SIMSBIOHUB-424: Publish Documents to BioHub from SIMS (#1193)

Submit artifacts to BioHub as part of Survey Submission.
---------
Co-authored-by: Curtis Upshall <[email protected]>
Co-authored-by: Al Rosenthal <[email protected]>
Co-authored-by: Nick Phura <[email protected]>
Co-authored-by: Nick Phura <[email protected]>

api/src/models/biohub-create.test.ts

@@ -7,7 +7,7 @@ import {
   PostSurveySubmissionToBioHubObject,
   PostSurveyToBiohubObject
 } from './biohub-create';
-import { GetSurveyData } from './survey-view';
+import { GetSurveyData, GetSurveyPurposeAndMethodologyData } from './survey-view';
 
 describe('PostSurveyObservationToBiohubObject', () => {
   describe('All values provided', () => {
@@ -114,7 +114,13 @@ describe('PostSurveyToBiohubObject', () => {
     } as GetSurveyData;
 
     before(() => {
-      data = new PostSurveyToBiohubObject(survey_obj, [observation_obj], { type: 'FeatureCollection', features: [] });
+      data = new PostSurveyToBiohubObject(
+        survey_obj,
+        [observation_obj],
+        { type: 'FeatureCollection', features: [] },
+        [],
+        []
+      );
     });
 
     it('sets id', () => {
@@ -139,7 +145,7 @@ describe('PostSurveyToBiohubObject', () => {
     });
 
     it('sets features', () => {
-      expect(data.features).to.eql([new PostSurveyObservationToBiohubObject(observation_obj)]);
+      expect(data.child_features).to.eql([new PostSurveyObservationToBiohubObject(observation_obj)]);
     });
   });
 });
@@ -180,19 +186,29 @@ describe('PostSurveySubmissionToBioHubObject', () => {
       revision_count: 1
     };
 
+    const purpose_and_methodology: GetSurveyPurposeAndMethodologyData = {
+      intended_outcome_ids: [],
+      additional_details: 'A description of the purpose',
+      revision_count: 0,
+      vantage_code_ids: []
+    };
+
     const survey_geometry: FeatureCollection = {
       type: 'FeatureCollection',
       features: []
     };
 
-    const additionalInformation = 'A description of the submission';
+    const submissionComment = 'A comment about the submission';
 
     before(() => {
       data = new PostSurveySubmissionToBioHubObject(
         survey_obj,
+        purpose_and_methodology,
         observation_obj,
         survey_geometry,
-        additionalInformation
+        [],
+        [],
+        submissionComment
       );
     });
 
@@ -205,11 +221,15 @@ describe('PostSurveySubmissionToBioHubObject', () => {
     });
 
     it('sets description', () => {
-      expect(data.description).to.equal('A description of the submission');
+      expect(data.description).to.equal('A description of the purpose');
     });
 
-    it('sets features', () => {
-      expect(data.features).to.eql([new PostSurveyToBiohubObject(survey_obj, observation_obj, survey_geometry)]);
+    it('sets comment', () => {
+      expect(data.comment).to.equal('A comment about the submission');
+    });
+
+    it('sets content', () => {
+      expect(data.content).to.eql(new PostSurveyToBiohubObject(survey_obj, observation_obj, survey_geometry, [], []));
     });
   });
 });

api/src/models/biohub-create.ts

@@ -1,15 +1,23 @@
 import { FeatureCollection } from 'geojson';
+import { ATTACHMENT_TYPE } from '../constants/attachments';
+import { ISurveyAttachment, ISurveyReportAttachment } from '../repositories/attachment-repository';
 import { ObservationRecord } from '../repositories/observation-repository';
 import { getLogger } from '../utils/logger';
-import { GetSurveyData } from './survey-view';
+import { GetSurveyData, GetSurveyPurposeAndMethodologyData } from './survey-view';
 
 const defaultLog = getLogger('models/biohub-create');
 
+export interface BioHubSubmission {
+  id: string;
+  name: string;
+  description: string;
+  content: BioHubSubmissionFeature;
+}
 export interface BioHubSubmissionFeature {
   id: string;
   type: string;
   properties: Record<string, any>;
-  features: BioHubSubmissionFeature[];
+  child_features: BioHubSubmissionFeature[];
 }
 
 /**
@@ -23,7 +31,7 @@ export class PostSurveyObservationToBiohubObject implements BioHubSubmissionFeat
   id: string;
   type: string;
   properties: Record<string, any>;
-  features: BioHubSubmissionFeature[];
+  child_features: BioHubSubmissionFeature[];
 
   constructor(observationRecord: ObservationRecord) {
     defaultLog.debug({ label: 'PostSurveyObservationToBiohubObject', message: 'params', observationRecord });
@@ -58,7 +66,68 @@ export class PostSurveyObservationToBiohubObject implements BioHubSubmissionFeat
             : []
       }
     };
-    this.features = [];
+    this.child_features = [];
+  }
+}
+
+/**
+ * Object to be sent to Biohub API for creating an artifact (for a SIMS attachment).
+ *
+ * @export
+ * @class PostSurveyAttachmentsToBiohubObject
+ * @implements {BioHubSubmissionFeature}
+ */
+export class PostSurveyAttachmentsToBiohubObject implements BioHubSubmissionFeature {
+  id: string;
+  type: string;
+  properties: Record<string, any>;
+  child_features: BioHubSubmissionFeature[];
+
+  constructor(attachmentRecord: ISurveyAttachment) {
+    defaultLog.debug({ label: 'PostSurveyAttachmentsToBiohubObject', message: 'params', attachmentRecord });
+
+    this.id = attachmentRecord.uuid;
+    this.type = BiohubFeatureType.ARTIFACT;
+    this.properties = {
+      artifact_id: attachmentRecord.survey_attachment_id,
+      filename: attachmentRecord.file_name,
+      file_type: attachmentRecord.file_type,
+      file_size: attachmentRecord.file_size,
+      title: attachmentRecord?.title || null,
+      description: attachmentRecord?.description || null
+    };
+    this.child_features = [];
+  }
+}
+
+/**
+ * Object to be sent to Biohub API for creating an artifact (for a SIMS report attachment).
+ *
+ * @export
+ * @class PostSurveyReportAttachmentsToBiohubObject
+ * @implements {BioHubSubmissionFeature}
+ */
+export class PostSurveyReportAttachmentsToBiohubObject implements BioHubSubmissionFeature {
+  id: string;
+  type: string;
+  properties: Record<string, any>;
+  child_features: BioHubSubmissionFeature[];
+
+  constructor(reportAttachmentRecord: ISurveyReportAttachment) {
+    defaultLog.debug({ label: 'PostSurveyReportAttachmentsToBiohubObject', message: 'params', reportAttachmentRecord });
+
+    this.id = reportAttachmentRecord.uuid;
+    this.type = BiohubFeatureType.ARTIFACT;
+    this.properties = {
+      artifact_id: reportAttachmentRecord.survey_report_attachment_id,
+      filename: reportAttachmentRecord.file_name,
+      file_type: ATTACHMENT_TYPE.REPORT,
+      file_size: reportAttachmentRecord.file_size,
+      title: reportAttachmentRecord.title,
+      description: reportAttachmentRecord.description,
+      year_published: reportAttachmentRecord.year_published
+    };
+    this.child_features = [];
   }
 }
 
@@ -73,11 +142,29 @@ export class PostSurveyToBiohubObject implements BioHubSubmissionFeature {
   id: string;
   type: string;
   properties: Record<string, any>;
-  features: PostSurveyObservationToBiohubObject[];
+  child_features: PostSurveyObservationToBiohubObject[];
 
-  constructor(surveyData: GetSurveyData, observationRecords: ObservationRecord[], surveyGeometry: FeatureCollection) {
+  constructor(
+    surveyData: GetSurveyData,
+    observationRecords: ObservationRecord[],
+    surveyGeometry: FeatureCollection,
+    surveyAttachments: ISurveyAttachment[],
+    surveyReports: ISurveyReportAttachment[]
+  ) {
     defaultLog.debug({ label: 'PostSurveyToBiohubObject', message: 'params', surveyData });
 
+    const observationFeatures = observationRecords.map(
+      (observation) => new PostSurveyObservationToBiohubObject(observation)
+    );
+
+    const attachmentFeatures = surveyAttachments.map(
+      (attachment) => new PostSurveyAttachmentsToBiohubObject(attachment)
+    );
+
+    const reportAttachmentFeatures = surveyReports.map(
+      (attachment) => new PostSurveyReportAttachmentsToBiohubObject(attachment)
+    );
+
     this.id = surveyData.uuid;
     this.type = BiohubFeatureType.DATASET;
     this.properties = {
@@ -90,32 +177,44 @@ export class PostSurveyToBiohubObject implements BioHubSubmissionFeature {
       revision_count: surveyData.revision_count,
       geometry: surveyGeometry
     };
-    this.features = observationRecords.map((observation) => new PostSurveyObservationToBiohubObject(observation));
+    this.child_features = [...observationFeatures, ...reportAttachmentFeatures, ...attachmentFeatures];
   }
 }
 
-export class PostSurveySubmissionToBioHubObject {
+export class PostSurveySubmissionToBioHubObject implements BioHubSubmission {
   id: string;
   name: string;
   description: string;
-  features: BioHubSubmissionFeature[];
+  comment: string;
+  content: BioHubSubmissionFeature;
 
   constructor(
     surveyData: GetSurveyData,
+    GetSurveyPurposeAndMethodologyData: GetSurveyPurposeAndMethodologyData,
     observationRecords: ObservationRecord[],
     surveyGeometry: FeatureCollection,
-    additionalInformation: string
+    surveyAttachments: ISurveyAttachment[],
+    surveyReports: ISurveyReportAttachment[],
+    submissionComment: string
   ) {
     defaultLog.debug({ label: 'PostSurveySubmissionToBioHubObject' });
 
     this.id = surveyData.uuid;
     this.name = surveyData.survey_name;
-    this.description = additionalInformation;
-    this.features = [new PostSurveyToBiohubObject(surveyData, observationRecords, surveyGeometry)];
+    this.description = GetSurveyPurposeAndMethodologyData.additional_details;
+    this.comment = submissionComment;
+    this.content = new PostSurveyToBiohubObject(
+      surveyData,
+      observationRecords,
+      surveyGeometry,
+      surveyAttachments,
+      surveyReports
+    );
   }
 }
 
 export enum BiohubFeatureType {
   DATASET = 'dataset',
-  OBSERVATION = 'observation'
+  OBSERVATION = 'observation',
+  ARTIFACT = 'artifact'
 }

api/src/models/project-survey-attachments.ts

@@ -1,4 +1,5 @@
 import { default as dayjs } from 'dayjs';
+import { ATTACHMENT_TYPE } from '../constants/attachments';
 import { getLogger } from '../utils/logger';
 import { SurveySupplementaryData } from './survey-view';
 
@@ -28,7 +29,7 @@ export class GetAttachmentsWithSupplementalData {
       attachment.project_attachment_id ||
       attachment.project_report_attachment_id;
     this.fileName = attachment.file_name;
-    this.fileType = attachment.file_type || 'Report';
+    this.fileType = attachment.file_type || ATTACHMENT_TYPE.REPORT;
     this.lastModified = dayjs(attachment.update_date || attachment.create_date).toISOString();
     this.size = attachment.file_size;
     this.status = attachment.status;

api/src/models/project-view.ts

@@ -22,7 +22,7 @@ export interface IGetProject {
 
 export const ProjectData = z.object({
   project_id: z.number(),
-  uuid: z.string(),
+  uuid: z.string().uuid(),
   project_name: z.string(),
   project_programs: z.array(z.number()),
   start_date: z.string(),
@@ -35,7 +35,7 @@ export type ProjectData = z.infer<typeof ProjectData>;
 
 export const ProjectListData = z.object({
   project_id: z.number(),
-  uuid: z.string(),
+  uuid: z.string().uuid(),
   project_name: z.string(),
   project_programs: z.array(z.number()).default([]),
   regions: z.array(z.string()).default([]),

api/src/paths/project/create.test.ts

@@ -30,7 +30,7 @@ describe('create', () => {
 
       sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
-      sinon.stub(ProjectService.prototype, 'createProjectAndUploadMetadataToBioHub').resolves(1);
+      sinon.stub(ProjectService.prototype, 'createProject').resolves(1);
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 
@@ -51,7 +51,7 @@ describe('create', () => {
 
       sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
-      sinon.stub(ProjectService.prototype, 'createProjectAndUploadMetadataToBioHub').rejects(new Error('a test error'));
+      sinon.stub(ProjectService.prototype, 'createProject').rejects(new Error('a test error'));
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 

api/src/paths/project/create.ts

@@ -95,7 +95,7 @@ export function createProject(): RequestHandler {
 
       const projectService = new ProjectService(connection);
 
-      const projectId = await projectService.createProjectAndUploadMetadataToBioHub(sanitizedProjectPostData);
+      const projectId = await projectService.createProject(sanitizedProjectPostData);
 
       await connection.commit();
 

api/src/paths/project/{projectId}/attachments/{attachmentId}/delete.test.ts

@@ -91,6 +91,6 @@ describe('deleteAttachment', () => {
 
     await result(sampleReq, (sampleRes as unknown) as any, (null as unknown) as any);
 
-    expect(handleDeleteProjectAttachmentStub).to.be.calledOnceWith(1, 2, 'Report', false);
+    expect(handleDeleteProjectAttachmentStub).to.be.calledOnceWith(1, 2, 'Report');
   });
 });

api/src/paths/project/{projectId}/attachments/{attachmentId}/delete.ts

@@ -2,10 +2,8 @@ import { RequestHandler } from 'express';
 import { Operation } from 'express-openapi';
 import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../constants/roles';
 import { getDBConnection } from '../../../../../database/db';
-import { SystemUser } from '../../../../../repositories/user-repository';
 import { authorizeRequestHandler } from '../../../../../request-handlers/security/authorization';
 import { AttachmentService } from '../../../../../services/attachment-service';
-import { UserService } from '../../../../../services/user-service';
 import { getLogger } from '../../../../../utils/logger';
 import { attachmentApiDocObject } from '../../../../../utils/shared-api-docs';
 
@@ -104,13 +102,10 @@ export function deleteAttachment(): RequestHandler {
 
       const attachmentService = new AttachmentService(connection);
 
-      const systemUserObject: SystemUser = req['system_user'];
-
       await attachmentService.handleDeleteProjectAttachment(
         Number(req.params.projectId),
         Number(req.params.attachmentId),
-        req.body.attachmentType,
-        UserService.isAdmin(systemUserObject)
+        req.body.attachmentType
       );
 
       await connection.commit();

api/src/paths/project/{projectId}/survey/create.test.ts

@@ -21,7 +21,7 @@ describe('survey/create', () => {
 
       sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
-      sinon.stub(SurveyService.prototype, 'createSurveyAndUploadMetadataToBioHub').resolves(2);
+      sinon.stub(SurveyService.prototype, 'createSurvey').resolves(2);
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 
@@ -45,7 +45,7 @@ describe('survey/create', () => {
 
       sinon.stub(db, 'getDBConnection').returns(dbConnectionObj);
 
-      sinon.stub(SurveyService.prototype, 'createSurveyAndUploadMetadataToBioHub').rejects(new Error('a test error'));
+      sinon.stub(SurveyService.prototype, 'createSurvey').rejects(new Error('a test error'));
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 

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

@@ -350,7 +350,7 @@ export function createSurvey(): RequestHandler {
       await connection.open();
 
       const surveyService = new SurveyService(connection);
-      const surveyId = await surveyService.createSurveyAndUploadMetadataToBioHub(projectId, sanitizedPostSurveyData);
+      const surveyId = await surveyService.createSurvey(projectId, sanitizedPostSurveyData);
 
       await connection.commit();