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161
api/src/paths/project/{projectId}/survey/{surveyId}/critters/measurements/import.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| import { RequestHandler } from 'express'; | ||
| import { Operation } from 'express-openapi'; | ||
| import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../../constants/roles'; | ||
| import { getDBConnection } from '../../../../../../../database/db'; | ||
| import { HTTP400 } from '../../../../../../../errors/http-error'; | ||
| import { csvFileSchema } from '../../../../../../../openapi/schemas/file'; | ||
| import { authorizeRequestHandler } from '../../../../../../../request-handlers/security/authorization'; | ||
| import { importCSV } from '../../../../../../../services/import-services/import-csv'; | ||
| import { ImportMeasurementsStrategy } from '../../../../../../../services/import-services/measurement/import-measurements-strategy'; | ||
| import { scanFileForVirus } from '../../../../../../../utils/file-utils'; | ||
| import { getLogger } from '../../../../../../../utils/logger'; | ||
| import { parseMulterFile } from '../../../../../../../utils/media/media-utils'; | ||
| import { getFileFromRequest } from '../../../../../../../utils/request'; | ||
|
|
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| const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/measurements/import'); | ||
|
|
||
| export const POST: Operation = [ | ||
| authorizeRequestHandler((req) => { | ||
| return { | ||
| or: [ | ||
| { | ||
| validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR], | ||
| surveyId: Number(req.params.surveyId), | ||
| discriminator: 'ProjectPermission' | ||
| }, | ||
| { | ||
| validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR], | ||
| discriminator: 'SystemRole' | ||
| } | ||
| ] | ||
| }; | ||
| }), | ||
| importCsv() | ||
| ]; | ||
|
|
||
| POST.apiDoc = { | ||
| description: 'Upload Critterbase CSV Measurements file', | ||
| tags: ['observations'], | ||
| security: [ | ||
| { | ||
| Bearer: [] | ||
| } | ||
| ], | ||
| parameters: [ | ||
| { | ||
| in: 'path', | ||
| description: 'SIMS survey id', | ||
| name: 'projectId', | ||
| required: true, | ||
| schema: { | ||
| type: 'integer', | ||
| minimum: 1 | ||
| } | ||
| }, | ||
| { | ||
| in: 'path', | ||
| description: 'SIMS survey id', | ||
| name: 'surveyId', | ||
| required: true, | ||
| schema: { | ||
| type: 'integer', | ||
| minimum: 1 | ||
| } | ||
| } | ||
| ], | ||
| requestBody: { | ||
| description: 'Critterbase Measurements CSV import file.', | ||
| content: { | ||
| 'multipart/form-data': { | ||
| schema: { | ||
| type: 'object', | ||
| additionalProperties: false, | ||
| required: ['media'], | ||
| properties: { | ||
| media: { | ||
| description: 'Critterbase Measurements CSV import file.', | ||
| type: 'array', | ||
| minItems: 1, | ||
| maxItems: 1, | ||
| items: csvFileSchema | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| responses: { | ||
| 201: { | ||
| description: 'Measurement import success.', | ||
| content: { | ||
| 'application/json': { | ||
| schema: { | ||
| type: 'object', | ||
| additionalProperties: false, | ||
| properties: { | ||
| measurementsCreated: { | ||
| description: 'Number of Critterbase measurements created.', | ||
| type: 'integer' | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| 400: { | ||
| $ref: '#/components/responses/400' | ||
| }, | ||
| 401: { | ||
| $ref: '#/components/responses/401' | ||
| }, | ||
| 403: { | ||
| $ref: '#/components/responses/403' | ||
| }, | ||
| 500: { | ||
| $ref: '#/components/responses/500' | ||
| }, | ||
| default: { | ||
| $ref: '#/components/responses/default' | ||
| } | ||
| } | ||
| }; | ||
|
|
||
| /** | ||
| * Imports a `Critterbase Measurement CSV` which bulk adds measurements to Critterbase. | ||
| * | ||
| * @return {*} {RequestHandler} | ||
| */ | ||
| export function importCsv(): RequestHandler { | ||
| return async (req, res) => { | ||
| const surveyId = Number(req.params.surveyId); | ||
| const rawFile = getFileFromRequest(req); | ||
|
|
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| const connection = getDBConnection(req.keycloak_token); | ||
|
|
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| try { | ||
| await connection.open(); | ||
|
|
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| // Check for viruses / malware | ||
| const virusScanResult = await scanFileForVirus(rawFile); | ||
|
|
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| if (!virusScanResult) { | ||
| throw new HTTP400('Malicious content detected, import cancelled.'); | ||
| } | ||
|
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| const importCsvMeasurementsStrategy = new ImportMeasurementsStrategy(connection, surveyId); | ||
|
|
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| // Pass CSV file and importer as dependencies | ||
| const measurementsCreated = await importCSV(parseMulterFile(rawFile), importCsvMeasurementsStrategy); | ||
|
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| await connection.commit(); | ||
|
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| return res.status(201).json({ measurementsCreated }); | ||
| } catch (error) { | ||
| defaultLog.error({ label: 'importMeasurementsCSV', message: 'error', error }); | ||
| await connection.rollback(); | ||
| throw error; | ||
| } finally { | ||
| connection.release(); | ||
| } | ||
| }; | ||
| } |
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22 changes: 22 additions & 0 deletions
22
api/src/services/import-services/measurement/import-measurements-strategy.interface.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| import { z } from 'zod'; | ||
|
|
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| export const CsvQualitativeMeasurementSchema = z.object({ | ||
| critter_id: z.string().uuid(), | ||
| capture_id: z.string().uuid(), | ||
| taxon_measurement_id: z.string().uuid(), | ||
| qualitative_option_id: z.string().uuid() | ||
| }); | ||
|
|
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| export const CsvQuantitativeMeasurementSchema = z.object({ | ||
| critter_id: z.string().uuid(), | ||
| capture_id: z.string().uuid(), | ||
| taxon_measurement_id: z.string().uuid(), | ||
| value: z.number() | ||
| }); | ||
|
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| export const CsvMeasurementSchema = CsvQualitativeMeasurementSchema.or(CsvQuantitativeMeasurementSchema); | ||
|
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| // Zod inferred types | ||
| export type CsvMeasurement = z.infer<typeof CsvMeasurementSchema>; | ||
| export type CsvQuantitativeMeasurement = z.infer<typeof CsvQuantitativeMeasurementSchema>; | ||
| export type CsvQualitativeMeasurement = z.infer<typeof CsvQualitativeMeasurementSchema>; |
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