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SIMSBIOHUB-451: Recognize 'Species' column in uploaded observation CSV #1196

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merged 5 commits into from
Jan 18, 2024
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SIMSBIOHUB-451: Recognize 'Species' column in uploaded observation CSV #1196

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be15a44
SIMSBIOHUB-451: Recognize 'Species' column in uploaded observation CSV
curtisupshall Jan 17, 2024
a4368a2
SIMSBIOHUB-451: Added taxon alias
curtisupshall Jan 17, 2024
4cb57b4
Merge branch 'dev' into SIMSBIOHUB-451
KjartanE Jan 17, 2024
9ac9f52
ignore-skip
curtisupshall Jan 18, 2024
41017e8
Turn down logging in dev
NickPhura Jan 18, 2024
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7 changes: 4 additions & 3 deletions api/src/services/observation-service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,12 @@ import { DBService } from './db-service';
const defaultLog = getLogger('services/observation-service');

const observationCSVColumnValidator: IXLSXCSVValidator = {
columnNames: ['SPECIES_TAXONOMIC_ID', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnNames: ['SPECIES', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'],
columnAliases: {
LATITUDE: ['LAT'],
LONGITUDE: ['LON', 'LONG', 'LNG']
LONGITUDE: ['LON', 'LONG', 'LNG'],
SPECIES: ['TAXON']
}
};

Expand Down Expand Up @@ -278,7 +279,7 @@ export class ObservationService extends DBService {
// Step 5. Merge all the table rows into an array of ObservationInsert[]
const insertRows: InsertObservation[] = worksheetRowObjects.map((row) => ({
survey_id: surveyId,
wldtaxonomic_units_id: row['SPECIES_TAXONOMIC_ID'],
wldtaxonomic_units_id: row['SPECIES'],
survey_sample_site_id: null,
survey_sample_method_id: null,
survey_sample_period_id: null,
Expand Down
11 changes: 6 additions & 5 deletions api/src/utils/xlsx-utils/worksheet-utils.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -12,19 +12,20 @@ describe('worksheet utils', () => {

it('should validate aliases', () => {
const observationCSVColumnValidator: worksheet_utils.IXLSXCSVValidator = {
columnNames: ['SPECIES_TAXONOMIC_ID', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnNames: ['SPECIES', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'],
columnAliases: {
LATITUDE: ['LAT'],
LONGITUDE: ['LON', 'LONG', 'LNG']
LONGITUDE: ['LON', 'LONG', 'LNG'],
SPECIES: ['TAXON']
}
};

const mockWorksheet = ({} as unknown) as xlsx.WorkSheet;

const getWorksheetHeaderssStub = sinon
.stub(worksheet_utils, 'getWorksheetHeaders')
.callsFake(() => ['SPECIES_TAXONOMIC_ID', 'COUNT', 'DATE', 'TIME', 'LAT', 'LON']);
.callsFake(() => ['TAXON', 'COUNT', 'DATE', 'TIME', 'LAT', 'LON']);

const result = worksheet_utils.validateWorksheetHeaders(mockWorksheet, observationCSVColumnValidator);

Expand All @@ -34,7 +35,7 @@ describe('worksheet utils', () => {

it('should fail for unknown aliases', () => {
const observationCSVColumnValidator: worksheet_utils.IXLSXCSVValidator = {
columnNames: ['SPECIES_TAXONOMIC_ID', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnNames: ['SPECIES', 'COUNT', 'DATE', 'TIME', 'LATITUDE', 'LONGITUDE'],
columnTypes: ['number', 'number', 'date', 'string', 'number', 'number'],
columnAliases: {
LATITUDE: ['LAT'],
Expand All @@ -46,7 +47,7 @@ describe('worksheet utils', () => {

const getWorksheetHeaderssStub = sinon
.stub(worksheet_utils, 'getWorksheetHeaders')
.callsFake(() => ['SPECIES_TAXONOMIC_ID', 'COUNT', 'DATE', 'TIME', 'SOMETHING_LAT', 'LON']);
.callsFake(() => ['SPECIES', 'COUNT', 'DATE', 'TIME', 'SOMETHING_LAT', 'LON']);

const result = worksheet_utils.validateWorksheetHeaders(mockWorksheet, observationCSVColumnValidator);

Expand Down
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