SIMSBIOHUB-458: Purge Old BioHub Code (#243)

- Remove all old/unused code from BioHub. - Validation/Transformation Schemas - access request endpoints - administrative activity endpoints/service/repo - dwc/eml enpoints/service - remove misc unused code --------- Co-authored-by: Nick Phura <[email protected]>
bcgov · May 1, 2024 · dd73aa0 · dd73aa0
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commit dd73aa0
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diff --git a/README/PR Based Deploy Pipeline.md b/README/PR Based Deploy Pipeline.md
diff --git a/README/handlebars.md b/README/handlebars.md
diff --git 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,
@@ -122,7 +116,7 @@ const phases = {
     cpuLimit: '1250m',
     memoryRequest: '100Mi',
     memoryLimit: '4Gi',
-    replicas: '2',
+    replicas: '1',
     replicasMax: '2'
   },
   prod: {
@@ -138,20 +132,17 @@ 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,
     sso: config.sso.prod,
     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/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
@@ -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
@@ -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
@@ -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
@@ -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