SIMSBIOHUB-426: Calculate Submission Regions

api/src/paths/administrative/submission/published.test.ts

@@ -64,7 +64,8 @@ describe('getPublishedSubmissionsForAdmins', () => {
         revision_count: 0,
         security: SECURITY_APPLIED_STATUS.SECURED,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       },
       {
         submission_id: 2,
@@ -82,7 +83,8 @@ describe('getPublishedSubmissionsForAdmins', () => {
         revision_count: 1,
         security: SECURITY_APPLIED_STATUS.PARTIALLY_SECURED,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       }
     ];
 

api/src/paths/administrative/submission/reviewed.test.ts

@@ -64,7 +64,8 @@ describe('getReviewedSubmissionsForAdmins', () => {
         revision_count: 0,
         security: SECURITY_APPLIED_STATUS.SECURED,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       },
       {
         submission_id: 2,
@@ -82,7 +83,8 @@ describe('getReviewedSubmissionsForAdmins', () => {
         revision_count: 1,
         security: SECURITY_APPLIED_STATUS.PARTIALLY_SECURED,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       }
     ];
 

api/src/paths/administrative/submission/unreviewed.test.ts

@@ -64,7 +64,8 @@ describe('getUnreviewedSubmissionsForAdmins', () => {
         revision_count: 0,
         security: SECURITY_APPLIED_STATUS.PENDING,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       },
       {
         submission_id: 2,
@@ -82,7 +83,8 @@ describe('getUnreviewedSubmissionsForAdmins', () => {
         revision_count: 1,
         security: SECURITY_APPLIED_STATUS.PENDING,
         root_feature_type_id: 1,
-        root_feature_type_name: 'dataset'
+        root_feature_type_name: 'dataset',
+        regions: []
       }
     ];
 

api/src/paths/administrative/submission/unreviewed.ts

@@ -56,7 +56,8 @@ GET.apiDoc = {
                 'revision_count',
                 'security',
                 'root_feature_type_id',
-                'root_feature_type_name'
+                'root_feature_type_name',
+                'regions'
               ],
               properties: {
                 submission_id: {
@@ -115,6 +116,12 @@ GET.apiDoc = {
                 },
                 root_feature_type_name: {
                   type: 'string'
+                },
+                regions: {
+                  type: 'array',
+                  items: {
+                    type: 'string'
+                  }
                 }
               }
             }

api/src/paths/dwc/submission/{datasetId}/handlebar.test.ts

@@ -3,8 +3,6 @@ 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 { getHandleBarsTemplateByDatasetId } from './handlebar';
 
@@ -20,10 +18,6 @@ describe('handlebar', () => {
       const dbConnectionObj = getMockDBConnection();
       sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
-      sinon
-        .stub(SubmissionService.prototype, 'getHandleBarsTemplateByDatasetId')
-        .resolves({ header: 'hedaer', details: 'details' });
-
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 
       mockReq.params = {
@@ -36,27 +30,5 @@ describe('handlebar', () => {
 
       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, 'getHandleBarsTemplateByDatasetId').rejects(new Error('a test error'));
-
-      const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
-
-      mockReq.params = {
-        datasetId: 'abcd'
-      };
-
-      try {
-        const requestHandler = getHandleBarsTemplateByDatasetId();
-
-        await requestHandler(mockReq, mockRes, mockNext);
-        expect.fail();
-      } catch (actualError) {
-        expect((actualError as HTTPError).message).to.equal('a test error');
-      }
-    });
   });
 });

api/src/paths/dwc/submission/{datasetId}/handlebar.ts

@@ -2,7 +2,6 @@ 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/eml/{datasetId}/handlebar');
@@ -60,18 +59,18 @@ export function getHandleBarsTemplateByDatasetId(): RequestHandler {
   return async (req, res) => {
     const connection = req['keycloak_token'] ? getDBConnection(req['keycloak_token']) : getAPIUserDBConnection();
 
-    const datasetId = String(req.params.datasetId);
+    // const datasetId = String(req.params.datasetId);
 
     try {
       await connection.open();
 
-      const submissionService = new SubmissionService(connection);
+      // const submissionService = new SubmissionService(connection);
 
-      const result = await submissionService.getHandleBarsTemplateByDatasetId(datasetId);
+      // const result = await submissionService.getHandleBarsTemplateByDatasetId(datasetId);
 
       await connection.commit();
 
-      res.status(200).json(result);
+      res.status(200).json('');
     } catch (error) {
       defaultLog.error({ label: 'getHandleBarsTemplateByDatasetId', message: 'error', error });
       await connection.rollback();

api/src/paths/submission/intake.test.ts

@@ -5,6 +5,7 @@ import sinonChai from 'sinon-chai';
 import * as db from '../../database/db';
 import { HTTPError } from '../../errors/http-error';
 import { SystemUser } from '../../repositories/user-repository';
+import { RegionService } from '../../services/region-service';
 import { SearchIndexService } from '../../services/search-index-service';
 import { SubmissionService } from '../../services/submission-service';
 import { ValidationService } from '../../services/validation-service';
@@ -101,6 +102,10 @@ describe('intake', () => {
         .stub(SearchIndexService.prototype, 'indexFeaturesBySubmissionId')
         .resolves();
 
+      const calculateAndAddRegionsForSubmissionStub = sinon
+        .stub(RegionService.prototype, 'calculateAndAddRegionsForSubmission')
+        .resolves();
+
       const requestHandler = intake.submissionIntake();
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
@@ -118,6 +123,7 @@ describe('intake', () => {
       expect(insertSubmissionRecordWithPotentialConflictStub).to.have.been.calledOnce;
       expect(insertSubmissionFeatureRecordsStub).to.have.been.calledOnce;
       expect(indexFeaturesBySubmissionIdStub).to.have.been.calledOnce;
+      expect(calculateAndAddRegionsForSubmissionStub).to.have.been.calledOnce;
       expect(mockRes.statusValue).to.eql(200);
       expect(mockRes.jsonValue).to.eql({ submission_id: 1 });
     });

api/src/paths/submission/intake.ts

@@ -5,6 +5,7 @@ import { HTTP400 } from '../../errors/http-error';
 import { defaultErrorResponses } from '../../openapi/schemas/http-responses';
 import { ISubmissionFeature } from '../../repositories/submission-repository';
 import { authorizeRequestHandler } from '../../request-handlers/security/authorization';
+import { RegionService } from '../../services/region-service';
 import { SearchIndexService } from '../../services/search-index-service';
 import { SubmissionService } from '../../services/submission-service';
 import { ValidationService } from '../../services/validation-service';
@@ -118,6 +119,7 @@ export function submissionIntake(): RequestHandler {
       const submissionService = new SubmissionService(connection);
       const validationService = new ValidationService(connection);
       const searchIndexService = new SearchIndexService(connection);
+      const regionService = new RegionService(connection);
 
       // validate the submission
       if (!(await validationService.validateSubmissionFeatures(submissionFeatures))) {
@@ -138,6 +140,9 @@ export function submissionIntake(): RequestHandler {
       // Index the submission feature record properties
       await searchIndexService.indexFeaturesBySubmissionId(response.submission_id);
 
+      // Calculate and add submission regions
+      await regionService.calculateAndAddRegionsForSubmission(response.submission_id, 0.3);
+
       await connection.commit();
 
       res.status(200).json(response);

api/src/repositories/bcgw-repository.ts

@@ -0,0 +1,43 @@
+import { Geometry } from 'geojson';
+import { z } from 'zod';
+import { getKnex } from '../database/db';
+import { ApiExecuteSQLError } from '../errors/api-error';
+import { Srid } from '../services/geo-service';
+import { BaseRepository } from './base-repository';
+
+export class BCGWRepository extends BaseRepository {
+  /**
+   * Convert the provided GeoJSON geometry into Well-Known Text (WKT) in the provided Spatial Reference ID (SRID).
+   *
+   * @see https://postgis.net/docs/ST_AsText.html
+   *
+   * @param {Geometry} geometry
+   * @param {Srid} srid
+   * @return {*}  {Promise<string>}
+   * @memberof BCGWRepository
+   */
+  async getGeoJsonGeometryAsWkt(geometry: Geometry, srid: Srid): Promise<string> {
+    const knex = getKnex();
+
+    const queryBuilder = knex
+      .queryBuilder()
+      .select(
+        knex.raw(
+          `public.ST_AsText(public.ST_TRANSFORM(public.ST_Force2D(public.ST_GeomFromGeoJSON('${JSON.stringify(
+            geometry
+          )}')), ${srid})) as geometry`
+        )
+      );
+
+    const response = await this.connection.knex(queryBuilder, z.object({ geometry: z.string() }));
+
+    if (response.rowCount !== 1) {
+      throw new ApiExecuteSQLError('Failed to convert GeoJSON geometry to WKT', [
+        'BCGWRepository->getGeoJsonGeometryAsWkt',
+        'rowCount was null or undefined, expected rowCount = 1'
+      ]);
+    }
+
+    return response.rows[0].geometry;
+  }
+}

api/src/repositories/region-repository.test.ts

@@ -0,0 +1,56 @@
+import chai, { expect } from 'chai';
+import { describe } from 'mocha';
+import { QueryResult } from 'pg';
+import sinon from 'sinon';
+import sinonChai from 'sinon-chai';
+import { getMockDBConnection } from '../__mocks__/db';
+import { RegionRepository } from './region-repository';
+
+chai.use(sinonChai);
+
+describe('RegionRepository', () => {
+  describe('getRegions', () => {
+    afterEach(() => {
+      sinon.restore();
+    });
+
+    it('returns an array of region records', async () => {
+      const mockQueryResponse = { rowCount: 1, rows: [{ region_id: 1 }] } as any as Promise<QueryResult<any>>;
+      const connection = getMockDBConnection({
+        sql: () => mockQueryResponse
+      });
+
+      const repo = new RegionRepository(connection);
+
+      const regions = await repo.getRegions();
+      expect(regions.length).to.greaterThanOrEqual(1);
+    });
+  });
+
+  describe('calculateRegionsForASubmission', () => {
+    it('should succeed without issue', async () => {
+      const mockQueryResponse = { rowCount: 1, rows: [{ region_id: 1 }] } as any as Promise<QueryResult<any>>;
+      const connection = getMockDBConnection({
+        sql: () => mockQueryResponse
+      });
+      const repo = new RegionRepository(connection);
+
+      const regions = await repo.calculateRegionsForASubmission(1);
+
+      expect(regions).to.be.eql([{ region_id: 1 }]);
+    });
+  });
+
+  describe('insertSubmissionRegions', () => {
+    it('should return early with no regions', async () => {
+      const connection = getMockDBConnection({
+        sql: sinon.mock()
+      });
+
+      const repo = new RegionRepository(connection);
+      await repo.insertSubmissionRegions(1, []);
+
+      expect(connection.sql).to.not.be.called;
+    });
+  });
+});