BHBC-1868: Push Observation Data to BioHub

api/src/models/occurrence-create.ts

@@ -1,7 +1,3 @@
-import { getLogger } from '../utils/logger';
-
-const defaultLog = getLogger('models/occurrence-create');
-
 /**
  * Pre-processes POST occurrences data
  *
@@ -21,8 +17,6 @@ export class PostOccurrence {
   eventDate: string;
 
   constructor(obj?: any) {
-    defaultLog.debug({ label: 'PostOccurrence', message: 'params', obj });
-
     this.associatedTaxa = obj?.associatedTaxa || null;
     this.lifeStage = obj?.lifeStage || null;
     this.sex = obj?.sex || null;

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

@@ -0,0 +1,95 @@
+import { RequestHandler } from 'express';
+import { Operation } from 'express-openapi';
+import { SYSTEM_ROLE } from '../../../../../constants/roles';
+import { getDBConnection } from '../../../../../database/db';
+import { HTTP400 } from '../../../../../errors/custom-error';
+import { authorizeRequestHandler } from '../../../../../request-handlers/security/authorization';
+import { PlatformService } from '../../../../../services/platform-service';
+import { getLogger } from '../../../../../utils/logger';
+
+const defaultLog = getLogger('/api/project/{projectId}/survey/{surveyId}/upload');
+
+export const POST: Operation = [
+  authorizeRequestHandler(() => {
+    return {
+      and: [
+        {
+          validSystemRoles: [SYSTEM_ROLE.SYSTEM_ADMIN],
+          discriminator: 'SystemRole'
+        }
+      ]
+    };
+  }),
+  uploadSurveyDataToBioHub()
+];
+
+POST.apiDoc = {
+  description: 'Upload survey/observation data to BioHub.',
+  tags: ['survey'],
+  security: [
+    {
+      Bearer: []
+    }
+  ],
+  parameters: [
+    {
+      in: 'path',
+      name: 'projectId',
+      schema: {
+        type: 'integer',
+        minimum: 1
+      },
+      required: true
+    },
+    {
+      in: 'path',
+      name: 'surveyId',
+      schema: {
+        type: 'integer',
+        minimum: 1
+      },
+      required: true
+    }
+  ],
+  responses: {
+    200: {
+      description: 'Upload survey/observation data to BioHub OK.'
+    },
+    401: {
+      $ref: '#/components/responses/401'
+    },
+    default: {
+      $ref: '#/components/responses/default'
+    }
+  }
+};
+
+export function uploadSurveyDataToBioHub(): RequestHandler {
+  return async (req, res) => {
+    const projectId = Number(req.params.projectId);
+    const surveyId = Number(req.params.surveyId);
+
+    if (!surveyId) {
+      throw new HTTP400('Missing required path param `surveyId`');
+    }
+
+    const connection = getDBConnection(req['keycloak_token']);
+
+    try {
+      await connection.open();
+
+      const platformService = new PlatformService(connection);
+      await platformService.uploadSurveyDataToBioHub(projectId, surveyId);
+
+      await connection.commit();
+
+      return res.status(200).send();
+    } catch (error) {
+      defaultLog.error({ label: 'uploadSurveyDataToBioHub', message: 'error', error });
+      await connection.rollback();
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}

api/src/queries/survey/survey-occurrence-queries.ts

@@ -159,6 +159,8 @@ export const getLatestSurveyOccurrenceSubmissionSQL = (surveyId: number): SQLSta
       os.event_timestamp,
       os.input_key,
       os.input_file_name,
+      os.output_key,
+      os.output_file_name,
       ss.submission_status_id,
       ss.submission_status_type_id,
       sst.name as submission_status_type_name,

api/src/services/platform-service.ts

@@ -2,9 +2,12 @@ import AdmZip from 'adm-zip';
 import axios from 'axios';
 import FormData from 'form-data';
 import { URL } from 'url';
+import { HTTP400 } from '../errors/custom-error';
+import { getFileFromS3 } from '../utils/file-utils';
 import { EmlService } from './eml-service';
 import { KeycloakService } from './keycloak-service';
 import { DBService } from './service';
+import { SurveyService } from './survey-service';
 
 export interface IDwCADataset {
   archiveFile: {
@@ -137,4 +140,51 @@ export class PlatformService extends DBService {
 
     return data;
   }
+
+  /**
+   * Upload Survey/Project/Observation data to Backbone
+   *
+   * @param {number} projectId
+   * @param {number} surveyId
+   * @return {*}
+   * @memberof PlatformService
+   */
+  async uploadSurveyDataToBioHub(projectId: number, surveyId: number) {
+    if (!this.BACKBONE_INTAKE_ENABLED) {
+      return;
+    }
+
+    const surveyService = new SurveyService(this.connection);
+    const surveyData = await surveyService.getLatestSurveyOccurrenceSubmission(surveyId);
+
+    if (!surveyData.output_key) {
+      throw new HTTP400('no s3Key found');
+    }
+    const s3File = await getFileFromS3(surveyData.output_key);
+
+    if (!s3File) {
+      throw new HTTP400('no s3File found');
+    }
+    const dwcArchiveZip = new AdmZip(s3File.Body as Buffer);
+
+    const emlService = new EmlService({ projectId: projectId }, this.connection);
+    const emlString = await emlService.buildProjectEml();
+
+    if (!emlString) {
+      throw new HTTP400('emlString failed to build');
+    }
+
+    dwcArchiveZip.addFile('eml.xml', Buffer.from(emlString));
+
+    const dwCADataset = {
+      archiveFile: {
+        data: dwcArchiveZip.toBuffer(),
+        fileName: 'DwCA.zip',
+        mimeType: 'application/zip'
+      },
+      dataPackageId: emlService.packageId
+    };
+
+    return this._submitDwCADatasetToBioHubBackbone(dwCADataset);
+  }
 }

api/src/services/survey-service.test.ts

@@ -1,5 +1,6 @@
 import chai, { expect } from 'chai';
 import { describe } from 'mocha';
+import { QueryResult } from 'pg';
 import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
 import { PutSurveyObject } from '../models/survey-update';
@@ -82,4 +83,25 @@ describe('SurveyService', () => {
       expect(updateSurveyProprietorDataStub).to.have.been.calledOnce;
     });
   });
+
+  describe('getLatestSurveyOccurrenceSubmission', () => {
+    afterEach(() => {
+      sinon.restore();
+    });
+
+    it('Gets latest survey submission', async () => {
+      const mockRowObj = { id: 123 };
+      const mockQueryResponse = ({ rows: [mockRowObj] } as unknown) as QueryResult<any>;
+
+      const mockDBConnection = getMockDBConnection({ query: async () => mockQueryResponse });
+
+      const surveyId = 1;
+
+      const surveyService = new SurveyService(mockDBConnection);
+
+      const response = await surveyService.getLatestSurveyOccurrenceSubmission(surveyId);
+
+      expect(response).to.eql({ id: 123 });
+    });
+  });
 });

api/src/services/survey-service.ts

@@ -223,6 +223,25 @@ export class SurveyService extends DBService {
     return (response && response.rows?.[0]) || null;
   }
 
+  /**
+   * Get latest survey data submission from id
+   *
+   * @param {number} surveyId
+   * @return {*}
+   * @memberof SurveyService
+   */
+  async getLatestSurveyOccurrenceSubmission(surveyId: number) {
+    const sqlStatement = queries.survey.getLatestSurveyOccurrenceSubmissionSQL(surveyId);
+
+    if (!sqlStatement) {
+      throw new ApiGeneralError('Failed to build SQL get statement');
+    }
+
+    const response = await this.connection.query(sqlStatement.text, sqlStatement.values);
+
+    return (response && response.rows?.[0]) || null;
+  }
+
   async getSummaryResultId(surveyId: number) {
     const sqlStatement = queries.survey.getLatestSummaryResultIdSQL(surveyId);