SIMSBIOHUB-457: Taxonomy Endpoints (#235)

Design BioHub taxonomy endpoint + services/repositories.
- Taxon Search endpoint
  - Search by term to SOLR service from frontend
- Taxon ids lookup endpoint
  - Query DB for cached tsn's
  - Search SOLR for tsn's not found in DB, update accordingly
  - Return list of Taxons

.vscode/settings.json

@@ -1,3 +1,3 @@
 {
-    "git.ignoreLimitWarning": true
-}
+  "git.ignoreLimitWarning": true
+}

api/.pipeline/config.js

@@ -83,6 +83,7 @@ const phases = {
     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,
     sso: config.sso.dev,
@@ -111,6 +112,7 @@ const phases = {
     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,
     sso: config.sso.test,
@@ -139,6 +141,7 @@ const phases = {
     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,

api/.pipeline/lib/api.deploy.js

@@ -38,6 +38,8 @@ const apiDeploy = async (settings) => {
         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)
         S3_KEY_PREFIX: phases[phase].s3KeyPrefix,
         OBJECT_STORE_SECRETS: 'biohubbc-object-store',

api/.pipeline/templates/api.dc.yaml

@@ -54,6 +54,11 @@ parameters:
     description: Application timezone
     required: false
     value: 'America/Vancouver'
+  # ITIS SOLR
+  - name: ITIS_SOLR_URL
+    description: ITIS SOLR API URL
+    value: 'https://services.itis.gov'
+    required: true
   # Keycloak
   - name: KEYCLOAK_HOST
     description: Key clock login url
@@ -263,6 +268,9 @@ objects:
                   value: ${ELASTICSEARCH_EML_INDEX}
                 - name: ELASTICSEARCH_TAXONOMY_INDEX
                   value: ${ELASTICSEARCH_TAXONOMY_INDEX}
+                # ITIS SOLR
+                - name: ITIS_SOLR_URL
+                  value: ${ITIS_SOLR_URL}
                 - name: S3_KEY_PREFIX
                   value: ${S3_KEY_PREFIX}
                 - name: TZ

api/src/__mocks__/db.ts

@@ -77,6 +77,18 @@ export class MockRes {
     return this;
   });
 
+  /**
+   * The value of the last `.setHeader(<value>)` call.
+   *
+   * @memberof MockRes
+   */
+  headerValue: any;
+  setHeader = sinon.fake((header: any) => {
+    this.headerValue = header;
+
+    return this;
+  });
+
   /**
    * The value of the last `.json(<value>)` call.
    *

api/src/paths/submission/intake.ts

@@ -147,7 +147,7 @@ export function submissionIntake(): RequestHandler {
       const searchIndexService = new SearchIndexService(connection);
       const regionService = new RegionService(connection);
 
-      // validate theubmission
+      // validate the submission
       if (!(await validationService.validateSubmissionFeatures([submissionFeature]))) {
         throw new HTTP400('Invalid submission'); // TODO return details on why the submission is invalid
       }

api/src/paths/taxonomy/taxon/index.test.ts

@@ -0,0 +1,97 @@
+import Ajv from 'ajv';
+import chai, { expect } from 'chai';
+import { describe } from 'mocha';
+import sinon from 'sinon';
+import sinonChai from 'sinon-chai';
+import { findTaxonBySearchTerms, GET } from '.';
+import * as db from '../../../database/db';
+import { HTTPError } from '../../../errors/http-error';
+import { ItisService } from '../../../services/itis-service';
+import { getMockDBConnection, getRequestHandlerMocks } from '../../../__mocks__/db';
+
+chai.use(sinonChai);
+
+describe('taxon', () => {
+  describe('openapi schema', () => {
+    const ajv = new Ajv();
+
+    it('is valid openapi v3 schema', () => {
+      expect(ajv.validateSchema(GET.apiDoc as unknown as object)).to.be.true;
+    });
+  });
+
+  describe('findTaxonBySearchTerms', () => {
+    afterEach(() => {
+      sinon.restore();
+    });
+
+    it('returns an empty array if no species are found', async () => {
+      const dbConnectionObj = getMockDBConnection();
+
+      sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
+
+      const getSpeciesFromIdsStub = sinon.stub(ItisService.prototype, 'searchItisByTerm').resolves([]);
+
+      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+      mockReq.query = {
+        terms: ''
+      };
+
+      const requestHandler = findTaxonBySearchTerms();
+
+      await requestHandler(mockReq, mockRes, mockNext);
+
+      expect(getSpeciesFromIdsStub).to.have.been.calledWith('');
+
+      expect(mockRes.statusValue).to.equal(200);
+      expect(mockRes.jsonValue).to.eql({ searchResponse: [] });
+    });
+
+    it('returns an array of species', async () => {
+      const dbConnectionObj = getMockDBConnection();
+
+      sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
+
+      const mock1 = { id: '1', commonName: 'something', scientificName: 'string' } as unknown as any;
+      const mock2 = { id: '2', commonName: null, scientificName: 'string' } as unknown as any;
+
+      const getSpeciesFromIdsStub = sinon.stub(ItisService.prototype, 'searchItisByTerm').resolves([mock1, mock2]);
+
+      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+      mockReq.query = {
+        terms: 't'
+      };
+
+      const requestHandler = findTaxonBySearchTerms();
+
+      await requestHandler(mockReq, mockRes, mockNext);
+
+      expect(getSpeciesFromIdsStub).to.have.been.calledWith('t');
+
+      expect(mockRes.jsonValue).to.eql({ searchResponse: [mock1, mock2] });
+      expect(mockRes.statusValue).to.equal(200);
+    });
+
+    it('catches error, and re-throws error', async () => {
+      const dbConnectionObj = getMockDBConnection({ rollback: sinon.stub(), release: sinon.stub() });
+
+      sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
+
+      sinon.stub(ItisService.prototype, 'searchItisByTerm').rejects(new Error('a test error'));
+
+      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+      mockReq.query = {
+        ids: 'a'
+      };
+
+      try {
+        const requestHandler = findTaxonBySearchTerms();
+
+        await requestHandler(mockReq, mockRes, mockNext);
+        expect.fail();
+      } catch (actualError) {
+        expect((actualError as HTTPError).message).to.equal('a test error');
+      }
+    });
+  });
+});