SIMSBIOHUB 217 - Edit Animal

api/src/paths/critter-data/critters/index.ts

@@ -1,7 +1,7 @@
 import { RequestHandler } from 'express';
 import { Operation } from 'express-openapi';
 import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../constants/roles';
-import { critterCreateRequestObject } from '../../../openapi/schemas/critter';
+import { critterBulkRequestObject } from '../../../openapi/schemas/critter';
 import { authorizeRequestHandler } from '../../../request-handlers/security/authorization';
 import { CritterbaseService, ICritterbaseUser } from '../../../services/critterbase-service';
 import { getLogger } from '../../../utils/logger';
@@ -39,7 +39,7 @@ POST.apiDoc = {
     description: 'Critterbase bulk creation request object',
     content: {
       'application/json': {
-        schema: critterCreateRequestObject
+        schema: critterBulkRequestObject
       }
     }
   },

api/src/paths/project/{projectId}/survey/{surveyId}/critters/index.test.ts

@@ -76,14 +76,11 @@ describe('addCritterToSurvey', () => {
   });
 
   const mockDBConnection = getMockDBConnection({ release: sinon.stub() });
-  const mockSurveyCritter = 123;
   const mockCBCritter = { critter_id: 'critterbase1' };
 
   it('returns critters from survey', async () => {
     const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
-    const mockAddCritterToSurvey = sinon
-      .stub(SurveyCritterService.prototype, 'addCritterToSurvey')
-      .resolves(mockSurveyCritter);
+    const mockAddCritterToSurvey = sinon.stub(SurveyCritterService.prototype, 'addCritterToSurvey').resolves();
     const mockCreateCritter = sinon.stub(CritterbaseService.prototype, 'createCritter').resolves(mockCBCritter);
     const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
 

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

@@ -2,7 +2,7 @@ import { RequestHandler } from 'express';
 import { Operation } from 'express-openapi';
 import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles';
 import { getDBConnection } from '../../../../../../database/db';
-import { critterCreateRequestObject } from '../../../../../../openapi/schemas/critter';
+import { bulkCreateResponse, critterBulkRequestObject } from '../../../../../../openapi/schemas/critter';
 import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization';
 import { CritterbaseService, ICritterbaseUser } from '../../../../../../services/critterbase-service';
 import { SurveyCritterService } from '../../../../../../services/survey-critter-service';
@@ -129,7 +129,7 @@ POST.apiDoc = {
     description: 'Critterbase bulk creation request object',
     content: {
       'application/json': {
-        schema: critterCreateRequestObject
+        schema: critterBulkRequestObject
       }
     }
   },
@@ -138,10 +138,7 @@ POST.apiDoc = {
       description: 'Responds with counts of objects created in critterbase.',
       content: {
         'application/json': {
-          schema: {
-            title: 'Bulk creation response object',
-            type: 'object'
-          }
+          schema: bulkCreateResponse
         }
       }
     },

api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}.test.ts

@@ -1,29 +1,42 @@
+import Ajv from 'ajv';
 import { expect } from 'chai';
 import sinon from 'sinon';
 import * as db from '../../../../../../database/db';
+import { HTTPError } from '../../../../../../errors/http-error';
+import { CritterbaseService } from '../../../../../../services/critterbase-service';
 import { SurveyCritterService } from '../../../../../../services/survey-critter-service';
 import { getMockDBConnection, getRequestHandlerMocks } from '../../../../../../__mocks__/db';
-import { removeCritterFromSurvey } from './{critterId}';
+import { DELETE, PATCH, removeCritterFromSurvey, updateSurveyCritter } from './{critterId}';
+
+describe('critterId openapi schema', () => {
+  const ajv = new Ajv();
+
+  it('PATCH is valid openapi v3 schema', () => {
+    expect(ajv.validateSchema((PATCH.apiDoc as unknown) as object)).to.be.true;
+  });
+
+  it('DELETE is valid openapi v3 schema', () => {
+    expect(ajv.validateSchema((DELETE.apiDoc as unknown) as object)).to.be.true;
+  });
+});
 
 describe('removeCritterFromSurvey', () => {
   afterEach(() => {
     sinon.restore();
   });
 
   const mockDBConnection = getMockDBConnection({ release: sinon.stub() });
-  const mockSurveyCritter = 123;
 
   it('removes critter from survey', async () => {
     sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
-    sinon.stub(SurveyCritterService.prototype, 'removeCritterFromSurvey').resolves(mockSurveyCritter);
+    sinon.stub(SurveyCritterService.prototype, 'removeCritterFromSurvey').resolves();
 
     const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
     const requestHandler = removeCritterFromSurvey();
 
     await requestHandler(mockReq, mockRes, mockNext);
 
     expect(mockRes.statusValue).to.equal(200);
-    expect(mockRes.jsonValue).to.equal(mockSurveyCritter);
   });
 
   it('catches and re-throws errors', async () => {
@@ -43,3 +56,81 @@ describe('removeCritterFromSurvey', () => {
     }
   });
 });
+
+describe('updateSurveyCritter', () => {
+  afterEach(() => {
+    sinon.restore();
+  });
+
+  const mockDBConnection = getMockDBConnection({ release: sinon.stub() });
+  const mockCBCritter = { critter_id: 'critterbase1' };
+
+  it('returns critters from survey', async () => {
+    const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
+    const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').resolves();
+    const mockCritterbaseUpdateCritter = sinon
+      .stub(CritterbaseService.prototype, 'updateCritter')
+      .resolves(mockCBCritter);
+    const mockCritterbaseCreateCritter = sinon
+      .stub(CritterbaseService.prototype, 'createCritter')
+      .resolves(mockCBCritter);
+    const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+    mockReq.body = {
+      create: {},
+      update: { critter_id: 'critterbase1' }
+    };
+    const requestHandler = updateSurveyCritter();
+    await requestHandler(mockReq, mockRes, mockNext);
+
+    expect(mockGetDBConnection.calledOnce).to.be.true;
+    expect(mockSurveyUpdateCritter.calledOnce).to.be.true;
+    expect(mockCritterbaseUpdateCritter.calledOnce).to.be.true;
+    expect(mockCritterbaseCreateCritter.calledOnce).to.be.true;
+    expect(mockRes.status).to.have.been.calledWith(200);
+    expect(mockRes.json).to.have.been.calledWith(mockCBCritter);
+  });
+
+  it('catches and re-throws errors', async () => {
+    const mockError = new Error('a test error');
+    const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
+    const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').rejects(mockError);
+    const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+    mockReq.body = {
+      create: {},
+      update: { critter_id: 'critterbase1' }
+    };
+    const requestHandler = updateSurveyCritter();
+
+    try {
+      await requestHandler(mockReq, mockRes, mockNext);
+      expect.fail();
+    } catch (actualError) {
+      expect(actualError).to.equal(mockError);
+      expect(mockSurveyUpdateCritter.calledOnce).to.be.true;
+      expect(mockGetDBConnection.calledOnce).to.be.true;
+      expect(mockDBConnection.release).to.have.been.called;
+    }
+  });
+
+  it('catches and re-throws errors', async () => {
+    const errMsg = 'No external critter ID was found.';
+    const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
+    const mockSurveyUpdateCritter = sinon.stub(SurveyCritterService.prototype, 'updateCritter').resolves();
+    const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
+    mockReq.body = {
+      update: {}
+    };
+    const requestHandler = updateSurveyCritter();
+
+    try {
+      await requestHandler(mockReq, mockRes, mockNext);
+      expect.fail();
+    } catch (actualError) {
+      expect((actualError as HTTPError).message).to.equal(errMsg);
+      expect((actualError as HTTPError).status).to.equal(400);
+      expect(mockSurveyUpdateCritter.calledOnce).to.be.false;
+      expect(mockGetDBConnection.calledOnce).to.be.true;
+      expect(mockDBConnection.release).to.have.been.called;
+    }
+  });
+});

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

@@ -2,7 +2,10 @@ import { RequestHandler } from 'express';
 import { Operation } from 'express-openapi';
 import { PROJECT_PERMISSION, SYSTEM_ROLE } from '../../../../../../constants/roles';
 import { getDBConnection } from '../../../../../../database/db';
+import { HTTPError, HTTPErrorType } from '../../../../../../errors/http-error';
+import { bulkUpdateResponse, critterBulkRequestObject } from '../../../../../../openapi/schemas/critter';
 import { authorizeRequestHandler } from '../../../../../../request-handlers/security/authorization';
+import { CritterbaseService, ICritterbaseUser } from '../../../../../../services/critterbase-service';
 import { SurveyCritterService } from '../../../../../../services/survey-critter-service';
 import { getLogger } from '../../../../../../utils/logger';
 
@@ -26,6 +29,25 @@ export const DELETE: Operation = [
   removeCritterFromSurvey()
 ];
 
+export const PATCH: Operation = [
+  authorizeRequestHandler((req) => {
+    return {
+      or: [
+        {
+          validProjectPermissions: [PROJECT_PERMISSION.COORDINATOR, PROJECT_PERMISSION.COLLABORATOR],
+          projectId: Number(req.params.projectId),
+          discriminator: 'ProjectPermission'
+        },
+        {
+          validSystemRoles: [SYSTEM_ROLE.DATA_ADMINISTRATOR],
+          discriminator: 'SystemRole'
+        }
+      ]
+    };
+  }),
+  updateSurveyCritter()
+];
+
 DELETE.apiDoc = {
   description: 'Removes association of this critter to this survey.',
   tags: ['critterbase'],
@@ -54,13 +76,58 @@ DELETE.apiDoc = {
   ],
   responses: {
     200: {
-      description: 'Responds with affected number of rows.',
+      description: 'Critter was removed from survey'
+    },
+    400: {
+      $ref: '#/components/responses/400'
+    },
+    401: {
+      $ref: '#/components/responses/401'
+    },
+    403: {
+      $ref: '#/components/responses/401'
+    },
+    500: {
+      $ref: '#/components/responses/500'
+    },
+    default: {
+      $ref: '#/components/responses/default'
+    }
+  }
+};
+
+PATCH.apiDoc = {
+  description: 'Patches a critter in critterbase, also capable of deleting relevant rows if marked with _delete.',
+  tags: ['critterbase'],
+  security: [
+    {
+      Bearer: []
+    }
+  ],
+  parameters: [
+    {
+      in: 'path',
+      name: 'surveyId',
+      schema: {
+        type: 'number'
+      },
+      required: true
+    }
+  ],
+  requestBody: {
+    description: 'Critterbase bulk patch request object',
+    content: {
+      'application/json': {
+        schema: critterBulkRequestObject
+      }
+    }
+  },
+  responses: {
+    200: {
+      description: 'Responds with counts of objects created in critterbase.',
       content: {
         'application/json': {
-          schema: {
-            title: 'Affected rows',
-            type: 'number'
-          }
+          schema: bulkUpdateResponse
         }
       }
     },
@@ -101,3 +168,40 @@ export function removeCritterFromSurvey(): RequestHandler {
     }
   };
 }
+
+export function updateSurveyCritter(): RequestHandler {
+  return async (req, res) => {
+    const user: ICritterbaseUser = {
+      keycloak_guid: req['system_user']?.user_guid,
+      username: req['system_user']?.user_identifier
+    };
+
+    const critterId = Number(req.params.critterId);
+    const connection = getDBConnection(req['keycloak_token']);
+    const surveyService = new SurveyCritterService(connection);
+    const cb = new CritterbaseService(user);
+    try {
+      await connection.open();
+      const critterbaseCritterId = req.body.update.critter_id;
+      if (!critterbaseCritterId) {
+        throw new HTTPError(HTTPErrorType.BAD_REQUEST, 400, 'No external critter ID was found.');
+      }
+      await surveyService.updateCritter(critterId, critterbaseCritterId);
+      let createResult, updateResult;
+      if (req.body.update) {
+        updateResult = await cb.updateCritter(req.body.update);
+      }
+      if (req.body.create) {
+        createResult = await cb.createCritter(req.body.create);
+      }
+      await connection.commit();
+      return res.status(200).json({ ...createResult, ...updateResult });
+    } catch (error) {
+      defaultLog.error({ label: 'updateCritter', message: 'error', error });
+      await connection.rollback();
+      throw error;
+    } finally {
+      connection.release();
+    }
+  };
+}

api/src/paths/project/{projectId}/survey/{surveyId}/critters/{critterId}/deployments.test.ts

@@ -13,7 +13,6 @@ describe('critter deployments', () => {
   });
 
   const mockDBConnection = getMockDBConnection({ release: sinon.stub() });
-  const mockSurveyEntry = 123;
 
   describe('openapi schema', () => {
     const ajv = new Ajv();
@@ -27,7 +26,7 @@ describe('critter deployments', () => {
   describe('upsertDeployment', () => {
     it('updates an existing deployment', async () => {
       const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
-      const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').resolves(1);
+      const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').resolves();
       const mockBctwService = sinon.stub(BctwService.prototype, 'updateDeployment');
 
       const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
@@ -39,7 +38,6 @@ describe('critter deployments', () => {
       expect(mockAddDeployment.calledOnce).to.be.true;
       expect(mockBctwService.calledOnce).to.be.true;
       expect(mockRes.status).to.have.been.calledWith(200);
-      expect(mockRes.json).to.have.been.calledWith(1);
     });
 
     it('catches and re-throws errors', async () => {
@@ -63,9 +61,7 @@ describe('critter deployments', () => {
     describe('deployDevice', () => {
       it('deploys a new telemetry device', async () => {
         const mockGetDBConnection = sinon.stub(db, 'getDBConnection').returns(mockDBConnection);
-        const mockAddDeployment = sinon
-          .stub(SurveyCritterService.prototype, 'upsertDeployment')
-          .resolves(mockSurveyEntry);
+        const mockAddDeployment = sinon.stub(SurveyCritterService.prototype, 'upsertDeployment').resolves();
         const mockBctwService = sinon.stub(BctwService.prototype, 'deployDevice');
 
         const { mockReq, mockRes, mockNext } = getRequestHandlerMocks();
@@ -77,7 +73,6 @@ describe('critter deployments', () => {
         expect(mockAddDeployment.calledOnce).to.be.true;
         expect(mockBctwService.calledOnce).to.be.true;
         expect(mockRes.status).to.have.been.calledWith(201);
-        expect(mockRes.json).to.have.been.calledWith(mockSurveyEntry);
       });
 
       it('catches and re-throws errors', async () => {