.length > 1 && ( - - - - - )} - {metadataObjectUrl && ( - - - - )} - - - ); -}; - -export default FeaturePopup; diff --git a/app/src/components/map/MapContainer.test.tsx b/app/src/components/map/MapContainer.test.tsx deleted file mode 100644 index 3e3571740..000000000 --- a/app/src/components/map/MapContainer.test.tsx +++ /dev/null @@ -1,97 +0,0 @@ -import bbox from '@turf/bbox'; -import { LatLngBoundsExpression } from 'leaflet'; -import { cleanup, render } from 'test-helpers/test-utils'; -import { IMarkerLayer } from './components/MarkerClusterControls'; -import { IStaticLayer } from './components/StaticLayersControls'; -import MapContainer from './MapContainer'; - -describe('MapContainer', () => { - afterEach(() => { - cleanup(); - }); - - it('renders with minimal settings', () => { - const { container } = render(); - - expect(container.querySelector('#myMap')).toBeInTheDocument(); - }); - - it('renders with static geometries', () => { - const staticLayers: IStaticLayer[] = [ - { - visible: true, - layerName: 'test layer', - features: [ - { - geoJSON: { - id: 'nonEditableGeo', - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [125.6, 10.1] - }, - properties: { - name: 'Biodiversity Land' - } - } - } - ] - } - ]; - - const { container } = render(); - - expect(container.querySelector('#myMap')).toBeInTheDocument(); - }); - - it('renders with bounds', () => { - const bboxCoords = bbox({ - id: 'myGeo', - type: 'Feature', - geometry: { - type: 'Polygon', - coordinates: [ - [ - [-128, 55], - [-128, 55.5], - [-128, 56], - [-126, 58], - [-128, 55] - ] - ] - }, - properties: { - name: 'Restoration Islands' - } - }); - - const bounds: LatLngBoundsExpression = [ - [bboxCoords[1], bboxCoords[0]], - [bboxCoords[3], bboxCoords[2]] - ]; - - const { container } = render(); - - expect(container.querySelector('#myMap')).toBeInTheDocument(); - }); - - it('renders with scrollWheelZoom', () => { - const { container } = render(); - - expect(container.querySelector('#myMap')).toBeInTheDocument(); - }); - - it('renders with markers', () => { - const markerLayers: IMarkerLayer[] = [ - { - visible: true, - layerName: 'test-marker-layer', - markers: [{ position: [55, 128], key: 'key', count: 1 }] - } - ]; - - const { container } = render(); - - expect(container.querySelector('#myMap')).toBeInTheDocument(); - }); -}); diff --git a/app/src/components/map/MapContainer.tsx b/app/src/components/map/MapContainer.tsx deleted file mode 100644 index 5796b6139..000000000 --- a/app/src/components/map/MapContainer.tsx +++ /dev/null @@ -1,137 +0,0 @@ -import { makeStyles } from '@mui/styles'; -import { MAP_DEFAULT_ZOOM, MAP_MAX_ZOOM, MAP_MIN_ZOOM } from 'constants/spatial'; -import L, { LatLngBoundsExpression, LeafletEventHandlerFnMap } from 'leaflet'; -import 'leaflet-draw/dist/leaflet.draw.css'; -import 'leaflet-fullscreen/dist/leaflet.fullscreen.css'; -import 'leaflet-fullscreen/dist/Leaflet.fullscreen.js'; -import iconRetina from 'leaflet/dist/images/marker-icon-2x.png'; -import icon from 'leaflet/dist/images/marker-icon.png'; -import iconShadow from 'leaflet/dist/images/marker-shadow.png'; -import 'leaflet/dist/leaflet.css'; -import { FeatureGroup, LayersControl, MapContainer as LeafletMapContainer } from 'react-leaflet'; -import BaseLayer from './components/BaseLayer'; -import BaseLayerControls from './components/BaseLayerControls'; -import { GetMapBounds, IMapBoundsOnChange, SetMapBounds } from './components/Bounds'; -import DrawControls, { IDrawControlsOnChange, IDrawControlsProps } from './components/DrawControls'; -import EventHandler from './components/EventHandler'; -import FullScreenScrollingEventHandler from './components/FullScreenScrollingEventHandler'; -import MarkerCluster from './components/MarkerCluster'; -import MarkerClusterControls, { IMarkerLayer } from './components/MarkerClusterControls'; -import StaticLayers from './components/StaticLayers'; -import StaticLayersControls, { IStaticLayer } from './components/StaticLayersControls'; - -const useStyles = makeStyles(() => ({ - map: { - height: '100%' - } -})); - -// @ts-ignore -delete L.Icon.Default.prototype._getIconUrl; -L.Icon.Default.mergeOptions({ - iconRetinaUrl: iconRetina, - iconUrl: icon, - shadowUrl: iconShadow -}); - -export interface IMapContainerProps { - mapId: string; - staticLayers?: IStaticLayer[]; - drawControls?: IDrawControlsProps; - zoomControlEnabled?: boolean; - doubleClickZoomEnabled?: boolean; - draggingEnabled?: boolean; - layerControlEnabled?: boolean; - onDrawChange?: IDrawControlsOnChange; - scrollWheelZoom?: boolean; - fullScreenControl?: boolean; - markerLayers?: IMarkerLayer[]; - bounds?: LatLngBoundsExpression; - zoom?: number; - eventHandlers?: LeafletEventHandlerFnMap; - LeafletMapContainerProps?: Partial>; - onBoundsChange?: IMapBoundsOnChange; -} - -const MapContainer: React.FC> = (props) => { - const classes = useStyles(); - - const { - mapId, - staticLayers, - drawControls, - onDrawChange, - scrollWheelZoom, - fullScreenControl, - markerLayers, - bounds, - zoom, - eventHandlers, - LeafletMapContainerProps, - onBoundsChange, - zoomControlEnabled, - doubleClickZoomEnabled, - draggingEnabled, - layerControlEnabled - } = props; - - const fullscreenControlProp = (fullScreenControl && { pseudoFullscreen: true }) || undefined; - - return ( - - - - - onBoundsChange?.(newBounds, newZoom)} /> - - {drawControls && ( - - - - )} - - - {layerControlEnabled ? ( - - - - - - ) : ( - // each of these layer components was duplicated and had any 'control' components removed - // without the and any of the internal control components these layers - // can properly render without the control - <> - - - - - )} - - ); -}; - -export default MapContainer; diff --git a/app/src/components/map/components/BaseLayer.tsx b/app/src/components/map/components/BaseLayer.tsx deleted file mode 100644 index dbc275cc4..000000000 --- a/app/src/components/map/components/BaseLayer.tsx +++ /dev/null @@ -1,16 +0,0 @@ -import { TileLayer } from 'react-leaflet'; - -// Compare this with BaseLayerControls.tsx -// Without the parent control component this component can only return a single Tile Layer -const BaseLayer: React.FC = () => { - return ( - <> - - - ); -}; - -export default BaseLayer; diff --git a/app/src/components/map/components/BaseLayerControls.tsx b/app/src/components/map/components/BaseLayerControls.tsx deleted file mode 100644 index 717e6ac05..000000000 --- a/app/src/components/map/components/BaseLayerControls.tsx +++ /dev/null @@ -1,19 +0,0 @@ -import { LayersControl, TileLayer } from 'react-leaflet'; - -const BaseLayerControls: React.FC = () => { - return ( - <> - - - - - - - - ); -}; - -export default BaseLayerControls; diff --git a/app/src/components/map/components/Bounds.tsx b/app/src/components/map/components/Bounds.tsx deleted file mode 100644 index d2a5821fd..000000000 --- a/app/src/components/map/components/Bounds.tsx +++ /dev/null @@ -1,60 +0,0 @@ -import { Feature, Polygon } from 'geojson'; -import { LatLngBoundsExpression } from 'leaflet'; -import { useMap, useMapEvents } from 'react-leaflet'; -import { getFeatureObjectFromLatLngBounds } from 'utils/Utils'; - -export interface ISetMapBoundsProps { - bounds?: LatLngBoundsExpression; - zoom?: number; -} - -export const SetMapBounds: React.FC> = (props) => { - const map = useMap(); - - // Set bounds if provided, ignore zoom - if (props.bounds) { - map.fitBounds(props.bounds); - - return null; - } - - // Set zoom if provided - if (props.zoom) { - map.setZoom(props.zoom); - - return null; - } - - return null; -}; - -export type IMapBoundsOnChange = (bounds: Feature, zoom: number) => void; - -export interface IGetMapBoundsProps { - onChange: IMapBoundsOnChange; -} - -export const GetMapBounds: React.FC> = (props) => { - const { onChange } = props; - - const map = useMapEvents({ - zoomend() { - const latLngBounds = map.getBounds(); - map.closePopup(); - - const featureBounds = getFeatureObjectFromLatLngBounds(latLngBounds); - - onChange(featureBounds, map.getZoom()); - }, - moveend() { - const latLngBounds = map.getBounds(); - map.closePopup(); - - const featureBounds = getFeatureObjectFromLatLngBounds(latLngBounds); - - onChange(featureBounds, map.getZoom()); - } - }); - - return null; -}; diff --git a/app/src/components/map/components/DrawControls.tsx b/app/src/components/map/components/DrawControls.tsx deleted file mode 100644 index 334bb2a5b..000000000 --- a/app/src/components/map/components/DrawControls.tsx +++ /dev/null @@ -1,226 +0,0 @@ -import { useLeafletContext } from '@react-leaflet/core'; -import { Feature } from 'geojson'; -import { useDeepCompareEffect } from 'hooks/useDeepCompareEffect'; -import * as L from 'leaflet'; -import 'leaflet-draw'; -import 'leaflet/dist/leaflet.css'; -import { useEffect, useRef } from 'react'; - -/* - * Supported draw events. - */ -const eventHandlers = { - onCreated: 'draw:created', - onEdited: 'draw:edited', - onDrawStart: 'draw:drawstart', - onDrawStop: 'draw:drawstop', - onDrawVertex: 'draw:drawvertex', - onEditStart: 'draw:editstart', - onEditMove: 'draw:editmove', - onEditResize: 'draw:editresize', - onEditVertex: 'draw:editvertex', - onEditStop: 'draw:editstop', - onDeleted: 'draw:deleted', - onDeleteStart: 'draw:deletestart', - onDeleteStop: 'draw:deletestop', - onMounted: 'draw:mounted' -}; - -/** - * Custom subset of `L.Control.DrawConstructorOptions` that omits `edit.Feature` as this will be added automatically - * by `DrawControls`. - * - * @export - * @interface IDrawControlsOptions - */ -export interface IDrawControlsOptions { - position?: L.Control.DrawConstructorOptions['position']; - draw?: L.Control.DrawConstructorOptions['draw']; - edit?: Omit; -} - -export type IDrawControlsOnChange = (features: Feature[]) => void; - -export interface IDrawControlsProps { - /** - * Initial features to add to the map. These features will be editable. - * - * @type {Feature[]} - * @memberof IDrawControlsProps - */ - initialFeatures?: Feature[]; - /** - * Options to control the draw/edit UI controls. - * - * @type {IDrawControlsOptions} - * @memberof IDrawControlsProps - */ - options?: IDrawControlsOptions; - /** - * Callback triggered anytime a feature is added or updated or removed. - * - * @type {IDrawControlsOnChange} - * @memberof IDrawControlsProps - */ - onChange?: IDrawControlsOnChange; - /** - * Clear any previously drawn features (layers) before drawing the next one. - * The result is that only 1 feature will be shown at a time. - * - * @type {boolean} - * @memberof IDrawControlsProps - */ - clearOnDraw?: boolean; -} - -const DrawControls: React.FC> = (props) => { - const context = useLeafletContext(); - - /** - * Fetch the layer used by the draw controls. - * - * @return {*} {L.FeatureGroup} - */ - const getFeatureGroup = () => { - const container = context.layerContainer; - - if (!container || !(container instanceof L.FeatureGroup)) { - throw new Error('Failed to get map layer'); - } - - return container; - }; - - /** - * Collects all current feature layers, and calls `props.onChange`. - * Adds `radius` to the properties if the source feature is a circle type. - */ - const handleFeatureUpdate = () => { - const container = getFeatureGroup(); - - const features: Feature[] = []; - - container.getLayers().forEach((layer: any) => { - const geoJSON = layer.toGeoJSON(); - - if (layer._mRadius) { - geoJSON.properties.radius = layer.getRadius(); - } - - features.push(geoJSON); - }); - - props.onChange?.([...features]); - }; - - /** - * Build and return a drawing map control. - * - * @return {*} {L.Control.Draw} - */ - const getDrawControls = (): L.Control.Draw => { - const options: L.Control.DrawConstructorOptions = { - edit: { - ...props.options?.edit, - // Add FeatureGroup automatically - featureGroup: getFeatureGroup() - } - }; - - options.draw = { ...props.options?.draw }; - - options.position = props.options?.position || 'topright'; - - return new L.Control.Draw(options); - }; - - /** - * Handle create events. - * - * @param {L.DrawEvents.Created} event - */ - const onDrawCreate = (event: L.DrawEvents.Created) => { - const container = getFeatureGroup(); - - if (props.clearOnDraw) { - // Clear previous layers - container.clearLayers(); - } - - container.addLayer(event.layer); - handleFeatureUpdate(); - }; - - /** - * Handle edit/delete events. - */ - const onDrawEditDelete = () => { - handleFeatureUpdate(); - }; - - /** - * Registers/draws features. - * - * @param {Feature[]} [features] - * @return {*} - */ - const drawFeatures = (features?: Feature[]) => { - if (!features) { - return; - } - - const container = getFeatureGroup(); - - container.clearLayers(); - - features?.forEach((item: Feature) => { - L.geoJSON(item, { - pointToLayer: (feature, latlng) => { - if (feature.properties?.radius) { - return new L.Circle([latlng.lat, latlng.lng], feature.properties.radius); - } - - return new L.Marker([latlng.lat, latlng.lng]); - }, - onEachFeature: function (_feature, layer) { - container.addLayer(layer); - } - }); - }); - }; - - useEffect(() => { - const { map } = context; - - // Remove any existing event handlers - map.removeEventListener(eventHandlers.onCreated); - map.removeEventListener(eventHandlers.onEdited); - map.removeEventListener(eventHandlers.onDeleted); - - // Register draw event handlers - map.on(eventHandlers.onCreated, onDrawCreate as L.LeafletEventHandlerFn); - map.on(eventHandlers.onEdited, onDrawEditDelete); - map.on(eventHandlers.onDeleted, onDrawEditDelete); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [props.options, props.onChange, props.clearOnDraw]); - - useDeepCompareEffect(() => { - drawFeatures(props.initialFeatures); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [props.initialFeatures]); - - const drawControlsRef = useRef(getDrawControls()); - - useDeepCompareEffect(() => { - const { map } = context; - // Update draw control - drawControlsRef.current.remove(); - drawControlsRef.current = getDrawControls(); - drawControlsRef.current.addTo(map); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [props.options]); - - return null; -}; - -export default DrawControls; diff --git a/app/src/components/map/components/EventHandler.tsx b/app/src/components/map/components/EventHandler.tsx deleted file mode 100644 index 97639797f..000000000 --- a/app/src/components/map/components/EventHandler.tsx +++ /dev/null @@ -1,16 +0,0 @@ -import { LeafletEventHandlerFnMap } from 'leaflet'; -import { useMapEvents } from 'react-leaflet'; - -export interface IEventHandlerProps { - eventHandlers?: LeafletEventHandlerFnMap; -} - -const EventHandler = (props: IEventHandlerProps) => { - useMapEvents({ - ...props.eventHandlers - }); - - return null; -}; - -export default EventHandler; diff --git a/app/src/components/map/components/FullScreenScrollingEventHandler.tsx b/app/src/components/map/components/FullScreenScrollingEventHandler.tsx deleted file mode 100644 index 146e8e9d3..000000000 --- a/app/src/components/map/components/FullScreenScrollingEventHandler.tsx +++ /dev/null @@ -1,64 +0,0 @@ -import { LatLngBoundsExpression } from 'leaflet'; -import { useMap } from 'react-leaflet'; - -export interface IFullScreenScrollingEventHandlerProps { - /** - * Whether or not scroll wheel zooming is enabled. - * - * Usage: - * - If `true`, scroll wheel zooming will always be enabled regardless of mode. - * - If `false`, scroll wheel zooming will only be enabled in full screen mode. - * - * @type {boolean} - * @memberof IFullScreenScrollingEventHandlerProps - */ - scrollWheelZoom?: boolean; - /** - * Bounds to set when exiting full screen mode. - * - * @type {LatLngBoundsExpression} - * @memberof IFullScreenScrollingEventHandlerProps - */ - bounds?: LatLngBoundsExpression; -} - -/** - * Special event handler that triggers when the map enters and exists full screen mode. - * - * @param {*} props - * @return {*} - */ -const FullScreenScrollingEventHandler: React.FC> = ( - props -) => { - const map = useMap(); - - if (props.scrollWheelZoom) { - map.scrollWheelZoom.enable(); - } else { - map.scrollWheelZoom.disable(); - } - - map.on('fullscreenchange', function () { - if (map.isFullscreen()) { - if (!props.scrollWheelZoom) { - // don't change scroll wheel zoom settings if it was enabled by default via props - map.scrollWheelZoom.enable(); - } - } else { - if (!props.scrollWheelZoom) { - // don't change scroll wheel zoom settings if it was enabled by default via props - map.scrollWheelZoom.disable(); - } - - if (props.bounds) { - // reset bounds, if provided, on exit fullscreen - map.fitBounds(props.bounds); - } - } - }); - - return null; -}; - -export default FullScreenScrollingEventHandler; diff --git a/app/src/components/map/components/MarkerCluster.tsx b/app/src/components/map/components/MarkerCluster.tsx deleted file mode 100644 index 4fb5dec9d..000000000 --- a/app/src/components/map/components/MarkerCluster.tsx +++ /dev/null @@ -1,56 +0,0 @@ -import 'leaflet.markercluster'; -import { ReactElement } from 'react'; -import { FeatureGroup, Popup, Tooltip } from 'react-leaflet'; -import { IMarkerLayersProps, Marker } from './MarkerClusterControls'; - -// Compare with MarkerClusterControls.tsx -// See that is removed here -// This allows the marker data to render properly without the component visible on the map -const MarkerCluster: React.FC> = (props) => { - if (!props.layers?.length) { - return null; - } - - const layerControls: ReactElement[] = []; - - props.layers.forEach((layer, index) => { - if (!layer.markers?.length) { - return; - } - - layerControls.push( - - {layer.markers.map((item) => { - const id = item.key; - return ( - - {item.tooltip && ( - - {item.tooltip} - - )} - {item.popup && ( - - {item.popup} - - )} - - ); - })} - - ); - }); - - return <>{layerControls}; -}; - -export default MarkerCluster; diff --git a/app/src/components/map/components/MarkerClusterControls.tsx b/app/src/components/map/components/MarkerClusterControls.tsx deleted file mode 100644 index 9f9edfe16..000000000 --- a/app/src/components/map/components/MarkerClusterControls.tsx +++ /dev/null @@ -1,149 +0,0 @@ -import { createLayerComponent } from '@react-leaflet/core'; -import L, { LatLngExpression } from 'leaflet'; -import 'leaflet.markercluster'; -import { ReactElement } from 'react'; -import { FeatureGroup, LayersControl, MarkerProps, Popup, PopupProps, Tooltip, TooltipProps } from 'react-leaflet'; - -export interface IMarker { - position: LatLngExpression; - count: number; - key: string | number; - MarkerProps?: Partial; - popup?: ReactElement; - PopupProps?: Partial; - tooltip?: ReactElement; - TooltipProps?: Partial; -} - -export interface IMarkerLayer { - visible: boolean; - layerName: string; - markers: IMarker[]; -} - -export interface IMarkerLayersProps { - layers?: IMarkerLayer[]; -} - -export const makeCountIcon = (count: number) => { - return L.divIcon({ - html: `
${count}
`, - className: 'marker-cluster marker-cluster-small', - iconSize: new L.Point(24, 24) - }); -}; - -export const CountMarker: any = L.Marker.extend({ - options: { - count: 1 - }, - - setCount(s: number) { - this.options.count = s; - }, - - initialize(latlng: number[], { count, ...options }: { count: number }) { - L.Util.setOptions(this, { - count, - ...options - }); - - (L.CircleMarker.prototype as any).initialize.call(this, latlng, { - count, - ...options, - icon: makeCountIcon(count) - }); - } -}); - -export const Marker = createLayerComponent< - L.Marker & { setCount: (count: number) => void }, - MarkerProps & { count: number } ->( - ({ position, ...options }: MarkerProps & { count: number }, ctx) => { - const instance = new CountMarker(position, options); - return { - instance, - context: { ...ctx, overlayContainer: instance } - }; - }, - (marker, props, prevProps) => { - if (props.count !== prevProps.count) { - marker.setCount(props.count); - } - if (props.position !== prevProps.position) { - marker.setLatLng(props.position); - } - - if (props.icon != null && props.icon !== prevProps.icon) { - marker.setIcon(props.icon); - } - - if (props.zIndexOffset != null && props.zIndexOffset !== prevProps.zIndexOffset) { - marker.setZIndexOffset(props.zIndexOffset); - } - - if (props.opacity != null && props.opacity !== prevProps.opacity) { - marker.setOpacity(props.opacity); - } - - if (marker.dragging != null && props.draggable !== prevProps.draggable) { - if (props.draggable === true) { - marker.dragging.enable(); - } else { - marker.dragging.disable(); - } - } - } -); - -const MarkerClusterControls: React.FC> = (props) => { - if (!props.layers?.length) { - return null; - } - - const layerControls: ReactElement[] = []; - - props.layers.forEach((layer, index) => { - if (!layer.markers?.length) { - return; - } - - layerControls.push( - - - {layer.markers.map((item) => { - const id = item.key; - return ( - - {item.tooltip && ( - - {item.tooltip} - - )} - {item.popup && ( - - {item.popup} - - )} - - ); - })} - - - ); - }); - - return <>{layerControls}; -}; - -export default MarkerClusterControls; diff --git a/app/src/components/map/components/StaticLayers.tsx b/app/src/components/map/components/StaticLayers.tsx deleted file mode 100644 index 30c9bc783..000000000 --- a/app/src/components/map/components/StaticLayers.tsx +++ /dev/null @@ -1,63 +0,0 @@ -import * as L from 'leaflet'; -import { ReactElement } from 'react'; -import { FeatureGroup, GeoJSON, Popup, Tooltip } from 'react-leaflet'; -import { IStaticLayersProps } from './StaticLayersControls'; - -// Compare with StaticLayersControl.tsx -// See that is removed here -// This allows the static layer data to render properly without the component visible on the map -const StaticLayers: React.FC> = (props) => { - if (!props.layers?.length) { - return null; - } - - const layerControls: ReactElement[] = []; - - props.layers.forEach((layer) => { - if (!layer.features?.length) { - return; - } - - layerControls.push( - - {layer.features.map((item, index) => { - const id = item.key || item.geoJSON.id || index; - - return ( - { - if (feature.properties?.radius) { - return new L.Circle([latlng.lat, latlng.lng], feature.properties.radius); - } - - return new L.Marker([latlng.lat, latlng.lng]); - }} - data={item.geoJSON} - {...item.GeoJSONProps}> - {item.tooltip && ( - - {item.tooltip} - - )} - {item.popup && ( - - {item.popup} - - )} - - ); - })} - - ); - }); - - return <>{layerControls}; -}; - -export default StaticLayers; diff --git a/app/src/components/map/components/StaticLayersControls.tsx b/app/src/components/map/components/StaticLayersControls.tsx deleted file mode 100644 index 883755ff0..000000000 --- a/app/src/components/map/components/StaticLayersControls.tsx +++ /dev/null @@ -1,91 +0,0 @@ -import { Feature } from 'geojson'; -import * as L from 'leaflet'; -import { ReactElement } from 'react'; -import { - FeatureGroup, - GeoJSON, - GeoJSONProps, - LayersControl, - Popup, - PopupProps, - Tooltip, - TooltipProps -} from 'react-leaflet'; - -export interface IStaticLayerFeature { - geoJSON: Feature; - key?: string | number; - GeoJSONProps?: Partial; - popup?: ReactElement; - PopupProps?: Partial; - tooltip?: ReactElement; - TooltipProps?: Partial; -} - -export interface IStaticLayer { - visible: boolean; - layerName: string; - features: IStaticLayerFeature[]; -} - -export interface IStaticLayersProps { - layers?: IStaticLayer[]; -} - -const StaticLayersControls: React.FC> = (props) => { - if (!props.layers?.length) { - return null; - } - - const layerControls: ReactElement[] = []; - - props.layers.forEach((layer) => { - if (!layer.features?.length) { - return; - } - - layerControls.push( - - - {layer.features.map((item, index) => { - const id = item.key || item.geoJSON.id || index; - - return ( - { - if (feature.properties?.radius) { - return new L.Circle([latlng.lat, latlng.lng], feature.properties.radius); - } - - return new L.Marker([latlng.lat, latlng.lng]); - }} - data={item.geoJSON} - {...item.GeoJSONProps}> - {item.tooltip && ( - - {item.tooltip} - - )} - {item.popup && ( - - {item.popup} - - )} - - ); - })} - - - ); - }); - - return <>{layerControls}; -}; - -export default StaticLayersControls; diff --git a/app/src/components/map/components/UploadAreaControls.tsx b/app/src/components/map/components/UploadAreaControls.tsx deleted file mode 100644 index 4ab151f44..000000000 --- a/app/src/components/map/components/UploadAreaControls.tsx +++ /dev/null @@ -1,51 +0,0 @@ -import { mdiTrayArrowUp } from '@mdi/js'; -import Icon from '@mdi/react'; -import { Button } from '@mui/material'; -import EditDialog from 'components/dialog/EditDialog'; -import UploadArea, { - AreaUploadYupSchema, - FormikAreaUploadInitialValues, - IFormikAreaUpload -} from 'components/upload/UploadArea'; -import { IDatasetSearchForm } from 'features/datasets/components/DatasetSearchForm'; -import { useFormikContext } from 'formik'; -import React, { useState } from 'react'; - -const UploadAreaControls: React.FC> = (props) => { - const formikProps = useFormikContext(); - - const [openUploadArea, setOpenUploadArea] = useState(false); - - const submitArea = (values: IFormikAreaUpload) => { - formikProps.setFieldValue('area', [...formikProps.values.area, values]); - setOpenUploadArea(false); - }; - - return ( - <> - , - initialValues: FormikAreaUploadInitialValues, - validationSchema: AreaUploadYupSchema - }} - onCancel={() => setOpenUploadArea(false)} - onSave={submitArea} - /> - - - ); -}; - -export default UploadAreaControls; diff --git a/app/src/components/security/SecurityRuleForm.tsx b/app/src/components/security/SecurityRuleForm.tsx index 433a6ee33..1a9a2e2c3 100644 --- a/app/src/components/security/SecurityRuleForm.tsx +++ b/app/src/components/security/SecurityRuleForm.tsx @@ -97,7 +97,12 @@ const SecurityRuleForm = () => { return ruleGroups; }, []) ); - }, [initialAppliedSecurityRules, submissionFeatureGroupsDataLoader.data]); + }, [ + allSecurityRules, + formikProps.initialValues.submissionFeatureIds, + initialAppliedSecurityRules, + submissionFeatureGroupsDataLoader.data + ]); const toggleStageApply = (securityRule: ISecurityRuleAndCategory) => { if ( diff --git a/app/src/contexts/submissionContext.tsx b/app/src/contexts/submissionContext.tsx index 9b0587ef0..c7ae727b7 100644 --- a/app/src/contexts/submissionContext.tsx +++ b/app/src/contexts/submissionContext.tsx @@ -120,6 +120,7 @@ export const SubmissionContextProvider: React.FC = (pro */ useEffect(() => { submissionFeaturesAppliedRulesDataLoader.refresh(); + // eslint-disable-next-line react-hooks/exhaustive-deps }, [allSubmissionFeatureIds]); const submissionContext: ISubmissionContext = useMemo(() => { diff --git a/app/src/features/datasets/DatasetPage.test.tsx b/app/src/features/datasets/DatasetPage.test.tsx deleted file mode 100644 index 3ea9f61bc..000000000 --- a/app/src/features/datasets/DatasetPage.test.tsx +++ /dev/null @@ -1,113 +0,0 @@ -import { ThemeProvider } from '@mui/styles'; -import { cleanup, render, waitFor } from '@testing-library/react'; -import { FeatureCollection } from 'geojson'; -import { createMemoryHistory } from 'history'; -import { useApi } from 'hooks/useApi'; -import { Router } from 'react-router'; -import appTheme from 'themes/appTheme'; -import DatasetPage from './DatasetPage'; - -const history = createMemoryHistory(); - -const renderContainer = () => { - return render( - - - - - - ); -}; - -jest.mock('../../hooks/useApi'); - -const mockUseApi = { - dataset: { - getDatasetEML: jest.fn(), - getDatasetArtifacts: jest.fn(), - getHandleBarsTemplateByDatasetId: jest.fn() - }, - search: { - getSpatialData: jest.fn(), - getSpatialDataFile: jest.fn() - } -}; - -const mockBiohubApi = useApi as jest.Mock; - -describe('DatasetPage', () => { - beforeEach(() => { - mockBiohubApi.mockImplementation(() => mockUseApi); - }); - - afterEach(() => { - cleanup(); - }); - - it('renders the empty page content correctly', async () => { - mockUseApi.search.getSpatialDataFile.mockResolvedValue([]); - - mockUseApi.search.getSpatialData.mockResolvedValue([]); - - mockUseApi.dataset.getDatasetEML.mockResolvedValue([]); - - mockUseApi.dataset.getDatasetArtifacts.mockResolvedValue([]); - - mockUseApi.dataset.getHandleBarsTemplateByDatasetId.mockResolvedValue({ header: 'header', details: 'details' }); - - const { getByTestId } = renderContainer(); - - await waitFor(() => { - expect(getByTestId('MapContainer')).toBeVisible(); - }); - }); - - it.skip('shows eml metadata as well as map points', async () => { - const validFeatureCollection: FeatureCollection = { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [-129.083298513, 55.40257311] - }, - properties: { - type: 'Occurrence', - eventDate: 'string' - } - } - ] - }; - - const hexDoc = ''; - - mockUseApi.search.getSpatialDataFile.mockResolvedValue(hexDoc); - - mockUseApi.search.getSpatialData.mockReturnValue(validFeatureCollection); - - mockUseApi.dataset.getDatasetEML.mockResolvedValue({ - 'eml:eml': { - dataset: { - contact: { - organizationName: 'organization name' - } - } - } - }); - - mockUseApi.dataset.getHandleBarsTemplateByDatasetId.mockResolvedValue({ - header: 'header', - details: '{{eml:eml.dataset.contact.organizationName}}' - }); - - mockUseApi.dataset.getDatasetArtifacts.mockResolvedValue([]); - - const { getByTestId, getByText } = renderContainer(); - - await waitFor(() => { - expect(getByTestId('MapContainer')).toBeVisible(); - expect(getByText('organization name')).toBeVisible(); - }); - }); -}); diff --git a/app/src/features/datasets/DatasetPage.tsx b/app/src/features/datasets/DatasetPage.tsx index 0f360dc8a..5fc4eb842 100644 --- a/app/src/features/datasets/DatasetPage.tsx +++ b/app/src/features/datasets/DatasetPage.tsx @@ -1,195 +1,16 @@ -import { Theme } from '@mui/material'; import Box from '@mui/material/Box'; import Container from '@mui/material/Container'; import Paper from '@mui/material/Paper'; -import { makeStyles } from '@mui/styles'; -import { ActionToolbar } from 'components/toolbar/ActionToolbars'; - -const useStyles = makeStyles((theme: Theme) => ({ - datasetTitleContainer: { - paddingBottom: theme.spacing(5), - background: '#f7f8fa', - '& h1': { - marginTop: '-4px' - } - }, - datasetDetailsLabel: { - borderBottom: '1pt solid #dadada' - }, - datasetDetailsContainer: {}, - datasetMapContainer: { - minHeight: '400px' - } -})); const DatasetPage: React.FC = () => { - const classes = useStyles(); - // const biohubApi = useApi(); - // const urlParams = useParams(); - // const dialogContext = useDialogContext(); - // const history = useHistory(); - - // const datasetId = urlParams['id']; - - // const datasetDataLoader = useDataLoader(() => biohubApi.dataset.getDataset(datasetId)); - // const templateDataLoader = useDataLoader(() => biohubApi.dataset.getHandleBarsTemplateByDatasetId(datasetId)); - - // const fileDataLoader = useDataLoader((searchBoundary: Feature, searchType: string[], searchZoom: number) => - // biohubApi.search.getSpatialDataFile({ - // boundary: [searchBoundary], - // type: searchType, - // zoom: searchZoom, - // datasetID: datasetId - // }) - // ); - - // useDataLoaderError(datasetDataLoader, () => { - // return { - // dialogTitle: 'Error Loading Dataset', - // dialogText: - // 'An error has occurred while attempting to load the dataset, please try again. If the error persists, please contact your system administrator.', - // onOk: () => { - // datasetDataLoader.clear(); - // dialogContext.setErrorDialog({ open: false }); - // history.replace('/search'); - // }, - // onClose: () => { - // datasetDataLoader.clear(); - // dialogContext.setErrorDialog({ open: false }); - // history.replace('/search'); - // } - // }; - // }); - - // datasetDataLoader.load(); - // console.log('datasetDataLoader.data', datasetDataLoader.data); - // // templateDataLoader.load(); - - // const mapDataLoader = useDataLoader((searchBoundary: Feature, searchType: string[], searchZoom: number) => - // biohubApi.search.getSpatialData({ - // boundary: [searchBoundary], - // type: searchType, - // zoom: searchZoom, - // datasetID: datasetId - // }) - // ); - - // useDataLoaderError(fileDataLoader, () => { - // return { - // dialogTitle: 'Error Exporting Data', - // dialogText: - // 'An error has occurred while attempting to archive and download occurrence data, please try again. If the error persists, please contact your system administrator.' - // }; - // }); - - // useDataLoaderError(mapDataLoader, () => { - // return { - // dialogTitle: 'Error Loading Map Data', - // dialogText: - // 'An error has occurred while attempting to load the map data, please try again. If the error persists, please contact your system administrator.' - // }; - // }); - - // const [markerLayers, setMarkerLayers] = useState([]); - // const [staticLayers, setStaticLayers] = useState([]); - // const [mapBoundary, setMapBoundary] = useState(undefined); - - // useEffect(() => { - // if (!fileDataLoader.data) { - // return; - // } - - // const data = fileDataLoader.data; - - // const content = Buffer.from(data, 'hex'); - - // const blob = new Blob([content], { type: 'application/zip' }); - - // const link = document.createElement('a'); - - // link.download = `${datasetId}.zip`; - - // link.href = URL.createObjectURL(blob); - - // link.click(); - - // URL.revokeObjectURL(link.href); - // }, [datasetId, fileDataLoader.data]); - - // useEffect(() => { - // if (!mapDataLoader.data) { - // return; - // } - - // const result = parseSpatialDataByType(mapDataLoader.data); - // if (result.staticLayers[0]?.features[0]?.geoJSON) { - // const bounds = calculateUpdatedMapBounds([result.staticLayers[0].features[0].geoJSON]); - // if (bounds) { - // const newBounds = new LatLngBounds(bounds[0] as LatLngTuple, bounds[1] as LatLngTuple); - // setMapBoundary(newBounds); - // } - // } - // setStaticLayers(result.staticLayers); - // setMarkerLayers(result.markerLayers); - // }, [mapDataLoader.data]); - - // mapDataLoader.load( - // ALL_OF_BC_BOUNDARY, - // [SPATIAL_COMPONENT_TYPE.BOUNDARY, SPATIAL_COMPONENT_TYPE.OCCURRENCE], - // MAP_DEFAULT_ZOOM - // ); - - // if (!datasetDataLoader.data) { - // // || !templateDataLoader.data) { - // return ; - // } - return ( - - - - - {/* */} - - - - - - - - - - {/* */} - - - {/* */} - - - - - {/* */} - - - {/* */} - - - - + + + + TBD + + + ); }; diff --git a/app/src/features/datasets/DatasetsRouter.tsx b/app/src/features/datasets/DatasetsRouter.tsx index a7c016027..fd615a94e 100644 --- a/app/src/features/datasets/DatasetsRouter.tsx +++ b/app/src/features/datasets/DatasetsRouter.tsx @@ -13,10 +13,6 @@ const DatasetsRouter: React.FC = () => { - {/* - - */} - diff --git a/app/src/features/datasets/components/AttachmentItemMenuButton.tsx b/app/src/features/datasets/components/AttachmentItemMenuButton.tsx deleted file mode 100644 index 713bfd0b0..000000000 --- a/app/src/features/datasets/components/AttachmentItemMenuButton.tsx +++ /dev/null @@ -1,119 +0,0 @@ -import { mdiDotsVertical, mdiLockOutline, mdiLockPlus, mdiTrashCanOutline, mdiTrayArrowDown } from '@mdi/js'; -import Icon from '@mdi/react'; -import { MenuList } from '@mui/material'; -import Box from '@mui/material/Box'; -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 { IArtifact, SECURITY_APPLIED_STATUS } from 'interfaces/useDatasetApi.interface'; -import { useState } from 'react'; - -interface IAttachmentItemMenuButtonProps { - artifact: IArtifact; - onDownload: (artifact: IArtifact) => void; - onDelete: (artifactUUID: string[]) => void; - onRequestAccess: (artifact: IArtifact) => void; - onApplySecurity: (artifact: IArtifact) => void; - hasAdministrativePermissions: boolean; - isPendingReview: boolean; -} - -const AttachmentItemMenuButton = (props: IAttachmentItemMenuButtonProps) => { - const [anchorEl, setAnchorEl] = useState(null); - const open = Boolean(anchorEl); - const canDownload = - props.hasAdministrativePermissions || - props.artifact.supplementaryData.persecutionAndHarmStatus === SECURITY_APPLIED_STATUS.UNSECURED; - - const handleClick = (event: any) => { - setAnchorEl(event.currentTarget); - }; - - const handleClose = () => { - setAnchorEl(null); - }; - - return ( - <> - - - - - - - - {canDownload ? ( - { - props.onDownload(props.artifact); - handleClose(); - }} - data-testid="attachment-action-menu-download"> - - - - Download Document - - ) : ( - { - props.onRequestAccess(props.artifact); - handleClose(); - }} - data-testid="attachment-action-menu-request-access"> - - - - Request Access - - )} - - {props.hasAdministrativePermissions && ( - <> - { - props.onApplySecurity(props.artifact); - setAnchorEl(null); - }} - data-testid="attachment-action-menu-download"> - - - - Apply Security to Document - - - { - props.onDelete([props.artifact.uuid]); - handleClose(); - }} - data-testid="attachment-action-menu-delete"> - - - - Delete Document - - - )} - - - - - - ); -}; - -export default AttachmentItemMenuButton; diff --git a/app/src/features/datasets/components/DatasetArtifacts.tsx b/app/src/features/datasets/components/DatasetArtifacts.tsx deleted file mode 100644 index 1d9e0ea22..000000000 --- a/app/src/features/datasets/components/DatasetArtifacts.tsx +++ /dev/null @@ -1,326 +0,0 @@ -import { mdiLockPlus, mdiTrayArrowDown } from '@mdi/js'; -import Icon from '@mdi/react'; -import Alert from '@mui/material/Alert'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; -import Chip from '@mui/material/Chip'; -import Divider from '@mui/material/Divider'; -import IconButton from '@mui/material/IconButton'; -import Typography from '@mui/material/Typography'; -import { DataGrid, GridColDef, GridRowSelectionModel } from '@mui/x-data-grid'; -import { ErrorDialog } from 'components/dialog/ErrorDialog'; -import YesNoDialog from 'components/dialog/YesNoDialog'; -import { ActionToolbar } from 'components/toolbar/ActionToolbars'; -import { DATE_FORMAT } from 'constants/dateTimeFormats'; -import { SYSTEM_ROLE } from 'constants/roles'; -import { ISnackbarProps } from 'contexts/dialogContext'; -import { useApi } from 'hooks/useApi'; -import { useAuthStateContext } from 'hooks/useAuthStateContext'; -import { useDialogContext } from 'hooks/useContext'; -import useDataLoader from 'hooks/useDataLoader'; -import { IArtifact, SECURITY_APPLIED_STATUS } from 'interfaces/useDatasetApi.interface'; -import { useState } from 'react'; -import { hasAtLeastOneValidValue } from 'utils/authUtils'; -import { downloadFile, getFormattedDate, getFormattedFileSize, pluralize as p } from 'utils/Utils'; -import SecureDataAccessRequestDialog from '../security/SecureDataAccessRequestDialog'; -import AttachmentItemMenuButton from './AttachmentItemMenuButton'; -import ApplySecurityDialog from './security/ApplySecurityDialog'; - -const VALID_SYSTEM_ROLES: SYSTEM_ROLE[] = [SYSTEM_ROLE.DATA_ADMINISTRATOR, SYSTEM_ROLE.SYSTEM_ADMIN]; - -export interface IDatasetAttachmentsProps { - datasetId: string; -} - -const NoArtifactRowsOverlay = () => ( - - - No Artifacts - - -); - -/** - * Dataset attachments content for a dataset. - * - * @return {*} - */ -const DatasetAttachments: React.FC = (props) => { - const { datasetId } = props; - const [showAlert, setShowAlert] = useState(true); - const [initialSecureDataAccessRequestSelection, setInitialSecureDataAccessRequestSelection] = useState( - null - ); - - const [rowSelectionModel, setRowSelectionModel] = useState([]); - - const [openApplySecurity, setOpenApplySecurity] = useState(false); - const [selectedArtifacts, setSelectedArtifacts] = useState([]); - const [showDeleteFileDialog, setShowDeleteFileDialog] = useState(false); - const [artifactToDelete, setArtifactToDelete] = useState(undefined); - const [showErrorDialog, setShowErrorDialog] = useState(false); - - const authStateContext = useAuthStateContext(); - const biohubApi = useApi(); - const dialogContext = useDialogContext(); - - const artifactsDataLoader = useDataLoader(() => biohubApi.dataset.getDatasetArtifacts(datasetId)); - artifactsDataLoader.load(); - - const artifactsList = artifactsDataLoader.data || []; - - const numPendingDocuments = artifactsList.filter( - (artifact) => artifact.supplementaryData.persecutionAndHarmStatus === SECURITY_APPLIED_STATUS.PENDING - ).length; - - const hasAdministrativePermissions = hasAtLeastOneValidValue( - VALID_SYSTEM_ROLES, - authStateContext.biohubUserWrapper.roleNames - ); - - const handleApplySecurity = (artifact: IArtifact) => { - setSelectedArtifacts([artifact]); - setOpenApplySecurity(true); - }; - - const handleDownloadAttachment = async (attachment: IArtifact) => { - const signedUrl = await biohubApi.dataset.getArtifactSignedUrl(attachment.artifact_id); - if (!signedUrl) { - return; - } - - await downloadFile(signedUrl); - }; - - const handleDeleteArtifact = async (artifactUUIDs: string[]): Promise => { - const data = await biohubApi.artifact.deleteArtifacts(artifactUUIDs); - artifactsDataLoader.refresh(); - - return data; - }; - - const showSnackBar = (textDialogProps?: Partial) => { - dialogContext.setSnackbar({ ...textDialogProps, open: true }); - }; - - const handleShowSnackBar = (message: string) => { - showSnackBar({ - snackbarMessage: ( - <> - - {message} - - - ), - open: true - }); - }; - - const columns: GridColDef[] = [ - { - field: 'file_name', - headerName: 'Title', - flex: 2, - disableColumnMenu: true - }, - { - field: 'file_type', - headerName: 'Type', - flex: 1 - }, - { - field: 'create_date', - headerName: 'Submitted', - valueGetter: ({ value }) => value && new Date(value), - valueFormatter: ({ value }) => getFormattedDate(DATE_FORMAT.ShortDateFormat, value), - flex: 1 - }, - { - field: 'file_size', - headerName: 'Size', - flex: 0, - valueFormatter: ({ value }) => getFormattedFileSize(value) - }, - { - field: 'status', - headerName: 'Status', - flex: 1, - renderCell: (params) => { - const { supplementaryData } = params.row; - if (supplementaryData.persecutionAndHarmStatus === SECURITY_APPLIED_STATUS.UNSECURED) { - return ; - } - - if (hasAdministrativePermissions) { - if (supplementaryData.persecutionAndHarmStatus === SECURITY_APPLIED_STATUS.PENDING) { - return ; - } - } - return ; - } - }, - { - field: 'action', - headerName: 'Action', - sortable: false, - renderCell: (params) => { - return ( - { - setArtifactToDelete(params.row); - setShowDeleteFileDialog(true); - }} - onRequestAccess={(artifact) => setInitialSecureDataAccessRequestSelection(artifact.artifact_id)} - onApplySecurity={handleApplySecurity} - isPendingReview={!params.row.security_review_timestamp} - hasAdministrativePermissions={hasAdministrativePermissions} - /> - ); - } - } - ]; - - return ( - <> - setInitialSecureDataAccessRequestSelection(null)} - artifacts={artifactsList} - initialArtifactSelection={ - initialSecureDataAccessRequestSelection ? [initialSecureDataAccessRequestSelection] : [] - } - /> - - { - setOpenApplySecurity(false); - artifactsDataLoader.refresh(); - - setSelectedArtifacts([]); - setRowSelectionModel([]); - }} - /> - - setShowErrorDialog(false)} - onOk={() => setShowErrorDialog(false)} - /> - - setShowDeleteFileDialog(false)} - onYes={async () => { - if (artifactToDelete) { - const response = await handleDeleteArtifact([artifactToDelete.uuid]); - if (response) { - handleShowSnackBar(`You successfully deleted ${artifactToDelete.file_name}.`); - } else { - setShowErrorDialog(true); - } - setShowDeleteFileDialog(false); - setArtifactToDelete(undefined); - } - }} - onNo={() => { - setShowDeleteFileDialog(false); - setArtifactToDelete(undefined); - }} - dialogTitle="Delete document?" - dialogText="Are you sure you want to permanently delete this document? This action cannot be undone." - yesButtonProps={{ color: 'error' }} - /> - - - - - - - - - - - - {hasAdministrativePermissions && numPendingDocuments > 0 && showAlert && ( - - setShowAlert(false)} severity="info"> - - {`You have ${numPendingDocuments} project ${p(numPendingDocuments, 'document')} to review.`} - - - - )} - - row.artifact_id} - autoHeight - rows={artifactsList} - columns={columns} - pageSizeOptions={[5]} - checkboxSelection - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - sortingOrder={['asc', 'desc']} - initialState={{ - sorting: { - sortModel: [{ field: 'create_date', sort: 'desc' }] - }, - pagination: { - paginationModel: { - pageSize: 5 - } - } - }} - slots={{ - noRowsOverlay: NoArtifactRowsOverlay - }} - rowSelectionModel={rowSelectionModel} - onRowSelectionModelChange={(newRowSelectionModel) => { - const selectedArtifacts = newRowSelectionModel.map((rowId) => { - const findArtifact = artifactsList.find((artifact) => artifact.artifact_id === rowId); - if (findArtifact === undefined) { - throw Error('Artifact not found'); - } else { - return findArtifact; - } - }); - - if (selectedArtifacts) { - setSelectedArtifacts(selectedArtifacts); - } - - setRowSelectionModel(newRowSelectionModel); - }} - /> - - - - ); -}; - -export default DatasetAttachments; diff --git a/app/src/features/datasets/components/DatasetSearchForm.tsx b/app/src/features/datasets/components/DatasetSearchForm.tsx deleted file mode 100644 index e5afbd692..000000000 --- a/app/src/features/datasets/components/DatasetSearchForm.tsx +++ /dev/null @@ -1,144 +0,0 @@ -import { InputLabel } from '@mui/material'; -import Box from '@mui/material/Box'; -import FormControl from '@mui/material/FormControl'; -import MenuItem from '@mui/material/MenuItem'; -import Select from '@mui/material/Select'; -import Typography from '@mui/material/Typography'; -import MultiAutocompleteField, { - IMultiAutocompleteFieldOption, - sortAutocompleteOptions -} from 'components/fields/MultiAutocompleteField'; -import MultiSelectList from 'components/fields/MultiSelectList'; -import UploadAreaControls from 'components/map/components/UploadAreaControls'; -import { IFormikAreaUpload } from 'components/upload/UploadArea'; -import { useFormikContext } from 'formik'; -import { useApi } from 'hooks/useApi'; -import React, { useEffect, useState } from 'react'; -import yup from 'utils/YupSchema'; - -export interface IDatasetSearchForm { - dataset: string; - species_list: IMultiAutocompleteFieldOption[]; - area: IFormikAreaUpload[]; -} - -export const DatasetSearchFormInitialValues: IDatasetSearchForm = { - dataset: 'Occurrence', - species_list: [], - area: [] -}; - -export const DatasetSearchFormYupSchema = yup.object().shape({ - dataset: yup.string(), - species_list: yup.mixed(), - area: yup.mixed() -}); - -export interface IDatasetSearchFormProps { - onAreaUpdate: (area: IFormikAreaUpload[]) => void; - toggleShowForm: () => void; - hasResults: boolean; -} - -/** - * Create project - Partnerships section - * - * @return {*} - */ -const DatasetSearchForm: React.FC = (props) => { - const api = useApi(); - const formikProps = useFormikContext(); - const [speciesList, setSpeciesList] = useState([]); - - const convertOptions = (value: any): IMultiAutocompleteFieldOption[] => - value.map((item: any) => { - return { value: item.code, label: item.label }; - }); - - const handleGetSpeciesList = async (value: string) => { - const response = await api.taxonomy.searchSpecies(value); - - const convertedOptions = convertOptions(response.searchResponse); - - setSpeciesList(convertedOptions); - }; - - useEffect(() => { - props.onAreaUpdate(formikProps.values.area); - - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [formikProps.values.area]); - - return ( - <> - - - What do you want to find? - - - Dataset - - - - - - - - - - - Refine Search Area - - - - Refine your search to a custom boundary by importing either KML files or Shapefiles. - - - - - - - ); -}; - -export default DatasetSearchForm; diff --git a/app/src/features/datasets/components/RelatedDatasets.tsx b/app/src/features/datasets/components/RelatedDatasets.tsx deleted file mode 100644 index 77097ebca..000000000 --- a/app/src/features/datasets/components/RelatedDatasets.tsx +++ /dev/null @@ -1,124 +0,0 @@ -import { Link, Typography } from '@mui/material'; -import Box from '@mui/material/Box'; -import Chip from '@mui/material/Chip'; -import Divider from '@mui/material/Divider'; -import { DataGrid, GridColDef, GridRenderCellParams, GridTreeNodeWithRender } from '@mui/x-data-grid'; -import { ActionToolbar } from 'components/toolbar/ActionToolbars'; -import { SYSTEM_ROLE } from 'constants/roles'; -import { useApi } from 'hooks/useApi'; -import { useAuthStateContext } from 'hooks/useAuthStateContext'; -import useDataLoader from 'hooks/useDataLoader'; -import { IRelatedDataset } from 'interfaces/useDatasetApi.interface'; -import { hasAtLeastOneValidValue } from 'utils/authUtils'; -import { ensureProtocol } from 'utils/Utils'; - -const VALID_SYSTEM_ROLES: SYSTEM_ROLE[] = [SYSTEM_ROLE.DATA_ADMINISTRATOR, SYSTEM_ROLE.SYSTEM_ADMIN]; - -export interface IRelatedDatasetsProps { - datasetId: string; -} - -const NoDatasetRowsOverlay = () => ( - - - No Related Datasets - - -); - -/** - * Dataset attachments content for a dataset. - * - * @return {*} - */ -const RelatedDatasets: React.FC = (props) => { - const { datasetId } = props; - - const biohubApi = useApi(); - const authStateContext = useAuthStateContext(); - - const relatedDatasetsDataLoader = useDataLoader(() => biohubApi.dataset.getRelatedDatasets(datasetId)); - relatedDatasetsDataLoader.load(); - - const relatedDatasetsList: IRelatedDataset[] = relatedDatasetsDataLoader.data?.datasetsWithSupplementaryData ?? []; - - const hasAdministrativePermissions = hasAtLeastOneValidValue( - VALID_SYSTEM_ROLES, - authStateContext.biohubUserWrapper.roleNames - ); - - const columns: GridColDef[] = [ - { - field: 'title', - headerName: 'Title', - flex: 1, - disableColumnMenu: true, - renderCell: (params: GridRenderCellParams) => { - return {params.row.title}; - } - }, - { - field: 'status', - headerName: 'Status', - flex: 1, - renderCell: (params) => { - const { supplementaryData } = params.row; - - if (hasAdministrativePermissions) { - if (supplementaryData.isPendingReview === true) { - return ; - } - } - return <>; - } - } - ]; - - return ( - <> - - - - - row.datasetId} - autoHeight - disableVirtualization - rows={relatedDatasetsList} - slots={{ - noRowsOverlay: NoDatasetRowsOverlay - }} - columns={columns} - pageSizeOptions={[5]} - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - sortingOrder={['asc', 'desc']} - initialState={{ - sorting: { - sortModel: [{ field: 'create_date', sort: 'desc' }] - }, - pagination: { - paginationModel: { - pageSize: 5 - } - } - }} - /> - - - - ); -}; - -export default RelatedDatasets; diff --git a/app/src/features/datasets/components/RenderWithHandlebars.test.tsx b/app/src/features/datasets/components/RenderWithHandlebars.test.tsx deleted file mode 100644 index 417407e62..000000000 --- a/app/src/features/datasets/components/RenderWithHandlebars.test.tsx +++ /dev/null @@ -1,44 +0,0 @@ -import { cleanup, render } from 'test-helpers/test-utils'; -import useHandlebars from 'utils/handlebarsUtils'; -import RenderWithHandlebars from './RenderWithHandlebars'; - -jest.mock('utils/handlebarsUtils'); - -const mockHandlebars = useHandlebars as jest.Mock; - -const HandlebarsComponent = () => { - const content = { - datasetEML: { - data: { - 'eml:eml': {} - } - }, - rawTemplate: {} - }; - - return ; -}; - -const mockHandlebarsImplementation = { - compileFromRawTemplate: (dataset: any) => { - return (dataset: any) => { - return '
ABCD
'; - }; - } -}; - -describe('RenderWithHandlebars', () => { - beforeEach(() => { - mockHandlebars.mockImplementation(() => mockHandlebarsImplementation); - }); - - afterEach(() => { - cleanup(); - }); - - it('renders a component', () => { - const { getByText } = render(); - - expect(getByText('ABCD')).toBeVisible(); - }); -}); diff --git a/app/src/features/datasets/components/RenderWithHandlebars.tsx b/app/src/features/datasets/components/RenderWithHandlebars.tsx deleted file mode 100644 index 460152df8..000000000 --- a/app/src/features/datasets/components/RenderWithHandlebars.tsx +++ /dev/null @@ -1,25 +0,0 @@ -import * as DOMPurify from 'dompurify'; -import 'styles/handlebar.scss'; -import { useHandlebars } from 'utils/handlebarsUtils'; - -export interface IRenderWithHandlebarsProps { - datasetEML: { - data: { - 'eml:eml': any; - }; - }; - rawTemplate: TemplateSpecification; -} - -const RenderWithHandlebars: React.FC = (props) => { - const dataset = props.datasetEML.data; - const rawTemplate = props.rawTemplate; - - const template = useHandlebars().compileFromRawTemplate(rawTemplate); - - const result = template(dataset); - - return
; -}; - -export default RenderWithHandlebars; diff --git a/app/src/features/datasets/components/security/ApplySecurityDialog.tsx b/app/src/features/datasets/components/security/ApplySecurityDialog.tsx deleted file mode 100644 index 42ea0a47d..000000000 --- a/app/src/features/datasets/components/security/ApplySecurityDialog.tsx +++ /dev/null @@ -1,292 +0,0 @@ -import { mdiInformationOutline, mdiLock } from '@mdi/js'; -import Icon from '@mdi/react'; -import LoadingButton from '@mui/lab/LoadingButton'; -import { Box, Divider, Typography } from '@mui/material'; -import Button from '@mui/material/Button'; -import Dialog from '@mui/material/Dialog'; -import DialogActions from '@mui/material/DialogActions'; -import DialogContent from '@mui/material/DialogContent'; -import DialogContentText from '@mui/material/DialogContentText'; -import DialogTitle from '@mui/material/DialogTitle'; -import { useTheme } from '@mui/material/styles'; -import useMediaQuery from '@mui/material/useMediaQuery'; -import YesNoDialog from 'components/dialog/YesNoDialog'; -import { ApplySecurityRulesI18N } from 'constants/i18n'; -import { ISnackbarProps } from 'contexts/dialogContext'; -import { Formik, FormikProps } from 'formik'; -import { useApi } from 'hooks/useApi'; -import { useDialogContext } from 'hooks/useContext'; -import useDataLoader from 'hooks/useDataLoader'; -import { IArtifact, IPersecutionAndHarmRule } from 'interfaces/useDatasetApi.interface'; -import React, { useRef, useState } from 'react'; -import { pluralize as p } from 'utils/Utils'; -import yup from 'utils/YupSchema'; -import { ISecurityReason } from './SecurityReasonCategory'; -import SecurityReasonSelector from './SecurityReasonSelector'; -import SelectedDocumentsDataset from './SelectedDocumentsDataset'; - -export interface IApplySecurityDialog { - selectedArtifacts: IArtifact[]; - open: boolean; - onClose: () => void; -} - -export interface ISelectSecurityReasonForm { - securityReasons: ISecurityReason[]; -} - -export const SecurityReasonsYupSchema = yup.object().shape({ - securityReasons: yup.array().of( - yup.object().shape({ - name: yup.string(), - description: yup.string(), - category: yup.string(), - id: yup.number(), - type_id: yup.number(), - wldtaxonomic_units_id: yup.number() - }) - ) -}); - -/** - * Publish button. - * - * @return {*} - */ -const ApplySecurityDialog: React.FC = (props) => { - const { selectedArtifacts, open, onClose } = props; - - const [yesNoDialogOpen, setYesNoDialogOpen] = useState(false); - const [isPendingApplySecurity, setIsPendingApplySecurity] = useState(false); - const [isPendingUnapplySecurity, setIsPendingUnapplySecurity] = useState(false); - const [formikRef] = useState(useRef>(null)); - - const biohubApi = useApi(); - const theme = useTheme(); - const fullScreen = useMediaQuery(theme.breakpoints.down('xl')); - const dialogContext = useDialogContext(); - - const persecutionHarmDataLoader = useDataLoader(() => biohubApi.security.listPersecutionHarmRules()); - persecutionHarmDataLoader.load(); - - const persecutionHarmRules: ISecurityReason[] = (persecutionHarmDataLoader.data ?? []).map((rule) => { - return { - category: 'Persecution or Harm', - name: rule.name, - description: rule.description, - id: rule.persecution_or_harm_id, - type_id: rule.persecution_or_harm_type_id, - wldtaxonomic_units_id: rule.wldtaxonomic_units_id - }; - }); - - const initialSecurityReasons: ISecurityReason[] = props.selectedArtifacts - // Find IDs of all applied security reasons - .reduce((securityRuleIds: number[], artifact: IArtifact) => { - const appliedSecurityReasons = artifact.supplementaryData.persecutionAndHarmRules.map( - (rule: IPersecutionAndHarmRule) => rule.persecution_or_harm_id - ); - - return [...securityRuleIds, ...appliedSecurityReasons]; - }, []) - - // Filter duplicate IDs - .filter((value, index, array) => array.indexOf(value) === index) - - // Map IDs to security rules - .map((securityRuleId: number) => { - return persecutionHarmRules.find((persecutionAndHarmRule) => persecutionAndHarmRule.id === securityRuleId); - }) - - // Filter missing security rules - .filter((value): value is ISecurityReason => Boolean(value)); - - const showSnackBar = (textDialogProps?: Partial) => { - dialogContext.setSnackbar({ ...textDialogProps, open: true }); - }; - - const handleSubmit = async (values: { securityReasons: ISecurityReason[] }) => { - if (values.securityReasons.length > 0) { - setIsPendingApplySecurity(true); - } else { - setIsPendingUnapplySecurity(true); - } - - return biohubApi.security.applySecurityReasonsToArtifacts(selectedArtifacts, values.securityReasons).finally(() => { - setIsPendingApplySecurity(false); - setIsPendingUnapplySecurity(false); - }); - }; - - const handleShowSnackBar = (message: string) => { - showSnackBar({ - snackbarMessage: ( - <> - - {message} - - - ), - open: true - }); - }; - - return ( - <> - - - innerRef={formikRef} - initialValues={{ - securityReasons: initialSecurityReasons - }} - validationSchema={SecurityReasonsYupSchema} - validateOnBlur={true} - validateOnChange={false} - onSubmit={async (values) => { - return handleSubmit(values) - .then(() => { - handleShowSnackBar( - `You successfully applied security reasons to ${selectedArtifacts.length} ${p( - selectedArtifacts.length, - 'file' - )}.` - ); - onClose(); - }) - .catch((apiError) => { - dialogContext.setErrorDialog({ - open: true, - dialogTitle: ApplySecurityRulesI18N.applySecurityRulesErrorTitle, - dialogText: ApplySecurityRulesI18N.applySecurityRulesErrorText, - dialogError: apiError.message, - dialogErrorDetails: apiError.errors, - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - } - }); - }); - }}> - {(formikProps) => ( - <> - setYesNoDialogOpen(false)} - onYes={() => { - handleSubmit({ securityReasons: [] }) - .then(() => { - handleShowSnackBar( - `You successfully unsecured ${selectedArtifacts.length} ${p(selectedArtifacts.length, 'file')}.` - ); - onClose(); - }) - .catch((apiError) => { - dialogContext.setErrorDialog({ - open: true, - dialogTitle: ApplySecurityRulesI18N.unapplySecurityRulesErrorTitle, - dialogText: ApplySecurityRulesI18N.unapplySecurityRulesErrorText, - dialogError: apiError.message, - dialogErrorDetails: apiError.errors, - onClose: () => { - dialogContext.setErrorDialog({ open: false }); - }, - onOk: () => { - dialogContext.setErrorDialog({ open: false }); - } - }); - }) - .finally(() => { - setYesNoDialogOpen(false); - }); - }} - yesButtonProps={{ loading: isPendingUnapplySecurity }} - onNo={() => setYesNoDialogOpen(false)} - dialogTitle="" - dialogText="" - dialogContent={ - - - - - - Warning - - - You are going to make this document available to the public. This document can be downloaded. - Also, if there are any security reasons, they will be removed. - - - Are you sure you would like to proceed? - - - } - /> - - Apply Security Reasons - - - {`Search for the security reasons and apply them to the selected ${p( - selectedArtifacts.length, - 'document' - )}`} - - - - - - - - - } - onClick={formikProps.submitForm}> - Apply Security - - - - - - - )} - - - - ); -}; - -export default ApplySecurityDialog; diff --git a/app/src/features/datasets/components/security/SecurityReasonCategory.tsx b/app/src/features/datasets/components/security/SecurityReasonCategory.tsx deleted file mode 100644 index 67e8c7969..000000000 --- a/app/src/features/datasets/components/security/SecurityReasonCategory.tsx +++ /dev/null @@ -1,108 +0,0 @@ -import { mdiArrowDown, mdiArrowUp, mdiMinus, mdiPlus } from '@mdi/js'; -import Icon from '@mdi/react'; -import { Collapse, Divider, IconButton, Paper, Typography } from '@mui/material'; -import Box from '@mui/material/Box'; -import { FieldArray } from 'formik'; -import { useState } from 'react'; - -export interface ISecurityReason { - name: string; - id: number; - type_id: number; - wldtaxonomic_units_id: number; - description: string | null; - category: string; -} - -export interface ISecurityReasonProps { - securityReason: ISecurityReason; - onClick: (securityReason: ISecurityReason) => void; - isSelected: boolean; -} - -export interface ISecurityReasonCategoryProps { - categoryName: string; - securityReasons: ISecurityReason[]; -} -/** - * Security Reason Selector for security application. - * - * @return {*} - */ -const SecurityReasonCategory = (props: ISecurityReasonCategoryProps) => { - const { categoryName, securityReasons } = props; - - const [open, setOpen] = useState(true); - - return ( - - - - {categoryName} - - - setOpen(!open)} color="primary" aria-label="dropdown arrow" component="label"> - - - - - - - ( - <> - {securityReasons - .sort((a, b) => a.name.localeCompare(b.name)) - .map((securityReason) => { - return ( - - { - if ( - !arrayHelpers.form.values.securityReasons.find( - (sr: ISecurityReason) => sr.name === securityReason.name - ) - ) { - arrayHelpers.push({ ...securityReason, category: categoryName }); - } - }} - isSelected={false} - /> - - ); - })} - - )} - /> - - - - ); -}; - -export const SecurityReason = (props: ISecurityReasonProps) => { - const { securityReason, onClick, isSelected } = props; - - return ( - - - - {securityReason.name} - {securityReason.description} - - {securityReason.category} - - - - onClick(securityReason)} color="primary" aria-label="add security"> - - - - - - ); -}; - -export default SecurityReasonCategory; diff --git a/app/src/features/datasets/components/security/SecurityReasonSelector.tsx b/app/src/features/datasets/components/security/SecurityReasonSelector.tsx deleted file mode 100644 index 00bcf2f31..000000000 --- a/app/src/features/datasets/components/security/SecurityReasonSelector.tsx +++ /dev/null @@ -1,82 +0,0 @@ -import { Button, Paper } from '@mui/material'; -import Box from '@mui/material/Box'; -import Divider from '@mui/material/Divider'; -import { ActionToolbar } from 'components/toolbar/ActionToolbars'; -import { FieldArray, useFormikContext } from 'formik'; -import { ISelectSecurityReasonForm } from './ApplySecurityDialog'; -import SecurityReasonCategory, { ISecurityReason, SecurityReason } from './SecurityReasonCategory'; - -/** - * Security Reason Selector for security application. - * - * @return {*} - */ -const SecurityReasonSelector = (props: ISelectSecurityReasonForm) => { - const { securityReasons } = props; - const { values, setFieldValue } = useFormikContext(); - - return ( - - - - - - { - return !values.securityReasons.some((reason) => reason.name === value.name); - })} - /> - - - - - - - - - - - {values.securityReasons.length > 1 && ( - - )} - - - - ( - <> - {values.securityReasons.map((securityReason, index) => { - return ( - - arrayHelpers.remove(index)} - isSelected={true} - /> - - ); - })} - - )} - /> - - - - ); -}; - -export default SecurityReasonSelector; diff --git a/app/src/features/datasets/components/security/SelectedDocumentsDataset.tsx b/app/src/features/datasets/components/security/SelectedDocumentsDataset.tsx deleted file mode 100644 index 9a4a811d3..000000000 --- a/app/src/features/datasets/components/security/SelectedDocumentsDataset.tsx +++ /dev/null @@ -1,57 +0,0 @@ -import { Paper } from '@mui/material'; -import Box from '@mui/material/Box'; -import Divider from '@mui/material/Divider'; -import { DataGrid, GridColDef } from '@mui/x-data-grid'; -import { ActionToolbar } from 'components/toolbar/ActionToolbars'; -import { IArtifact } from 'interfaces/useDatasetApi.interface'; - -export interface IRelatedDatasetsProps { - selectedArtifacts: IArtifact[]; -} - -/** - * Selected Documents Dataset for security application. - * - * @return {*} - */ -const SelectedDocumentsDataset: React.FC = (props) => { - const { selectedArtifacts } = props; - - const columns: GridColDef[] = [ - { - field: 'file_type', - headerName: 'Type', - flex: 0.5 - }, - { - field: 'file_name', - headerName: 'Title', - flex: 2, - disableColumnMenu: true - } - ]; - - return ( - - - - - row.artifact_id} - autoHeight - rows={selectedArtifacts} - columns={columns} - disableVirtualization - disableRowSelectionOnClick - disableColumnSelector - disableColumnFilter - disableColumnMenu - disableDensitySelector - hideFooter - /> - - - ); -}; - -export default SelectedDocumentsDataset; diff --git a/app/src/features/home/HomePage.tsx b/app/src/features/home/HomePage.tsx deleted file mode 100644 index fd6773e81..000000000 --- a/app/src/features/home/HomePage.tsx +++ /dev/null @@ -1,64 +0,0 @@ -import { Container, Paper, Typography } from '@mui/material'; -import Box from '@mui/material/Box'; -import SearchComponent from 'features/search/SearchComponent'; -import { Formik, FormikProps } from 'formik'; -import { IAdvancedSearch } from 'interfaces/useSearchApi.interface'; -import { useRef } from 'react'; -import { useHistory } from 'react-router'; - -const HomePage = () => { - const formikRef = useRef>(null); - const history = useHistory(); - - const handleSubmit = () => { - const query = formikRef.current?.values?.keywords || ''; - - if (!query) { - return; - } - - history.push(`/search?keywords=${query}`); - }; - - return ( - - - - Biodiversity Hub B.C. - - - Open access to British Columbia's terrestrial, aquatic species and habitat inventory data - - - - - - - - - ); -}; - -export default HomePage; diff --git a/app/src/features/home/HomeRouter.tsx b/app/src/features/home/HomeRouter.tsx deleted file mode 100644 index baaadc629..000000000 --- a/app/src/features/home/HomeRouter.tsx +++ /dev/null @@ -1,21 +0,0 @@ -import { Switch } from 'react-router'; -import RouteWithTitle from 'utils/RouteWithTitle'; -import { getTitle } from 'utils/Utils'; -import HomePage from './HomePage'; - -/** - * Router for all `/*` pages. - * - * @return {*} - */ -const HomeRouter: React.FC = () => { - return ( - - - - - - ); -}; - -export default HomeRouter; diff --git a/app/src/features/map/MapPage.test.tsx b/app/src/features/map/MapPage.test.tsx deleted file mode 100644 index eb198a3fa..000000000 --- a/app/src/features/map/MapPage.test.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import { FeatureCollection } from 'geojson'; -import { createMemoryHistory } from 'history'; -import { useApi } from 'hooks/useApi'; -import { Router } from 'react-router'; -import { cleanup, render, waitFor } from 'test-helpers/test-utils'; -import MapPage from './MapPage'; - -jest.mock('../../hooks/useApi'); - -const mockBiohubApi = useApi as jest.Mock; - -const mockUseApi = { - search: { - getSpatialData: jest.fn() - } -}; - -const history = createMemoryHistory(); - -const renderContainer = () => { - return render( - - - - ); -}; - -jest.mock('./SideSearchBar', () => () =>
); - -describe('MapPage', () => { - beforeEach(() => { - mockBiohubApi.mockImplementation(() => mockUseApi); - }); - - afterEach(() => { - cleanup(); - }); - - it('shows `Map` and map container when there are no occurrences', async () => { - mockUseApi.search.getSpatialData.mockReturnValue([]); - - const { getByTestId } = renderContainer(); - - await waitFor(() => { - expect(getByTestId('MapContainer')).toBeVisible(); - }); - }); - - it('shows `Map` and map container with data points when there is occurrences', async () => { - const vaildFeatureCollection: FeatureCollection = { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [-129.083298513, 55.40257311] - }, - properties: { - type: 'Occurrence', - eventDate: 'string' - } - } - ] - }; - - mockUseApi.search.getSpatialData.mockReturnValue(vaildFeatureCollection); - - const { getByTestId } = renderContainer(); - - await waitFor(() => { - expect(getByTestId('MapContainer')).toBeVisible(); - }); - }); -}); diff --git a/app/src/features/map/MapPage.tsx b/app/src/features/map/MapPage.tsx deleted file mode 100644 index 1651fdb8c..000000000 --- a/app/src/features/map/MapPage.tsx +++ /dev/null @@ -1,210 +0,0 @@ -import Box from '@mui/material/Box'; -import Paper from '@mui/material/Paper'; -import intersect from '@turf/intersect'; -import { IMarkerLayer } from 'components/map/components/MarkerClusterControls'; -import { IStaticLayer, IStaticLayerFeature } from 'components/map/components/StaticLayersControls'; -import MapContainer from 'components/map/MapContainer'; -import { AreaToolTip, IFormikAreaUpload } from 'components/upload/UploadArea'; -import { ALL_OF_BC_BOUNDARY, MAP_DEFAULT_ZOOM, SPATIAL_COMPONENT_TYPE } from 'constants/spatial'; -import { IDatasetVisibility, ISearchResult } from 'features/datasets/components/SearchResultList'; -import { Feature, Polygon } from 'geojson'; -import { useApi } from 'hooks/useApi'; -import useDataLoader from 'hooks/useDataLoader'; -import useDataLoaderError from 'hooks/useDataLoaderError'; -import useURL from 'hooks/useURL'; -import { LatLngBounds, LatLngBoundsExpression, LatLngTuple } from 'leaflet'; -import React, { useEffect, useRef, useState } from 'react'; -import { calculateUpdatedMapBounds } from 'utils/mapUtils'; -import { parseBoundaryCentroidResults, parseOccurrenceResults, parseSpatialDataByType } from 'utils/spatial-utils'; -import SideSearchBar from './SideSearchBar'; - -const MapPage: React.FC = () => { - const api = useApi(); - - const url = useURL<{ - mapViewBoundary: Feature | undefined; - drawnBoundary: Feature | undefined; - type: string[] | undefined; - zoom: number | undefined; - }>(); - - const mapDataLoader = useDataLoader( - (searchBoundary: Feature[], searchType: string[], species?: string[], searchZoom?: number, datasetID?: string) => - api.search.getSpatialData({ - boundary: searchBoundary, - type: searchType, - species: species, - zoom: searchZoom, - datasetID: datasetID - }) - ); - - const loadedFromUrl = useRef(false); - - useDataLoaderError(mapDataLoader, () => { - return { - dialogTitle: 'Error Loading Map Data', - dialogText: - 'An error has occurred while attempting to load map data, please try again. If the error persists, please contact your system administrator.' - }; - }); - - const [mapViewBoundary] = useState | undefined>(url.queryParams.mapViewBoundary); - const [drawnBoundary, setDrawnBoundary] = useState | undefined>(url.queryParams.drawnBoundary); - - const [type] = useState(url.queryParams.type || [SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID]); - const [zoom, setZoom] = useState(url.queryParams.zoom || MAP_DEFAULT_ZOOM); - - const [markerLayers, setMarkerLayers] = useState([]); - const [staticLayers, setStaticLayers] = useState([]); - const [shouldUpdateBounds, setShouldUpdateBounds] = useState(false); - const [updatedBounds, setUpdatedBounds] = useState(undefined); - const [areaStaticLayers, setAreaStaticLayers] = useState([]); - const [datasetVisibility, setDatasetVisibility] = useState({}); - - const [parsedSearchResults, setParsedSearchResults] = useState([]); - - useEffect(() => { - if (!mapDataLoader.data) { - return; - } - - const result = parseSpatialDataByType(mapDataLoader.data, datasetVisibility); - - setMarkerLayers(result.markerLayers); - setStaticLayers(result.staticLayers); - - setParsedSearchResults([ - ...parseOccurrenceResults(mapDataLoader.data, datasetVisibility), - ...parseBoundaryCentroidResults(mapDataLoader.data, datasetVisibility) - ]); - - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [mapDataLoader.data, datasetVisibility]); - - useEffect(() => { - if (!loadedFromUrl.current) { - loadedFromUrl.current = true; - if (drawnBoundary) { - const searchBoundary = getSearchBoundary(mapViewBoundary, drawnBoundary); - mapDataLoader.refresh([searchBoundary], type, [], zoom); - } - } - }); - - const getSearchBoundary = (boundary1?: Feature, boundary2?: Feature) => { - return (boundary2 && boundary1 && intersect(boundary2, boundary1)) || boundary1 || boundary2 || ALL_OF_BC_BOUNDARY; - }; - - const onDrawChange = (features: Feature[]) => { - // In this case, we have disabled all draw controls except Polygons, and limited it to only 1 at a time, so - // assuming the type should be safe. This will need to be updated if the draw control options are changed. - const bounds = features?.[0] as Feature | undefined; - - // Store user drawn boundary - setDrawnBoundary(bounds); - - // Calculate search boundary based on drawn and map view boundaries - const searchBoundary = getSearchBoundary(mapViewBoundary, bounds); - - // Store drawn bounds in URL - url.appendQueryParams({ drawnBoundary: bounds }); - - mapDataLoader.refresh([searchBoundary], type, [], zoom); - }; - - const onAreaUpdate = (areas: IFormikAreaUpload[]) => { - const staticLayers: IStaticLayer[] = []; - const featureArray: Feature[] = []; - - areas.forEach((area) => { - const layers: IStaticLayerFeature[] = []; - area.features.forEach((feature: Feature) => { - const staticLayerFeature: IStaticLayerFeature = { - geoJSON: feature, - tooltip: - }; - layers.push(staticLayerFeature); - featureArray.push(feature); - }); - const staticLayer: IStaticLayer = { layerName: area.name, features: layers, visible: true }; - staticLayers.push(staticLayer); - }); - - setAreaStaticLayers(staticLayers); - setBounds(featureArray); - }; - - const setBounds = (features: Feature[]) => { - const bounds = calculateUpdatedMapBounds(features); - - if (bounds) { - const newBounds = new LatLngBounds(bounds[0] as LatLngTuple, bounds[1] as LatLngTuple); - setShouldUpdateBounds(true); - setUpdatedBounds(newBounds); - } else { - const boundsBC = calculateUpdatedMapBounds([ALL_OF_BC_BOUNDARY]); - if (boundsBC) { - const newBounds = new LatLngBounds(boundsBC[0] as LatLngTuple, boundsBC[1] as LatLngTuple); - setShouldUpdateBounds(true); - setUpdatedBounds(newBounds); - } - } - }; - - const onToggleDataVisibility = (visibility: IDatasetVisibility) => { - setDatasetVisibility({ ...visibility }); - }; - - return ( - - - - - - , zoom: number) => { - setZoom(zoom); - setShouldUpdateBounds(false); - }} - drawControls={{ - initialFeatures: drawnBoundary && [drawnBoundary], - options: { - // Disable all controls except for Polygon (and Rectangle, which is just a type of Polygon) - draw: { circle: false, circlemarker: false, marker: false, polyline: false } - }, - // Limit drawing to 1 shape at a time - clearOnDraw: true - }} - onDrawChange={onDrawChange} - scrollWheelZoom={true} - zoom={zoom} - fullScreenControl={true} - markerLayers={markerLayers} - staticLayers={[...staticLayers, ...areaStaticLayers]} - bounds={(shouldUpdateBounds && updatedBounds) || undefined} - zoomControlEnabled={true} - doubleClickZoomEnabled={true} - draggingEnabled={true} - layerControlEnabled={true} - /> - - - ); -}; - -export default MapPage; diff --git a/app/src/features/map/MapRouter.tsx b/app/src/features/map/MapRouter.tsx deleted file mode 100644 index 7ba5dbd78..000000000 --- a/app/src/features/map/MapRouter.tsx +++ /dev/null @@ -1,21 +0,0 @@ -import { Switch } from 'react-router'; -import RouteWithTitle from 'utils/RouteWithTitle'; -import { getTitle } from 'utils/Utils'; -import MapPage from './MapPage'; - -/** - * Router for all `/map` pages. - * - * @return {*} - */ -const MapRouter: React.FC = () => { - return ( - - - - - - ); -}; - -export default MapRouter; diff --git a/app/src/features/map/SideSearchBar.test.tsx b/app/src/features/map/SideSearchBar.test.tsx deleted file mode 100644 index 6eb064585..000000000 --- a/app/src/features/map/SideSearchBar.test.tsx +++ /dev/null @@ -1,58 +0,0 @@ -import { Feature, GeoJsonProperties, Geometry } from 'geojson'; -import { useApi } from 'hooks/useApi'; -import useDataLoader from 'hooks/useDataLoader'; -import { ISpatialData } from 'interfaces/useSearchApi.interface'; -import { cleanup, render } from 'test-helpers/test-utils'; -import SideSearchBar from './SideSearchBar'; - -jest.mock('../../hooks/useApi'); - -const mockBiohubApi = useApi as jest.Mock; - -const mockUseApi = { - taxonomy: { - searchSpecies: jest.fn() - } -}; - -describe('SideSearchBar', () => { - beforeEach(() => { - mockBiohubApi.mockImplementation(() => mockUseApi); - }); - afterEach(() => { - cleanup(); - }); - - it('renders an empty component', () => { - const TestComponent = () => { - const mockCallBack = jest.fn().mockResolvedValue({}); - const mockMapDataLoader = useDataLoader< - [ - searchBoundary: Feature[], - searchType: string[], - species?: string[], - searchZoom?: number, - datasetID?: string - ], - ISpatialData[], - unknown - >(mockCallBack); - const mockAreaUpdate = jest.fn(); - const mockOnToggleDataVisibility = jest.fn(); - return ( - - ); - }; - - const { getByText } = render(); - - expect(getByText('What do you want to find?', { exact: false })).toBeVisible(); - expect(getByText('Refine Search Area', { exact: false })).toBeVisible(); - expect(getByText('Find Data', { exact: false })).toBeVisible(); - }); -}); diff --git a/app/src/features/map/SideSearchBar.tsx b/app/src/features/map/SideSearchBar.tsx deleted file mode 100644 index 7a8521d07..000000000 --- a/app/src/features/map/SideSearchBar.tsx +++ /dev/null @@ -1,210 +0,0 @@ -import { mdiArrowRight } from '@mdi/js'; -import Icon from '@mdi/react'; -import LoadingButton from '@mui/lab/LoadingButton'; -import { Box, Button } from '@mui/material'; -import Divider from '@mui/material/Divider'; -import Typography from '@mui/material/Typography'; -import simplify from '@turf/simplify'; -import { ErrorDialog } from 'components/dialog/ErrorDialog'; -import { IMultiAutocompleteFieldOption } from 'components/fields/MultiAutocompleteField'; -import { IFormikAreaUpload } from 'components/upload/UploadArea'; -import DatasetSearchForm, { - DatasetSearchFormInitialValues, - DatasetSearchFormYupSchema, - IDatasetSearchForm -} from 'features/datasets/components/DatasetSearchForm'; -import SearchResultList, { IDatasetVisibility, ISearchResult } from 'features/datasets/components/SearchResultList'; -import { Form, Formik, FormikProps } from 'formik'; -import { Feature, GeoJsonProperties, Geometry, Polygon } from 'geojson'; -import { DataLoader } from 'hooks/useDataLoader'; -import { ISpatialData } from 'interfaces/useSearchApi.interface'; -import { useEffect, useRef, useState } from 'react'; - -export interface IDatasetRequest { - criteria: { - boundary: Feature; - type: string[]; - species?: IMultiAutocompleteFieldOption[]; - zoom?: number; // TODO include in request params when backend is updated to receive it - datasetID?: string; - datasetName?: string; - }; -} - -export interface SideSearchBarProps { - mapDataLoader: DataLoader< - [ - searchBoundary: Feature[], - searchType: string[], - species?: string[], - searchZoom?: number, - datasetID?: string - ], - ISpatialData[], - unknown - >; - searchResults: ISearchResult[]; - onAreaUpdate: (area: IFormikAreaUpload[]) => void; - onToggleDataVisibility: (datasets: IDatasetVisibility) => void; -} - -const SideSearchBar: React.FC = (props) => { - const formikRef = useRef>(null); - const [showForm, setShowForm] = useState(true); - const [showNoData, setShowNoData] = useState(false); - const [showSpinner, setShowSpinner] = useState(false); - - const [formData, setFormData] = useState(null); - /** - * Handle dataset requests. - */ - const handleDatasetRequestCreation = async (values: IDatasetSearchForm) => { - const featureArray: Feature[] = []; - values.area.forEach((area: IFormikAreaUpload) => { - area.features.forEach((feature: Feature) => { - const newFeature: Feature = { - type: 'Feature', - geometry: simplify(feature.geometry, { tolerance: 0.01, highQuality: false }), - properties: feature.properties - }; - featureArray.push(newFeature); - }); - }); - - const species_array: string[] = []; - values.species_list.forEach((item) => { - species_array.push(item.value.toString()); - }); - - props.mapDataLoader.refresh(featureArray, [values.dataset], species_array); - setFormData(values); - }; - - const toggleShowForm = () => { - setShowForm(!showForm); - }; - - useEffect(() => { - setShowSpinner(true); - if (props.mapDataLoader.isReady) { - if (!props.mapDataLoader.data?.length) { - setShowNoData(true); - setShowForm(true); - } else { - setShowForm(false); - } - } - - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [props.mapDataLoader.isLoading, props.mapDataLoader.isReady]); - - const hasResults = props.searchResults.length > 0; - - return ( - <> - setShowNoData(false)} - onOk={() => setShowNoData(false)} - /> - {showForm && ( - - - - - Map Search - - {hasResults && ( - - )} - - - - - - innerRef={formikRef} - enableReinitialize={true} - initialValues={formData || DatasetSearchFormInitialValues} - validationSchema={DatasetSearchFormYupSchema} - validateOnBlur={true} - validateOnChange={false} - onSubmit={handleDatasetRequestCreation}> - {(formikProps) => ( - -
- - - - {showSpinner && - (props.mapDataLoader.isLoading ? ( - - Submit - - ) : ( - - ))} - - -
- )} - - - - )} - - {!showForm && hasResults && ( - toggleShowForm()} - onToggleDataVisibility={props.onToggleDataVisibility} - /> - )} - - ); -}; - -export default SideSearchBar; diff --git a/app/src/features/search/SearchComponent.tsx b/app/src/features/search/SearchComponent.tsx index d9f8c1ab7..72d7f3830 100644 --- a/app/src/features/search/SearchComponent.tsx +++ b/app/src/features/search/SearchComponent.tsx @@ -1,13 +1,9 @@ import { mdiMagnify } from '@mdi/js'; import { Icon } from '@mdi/react'; import { Theme } from '@mui/material'; -import Box from '@mui/material/Box'; -import Button from '@mui/material/Button'; import Input from '@mui/material/Input'; import InputAdornment from '@mui/material/InputAdornment'; import { makeStyles } from '@mui/styles'; -import { useFormikContext } from 'formik'; -import { IAdvancedSearch } from 'interfaces/useSearchApi.interface'; import { ChangeEvent } from 'react'; export const useSearchInputStyles = makeStyles((theme: Theme) => ({ @@ -86,35 +82,3 @@ export const SearchInput = (props: ISearchInputProps) => { /> ); }; - -const SearchComponent: React.FC = () => { - const classes = useSearchInputStyles(); - - const formikProps = useFormikContext(); - const { handleSubmit, handleChange, values } = formikProps; - - return ( -
- - - - -
- ); -}; - -export default SearchComponent; diff --git a/app/src/hooks/api/useDatasetApi.test.ts b/app/src/hooks/api/useDatasetApi.test.ts index d97b085f1..e7f01a331 100644 --- a/app/src/hooks/api/useDatasetApi.test.ts +++ b/app/src/hooks/api/useDatasetApi.test.ts @@ -13,16 +13,6 @@ describe('useDatasetApi', () => { mock.restore(); }); - it('getDatasetEML works as expected', async () => { - const response = 'response'; - - mock.onGet('api/dwc/submission/a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf/get').reply(200, response); - - const actualResult = await useDatasetApi(axios).getDatasetEML('a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf'); - - expect(actualResult).toEqual('response'); - }); - it('getDatasetArtifacts works as expected', async () => { const response = { artifacts: [{ artifact_id: 1 }, { artifact_id: 2 }] @@ -44,29 +34,4 @@ describe('useDatasetApi', () => { expect(actualResult).toEqual('http://example.com'); }); - - it('getRelatedDatasets works as expected', async () => { - mock.onGet(`api/dwc/submission/${'123-456-789'}/related`).reply(200, { - datasets: [{ datasetId: '123' }, { datasetId: '456' }] - }); - - const actualResult = await useDatasetApi(axios).getRelatedDatasets('123-456-789'); - - expect(actualResult).toEqual({ - datasets: [{ datasetId: '123' }, { datasetId: '456' }] - }); - }); - - it('getHandleBarsTemplateByDatasetId works as expected', async () => { - mock.onGet(`api/dwc/submission/uuid/handlebar`).reply(200, { - header: 'Header Template', - details: 'Details Template' - }); - - const results = await useDatasetApi(axios).getHandleBarsTemplateByDatasetId('uuid'); - expect(results).toEqual({ - header: 'Header Template', - details: 'Details Template' - }); - }); }); diff --git a/app/src/hooks/api/useDatasetApi.ts b/app/src/hooks/api/useDatasetApi.ts index cc764c050..b1b7905d2 100644 --- a/app/src/hooks/api/useDatasetApi.ts +++ b/app/src/hooks/api/useDatasetApi.ts @@ -1,5 +1,5 @@ import { AxiosInstance } from 'axios'; -import { IArtifact, IHandlebarsTemplates, IListRelatedDatasetsResponse } from 'interfaces/useDatasetApi.interface'; +import { IArtifact } from 'interfaces/useDatasetApi.interface'; /** * Returns a set of supported api methods for working with datasets. @@ -8,18 +8,6 @@ import { IArtifact, IHandlebarsTemplates, IListRelatedDatasetsResponse } from 'i * @return {*} object whose properties are supported api methods. */ const useDatasetApi = (axios: AxiosInstance) => { - /** - * Fetch dataset metadata by datasetId. - * - * @param {string} datasetId - * @return {*} {Promise} - */ - const getDatasetEML = async (datasetId: string): Promise => { - const { data } = await axios.get(`api/dwc/submission/${datasetId}/get`); - - return data; - }; - /** * Fetch dataset data by datasetUUID. * @@ -55,37 +43,10 @@ const useDatasetApi = (axios: AxiosInstance) => { return data; }; - /** - * Fetch the signed handlebar template for a given dataset ID. - * - * @param {string} datasetId - * @return {*} {Promise} - */ - const getHandleBarsTemplateByDatasetId = async (datasetId: string): Promise => { - const { data } = await axios.get(`api/dwc/submission/${datasetId}/handlebar`); - - return data; - }; - - /** - * Fetch a list of datasets related to the given dataset - * - * @param {string} datasetId - * @return {*} {Promise} - */ - const getRelatedDatasets = async (datasetId: string): Promise => { - const { data } = await axios.get(`api/dwc/submission/${datasetId}/related`); - - return data; - }; - return { - getDatasetEML, getDataset, getDatasetArtifacts, - getArtifactSignedUrl, - getHandleBarsTemplateByDatasetId, - getRelatedDatasets + getArtifactSignedUrl }; }; diff --git a/app/src/hooks/api/useSearchApi.test.ts b/app/src/hooks/api/useSearchApi.test.ts deleted file mode 100644 index 531306964..000000000 --- a/app/src/hooks/api/useSearchApi.test.ts +++ /dev/null @@ -1,89 +0,0 @@ -import axios from 'axios'; -import MockAdapter from 'axios-mock-adapter'; -import { Feature, FeatureCollection } from 'geojson'; -import useSearchApi, { usePublicSearchApi } from './useSearchApi'; - -describe('useSearchApi', () => { - let mock: any; - - beforeEach(() => { - mock = new MockAdapter(axios); - }); - - afterEach(() => { - mock.restore(); - }); - - describe('getSpatialData', () => { - it('with criteria `type` works as expected', async () => { - const res = [{ type: 'FeatureCollection' } as FeatureCollection]; - - mock.onGet('/api/dwc/spatial/search').reply(200, res); - - const result = await useSearchApi(axios).getSpatialData({ - boundary: [{ type: 'Feature' }] as Feature[], - type: ['type'] - }); - - expect(result[0]).toEqual({ type: 'FeatureCollection' }); - }); - - it('with criteria `species` works as expected', async () => { - const res = [{ species: 'Spotted Owl' }]; - - mock.onGet('/api/dwc/spatial/search').reply(200, res); - - const result = await useSearchApi(axios).getSpatialData({ - boundary: [{ type: 'Feature' }] as Feature[], - type: ['type'], - species: ['species'] - }); - - expect(result[0]).toEqual({ species: 'Spotted Owl' }); - }); - }); - - it('getSpatialFile works as expected', async () => { - const res = 'zipped file contents'; - - mock.onGet('/api/dwc/spatial/download').reply(200, res); - - const result = await useSearchApi(axios).getSpatialDataFile({ - boundary: [{ type: 'Feature' }] as Feature[], - type: ['type'], - datasetID: '123' - }); - - expect(typeof result).toBe('string'); - expect(result).toEqual('zipped file contents'); - }); -}); - -describe('usePublicSearchApi', () => { - let mock: any; - - beforeEach(() => { - mock = new MockAdapter(axios); - }); - - afterEach(() => { - mock.restore(); - }); - - it('getSearchResults works as expected', async () => { - const res = [ - { - id: '1', - name: 'name', - objectives: 'objectives', - geometry: [] - } - ]; - - mock.onGet('api/public/search').reply(200, res); - - const result = await usePublicSearchApi(axios).getSearchResults(); - - expect(result[0].id).toEqual('1'); - }); -}); diff --git a/app/src/hooks/api/useSearchApi.ts b/app/src/hooks/api/useSearchApi.ts deleted file mode 100644 index bb72ed935..000000000 --- a/app/src/hooks/api/useSearchApi.ts +++ /dev/null @@ -1,82 +0,0 @@ -import { AxiosInstance } from 'axios'; -import { Feature, GeoJsonProperties } from 'geojson'; -import { IGetSearchResultsResponse, ISpatialData } from 'interfaces/useSearchApi.interface'; - -/** - * Returns a set of supported api methods for working with search functionality - * - * @param {AxiosInstance} axios - * @return {*} object whose properties are supported api methods. - */ -const useSearchApi = (axios: AxiosInstance) => { - const getSpatialData = async (criteria: { - boundary: Feature[]; - type: string[]; - species?: string[]; - zoom?: number; // TODO include in request params when backend is updated to receive it - datasetID?: string; - }): Promise => { - const { data } = await axios.get(`/api/dwc/spatial/search`, { - params: { - boundary: criteria.boundary, - species: criteria.species, - type: criteria.type, - datasetID: criteria.datasetID - } - }); - - return data; - }; - - const getSpatialMetadata = async (submissionSpatialComponentIds: number[]): Promise => { - const { data } = await axios.get(`/api/dwc/spatial/metadata`, { - params: { submissionSpatialComponentIds } - }); - - return data; - }; - - const getSpatialDataFile = async (criteria: { - boundary: Feature[]; - type: string[]; - zoom?: number; // TODO include in request params when backend is updated to receive it - datasetID?: string; - }): Promise => { - const { data } = await axios.get(`/api/dwc/spatial/download`, { - params: { boundary: criteria.boundary, type: criteria.type, datasetID: criteria.datasetID } - }); - - return data; - }; - - return { - getSpatialData, - getSpatialMetadata, - getSpatialDataFile - }; -}; - -export default useSearchApi; - -/** - * Returns a set of supported api methods for working with public search functionality. - * - * @param {AxiosInstance} axios - * @return {*} object whose properties are supported api methods. - */ -export const usePublicSearchApi = (axios: AxiosInstance) => { - /** - * Get public search results (spatial) - * - * @return {*} {Promise} - */ - const getSearchResults = async (): Promise => { - const { data } = await axios.get(`/api/public/search`); - - return data; - }; - - return { - getSearchResults - }; -}; diff --git a/app/src/hooks/api/useSubmissionsApi.test.ts b/app/src/hooks/api/useSubmissionsApi.test.ts index 81d4869b8..3928c102e 100644 --- a/app/src/hooks/api/useSubmissionsApi.test.ts +++ b/app/src/hooks/api/useSubmissionsApi.test.ts @@ -13,34 +13,6 @@ describe('useSubmissionApi', () => { mock.restore(); }); - it('listSubmissions works as expected', async () => { - const res = [ - { - create_date: '2022-05-24T18:41:42.056Z', - create_user: 15, - darwin_core_source: {}, - delete_timestamp: null, - eml_source: null, - event_timestamp: '2022-05-24T18:41:42.211Z', - input_file_name: 'moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - input_key: 'biohub/1/moose_aerial_stratifiedrandomblock_composition_recruitment_survey_2.5_withdata.zip', - revision_count: 1, - source: 'SIMS', - submission_id: 1, - submission_status: null, - update_date: '2022-05-24T18:41:42.056Z', - update_user: 15, - uuid: '2267501d-c6a9-43b5-b951-2324faff6397' - } - ]; - - mock.onGet('/api/dwc/submission/list').reply(200, res); - - const result = await useSubmissionsApi(axios).listSubmissions(); - - expect(result[0].submission_id).toEqual(1); - }); - it('getSignedUrl works as expected', async () => { const res = 'test-signed-url'; const testSubmissionId = 1; diff --git a/app/src/hooks/api/useSubmissionsApi.ts b/app/src/hooks/api/useSubmissionsApi.ts index 69211fb9b..a73446780 100644 --- a/app/src/hooks/api/useSubmissionsApi.ts +++ b/app/src/hooks/api/useSubmissionsApi.ts @@ -2,7 +2,6 @@ import { AxiosInstance } from 'axios'; import { IGetDownloadSubmissionResponse, IGetSubmissionGroupedFeatureResponse, - IListSubmissionsResponse, SubmissionFeatureSignedUrlPayload, SubmissionRecordPublishedForPublic, SubmissionRecordWithSecurity, @@ -16,17 +15,6 @@ import { * @return {*} object whose properties are supported api methods. */ const useSubmissionsApi = (axios: AxiosInstance) => { - /** - * Fetch all submissions. - * - * @return {*} {Promise} - */ - const listSubmissions = async (): Promise => { - const { data } = await axios.get('/api/dwc/submission/list'); - - return data; - }; - /** * Fetch the signed URL of a submission by submission ID. * @@ -169,7 +157,6 @@ const useSubmissionsApi = (axios: AxiosInstance) => { }; return { - listSubmissions, getSignedUrl, getSubmissionDownloadPackage, getSubmissionPublishedDownloadPackage, diff --git a/app/src/hooks/useApi.ts b/app/src/hooks/useApi.ts index 4af2637da..a2be22539 100644 --- a/app/src/hooks/useApi.ts +++ b/app/src/hooks/useApi.ts @@ -5,7 +5,6 @@ import useArtifactApi from './api/useArtifactApi'; import useAxios from './api/useAxios'; import useCodesApi from './api/useCodesApi'; import useDatasetApi from './api/useDatasetApi'; -import useSearchApi, { usePublicSearchApi } from './api/useSearchApi'; import useSecurityApi from './api/useSecurityApi'; import useSubmissionsApi from './api/useSubmissionsApi'; import useTaxonomyApi from './api/useTaxonomyApi'; @@ -28,12 +27,6 @@ export const useApi = () => { const taxonomy = useTaxonomyApi(apiAxios); - const publicApis = { - search: usePublicSearchApi(apiAxios) - }; - - const search = useSearchApi(apiAxios); - const dataset = useDatasetApi(apiAxios); const artifact = useArtifactApi(apiAxios); @@ -46,8 +39,6 @@ export const useApi = () => { user, admin, submissions, - public: publicApis, - search, dataset, taxonomy, security, diff --git a/app/src/interfaces/useDatasetApi.interface.ts b/app/src/interfaces/useDatasetApi.interface.ts index f09ecba4a..25afd6211 100644 --- a/app/src/interfaces/useDatasetApi.interface.ts +++ b/app/src/interfaces/useDatasetApi.interface.ts @@ -47,10 +47,6 @@ export interface IListRelatedDatasetsResponse { datasetsWithSupplementaryData: IRelatedDataset[]; } -export interface IHandlebarsTemplates { - header: string; - details: string; -} export interface IDatasetForReview { dataset_id: string; // UUID artifacts_to_review: number; diff --git a/app/src/interfaces/useSearchApi.interface.ts b/app/src/interfaces/useSearchApi.interface.ts deleted file mode 100644 index 8e56d706c..000000000 --- a/app/src/interfaces/useSearchApi.interface.ts +++ /dev/null @@ -1,71 +0,0 @@ -import { Feature, FeatureCollection } from 'geojson'; - -/** - * Get search results response object. - * - * @export - * @interface IGetSearchResultsResponse - */ -export interface IGetSearchResultsResponse { - id: string; - name?: string; - objectives?: string; - taxonID?: string; - lifestage?: string; - geometry: Feature[]; -} - -export type EmptyObject = Record; - -export interface ITaxaData { - taxon_id?: string; - vernacular_name?: string; - submission_spatial_component_id: number; -} -export interface ISpatialData { - taxa_data: ITaxaData[]; - spatial_data: FeatureCollection | EmptyObject; -} - -/** - * An interface for an instance of filter fields for search results - */ -export interface ISearchResultsAdvancedFilterRequest { - record_type: string; - geometry: Feature[]; -} - -/** - * Interface for Occurrence table return. - * Check api\src\repositories\occurrence-repository.ts for updates - * @export - * @interface IGetOccurrenceData - */ -export interface IGetOccurrenceData { - occurrenceId: number; - submissionId: number; - taxonId: string | null; - lifeStage: string | null; - sex: string | null; - eventDate: object | null; - vernacularName: string | null; - individualCount: number | null; - organismQuantity: number | null; - organismQuantityType: string | null; - geometry: Feature | null; -} - -export type IElasticSearchResponse = { - id: string; - fields: Fields; - source: Source; -}; - -export interface IKeywordSearchResponse, Source = Record> - extends IElasticSearchResponse { - observation_count: number; -} - -export interface IAdvancedSearch { - keywords: string; -} diff --git a/app/src/interfaces/useSubmissionsApi.interface.ts b/app/src/interfaces/useSubmissionsApi.interface.ts index 0912f52e5..7578c23ba 100644 --- a/app/src/interfaces/useSubmissionsApi.interface.ts +++ b/app/src/interfaces/useSubmissionsApi.interface.ts @@ -1,23 +1,5 @@ import { SECURITY_APPLIED_STATUS } from './useDatasetApi.interface'; -export type IListSubmissionsResponse = Array<{ - submission_id: number; - submission_status: string; - source_transform_id: string; - uuid: string; - event_timestamp: string; - delete_timestamp: string | null; - input_key: string | null; - input_file_name: string | null; - eml_source: string | null; - darwin_core_source: string | null; - create_date: string; - create_user: number; - update_date: string | null; - update_user: number | null; - revision_count: number; -}>; - /** NET-NEW INTERFACES FOR UPDATED SCHEMA **/ export type SubmissionRecord = { diff --git a/app/src/styles/handlebar.scss b/app/src/styles/handlebar.scss deleted file mode 100644 index d759e4097..000000000 --- a/app/src/styles/handlebar.scss +++ /dev/null @@ -1,62 +0,0 @@ -.hbr-header { - display: flex; - flex-direction: column; - - .hbr-header-title-primary { - font-size: 32px; - color: #313132; - font-weight: bold; - margin: 0; - } - - .hbr-header-badge { - background-color: #d9eaf7; - border-radius: 16px; - padding: 5px 10px; - width: fit-content; - font-size: 10px; - font-weight: bold; - color: #313132; - text-transform: uppercase; - margin-top: 6px; - } -} - -.hbr-container { - .hbr-project-coordinator { - list-style-type: none; - padding: 0; - margin: 0; - } - - .details-container { - border-radius: 6px; - background-color: #ffffff; - margin: 0 24px; - .details-container-title { - background-color: #ffffff; - background-size: cover; - font-size: 20px; - font-weight: bold; - padding: 18px 25px; - border-bottom: solid thin #dadada; - border-radius: 6px 6px 0 0; - } - - .details-container-metadata { - div { - display: flex; - padding: 10px 0px; - border-bottom: solid thin #dadada; - dt { - color: #787f81; - flex: 1; - max-width: 200px; - } - dd { - flex: 1; - } - } - } - } -} diff --git a/app/src/utils/handlebarsUtils.ts b/app/src/utils/handlebarsUtils.ts deleted file mode 100644 index b60d7030a..000000000 --- a/app/src/utils/handlebarsUtils.ts +++ /dev/null @@ -1,106 +0,0 @@ -import dayjs from 'dayjs'; -import Handlebars, { HelperOptions } from 'handlebars'; - -export const useHandlebars = () => { - /** - * This functions allows us to conditionally check values - * - */ - const applyConditionalChecks = () => { - Handlebars.registerHelper('ifCond', (v1, operator, v2, options: HelperOptions) => { - switch (operator) { - case '==': - return v1 === v2 ? options.fn(this) : options.inverse(this); - case '===': - return v1 === v2 ? options.fn(this) : options.inverse(this); - case '!=': - return v1 !== v2 ? options.fn(this) : options.inverse(this); - case '!==': - return v1 !== v2 ? options.fn(this) : options.inverse(this); - case '<': - return v1 < v2 ? options.fn(this) : options.inverse(this); - case '<=': - return v1 <= v2 ? options.fn(this) : options.inverse(this); - case '>': - return v1 > v2 ? options.fn(this) : options.inverse(this); - case '>=': - return v1 >= v2 ? options.fn(this) : options.inverse(this); - case '&&': - return v1 && v2 ? options.fn(this) : options.inverse(this); - case '||': - return v1 || v2 ? options.fn(this) : options.inverse(this); - default: - return options.inverse(this); - } - }); - }; - - /** - * This is a Handlesbars helper to format date strings from a given format to another using dayjs - * Example of use - * - * {{formatDate MyDateProperty 'YYYY-MM-DD' 'MMM YYYY'}} - * - */ - const formatDateHelper = () => { - Handlebars.registerHelper('formatDate', (dateString: string, ogFormat: string, newFormat: string) => { - return dayjs(dateString, ogFormat).format(newFormat).toString(); - }); - }; - - /** - * This is a Handlesbars helper to check if a passed item is an array or not - * Example of use in a template - * - * - * {{#if (isAnArray AnyObject)}} - * - * {{else}} - * - * {{/if}} - * - */ - const isAnArray = () => { - Handlebars.registerHelper('isAnArray', (item: any) => { - return Array.isArray(item); - }); - }; - - /** - * This function converts a rawTemplate to a template - * - * @param {string} template - * @return {*} {HandlebarsTemplateDelegate} - */ - const compileFromRawTemplate = (template: TemplateSpecification): HandlebarsTemplateDelegate => { - applyConditionalChecks(); - formatDateHelper(); - isAnArray(); - return Handlebars.compile(template); - }; - - /** - * This function converts a precompiled template - * see Readme/handlebars.md for more information - * - * @param {TemplateSpecification} preCompiledTemplate - * @return {*} {HandlebarsTemplateDelegate} - */ - const compileFromPrecompiledTemplate = (preCompiledTemplate: TemplateSpecification): HandlebarsTemplateDelegate => { - // This is a workaround to using Handlebars.template(preCompiledTemplate) - // in order to avoid an unknown object exception - - const encodedHandlebarsFunction = `(handlebars) => handlebars.template(${preCompiledTemplate})`; - // eslint-disable-next-line no-eval - const handlebarsFunction = eval(encodedHandlebarsFunction); - - return handlebarsFunction(Handlebars); - }; - - return { - compileFromRawTemplate, - compileFromPrecompiledTemplate - }; -}; - -export default useHandlebars; diff --git a/app/src/utils/spatial-utils.test.tsx b/app/src/utils/spatial-utils.test.tsx deleted file mode 100644 index 4507bc8ad..000000000 --- a/app/src/utils/spatial-utils.test.tsx +++ /dev/null @@ -1,143 +0,0 @@ -import { LAYER_NAME, SPATIAL_COMPONENT_TYPE } from 'constants/spatial'; -import { ISpatialData } from 'interfaces/useSearchApi.interface'; -import { parseSpatialDataByType } from './spatial-utils'; - -describe('parseSpatialDataByType', () => { - it('returns empty responses if featureCollections param is empty', () => { - const spatialData: ISpatialData[] = []; - - const result = parseSpatialDataByType(spatialData); - - expect(result.markerLayers).toEqual([{ layerName: LAYER_NAME.OCCURRENCES, markers: [], visible: true }]); - - expect(result.staticLayers).toEqual([{ layerName: LAYER_NAME.BOUNDARIES, features: [], visible: true }]); - }); - - it('returns empty responses if featureCollections param is has no features', () => { - const spatialData: ISpatialData[] = [ - { - taxa_data: [ - { - submission_spatial_component_id: 1 - } - ], - spatial_data: { - type: 'FeatureCollection', - features: [] - } - } - ]; - - const result = parseSpatialDataByType(spatialData); - - expect(result.markerLayers).toEqual([{ layerName: LAYER_NAME.OCCURRENCES, markers: [], visible: true }]); - - expect(result.staticLayers).toEqual([{ layerName: LAYER_NAME.BOUNDARIES, features: [], visible: true }]); - }); - - it('returns non-empty responses if featureCollections has features', () => { - const spatialData: ISpatialData[] = [ - { - taxa_data: [ - { - taxon_id: 'M-ALAM', - vernacular_name: 'Moose', - submission_spatial_component_id: 1 - } - ], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [123, 456] - }, - properties: { - type: SPATIAL_COMPONENT_TYPE.OCCURRENCE - } - } - ] - } - }, - { - taxa_data: [ - { - submission_spatial_component_id: 2 - } - ], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'GeometryCollection', - geometries: [] - }, - properties: {} - } - ] - } - }, - { - taxa_data: [ - { - submission_spatial_component_id: 3 - } - ], - spatial_data: { - type: 'FeatureCollection', - features: [ - { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [321, 654] - }, - properties: { - type: SPATIAL_COMPONENT_TYPE.BOUNDARY - } - } - ] - } - } - ]; - - const result = parseSpatialDataByType(spatialData); - - expect(result.markerLayers.length).toEqual(1); - expect(result.markerLayers[0]).toMatchObject({ - layerName: LAYER_NAME.OCCURRENCES, - markers: [ - { - position: [123, 456], - key: '1', - popup: expect.any(Object) - } - ] - }); - - expect(result.staticLayers.length).toEqual(1); - expect(result.staticLayers[0]).toMatchObject({ - layerName: LAYER_NAME.BOUNDARIES, - features: [ - { - geoJSON: { - type: 'Feature', - geometry: { - type: 'Point', - coordinates: [321, 654] - }, - properties: { - type: SPATIAL_COMPONENT_TYPE.BOUNDARY - } - }, - key: undefined, - popup: expect.any(Object) - } - ] - }); - }); -}); diff --git a/app/src/utils/spatial-utils.tsx b/app/src/utils/spatial-utils.tsx deleted file mode 100644 index 9f06a3c2e..000000000 --- a/app/src/utils/spatial-utils.tsx +++ /dev/null @@ -1,230 +0,0 @@ -import { IMarker, IMarkerLayer } from 'components/map/components/MarkerClusterControls'; -import { IStaticLayer } from 'components/map/components/StaticLayersControls'; -import DatasetPopup from 'components/map/DatasetPopup'; -import FeaturePopup, { BoundaryCentroidFeature, BoundaryFeature, OccurrenceFeature } from 'components/map/FeaturePopup'; -import { LAYER_NAME, SPATIAL_COMPONENT_TYPE } from 'constants/spatial'; -import { IDatasetVisibility, ISearchResult } from 'features/datasets/components/SearchResultList'; -import { Feature } from 'geojson'; -import { EmptyObject, ISpatialData, ITaxaData } from 'interfaces/useSearchApi.interface'; -import { LatLngTuple } from 'leaflet'; -import { isObject } from './Utils'; - -const UNKNOWN_TAXON = 'Unknown'; - -export interface ISpatialDataGroupedBySpecies { - [species: string]: ISpatialData[]; -} - -export const parseSpatialDataByType = ( - spatialDataRecords: ISpatialData[], - datasetVisibility: IDatasetVisibility = {} -) => { - const occurrencesMarkerLayer: IMarkerLayer = { layerName: LAYER_NAME.OCCURRENCES, markers: [], visible: true }; - const boundaryStaticLayer: IStaticLayer = { layerName: LAYER_NAME.BOUNDARIES, features: [], visible: true }; - - for (const spatialRecord of spatialDataRecords) { - if (isEmptyObject(spatialRecord.spatial_data)) { - continue; - } - - for (const feature of spatialRecord.spatial_data.features) { - let visible = true; - - if (feature.geometry.type === 'GeometryCollection') { - // Not expecting or supporting geometry collections - continue; - } - - if (isOccurrenceFeature(feature)) { - // check if species has been toggled on/ off - const marker = occurrenceMarkerSetup( - feature.geometry.coordinates as LatLngTuple, - spatialRecord.taxa_data, - datasetVisibility - ); - if (marker) { - occurrencesMarkerLayer.markers.push(marker); - } - } - - if (isBoundaryFeature(feature)) { - // check if dataset has been toggled - const ids = getSubmissionSpatialComponentIds(spatialRecord); - const key = makeKeyFromIds(ids); - if (ids.length > 0) { - visible = datasetVisibility[key] === undefined ? true : datasetVisibility[key]; - } - - if (visible) { - boundaryStaticLayer.features.push({ - geoJSON: feature, - key: feature.id, - popup: - }); - } - } - - if (isBoundaryCentroidFeature(feature)) { - // check if dataset has been toggled - const ids = getSubmissionSpatialComponentIds(spatialRecord); - const key = makeKeyFromIds(ids); - if (ids.length > 0) { - visible = datasetVisibility[key] === undefined ? true : datasetVisibility[key]; - } - - if (visible) { - boundaryStaticLayer.features.push({ - geoJSON: feature, - key: feature.id || feature.properties.datasetID, - popup: - }); - } - } - } - } - - return { markerLayers: [occurrencesMarkerLayer], staticLayers: [boundaryStaticLayer] }; -}; - -/** - * Helper function to *consistently* make React keys from an array of submission_spatial_component_ids. - * @param submissionSpatialComponentIds A list of IDs - * @returns A string joining all the id's by a seperator - */ -const makeKeyFromIds = (submissionSpatialComponentIds: number[]): string => { - return submissionSpatialComponentIds.join('-'); -}; - -/** - * Gleans submission spatial component IDs from a spatial component. - * @param spatialRecord A spatial component record - * @returns an array of submission_spatial_component_ids - */ -const getSubmissionSpatialComponentIds = (spatialRecord: ISpatialData): number[] => { - return spatialRecord.taxa_data.map((record) => record.submission_spatial_component_id); -}; - -/** - * Takes a geographic point, an array of taxonomy data, and a Record denoting dataset visibility, - * and produces an IMarker whose FeaturePopup contains submission spatial component IDs - * commensurate with the given dataset visibility. - * @param latLng The geograhic point of the marker - * @param taxaData The taxonomic data for the point (namely submission_spatial_component_ids) - * @param datasetVisibility The dataset visiblity record - * @returns An IMarker - */ -const occurrenceMarkerSetup = ( - latLng: LatLngTuple, - taxaData: ITaxaData[], - datasetVisibility: IDatasetVisibility -): IMarker | null => { - const submission_ids: number[] = taxaData - .filter((item: ITaxaData) => { - const taxonId = item.taxon_id || UNKNOWN_TAXON; - - return datasetVisibility[taxonId] === undefined ? true : datasetVisibility[taxonId]; - }) - .map((item: ITaxaData) => item.submission_spatial_component_id); - - if (submission_ids.length > 0) { - return { - position: latLng, - key: makeKeyFromIds(submission_ids), - popup: , - count: submission_ids.length - }; - } - - return null; -}; - -/** - * Takes an array of ISpatialData and maps it to an ISearchResult array denoting visibility based - * on the given datasetVisibility Record. - * @param data The array of spatial data - * @param datasetVisibility a Record denoting dataset visiblity - * @returns an array of type ISearchResult - */ -export const parseBoundaryCentroidResults = ( - data: ISpatialData[], - datasetVisibility: IDatasetVisibility -): ISearchResult[] => { - const results: ISearchResult[] = []; - data.forEach((spatialData: ISpatialData) => { - if (isBoundaryCentroidFeature(spatialData.spatial_data.features[0])) { - const key = makeKeyFromIds(getSubmissionSpatialComponentIds(spatialData)); - results.push({ - key: key, - name: `${spatialData.spatial_data?.features[0]?.properties?.datasetTitle}`, - count: 0, - visible: datasetVisibility[key] !== undefined ? datasetVisibility[key] : true - }); - } - }); - - return results; -}; - -/** - * Takes an array of ISpatialData and maps it to an ISearchResult array denoting visibility based - * on the given datasetVisibility Record, while numerating the count of each species. - * @param data The array of spatial data - * @param datasetVisibility a Record denoting dataset visiblity - * @returns an array of type ISearchResult - */ -export const parseOccurrenceResults = ( - data: ISpatialData[], - datasetVisibility: IDatasetVisibility -): ISearchResult[] => { - const taxaMap: Record = {}; - data.forEach((spatialData) => { - spatialData.taxa_data.forEach((item) => { - // need to check if it is an occurrence or not - if (isOccurrenceFeature(spatialData.spatial_data.features[0])) { - const taxonId = item.taxon_id || UNKNOWN_TAXON; - const taxonName = item.vernacular_name || UNKNOWN_TAXON; - - if (taxaMap[taxonId] === undefined) { - taxaMap[taxonId] = { - key: taxonId, - name: `${taxonName} (${taxonId})`, - count: 0, - visible: datasetVisibility[taxonId] !== undefined ? datasetVisibility[taxonId] : true - }; - } - - taxaMap[taxonId].count++; - } - }); - }); - - return Object.values(taxaMap); -}; - -/** - * Checks if `obj` is an object with no keys (aka: an empty object) - */ -export const isEmptyObject = (obj: any): obj is EmptyObject => { - return !!(isObject(obj) && !Object.keys(obj).length); -}; - -/** - * Asserts if a feature is an OccurrenceFeature. - */ -export const isOccurrenceFeature = (feature: Feature): feature is OccurrenceFeature => { - return feature.geometry.type === 'Point' && feature.properties?.['type'] === SPATIAL_COMPONENT_TYPE.OCCURRENCE; -}; - -/** - * Asserts if a feature is an BoundaryFeature. - */ -export const isBoundaryFeature = (feature: Feature): feature is BoundaryFeature => { - return feature?.properties?.['type'] === SPATIAL_COMPONENT_TYPE.BOUNDARY; -}; - -/** - * Asserts if a feature is an BoundaryCentroidFeature. - */ -export const isBoundaryCentroidFeature = (feature: Feature): feature is BoundaryCentroidFeature => { - return feature?.properties?.['type'] === SPATIAL_COMPONENT_TYPE.BOUNDARY_CENTROID; -}; diff --git a/database/liquibase/changelog.xml b/database/liquibase/changelog.xml deleted file mode 100644 index e69de29bb..000000000 diff --git a/database/liquibase/docker-compose.yml b/database/liquibase/docker-compose.yml deleted file mode 100644 index fd756bfb8..000000000 --- a/database/liquibase/docker-compose.yml +++ /dev/null @@ -1,25 +0,0 @@ -version: "3.5" - -services: - ## Build liquibase docker image - lquibase: - image: liquibase/liquibase:latest - container_name: liquibase-container - environment: - - LIQUIBASE_COMMAND_USERNAME=${LIQUIBASE_COMMAND_USERNAME} - - LIQUIBASE_COMMAND_PASSWORD=${LIQUIBASE_COMMAND_PASSWORD} - - LIQUIBASE_COMMAND_URL=${LIQUIBASE_COMMAND_URL} - - LIQUIBASE_PRO_LICENSE_KEY=${LIQUIBASE_PRO_LICENSE_KEY} - - LIQUIBASE_COMMAND_CHANGELOG_FILE=${LIQUIBASE_COMMAND_CHANGELOG_FILE} - networks: - - local-network - volumes: - - liquibase:/liquibase/changelog - command: ["update-sql"] -networks: - local-network: - driver: bridge - -volumes: - liquibase: - name: liquibase-vol diff --git a/database/liquibase/liquibase.docker.properties b/database/liquibase/liquibase.docker.properties deleted file mode 100644 index 4de906d4f..000000000 --- a/database/liquibase/liquibase.docker.properties +++ /dev/null @@ -1,6 +0,0 @@ -classpath: /liquibase/changelog -url: jdbc:postgresql://localhost:5432/restoration-tracker?currentSchema=restoration -changeLogFile: changelog.xml -username: postgres -password: postgres -liquibaseProLicenseKey= diff --git a/database/package-lock.json b/database/package-lock.json index 2148757cf..958af2e67 100644 --- a/database/package-lock.json +++ b/database/package-lock.json @@ -14,20 +14,21 @@ } }, "@babel/helper-validator-identifier": { - 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"version": "1.0.4", - "resolved": "https://registry.npmjs.org/typed-array-length/-/typed-array-length-1.0.4.tgz", - "integrity": "sha512-KjZypGq+I/H7HI5HlOoGHkWUUGq+Q0TPhQurLbyrVrvnKTBgzLhIJ7j6J/XTQOi0d1RjyZ0wdas8bKs2p0x3Ng==", + "version": "1.0.6", + "resolved": "https://registry.npmjs.org/typed-array-length/-/typed-array-length-1.0.6.tgz", + "integrity": "sha512-/OxDN6OtAk5KBpGb28T+HZc2M+ADtvRxXrKKbUwtsLgdoxgX13hyy7ek6bFRl5+aBs2yZzB0c4CnQfAtVypW/g==", "dev": true, "requires": { - "call-bind": "^1.0.2", + "call-bind": "^1.0.7", "for-each": "^0.3.3", - "is-typed-array": "^1.1.9" + "gopd": "^1.0.1", + "has-proto": "^1.0.3", + "is-typed-array": "^1.1.13", + "possible-typed-array-names": "^1.0.0" } }, "typescript": { @@ -2458,9 +2689,9 @@ "dev": true }, "v8-compile-cache": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz", - "integrity": "sha512-l8lCEmLcLYZh4nbunNZvQCJc5pv7+RCwa8q/LdUx8u7lsWvPDKmpodJAJNwkAhJC//dFY48KuIEmjtd4RViDrA==", + "version": "2.4.0", + "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.4.0.tgz", + "integrity": "sha512-ocyWc3bAHBB/guyqJQVI5o4BZkPhznPYUG2ea80Gond/BgNWpap8TOmLSeeQG7bnh2KMISxskdADG59j7zruhw==", "dev": true }, "validate-npm-package-license": { @@ -2496,29 +2727,28 @@ } }, "which-typed-array": { - "version": "1.1.9", - "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.9.tgz", - "integrity": "sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA==", + "version": "1.1.15", + "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.15.tgz", + "integrity": "sha512-oV0jmFtUky6CXfkqehVvBP/LSWJ2sy4vWMioiENyJLePrBO/yKyV9OyJySfAKosh+RYkIl5zJCNZ8/4JncrpdA==", "dev": true, "requires": { - "available-typed-arrays": "^1.0.5", - "call-bind": "^1.0.2", + "available-typed-arrays": "^1.0.7", + "call-bind": "^1.0.7", "for-each": "^0.3.3", "gopd": "^1.0.1", - "has-tostringtag": "^1.0.0", - "is-typed-array": "^1.1.10" + "has-tostringtag": "^1.0.2" } }, "word-wrap": { - "version": "1.2.3", - "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz", - "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==", + "version": "1.2.5", + "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz", + "integrity": "sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==", "dev": true }, "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", "dev": true }, "xtend": { diff --git a/docker-compose.yml b/docker-compose.yml index e52180c32..08a2e4dc3 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -42,9 +42,6 @@ services: environment: - NODE_ENV=${NODE_ENV} - NODE_OPTIONS=${API_NODE_OPTIONS} - - ELASTICSEARCH_URL=${ELASTICSEARCH_URL} - - ELASTICSEARCH_EML_INDEX=${ELASTICSEARCH_EML_INDEX} - - ELASTICSEARCH_TAXONOMY_INDEX=${ELASTICSEARCH_TAXONOMY_INDEX} # ITIS API - ITIS_SOLR_URL=${ITIS_SOLR_URL} - S3_KEY_PREFIX=${S3_KEY_PREFIX} @@ -111,9 +108,6 @@ services: dockerfile: ./.docker/queue/Dockerfile environment: - NODE_ENV=${NODE_ENV} - - ELASTICSEARCH_URL=${ELASTICSEARCH_URL} - - ELASTICSEARCH_EML_INDEX=${ELASTICSEARCH_EML_INDEX} - - ELASTICSEARCH_TAXONOMY_INDEX=${ELASTICSEARCH_TAXONOMY_INDEX} - S3_KEY_PREFIX=${S3_KEY_PREFIX} - API_HOST=${API_HOST} - API_PORT=${API_PORT} diff --git a/env_config/env.docker b/env_config/env.docker index d50d74799..13e28f305 100644 --- a/env_config/env.docker +++ b/env_config/env.docker @@ -143,13 +143,6 @@ GCNOTIFY_ONBOARDING_REQUEST_SMS_TEMPLATE=af2f1e40-bd72-4612-9c5a-567ee5b26ca5 GCNOTIFY_EMAIL_URL=https://api.notification.canada.ca/v2/notifications/email GCNOTIFY_SMS_URL=https://api.notification.canada.ca/v2/notifications/sms -# ------------------------------------------------------------------------------ -# Elasticsearch Platform API -# ------------------------------------------------------------------------------ -ELASTICSEARCH_URL=https://elasticsearch-a0ec71-dev.apps.silver.devops.gov.bc.ca -ELASTICSEARCH_EML_INDEX=eml -ELASTICSEARCH_TAXONOMY_INDEX=taxonomy_3.0.0 - # ------------------------------------------------------------------------------ # ITIS Platform API # ------------------------------------------------------------------------------ From 80c57ce233b9526e8e866af601eed12eec4cbf04 Mon Sep 17 00:00:00 2001 From: Nick Phura Date: Wed, 1 May 2024 16:01:05 -0700 Subject: [PATCH 6/7] Remove more unused code --- .../{submissionId}/download/index.ts | 2 +- .../{submissionId}/features/index.ts | 2 +- .../{submissionFeatureId}/signed-url.ts | 2 +- .../published/download/index.ts | 2 +- api/src/queue/queue-registry.test.ts | 9 +-- api/src/queue/queue-registry.ts | 2 - api/src/queue/queue.ts | 4 +- .../submission-job-queue-repository.test.ts | 31 ---------- .../submission-repository.test.ts | 61 +------------------ api/src/repositories/submission-repository.ts | 55 ----------------- api/src/services/submission-service.test.ts | 21 ------- api/src/services/submission-service.ts | 14 ----- app/src/hooks/api/useDatasetApi.test.ts | 37 ----------- app/src/hooks/api/useDatasetApi.ts | 53 ---------------- app/src/hooks/api/useSubmissionsApi.test.ts | 11 ---- app/src/hooks/api/useSubmissionsApi.ts | 14 ----- app/src/hooks/useApi.ts | 4 -- app/src/layouts/BaseLayout.test.tsx | 2 - 18 files changed, 10 insertions(+), 316 deletions(-) delete mode 100644 app/src/hooks/api/useDatasetApi.test.ts delete mode 100644 app/src/hooks/api/useDatasetApi.ts diff --git a/api/src/paths/submission/{submissionId}/download/index.ts b/api/src/paths/submission/{submissionId}/download/index.ts index 1140eddc2..a4fbc2732 100644 --- a/api/src/paths/submission/{submissionId}/download/index.ts +++ b/api/src/paths/submission/{submissionId}/download/index.ts @@ -11,7 +11,7 @@ export const GET: Operation = [downloadSubmission()]; GET.apiDoc = { description: 'Downloads a submission record and all associated features from the submission table', - tags: ['eml'], + tags: ['submission'], security: [ { OptionalBearer: [] diff --git a/api/src/paths/submission/{submissionId}/features/index.ts b/api/src/paths/submission/{submissionId}/features/index.ts index 6a7de1b49..62c87f98a 100644 --- a/api/src/paths/submission/{submissionId}/features/index.ts +++ b/api/src/paths/submission/{submissionId}/features/index.ts @@ -11,7 +11,7 @@ export const GET: Operation = [getSubmissionFeatures()]; GET.apiDoc = { description: 'Retrieves a submission record from the submission table', - tags: ['eml'], + tags: ['submission'], security: [ { OptionalBearer: [] diff --git a/api/src/paths/submission/{submissionId}/features/{submissionFeatureId}/signed-url.ts b/api/src/paths/submission/{submissionId}/features/{submissionFeatureId}/signed-url.ts index eaec2742d..d782a6e9c 100644 --- a/api/src/paths/submission/{submissionId}/features/{submissionFeatureId}/signed-url.ts +++ b/api/src/paths/submission/{submissionId}/features/{submissionFeatureId}/signed-url.ts @@ -12,7 +12,7 @@ export const GET: Operation = [getSubmissionFeatureSignedUrl()]; GET.apiDoc = { description: 'Retrieves a signed url of a submission feature', - tags: ['eml'], + tags: ['submission'], security: [ { OptionalBearer: [] diff --git a/api/src/paths/submission/{submissionId}/published/download/index.ts b/api/src/paths/submission/{submissionId}/published/download/index.ts index 92e75f569..5e7afb692 100644 --- a/api/src/paths/submission/{submissionId}/published/download/index.ts +++ b/api/src/paths/submission/{submissionId}/published/download/index.ts @@ -11,7 +11,7 @@ export const GET: Operation = [downloadPublishedSubmission()]; GET.apiDoc = { description: 'Downloads a submission record and all associated features from the submission table', - tags: ['eml'], + tags: ['submission'], security: [ { OptionalBearer: [] diff --git a/api/src/queue/queue-registry.test.ts b/api/src/queue/queue-registry.test.ts index 7e6d9aaa7..8e994605b 100644 --- a/api/src/queue/queue-registry.test.ts +++ b/api/src/queue/queue-registry.test.ts @@ -5,16 +5,9 @@ import * as db from '../database/db'; import { ISubmissionJobQueueRecord } from '../repositories/submission-job-queue-repository'; import { SubmissionJobQueueService } from '../services/submission-job-queue-service'; import { getMockDBConnection } from '../__mocks__/db'; -import { DWC_DATASET_SUBMISSION_JOB, jobQueueAttemptsWrapper, QueueJobRegistry } from './queue-registry'; +import { jobQueueAttemptsWrapper, QueueJobRegistry } from './queue-registry'; describe('QueueJobRegistry', () => { - it.skip('returns a known job function', () => { - const job = QueueJobRegistry.findMatchingJob(DWC_DATASET_SUBMISSION_JOB); - - expect(job).not.to.be.undefined; - expect(typeof job).to.equal('function'); - }); - it('returns null if no matching job found', () => { const job = QueueJobRegistry.findMatchingJob('not_a_real_job'); diff --git a/api/src/queue/queue-registry.ts b/api/src/queue/queue-registry.ts index cb9620cf0..b11549ade 100644 --- a/api/src/queue/queue-registry.ts +++ b/api/src/queue/queue-registry.ts @@ -7,8 +7,6 @@ const defaultLog = getLogger('queue/queue-registry'); type QueueJob = (jobQueueRecord: ISubmissionJobQueueRecord) => Promise; -export const DWC_DATASET_SUBMISSION_JOB = 'dwc_dataset_submission_job'; - /** * Translates a string to a queue-job compatible function. */ diff --git a/api/src/queue/queue.ts b/api/src/queue/queue.ts index 860182b57..6b852e141 100644 --- a/api/src/queue/queue.ts +++ b/api/src/queue/queue.ts @@ -1,6 +1,6 @@ import fastq from 'fastq'; import { ISubmissionJobQueueRecord } from '../repositories/submission-job-queue-repository'; -import { DWC_DATASET_SUBMISSION_JOB, QueueJobRegistry } from './queue-registry'; +import { QueueJobRegistry } from './queue-registry'; import { QUEUE_DEFAULT_CONCURRENCY, QUEUE_DEFAULT_TIMEOUT } from './queue-scheduler'; export class Queue { @@ -39,7 +39,7 @@ export class Queue { * @memberof Queue */ async _queueWorker(jobQueueRecord: ISubmissionJobQueueRecord) { - const job = QueueJobRegistry.findMatchingJob(DWC_DATASET_SUBMISSION_JOB); + const job = QueueJobRegistry.findMatchingJob('placeholder-not_a_real_job'); if (!job) { throw new Error('Failed to find matching queue job handler'); diff --git a/api/src/repositories/submission-job-queue-repository.test.ts b/api/src/repositories/submission-job-queue-repository.test.ts index bdb08e82c..380859663 100644 --- a/api/src/repositories/submission-job-queue-repository.test.ts +++ b/api/src/repositories/submission-job-queue-repository.test.ts @@ -73,37 +73,6 @@ describe('SubmissionJobQueueRepository', () => { }); }); - describe('getSourceTransformIdForUserId', () => { - it('should return with transform id', async () => { - const mockQueryResponse = { rowCount: 1, rows: [{ source_transform_id: 3 }] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - const repo = new SubmissionJobQueueRepository(mockDBConnection); - - const transformId = await repo.getSourceTransformIdForUserId(1); - expect(transformId).to.be.eql(3); - }); - - it('should throw an error when no transforms are found', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ - sql: () => mockQueryResponse - }); - - const repo = new SubmissionJobQueueRepository(mockDBConnection); - - try { - await repo.getSourceTransformIdForUserId(1); - expect.fail(); - } catch (error) { - expect((error as ApiGeneralError).message).to.equal('Failed to get source transform Id'); - } - }); - }); - describe('getNextUnprocessedJobQueueRecords', () => { it('should return all matching rows with no optional parameters', async () => { const mockQueryResponse = { diff --git a/api/src/repositories/submission-repository.test.ts b/api/src/repositories/submission-repository.test.ts index 79e98b991..edf5dffec 100644 --- a/api/src/repositories/submission-repository.test.ts +++ b/api/src/repositories/submission-repository.test.ts @@ -10,6 +10,7 @@ import { SECURITY_APPLIED_STATUS } from './security-repository'; import { ISourceTransformModel, ISpatialComponentCount, + ISubmissionModel, PatchSubmissionRecord, SubmissionFeatureRecord, SubmissionRecord, @@ -86,14 +87,8 @@ describe('SubmissionRepository', () => { }); it('should succeed with valid data', async () => { - const mockResponse = { - source_transform_id: 'test', - input_file_name: 'test', - input_key: 'test', - record_effective_date: 'test', - eml_source: 'test', - darwin_core_source: 'test', - uuid: 'test' + const mockResponse: ISubmissionModel = { + uuid: '123-456-789' }; const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; @@ -423,56 +418,6 @@ describe('SubmissionRepository', () => { }); }); - describe('insertSubmissionObservationRecord', () => { - afterEach(() => { - sinon.restore(); - }); - - it('should throw an error when insert sql fails', async () => { - const mockQueryResponse = { rowCount: 0 } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const submissionData = { - submission_id: 1, - darwin_core_source: '', - submission_security_request: '', - foi_reason: '' - }; - try { - await submissionRepository.insertSubmissionObservationRecord(submissionData); - expect.fail(); - } catch (actualError) { - expect((actualError as ApiGeneralError).message).to.equal('Failed to insert submission observation record'); - } - }); - - it('should succeed with valid data', async () => { - const mockResponse = { - id: 1 - }; - - const mockQueryResponse = { rowCount: 1, rows: [mockResponse] } as any as Promise>; - - const mockDBConnection = getMockDBConnection({ sql: () => mockQueryResponse }); - - const submissionRepository = new SubmissionRepository(mockDBConnection); - - const submissionData = { - submission_id: 1, - darwin_core_source: '', - submission_security_request: '', - foi_reason: '' - }; - - const response = await submissionRepository.insertSubmissionObservationRecord(submissionData); - - expect(response).to.eql(mockResponse); - }); - }); - describe('getUnreviewedSubmissionsForAdmins', () => { beforeEach(() => { sinon.restore(); diff --git a/api/src/repositories/submission-repository.ts b/api/src/repositories/submission-repository.ts index 6d45bcc78..fa4c32e3b 100644 --- a/api/src/repositories/submission-repository.ts +++ b/api/src/repositories/submission-repository.ts @@ -186,20 +186,6 @@ export interface ISubmissionJobQueueRecord { revision_count: number; } -export interface ISubmissionMetadataRecord { - submission_metadata_id?: number; - submission_id: number; - eml_source: string; - eml_json_source?: any; - record_effective_timestamp?: string | null; - record_end_timestamp?: string | null; - create_date?: string; - create_user?: string; - update_date?: string; - update_user?: string; - revision_count?: string; -} - export interface ISubmissionObservationRecord { submission_observation_id?: number; submission_id: number; @@ -736,47 +722,6 @@ export class SubmissionRepository extends BaseRepository { return response.rows[0]; } - /** - * Insert a new Observation Record - * - * @param {ISubmissionObservationRecord} submissionObservation - * @return {*} {Promise<{ submission_observation_id: number }>} - * @memberof SubmissionRepository - */ - async insertSubmissionObservationRecord( - submissionObservation: ISubmissionObservationRecord - ): Promise<{ submission_observation_id: number }> { - const sqlStatement = SQL` - INSERT INTO submission_observation ( - submission_id, - darwin_core_source, - submission_security_request, - foi_reason, - record_effective_timestamp - ) VALUES ( - ${submissionObservation.submission_id}, - ${submissionObservation.darwin_core_source}, - ${submissionObservation.submission_security_request}, - ${submissionObservation.foi_reason}, - now() - ) - RETURNING - submission_observation_id - ; - `; - - const response = await this.connection.sql<{ submission_observation_id: number }>(sqlStatement); - - if (!response.rowCount) { - throw new ApiExecuteSQLError('Failed to insert submission observation record', [ - 'SubmissionRepository->insertSubmissionObservationRecord', - 'rowCount was null or undefined, expected rowCount >= 0' - ]); - } - - return response.rows[0]; - } - /** * Get all submissions that have not completed security review. * diff --git a/api/src/services/submission-service.test.ts b/api/src/services/submission-service.test.ts index f38e504f4..dfd868c1f 100644 --- a/api/src/services/submission-service.test.ts +++ b/api/src/services/submission-service.test.ts @@ -9,7 +9,6 @@ import { ISubmissionFeature, ISubmissionJobQueueRecord, ISubmissionModel, - ISubmissionObservationRecord, PatchSubmissionRecord, SubmissionFeatureDownloadRecord, SubmissionFeatureRecord, @@ -401,26 +400,6 @@ describe('SubmissionService', () => { }); }); - describe('insertSubmissionObservationRecord', () => { - it('should return a submission observation record', async () => { - const mockDBConnection = getMockDBConnection(); - const submissionService = new SubmissionService(mockDBConnection); - - const repo = sinon.stub(SubmissionRepository.prototype, 'insertSubmissionObservationRecord').resolves({ - submission_observation_id: 1 - }); - - const response = await submissionService.insertSubmissionObservationRecord({ - test: 'test' - } as unknown as ISubmissionObservationRecord); - - expect(repo).to.be.calledOnce; - expect(response).to.be.eql({ - submission_observation_id: 1 - }); - }); - }); - describe('getUnreviewedSubmissionsForAdmins', () => { it('should return an array of submission records', async () => { const mockSubmissionRecords: SubmissionRecordWithSecurityAndRootFeatureType[] = [ diff --git a/api/src/services/submission-service.ts b/api/src/services/submission-service.ts index f56254366..29f1c0df6 100644 --- a/api/src/services/submission-service.ts +++ b/api/src/services/submission-service.ts @@ -6,7 +6,6 @@ import { ISubmissionFeature, ISubmissionJobQueueRecord, ISubmissionModel, - ISubmissionObservationRecord, ISubmissionRecord, PatchSubmissionRecord, SubmissionFeatureDownloadRecord, @@ -262,19 +261,6 @@ export class SubmissionService extends DBService { return this.submissionRepository.getSubmissionJobQueue(submissionId); } - /** - * Insert a new Observation Record - * - * @param {ISubmissionObservationRecord} submissionObservation - * @return {*} {Promise<{ submission_observation_id: number }>} - * @memberof SubmissionService - */ - async insertSubmissionObservationRecord( - submissionObservation: ISubmissionObservationRecord - ): Promise<{ submission_observation_id: number }> { - return this.submissionRepository.insertSubmissionObservationRecord(submissionObservation); - } - /** * Get all submissions that are pending security review (are unreviewed). * diff --git a/app/src/hooks/api/useDatasetApi.test.ts b/app/src/hooks/api/useDatasetApi.test.ts deleted file mode 100644 index e7f01a331..000000000 --- a/app/src/hooks/api/useDatasetApi.test.ts +++ /dev/null @@ -1,37 +0,0 @@ -import axios from 'axios'; -import MockAdapter from 'axios-mock-adapter'; -import useDatasetApi from './useDatasetApi'; - -describe('useDatasetApi', () => { - let mock: any; - - beforeEach(() => { - mock = new MockAdapter(axios); - }); - - afterEach(() => { - mock.restore(); - }); - - it('getDatasetArtifacts works as expected', async () => { - const response = { - artifacts: [{ artifact_id: 1 }, { artifact_id: 2 }] - }; - - mock.onGet('api/dwc/submission/a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf/artifacts').reply(200, response); - - const actualResult = await useDatasetApi(axios).getDatasetArtifacts('a6f90fb7-2f20-4d6e-b1cd-75f3336c2dcf'); - - expect(actualResult).toEqual({ - artifacts: [{ artifact_id: 1 }, { artifact_id: 2 }] - }); - }); - - it('getArtifactSignedUrl works as expected', async () => { - mock.onGet(`api/artifact/${1}/getSignedUrl`).reply(200, 'http://example.com'); - - const actualResult = await useDatasetApi(axios).getArtifactSignedUrl(1); - - expect(actualResult).toEqual('http://example.com'); - }); -}); diff --git a/app/src/hooks/api/useDatasetApi.ts b/app/src/hooks/api/useDatasetApi.ts deleted file mode 100644 index b1b7905d2..000000000 --- a/app/src/hooks/api/useDatasetApi.ts +++ /dev/null @@ -1,53 +0,0 @@ -import { AxiosInstance } from 'axios'; -import { IArtifact } from 'interfaces/useDatasetApi.interface'; - -/** - * Returns a set of supported api methods for working with datasets. - * - * @param {AxiosInstance} axios - * @return {*} object whose properties are supported api methods. - */ -const useDatasetApi = (axios: AxiosInstance) => { - /** - * Fetch dataset data by datasetUUID. - * - * @param {string} datasetUUID - * @return {*} {Promise} - */ - const getDataset = async (datasetUUID: string): Promise => { - const { data } = await axios.get(`api/dataset/${datasetUUID}`); - - return data; - }; - - /** - * Fetch dataset artifacts by datasetId. - * - * @param {string} datasetId - * @return {*} {Promise} - */ - const getDatasetArtifacts = async (datasetId: string): Promise => { - const { data } = await axios.get(`api/dwc/submission/${datasetId}/artifacts`); - - return data; - }; - - /** - * Fetch the signed URL of an artifact by its artifact ID. - * - * @return {*} {Promise} - */ - const getArtifactSignedUrl = async (artifactId: number): Promise => { - const { data } = await axios.get(`api/artifact/${artifactId}/getSignedUrl`); - - return data; - }; - - return { - getDataset, - getDatasetArtifacts, - getArtifactSignedUrl - }; -}; - -export default useDatasetApi; diff --git a/app/src/hooks/api/useSubmissionsApi.test.ts b/app/src/hooks/api/useSubmissionsApi.test.ts index 3928c102e..41ae2c0e1 100644 --- a/app/src/hooks/api/useSubmissionsApi.test.ts +++ b/app/src/hooks/api/useSubmissionsApi.test.ts @@ -13,17 +13,6 @@ describe('useSubmissionApi', () => { mock.restore(); }); - it('getSignedUrl works as expected', async () => { - const res = 'test-signed-url'; - const testSubmissionId = 1; - - mock.onGet(`/api/dwc/submission/${testSubmissionId}/getSignedUrl`).reply(200, res); - - const result = await useSubmissionsApi(axios).getSignedUrl(testSubmissionId); - - expect(result).toEqual('test-signed-url'); - }); - describe('getSubmissionFeatureSignedUrl', () => { it('should return signed URL', async () => { const payload = { diff --git a/app/src/hooks/api/useSubmissionsApi.ts b/app/src/hooks/api/useSubmissionsApi.ts index a73446780..00ba6beac 100644 --- a/app/src/hooks/api/useSubmissionsApi.ts +++ b/app/src/hooks/api/useSubmissionsApi.ts @@ -15,19 +15,6 @@ import { * @return {*} object whose properties are supported api methods. */ const useSubmissionsApi = (axios: AxiosInstance) => { - /** - * Fetch the signed URL of a submission by submission ID. - * - * @return {*} {Promise} - */ - const getSignedUrl = async (submissionId: number): Promise => { - const { data } = await axios.get(`/api/dwc/submission/${submissionId}/getSignedUrl`); - - return data; - }; - - /** NET-NEW FRONTEND REQUESTS FOR UPDATED SCHEMA **/ - /** * repackages and retrieves json data from self and each child under submission * @@ -157,7 +144,6 @@ const useSubmissionsApi = (axios: AxiosInstance) => { }; return { - getSignedUrl, getSubmissionDownloadPackage, getSubmissionPublishedDownloadPackage, getSubmissionFeatureGroups, diff --git a/app/src/hooks/useApi.ts b/app/src/hooks/useApi.ts index a2be22539..074a50f9f 100644 --- a/app/src/hooks/useApi.ts +++ b/app/src/hooks/useApi.ts @@ -4,7 +4,6 @@ import useAdminApi from './api/useAdminApi'; import useArtifactApi from './api/useArtifactApi'; import useAxios from './api/useAxios'; import useCodesApi from './api/useCodesApi'; -import useDatasetApi from './api/useDatasetApi'; import useSecurityApi from './api/useSecurityApi'; import useSubmissionsApi from './api/useSubmissionsApi'; import useTaxonomyApi from './api/useTaxonomyApi'; @@ -27,8 +26,6 @@ export const useApi = () => { const taxonomy = useTaxonomyApi(apiAxios); - const dataset = useDatasetApi(apiAxios); - const artifact = useArtifactApi(apiAxios); const security = useSecurityApi(apiAxios); @@ -39,7 +36,6 @@ export const useApi = () => { user, admin, submissions, - dataset, taxonomy, security, artifact, diff --git a/app/src/layouts/BaseLayout.test.tsx b/app/src/layouts/BaseLayout.test.tsx index a45ee1257..498a6a369 100644 --- a/app/src/layouts/BaseLayout.test.tsx +++ b/app/src/layouts/BaseLayout.test.tsx @@ -9,8 +9,6 @@ const history = createMemoryHistory(); describe.skip('BaseLayout', () => { it('renders correctly', () => { - process.env.REACT_APP_NODE_ENV = 'local'; - const authState = getMockAuthState({ base: SystemAdminAuthState }); const { getByText } = render( From 4180e4f4ca9dd99f61b0af0b8e9b9db93f96b4fe Mon Sep 17 00:00:00 2001 From: Nick Phura Date: Wed, 1 May 2024 16:03:18 -0700 Subject: [PATCH 7/7] Update pipeline settings --- api/.pipeline/config.js | 8 ++++---- app/.pipeline/config.js | 4 ++-- database/.pipeline/config.js | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/api/.pipeline/config.js b/api/.pipeline/config.js index 1c09c7c12..3ab7df0f9 100644 --- a/api/.pipeline/config.js +++ b/api/.pipeline/config.js @@ -116,7 +116,7 @@ const phases = { cpuLimit: '1250m', memoryRequest: '100Mi', memoryLimit: '4Gi', - replicas: '2', + replicas: '1', replicasMax: '2' }, prod: { @@ -139,10 +139,10 @@ const phases = { logLevel: 'warn', nodeOptions: '--max_old_space_size=6000', // 75% of memoryLimit (bytes) cpuRequest: '50m', - cpuLimit: '1750m', + cpuLimit: '1500m', memoryRequest: '100Mi', - memoryLimit: '8Gi', - replicas: '2', + memoryLimit: '6Gi', + replicas: '1', replicasMax: '2' } }; diff --git a/app/.pipeline/config.js b/app/.pipeline/config.js index f6dd04eb6..54e8fb829 100644 --- a/app/.pipeline/config.js +++ b/app/.pipeline/config.js @@ -111,7 +111,7 @@ const phases = { cpuLimit: '400m', memoryRequest: '100Mi', memoryLimit: '750Mi', - replicas: '2', + replicas: '1', replicasMax: '2' }, prod: { @@ -134,7 +134,7 @@ const phases = { cpuLimit: '500m', memoryRequest: '100Mi', memoryLimit: '1Gi', - replicas: '2', + replicas: '1', replicasMax: '2' } }; diff --git a/database/.pipeline/config.js b/database/.pipeline/config.js index f83e03428..0ee612f73 100644 --- a/database/.pipeline/config.js +++ b/database/.pipeline/config.js @@ -117,9 +117,9 @@ const phases = { dbSetupDockerfilePath: dbSetupDockerfilePath, volumeCapacity: '5Gi', cpuRequest: '50m', - cpuLimit: '2000m', + cpuLimit: '1500m', memoryRequest: '100Mi', - memoryLimit: '8Gi', + memoryLimit: '6Gi', replicas: '1' } };