Merge branch 'dataset_security_feature' into SIMSBIOHUB-397

api/src/openapi/root-api-doc.ts

@@ -168,6 +168,28 @@ export const rootAPIDoc = {
           }
         },
         additionalProperties: false
+      },
+      feature: {
+        type: 'object',
+        required: ['submission_feature_id', 'submission_id', 'feature_type', 'data', 'parent_submission_feature_id'],
+        properties: {
+          submission_feature_id: {
+            type: 'number'
+          },
+          submission_id: {
+            type: 'number'
+          },
+          feature_type: {
+            type: 'string'
+          },
+          data: {
+            type: 'object'
+          },
+          parent_submission_feature_id: {
+            type: 'number',
+            nullable: true
+          }
+        }
       }
     }
   }

api/src/paths/administrative/submission/unreviewed/index.test.ts

@@ -2,7 +2,7 @@ import chai, { expect } from 'chai';
 import { describe } from 'mocha';
 import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
-import { getUnreviewedSubmissions } from '.';
+import { getUnreviewedSubmissionsForAdmins } from '.';
 import * as db from '../../../../database/db';
 import { HTTPError } from '../../../../errors/http-error';
 import { SubmissionService } from '../../../../services/submission-service';
@@ -26,7 +26,7 @@ describe('list', () => {
 
     const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 
-    const requestHandler = getUnreviewedSubmissions();
+    const requestHandler = getUnreviewedSubmissionsForAdmins();
 
     try {
       await requestHandler(mockReq, mockRes, mockNext);
@@ -48,10 +48,10 @@ describe('list', () => {
     const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 
     const getUnreviewedSubmissionsStub = sinon
-      .stub(SubmissionService.prototype, 'getUnreviewedSubmissions')
+      .stub(SubmissionService.prototype, 'getUnreviewedSubmissionsForAdmins')
       .resolves([]);
 
-    const requestHandler = getUnreviewedSubmissions();
+    const requestHandler = getUnreviewedSubmissionsForAdmins();
 
     await requestHandler(mockReq, mockRes, mockNext);
 

api/src/paths/dwc/submission/{datasetId}/artifacts.test.ts

@@ -6,7 +6,6 @@ import sinon from 'sinon';
 import sinonChai from 'sinon-chai';
 import * as db from '../../../../database/db';
 import { HTTPError } from '../../../../errors/http-error';
-import { Artifact } from '../../../../repositories/artifact-repository';
 import { SECURITY_APPLIED_STATUS } from '../../../../repositories/security-repository';
 import { ArtifactService } from '../../../../services/artifact-service';
 import { SecurityService } from '../../../../services/security-service';
@@ -219,7 +218,7 @@ describe('getArtifactsByDatasetId', () => {
     const artifactServiceStub = sinon.stub(ArtifactService.prototype, 'getArtifactsByDatasetId').resolves([
       { artifact_id: 1, security_review_timestamp: new Date('1970-01-01T00:00:00.000Z') },
       { artifact_id: 2, security_review_timestamp: new Date('1970-01-01T00:00:00.000Z') }
-    ] as Artifact[]);
+    ] as any[]);
 
     const isSystemUserAdminStub = sinon.stub(UserService.prototype, 'isSystemUserAdmin').resolves(true);
 

api/src/paths/submission/index.ts

@@ -0,0 +1,105 @@
+import { RequestHandler } from 'express';
+import { Operation } from 'express-openapi';
+import { getAPIUserDBConnection } from '../../database/db';
+import { defaultErrorResponses } from '../../openapi/schemas/http-responses';
+import { SubmissionService } from '../../services/submission-service';
+import { getLogger } from '../../utils/logger';
+
+const defaultLog = getLogger('paths/submission');
+
+export const GET: Operation = [getReviewedSubmissionsWithSecurity()];
+
+GET.apiDoc = {
+  description: 'Get a list of reviewed submissions',
+  tags: ['submisssion', 'reviewed'],
+  security: [],
+  responses: {
+    200: {
+      description: 'List of reviewed submissions',
+      content: {
+        'application/json': {
+          schema: {
+            type: 'array',
+            items: {
+              type: 'object',
+              properties: {
+                submission_id: {
+                  type: 'integer',
+                  minimum: 1
+                },
+                uuid: {
+                  type: 'string',
+                  format: 'uuid'
+                },
+                security_review_timestamp: {
+                  type: 'string',
+                  nullable: true
+                },
+                source_system: {
+                  type: 'string'
+                },
+                name: {
+                  type: 'string',
+                  maxLength: 200
+                },
+                description: {
+                  type: 'string',
+                  maxLength: 3000
+                },
+                create_date: {
+                  type: 'string'
+                },
+                create_user: {
+                  type: 'integer',
+                  minimum: 1
+                },
+                update_date: {
+                  type: 'string',
+                  nullable: true
+                },
+                update_user: {
+                  type: 'integer',
+                  minimum: 1,
+                  nullable: true
+                },
+                revision_count: {
+                  type: 'integer',
+                  minimum: 0
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    ...defaultErrorResponses
+  }
+};
+
+/**
+ * Get all reviewed submissions (with security status).
+ *
+ * @returns {RequestHandler}
+ */
+export function getReviewedSubmissionsWithSecurity(): RequestHandler {
+  return async (_req, res) => {
+    const connection = getAPIUserDBConnection();
+
+    try {
+      await connection.open();
+
+      const service = new SubmissionService(connection);
+      const response = await service.getReviewedSubmissionsWithSecurity();
+
+      await connection.commit();
+
+      return res.status(200).json(response);
+    } catch (error) {
+      await connection.rollback();
+      defaultLog.error({ label: 'getReviewedSubmissionsWithSecurity', message: 'error', error });
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}

api/src/paths/dataset/intake.ts → api/src/paths/submission/intake.ts

@@ -10,7 +10,11 @@ import { ValidationService } from '../../services/validation-service';
 import { getKeycloakSource } from '../../utils/keycloak-utils';
 import { getLogger } from '../../utils/logger';
 
-const defaultLog = getLogger('paths/dataset/intake');
+const defaultLog = getLogger('paths/submission/intake');
+
+/*
+TODO: UPDATED PATH TO SUBMISSION/INTAKE NEED TO UPDATE SIMS TO USE THIS PATH
+*/
 
 export const POST: Operation = [
   authorizeRequestHandler(() => {
@@ -23,12 +27,12 @@ export const POST: Operation = [
       ]
     };
   }),
-  datasetIntake()
+  submissionIntake()
 ];
 
 POST.apiDoc = {
-  description: 'Submit dataset to BioHub',
-  tags: ['dataset'],
+  description: 'Submit submission to BioHub',
+  tags: ['submission'],
   security: [
     {
       Bearer: []
@@ -48,7 +52,7 @@ POST.apiDoc = {
             },
             type: {
               type: 'string',
-              enum: ['dataset']
+              enum: ['submission']
             },
             properties: {
               title: 'Dataset properties',
@@ -89,7 +93,7 @@ POST.apiDoc = {
   }
 };
 
-export function datasetIntake(): RequestHandler {
+export function submissionIntake(): RequestHandler {
   return async (req, res) => {
     const sourceSystem = getKeycloakSource(req['keycloak_token']);
 
@@ -99,7 +103,7 @@ export function datasetIntake(): RequestHandler {
       ]);
     }
 
-    const dataset = {
+    const submission = {
       ...req.body,
       properties: { ...req.body.properties, additionalInformation: req.body.properties.additionalInformation }
     };
@@ -113,21 +117,21 @@ export function datasetIntake(): RequestHandler {
       const submissionService = new SubmissionService(connection);
       const validationService = new ValidationService(connection);
 
-      // validate the dataset submission
-      if (!(await validationService.validateDatasetSubmission(dataset))) {
-        throw new HTTP400('Invalid dataset submission');
+      // validate the submission submission
+      if (!(await validationService.validateDatasetSubmission(submission))) {
+        throw new HTTP400('Invalid submission submission');
       }
 
       // insert the submission record
       const response = await submissionService.insertSubmissionRecordWithPotentialConflict(id);
 
       // insert each submission feature record
-      await submissionService.insertSubmissionFeatureRecords(response.submission_id, dataset.features);
+      await submissionService.insertSubmissionFeatureRecords(response.submission_id, submission.features);
 
       await connection.commit();
       res.status(200).json(response);
     } catch (error) {
-      defaultLog.error({ label: 'datasetIntake', message: 'error', error });
+      defaultLog.error({ label: 'submissionIntake', message: 'error', error });
       await connection.rollback();
       throw error;
     } finally {