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SIMSBIOHUB-288: Sample Site Dropdowns (#1110)
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* 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
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@al-rosenthal
al-rosenthal authored Oct 11, 2023
1 parent dfd11f5 commit e976b83
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Showing 53 changed files with 2,067 additions and 437 deletions.
12 changes: 6 additions & 6 deletions api/package-lock.json
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5 changes: 5 additions & 0 deletions api/src/database/db.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion api/src/paths/project/{projectId}/survey/list.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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) => {
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24 changes: 18 additions & 6 deletions api/src/paths/project/{projectId}/survey/{surveyId}/observation/index.test.ts
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Expand Up @@ -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, [
Expand All @@ -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,
Expand All @@ -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);
Expand Down Expand Up @@ -533,7 +545,7 @@ describe('insertUpdateSurveyObservations', () => {
};

try {
const requestHandler = observationRecords.insertUpdateSurveyObservations();
const requestHandler = observationRecords.insertUpdateDeleteSurveyObservations();

await requestHandler(mockReq, mockRes, mockNext);
expect.fail();
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39 changes: 28 additions & 11 deletions api/src/paths/project/{projectId}/survey/{surveyId}/observation/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ export const PUT: Operation = [
]
};
}),
insertUpdateSurveyObservations()
insertUpdateDeleteSurveyObservations()
];

const surveyObservationsResponseSchema: SchemaObject = {
Expand Down Expand Up @@ -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: [
{
Expand Down Expand Up @@ -170,7 +170,7 @@ GET.apiDoc = {
$ref: '#/components/responses/401'
},
403: {
$ref: '#/components/responses/401'
$ref: '#/components/responses/403'
},
500: {
$ref: '#/components/responses/500'
Expand All @@ -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: []
Expand Down Expand Up @@ -250,7 +250,7 @@ PUT.apiDoc = {
},
responses: {
200: {
description: 'Upload OK',
description: 'Update OK',
content: {
'application/json': {
schema: { ...surveyObservationsResponseSchema }
Expand All @@ -264,7 +264,7 @@ PUT.apiDoc = {
$ref: '#/components/responses/401'
},
403: {
$ref: '#/components/responses/401'
$ref: '#/components/responses/403'
},
500: {
$ref: '#/components/responses/500'
Expand All @@ -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);
Expand All @@ -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']);

Expand All @@ -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);
Expand All @@ -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 {
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2 changes: 2 additions & 0 deletions api/src/paths/project/{projectId}/survey/{surveyId}/sample-site/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
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2 changes: 2 additions & 0 deletions ...src/paths/project/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
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2 changes: 2 additions & 0 deletions ...ect/{projectId}/survey/{surveyId}/sample-site/{surveySampleSiteId}/sample-method/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
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2 changes: 2 additions & 0 deletions ...{surveyId}/sample-site/{surveySampleSiteId}/sample-method/{surveySampleMethodId}/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
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2 changes: 2 additions & 0 deletions ...ple-site/{surveySampleSiteId}/sample-method/{surveySampleMethodId}/sample-period/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
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2 changes: 2 additions & 0 deletions ...ampleSiteId}/sample-method/{surveySampleMethodId}/sample-period/{surveySamplePeriodId}.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down Expand Up @@ -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();
Expand Down
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