SIMSBIOHUB-342: Delete Sampling Site (#1147)

* Add delete sample site button to menu drop down * Check for any associated observations to sample site. * hook up api sample-site delete function. * SIMSBIOHUB-336/337 (#1142) * Adds Sampling Site record count to title area, Example: Sampling Sites (10) * Adds Observation record count to title area of observations map component and manage observations page, Example: Observations (10) * Adds 'supplementaryObservationData' section to get survey observations endpoint. This allows observation record counts to be displayed, even if the get observations response becomes paginated or virtualized at a later date * SIMSBIOHUB 343 - Incorrect date overlap error in sampling methods (#1144) * Fixed an issue where the yup schema used for editing sampling methods used the wrong field for a date overlap check. * Removed an unintended required(). * Added a refresh call when submitting sampling method changes so they are reflected in the UI. Otherwise you will still see the previous value if you go back to the sampling methods view even though the new value did save to the db. * SIMSBIOHUB-334/350/352 (#1143) * Added snackbar popup upon successfully saving observations. * Removed single-click to edit; Fixed bug that made row go into edit mode when clicking row delete icon. * Added seconds to the observation time * Clean up functions and excess data calls * fix tests --------- Co-authored-by: JeremyQuartech <[email protected]> Co-authored-by: GrahamS-Quartech <[email protected]> Co-authored-by: Curtis Upshall <[email protected]>
bcgov · Oct 31, 2023 · a284963 · a284963
1 parent 7cb5142
commit a284963
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Showing 10 changed files with 164 additions and 13 deletions.
diff --git a/...aths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.test.ts b/...aths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.test.ts
@@ -4,6 +4,7 @@ import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
 import * as db from '../../../../../../../database/db';
 import { HTTPError } from '../../../../../../../errors/http-error';
+import { ObservationService } from '../../../../../../../services/observation-service';
 import { SampleLocationService } from '../../../../../../../services/sample-location-service';
 import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../../__mocks__/db';
 import * as delete_survey_sample_site_record from './index';
@@ -198,6 +199,10 @@ describe('deleteSurveySampleSiteRecord', () => {
   it('should work', async () => {
     sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
+    const getObservationsCountBySampleSiteIdStub = sinon
+      .stub(ObservationService.prototype, 'getObservationsCountBySampleSiteId')
+      .resolves({ observationCount: 0 });
+
     const deleteSampleLocationRecordStub = sinon
       .stub(SampleLocationService.prototype, 'deleteSampleLocationRecord')
       .resolves();
@@ -219,5 +224,6 @@ describe('deleteSurveySampleSiteRecord', () => {
 
     expect(mockRes.status).to.have.been.calledWith(204);
     expect(deleteSampleLocationRecordStub).to.have.been.calledOnce;
+    expect(getObservationsCountBySampleSiteIdStub).to.have.been.calledOnce;
   });
 });
diff --git a/...src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.ts b/...src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.ts
@@ -5,6 +5,7 @@ import { getDBConnection } from '../../../../../../../database/db';
 import { HTTP400 } from '../../../../../../../errors/http-error';
 import { GeoJSONFeature } from '../../../../../../../openapi/schemas/geoJson';
 import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization';
+import { ObservationService } from '../../../../../../../services/observation-service';
 import { SampleLocationService } from '../../../../../../../services/sample-location-service';
 import { getLogger } from '../../../../../../../utils/logger';
 
@@ -268,6 +269,7 @@ DELETE.apiDoc = {
 
 export function deleteSurveySampleSiteRecord(): RequestHandler {
   return async (req, res) => {
+    const surveyId = Number(req.params.surveyId);
     const surveySampleSiteId = Number(req.params.surveySampleSiteId);
 
     if (!surveySampleSiteId) {
@@ -279,6 +281,14 @@ export function deleteSurveySampleSiteRecord(): RequestHandler {
     try {
       await connection.open();
 
+      const observationService = new ObservationService(connection);
+
+      if (
+        (await observationService.getObservationsCountBySampleSiteId(surveyId, surveySampleSiteId)).observationCount > 0
+      ) {
+        throw new HTTP400('Cannot delete a sample site that is associated with an observation');
+      }
+
       const sampleLocationService = new SampleLocationService(connection);
 
       await sampleLocationService.deleteSampleLocationRecord(surveySampleSiteId);

diff --git a/api/src/repositories/observation-repository.ts b/api/src/repositories/observation-repository.ts
@@ -301,4 +301,29 @@ export class ObservationRepository extends BaseRepository {
 
     return response.rows[0];
   }
+
+  /**
+   * Retrieves all observation records for the given survey and sample site ids
+   *
+   * @param {number} surveyId
+   * @param {number} sampleSiteId
+   * @return {*}  {Promise<{ observationCount: number }>}
+   * @memberof ObservationRepository
+   */
+  async getObservationsCountBySampleSiteId(
+    surveyId: number,
+    sampleSiteId: number
+  ): Promise<{ observationCount: number }> {
+    const knex = getKnex();
+    const sqlStatement = knex
+      .queryBuilder()
+      .count('survey_observation_id as rowCount')
+      .from('survey_observation')
+      .where('survey_id', surveyId)
+      .where('survey_sample_site_id', sampleSiteId);
+
+    const response = await this.connection.knex(sqlStatement);
+    const observationCount = Number(response.rows[0].rowCount);
+    return { observationCount };
+  }
 }
diff --git a/api/src/repositories/sample-period-repository.ts b/api/src/repositories/sample-period-repository.ts
@@ -1,5 +1,6 @@
 import SQL from 'sql-template-strings';
 import { z } from 'zod';
+import { getKnex } from '../database/db';
 import { ApiExecuteSQLError } from '../errors/api-error';
 import { BaseRepository } from './base-repository';
 
@@ -151,19 +152,19 @@ export class SamplePeriodRepository extends BaseRepository {
    * @memberof SamplePeriodRepository
    */
   async deleteSamplePeriods(periodsToDelete: number[]): Promise<SamplePeriodRecord[]> {
-    const sqlStatement = SQL`
-      DELETE FROM
-        survey_sample_period
-      WHERE
-        survey_sample_period_id IN (${periodsToDelete.join(',')})
-      RETURNING
-        *;
-    `;
+    const knex = getKnex();
 
-    const response = await this.connection.sql(sqlStatement, SamplePeriodRecord);
+    const sqlStatement = knex
+      .queryBuilder()
+      .delete()
+      .from('survey_sample_period')
+      .whereIn('survey_sample_period_id', periodsToDelete)
+      .returning('*');
+
+    const response = await this.connection.knex(sqlStatement, SamplePeriodRecord);
 
     if (!response?.rowCount) {
-      throw new ApiExecuteSQLError('Failed to delete sample period', [
+      throw new ApiExecuteSQLError('Failed to delete sample periods', [
         'SamplePeriodRepository->deleteSamplePeriods',
         'rows was null or undefined, expected rows != null'
       ]);

diff --git a/api/src/services/observation-service.ts b/api/src/services/observation-service.ts
@@ -151,6 +151,21 @@ export class ObservationService extends DBService {
     return this.observationRepository.getObservationSubmissionById(submissionId);
   }
 
+  /**
+   * Retrieves all observation records for the given survey and sample site ids
+   *
+   * @param {number} surveyId
+   * @param {number} sampleSiteId
+   * @return {*}  {Promise<{ observationCount: number }>}
+   * @memberof ObservationService
+   */
+  async getObservationsCountBySampleSiteId(
+    surveyId: number,
+    sampleSiteId: number
+  ): Promise<{ observationCount: number }> {
+    return this.observationRepository.getObservationsCountBySampleSiteId(surveyId, sampleSiteId);
+  }
+
   /**
    * Processes a observation upload submission. This method receives an ID belonging to an
    * observation submission, gets the CSV file associated with the submission, and appends

diff --git a/api/src/services/sample-location-service.test.ts b/api/src/services/sample-location-service.test.ts
@@ -116,6 +116,14 @@ describe('SampleLocationService', () => {
       const mockDBConnection = getMockDBConnection();
       const service = new SampleLocationService(mockDBConnection);
 
+      const getSampleMethodsForSurveySampleSiteIdStub = sinon
+        .stub(SampleMethodService.prototype, 'getSampleMethodsForSurveySampleSiteId')
+        .resolves([{ survey_sample_method_id: 1 } as any]);
+
+      const deleteSampleMethodRecordStub = sinon
+        .stub(SampleMethodService.prototype, 'deleteSampleMethodRecord')
+        .resolves();
+
       sinon.stub(SampleLocationRepository.prototype, 'deleteSampleLocationRecord').resolves({
         survey_sample_site_id: 1,
         survey_id: 1,
@@ -134,6 +142,8 @@ describe('SampleLocationService', () => {
       const { survey_sample_site_id } = await service.deleteSampleLocationRecord(1);
 
       expect(survey_sample_site_id).to.be.eq(1);
+      expect(getSampleMethodsForSurveySampleSiteIdStub).to.be.calledOnceWith(1);
+      expect(deleteSampleMethodRecordStub).to.be.calledOnceWith(1);
     });
   });
 

diff --git a/api/src/services/sample-location-service.ts b/api/src/services/sample-location-service.ts
@@ -52,6 +52,14 @@ export class SampleLocationService extends DBService {
    * @memberof SampleLocationService
    */
   async deleteSampleLocationRecord(surveySampleSiteId: number): Promise<SampleLocationRecord> {
+    const sampleMethodService = new SampleMethodService(this.connection);
+
+    // Delete all methods associated with the sample location
+    const existingSampleMethods = await sampleMethodService.getSampleMethodsForSurveySampleSiteId(surveySampleSiteId);
+    for (const item of existingSampleMethods) {
+      await sampleMethodService.deleteSampleMethodRecord(item.survey_sample_method_id);
+    }
+
     return this.sampleLocationRepository.deleteSampleLocationRecord(surveySampleSiteId);
   }
 

diff --git a/api/src/services/sample-method-service.ts b/api/src/services/sample-method-service.ts
@@ -44,9 +44,10 @@ export class SampleMethodService extends DBService {
   async deleteSampleMethodRecord(surveySampleMethodId: number): Promise<SampleMethodRecord> {
     const samplePeriodService = new SamplePeriodService(this.connection);
 
-    // Delete all associated sample periods
+    // Collect list of periods to delete
     const existingSamplePeriods = await samplePeriodService.getSamplePeriodsForSurveyMethodId(surveySampleMethodId);
     const periodsToDelete = existingSamplePeriods.map((item) => item.survey_sample_period_id);
+    // Delete all associated sample periods
     await samplePeriodService.deleteSamplePeriodRecords(periodsToDelete);
 
     return this.sampleMethodRepository.deleteSampleMethodRecord(surveySampleMethodId);

diff --git a/app/src/features/surveys/observations/sampling-sites/SamplingSiteList.tsx b/app/src/features/surveys/observations/sampling-sites/SamplingSiteList.tsx
@@ -25,7 +25,9 @@ import Skeleton from '@mui/material/Skeleton';
 import Toolbar from '@mui/material/Toolbar';
 import Typography from '@mui/material/Typography';
 import { CodesContext } from 'contexts/codesContext';
+import { DialogContext } from 'contexts/dialogContext';
 import { SurveyContext } from 'contexts/surveyContext';
+import { useBiohubApi } from 'hooks/useBioHubApi';
 import { useContext, useEffect, useState } from 'react';
 import { Link as RouterLink } from 'react-router-dom';
 import { getCodesName } from 'utils/Utils';
@@ -47,6 +49,8 @@ const SampleSiteSkeleton = () => (
 const SamplingSiteList = () => {
   const surveyContext = useContext(SurveyContext);
   const codesContext = useContext(CodesContext);
+  const dialogContext = useContext(DialogContext);
+  const biohubApi = useBiohubApi();
 
   useEffect(() => {
     codesContext.codesDataLoader.load();
@@ -64,6 +68,64 @@ const SamplingSiteList = () => {
     setSelectedSampleSiteId(sample_site_id);
   };
 
+  /**
+   * Handle the delete sampling site API call.
+   *
+   */
+  const handleDeleteSampleSite = async () => {
+    await biohubApi.samplingSite
+      .deleteSampleSite(surveyContext.projectId, surveyContext.surveyId, Number(selectedSampleSiteId))
+      .then(() => {
+        dialogContext.setYesNoDialog({ open: false });
+        setAnchorEl(null);
+        surveyContext.sampleSiteDataLoader.refresh(surveyContext.projectId, surveyContext.surveyId);
+      })
+      .catch((error: any) => {
+        dialogContext.setYesNoDialog({ open: false });
+        setAnchorEl(null);
+        dialogContext.setSnackbar({
+          snackbarMessage: (
+            <>
+              <Typography variant="body2" component="div">
+                <strong>Error Deleting Sampling Site</strong>
+              </Typography>
+              <Typography variant="body2" component="div">
+                {String(error)}
+              </Typography>
+            </>
+          ),
+          open: true
+        });
+      });
+  };
+
+  /**
+   * Display the delete sampling site dialog.
+   *
+   */
+  const deleteSampleSiteDialog = () => {
+    dialogContext.setYesNoDialog({
+      dialogTitle: 'Delete Sampling Site?',
+      dialogContent: (
+        <Typography variant="body1" component="div" color="textSecondary">
+          Are you sure you want to delete this sampling site?
+        </Typography>
+      ),
+      yesButtonLabel: 'Delete Sampling Site',
+      noButtonLabel: 'Cancel',
+      yesButtonProps: { color: 'error' },
+      onClose: () => {
+        dialogContext.setYesNoDialog({ open: false });
+      },
+      onNo: () => {
+        dialogContext.setYesNoDialog({ open: false });
+      },
+      open: true,
+      onYes: () => {
+        handleDeleteSampleSite();
+      }
+    });
+  };
   const samplingSiteCount = surveyContext.sampleSiteDataLoader.data?.sampleSites.length ?? 0;
 
   return (
@@ -102,7 +164,7 @@ const SamplingSiteList = () => {
             <ListItemText>Edit Details</ListItemText>
           </RouterLink>
         </MenuItem>
-        <MenuItem onClick={() => console.log('DELETE THIS SAMPLING SITE')}>
+        <MenuItem onClick={deleteSampleSiteDialog}>
           <ListItemIcon>
             <Icon path={mdiTrashCanOutline} size={1} />
           </ListItemIcon>

diff --git a/app/src/hooks/api/useSamplingSiteApi.ts b/app/src/hooks/api/useSamplingSiteApi.ts
@@ -56,10 +56,23 @@ const useSamplingSiteApi = (axios: AxiosInstance) => {
     await axios.put(`/api/project/${projectId}/survey/${surveyId}/sample-site/${sampleSiteId}`, sampleSite);
   };
 
+  /**
+   * Delete Sample Site
+   *
+   * @param {number} projectId
+   * @param {number} surveyId
+   * @param {number} sampleSiteId
+   * @return {*}  {Promise<void>}
+   */
+  const deleteSampleSite = async (projectId: number, surveyId: number, sampleSiteId: number): Promise<void> => {
+    await axios.delete(`/api/project/${projectId}/survey/${surveyId}/sample-site/${sampleSiteId}`);
+  };
+
   return {
     createSamplingSites,
     getSampleSites,
-    editSampleSite
+    editSampleSite,
+    deleteSampleSite
   };
 };