Done CancerRelatedMeds; minor fixes to CDS and AE

Author: Dtphelan1

test/extractors/CSVAdverseEventExtractor.test.js

@@ -2,9 +2,9 @@ const path = require('path');
 const rewire = require('rewire');
 const _ = require('lodash');
 const { CSVAdverseEventExtractor } = require('../../src/extractors');
-const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVAdverseEventModuleResponse = require('./fixtures/csv-adverse-event-module-response.json');
 const exampleCSVAdverseEventBundle = require('./fixtures/csv-adverse-event-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests

test/extractors/CSVCancerDiseaseStatusExtractor.test.js

@@ -1,9 +1,9 @@
 const path = require('path');
 const _ = require('lodash');
 const { CSVCancerDiseaseStatusExtractor } = require('../../src/extractors');
-const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVDiseaseStatusModuleResponse = require('./fixtures/csv-cancer-disease-status-module-response.json');
 const exampleCSVDiseaseStatusBundle = require('./fixtures/csv-cancer-disease-status-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
@@ -29,22 +29,24 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
       const expectedErrorString = 'DiseaseStatusData missing an expected property: conditionId, diseaseStatusCode, and dateOfObservation are required.';
       const localData = _.cloneDeep(exampleCSVDiseaseStatusModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
       // Test that valid data works fine
-      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(exampleCSVDiseaseStatusModuleResponse)).toEqual(expect.anything());
+      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(exampleCSVDiseaseStatusModuleResponse, patientId)).toEqual(expect.anything());
 
       localData[0].evidence = ''; // Evidence is not required and will not throw an error
       localData[0].observationStatus = ''; // Observation Status is not required and will not throw an error
 
       // Only including required properties is valid
-      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(localData)).toEqual(expect.anything());
+      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(localData, patientId)).toEqual(expect.anything());
 
       const requiredProperties = ['conditionId', 'diseaseStatusCode', 'dateOfObservation'];
 
       // Removing each required property should throw an error
       requiredProperties.forEach((key) => {
         const clonedData = _.cloneDeep(localData);
         clonedData[0][key] = '';
-        expect(() => csvCancerDiseaseStatusExtractor.joinAndReformatData(clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => csvCancerDiseaseStatusExtractor.joinAndReformatData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
     });
   });

test/extractors/CSVCancerRelatedMedicationExtractor.test.js

@@ -4,6 +4,8 @@ const _ = require('lodash');
 const { CSVCancerRelatedMedicationExtractor } = require('../../src/extractors');
 const exampleCSVMedicationModuleResponse = require('./fixtures/csv-medication-module-response.json');
 const exampleCSVMedicationBundle = require('./fixtures/csv-medication-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Rewired extractor for helper tests
 const CSVCancerRelatedMedicationExtractorRewired = rewire('../../src/extractors/CSVCancerRelatedMedicationExtractor.js');
@@ -35,24 +37,25 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
       const expectedErrorString = 'The cancer-related medication is missing an expected element; mrn, code, code system, and status are all required values.';
       const localData = _.cloneDeep(exampleCSVMedicationModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test that valid maximal data works fine
-      expect(formatData(exampleCSVMedicationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that deleting an optional value works fine
       delete localData[0].treatmentIntent;
-      expect(formatData(exampleCSVMedicationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that deleting a mandatory value throws an error
       delete localData[0].code;
-      expect(() => formatData(localData)).toThrow(new Error(expectedErrorString));
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedErrorString));
     });
   });
 
   describe('get', () => {
     test('should return bundle with a CancerRelatedMedication', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVMedicationModuleResponse);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -62,7 +65,7 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -72,8 +75,7 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
     test('get() should return an array of 2 when two medication statements are tied to a single patient', async () => {
       exampleCSVMedicationModuleResponse.push(exampleEntry);
       csvModuleSpy.mockReturnValue(exampleCSVMedicationModuleResponse);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
-
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();