SIMSBIOHUB-288: Sample Site Dropdowns (#1110)

* Add datagrid autocomplete components
* Add datagrid support for sample site, method, and period columns
* Add time component to data grid.
* Added node-pg float type parser
* Save/Edit datagrid observations working

api/src/database/db.ts

@@ -51,6 +51,11 @@ pg.types.setTypeParser(pg.types.builtins.TIMESTAMP, (stringValue: string) => {
 pg.types.setTypeParser(pg.types.builtins.TIMESTAMPTZ, (stringValue: string) => {
   return stringValue; // 1082 for `DATE` type
 });
+// NUMERIC column types return as strings to maintain precision. Converting this to a float so it is usable by the system
+// Explanation of why Numeric returns as a string: https://github.com/brianc/node-postgres/issues/811
+pg.types.setTypeParser(pg.types.builtins.NUMERIC, (stringValue: string) => {
+  return parseFloat(stringValue);
+});
 
 // singleton pg pool instance used by the api
 let DBPool: pg.Pool | undefined;

api/src/paths/project/{projectId}/survey/list.ts

@@ -8,7 +8,7 @@ import { authorizeRequestHandler } from '../../../../request-handlers/security/a
 import { SurveyService } from '../../../../services/survey-service';
 import { getLogger } from '../../../../utils/logger';
 
-const defaultLog = getLogger('paths/project/{projectId}/surveys');
+const defaultLog = getLogger('paths/project/{projectId}/survey/list');
 
 export const GET: Operation = [
   authorizeRequestHandler((req) => {

api/src/paths/project/{projectId}/survey/{surveyId}/observation/index.test.ts

@@ -462,20 +462,26 @@ describe('insertUpdateSurveyObservations', () => {
           latitude: 48.103322,
           longitude: -122.798892,
           observation_date: '1970-01-01',
-          observation_time: '00:00:00'
+          observation_time: '00:00:00',
+          survey_sample_site_id: 1,
+          survey_sample_method_id: 1,
+          survey_sample_period_id: 1
         },
         {
           wldtaxonomic_units_id: 1234,
           count: 99,
           latitude: 48.103322,
           longitude: -122.798892,
           observation_date: '1970-01-01',
-          observation_time: '00:00:00'
+          observation_time: '00:00:00',
+          survey_sample_site_id: 1,
+          survey_sample_method_id: 1,
+          survey_sample_period_id: 1
         }
       ]
     };
 
-    const requestHandler = observationRecords.insertUpdateSurveyObservations();
+    const requestHandler = observationRecords.insertUpdateDeleteSurveyObservations();
     await requestHandler(mockReq, mockRes, mockNext);
 
     expect(insertUpdateSurveyObservationsStub).to.have.been.calledOnceWith(2, [
@@ -486,7 +492,10 @@ describe('insertUpdateSurveyObservations', () => {
         longitude: -122.798892,
         count: 99,
         observation_date: '1970-01-01',
-        observation_time: '00:00:00'
+        observation_time: '00:00:00',
+        survey_sample_site_id: 1,
+        survey_sample_method_id: 1,
+        survey_sample_period_id: 1
       },
       {
         survey_observation_id: undefined,
@@ -495,7 +504,10 @@ describe('insertUpdateSurveyObservations', () => {
         longitude: -122.798892,
         count: 99,
         observation_date: '1970-01-01',
-        observation_time: '00:00:00'
+        observation_time: '00:00:00',
+        survey_sample_site_id: 1,
+        survey_sample_method_id: 1,
+        survey_sample_period_id: 1
       }
     ]);
     expect(mockRes.statusValue).to.equal(200);
@@ -533,7 +545,7 @@ describe('insertUpdateSurveyObservations', () => {
     };
 
     try {
-      const requestHandler = observationRecords.insertUpdateSurveyObservations();
+      const requestHandler = observationRecords.insertUpdateDeleteSurveyObservations();
 
       await requestHandler(mockReq, mockRes, mockNext);
       expect.fail();

api/src/paths/project/{projectId}/survey/{surveyId}/observation/index.ts

@@ -49,7 +49,7 @@ export const PUT: Operation = [
       ]
     };
   }),
-  insertUpdateSurveyObservations()
+  insertUpdateDeleteSurveyObservations()
 ];
 
 const surveyObservationsResponseSchema: SchemaObject = {
@@ -127,7 +127,7 @@ const surveyObservationsResponseSchema: SchemaObject = {
 };
 
 GET.apiDoc = {
-  description: 'Fetches observation records for the given survey.',
+  description: 'Get all observations for the survey.',
   tags: ['observation'],
   security: [
     {
@@ -170,7 +170,7 @@ GET.apiDoc = {
       $ref: '#/components/responses/401'
     },
     403: {
-      $ref: '#/components/responses/401'
+      $ref: '#/components/responses/403'
     },
     500: {
       $ref: '#/components/responses/500'
@@ -182,8 +182,8 @@ GET.apiDoc = {
 };
 
 PUT.apiDoc = {
-  description: 'Fetches observation records for the given survey.',
-  tags: ['attachments'],
+  description: 'Insert/update/delete observations for the survey.',
+  tags: ['observation'],
   security: [
     {
       Bearer: []
@@ -250,7 +250,7 @@ PUT.apiDoc = {
   },
   responses: {
     200: {
-      description: 'Upload OK',
+      description: 'Update OK',
       content: {
         'application/json': {
           schema: { ...surveyObservationsResponseSchema }
@@ -264,7 +264,7 @@ PUT.apiDoc = {
       $ref: '#/components/responses/401'
     },
     403: {
-      $ref: '#/components/responses/401'
+      $ref: '#/components/responses/403'
     },
     500: {
       $ref: '#/components/responses/500'
@@ -275,6 +275,12 @@ PUT.apiDoc = {
   }
 };
 
+/**
+ * Fetch all observations for a survey.
+ *
+ * @export
+ * @return {*}  {RequestHandler}
+ */
 export function getSurveyObservations(): RequestHandler {
   return async (req, res) => {
     const surveyId = Number(req.params.surveyId);
@@ -300,11 +306,19 @@ export function getSurveyObservations(): RequestHandler {
   };
 }
 
-export function insertUpdateSurveyObservations(): RequestHandler {
+/**
+ * Inserts new observation records.
+ * Updates existing observation records.
+ * Deletes missing observation records.
+ *
+ * @export
+ * @return {*}  {RequestHandler}
+ */
+export function insertUpdateDeleteSurveyObservations(): RequestHandler {
   return async (req, res) => {
     const surveyId = Number(req.params.surveyId);
 
-    defaultLog.debug({ label: 'insertUpdateSurveyObservations', surveyId });
+    defaultLog.debug({ label: 'insertUpdateDeleteSurveyObservations', surveyId });
 
     const connection = getDBConnection(req['keycloak_token']);
 
@@ -318,12 +332,15 @@ export function insertUpdateSurveyObservations(): RequestHandler {
         return {
           survey_observation_id: record.survey_observation_id,
           wldtaxonomic_units_id: Number(record.wldtaxonomic_units_id),
+          survey_sample_site_id: record.survey_sample_site_id,
+          survey_sample_method_id: record.survey_sample_method_id,
+          survey_sample_period_id: record.survey_sample_period_id,
           latitude: record.latitude,
           longitude: record.longitude,
           count: record.count,
           observation_date: record.observation_date,
           observation_time: record.observation_time
-        };
+        } as InsertObservation | UpdateObservation;
       });
 
       const surveyObservations = await observationService.insertUpdateDeleteSurveyObservations(surveyId, records);
@@ -332,7 +349,7 @@ export function insertUpdateSurveyObservations(): RequestHandler {
 
       return res.status(200).json({ surveyObservations });
     } catch (error) {
-      defaultLog.error({ label: 'insertUpdateSurveyObservations', message: 'error', error });
+      defaultLog.error({ label: 'insertUpdateDeleteSurveyObservations', message: 'error', error });
       await connection.rollback();
       throw error;
     } finally {

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/index.ts

@@ -158,6 +158,7 @@ export function getSurveySampleLocationRecords(): RequestHandler {
       return res.status(200).json({ sampleSites: result });
     } catch (error) {
       defaultLog.error({ label: 'getSurveySampleLocationRecords', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -309,6 +310,7 @@ export function createSurveySampleSiteRecord(): RequestHandler {
       return res.status(201).send();
     } catch (error) {
       defaultLog.error({ label: 'insertProjectParticipants', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.ts

@@ -146,6 +146,7 @@ export function updateSurveySampleSite(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'updateSurveySampleSite', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -253,6 +254,7 @@ export function deleteSurveySampleSiteRecord(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'deleteSurveySampleSiteRecord', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts

@@ -163,6 +163,7 @@ export function getSurveySampleMethodRecords(): RequestHandler {
       return res.status(200).json({ sampleMethods: result });
     } catch (error) {
       defaultLog.error({ label: 'getSurveySampleMethodRecords', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -298,6 +299,7 @@ export function createSurveySampleSiteRecord(): RequestHandler {
       return res.status(201).send();
     } catch (error) {
       defaultLog.error({ label: 'insertProjectParticipants', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/{surveySampleMethodId}/index.ts

@@ -143,6 +143,7 @@ export function updateSurveySampleMethod(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'updateSurveySampleMethod', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -250,6 +251,7 @@ export function deleteSurveySampleMethodRecord(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'deleteSurveySampleMethodRecord', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/{surveySampleMethodId}/sample-period/index.ts

@@ -172,6 +172,7 @@ export function getSurveySamplePeriodRecords(): RequestHandler {
       return res.status(200).json({ samplePeriods: result });
     } catch (error) {
       defaultLog.error({ label: 'getSurveySamplePeriodRecords', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -311,6 +312,7 @@ export function createSurveySamplePeriodRecord(): RequestHandler {
       return res.status(201).send();
     } catch (error) {
       defaultLog.error({ label: 'createSurveySamplePeriodRecord', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();

api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/{surveySampleMethodId}/sample-period/{surveySamplePeriodId}.ts

@@ -162,6 +162,7 @@ export function updateSurveySamplePeriod(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'updateSurveySamplePeriod', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();
@@ -287,6 +288,7 @@ export function deleteSurveySamplePeriodRecord(): RequestHandler {
       return res.status(204).send();
     } catch (error) {
       defaultLog.error({ label: 'deleteSurveySamplePeriodRecord', message: 'error', error });
+      await connection.rollback();
       throw error;
     } finally {
       connection.release();