updates to CTI tests

Author: Dtphelan1

src/extractors/CSVClinicalTrialInformationExtractor.js

@@ -22,8 +22,8 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
     } = clinicalTrialData;
     const { clinicalSiteID, clinicalSiteSystem } = this;
 
-    if (!(patientId && clinicalSiteID && trialSubjectID && enrollmentStatus && trialResearchID && trialStatus)) {
-      throw new Error('Clinical trial missing an expected property: patientId, clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.');
+    if (!(clinicalSiteID && trialSubjectID && enrollmentStatus && trialResearchID && trialStatus)) {
+      throw new Error('Clinical trial missing an expected property: clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.');
     }
 
     // Need separate data objects for ResearchSubject and ResearchStudy so that they get different resource ids

test/extractors/CSVClinicalTrialInformationExtractor.test.js

@@ -1,9 +1,10 @@
 const path = require('path');
-const rewire = require('rewire');
 const _ = require('lodash');
 const { CSVClinicalTrialInformationExtractor } = require('../../src/extractors');
 const exampleClinicalTrialInformationResponse = require('./fixtures/csv-clinical-trial-information-module-response.json');
 const exampleClinicalTrialInformationBundle = require('./fixtures/csv-clinical-trial-information-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for mock tests
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
@@ -26,34 +27,30 @@ const csvModuleSpy = jest.spyOn(csvModule, 'get');
 csvModuleSpy
   .mockReturnValue(exampleClinicalTrialInformationResponse);
 
-const getPatientId = rewire('../../src/extractors/CSVClinicalTrialInformationExtractor.js').__get__('getPatientId');
-
 describe('CSVClinicalTrialInformationExtractor', () => {
   describe('joinClinicalTrialData', () => {
     test('should join clinical trial data appropriately and throw errors when missing required properties', () => {
       const firstClinicalTrialInfoResponse = exampleClinicalTrialInformationResponse[0]; // Each patient will only have one entry per clinical trial
-      const expectedErrorString = 'Clinical trial missing an expected property: patientId, clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.';
+      const expectedErrorString = 'Clinical trial missing an expected property: clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.';
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test required properties in CSV throw error
       Object.keys(firstClinicalTrialInfoResponse).forEach((key) => {
         const clonedData = _.cloneDeep(firstClinicalTrialInfoResponse);
-        expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, clonedData)).toEqual(expect.anything());
+        expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toEqual(expect.anything());
         if (key === 'mrn') return; // MRN is not required from CSV
         if (key === 'trialResearchSystem') return; // trialResearchSystem is an optional field
         delete clonedData[key];
-        expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
 
-      // patientId is required to be passed in
-      expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(undefined, firstClinicalTrialInfoResponse)).toThrow(new Error(expectedErrorString));
-
       // joinClinicalTrialData should return correct format
-      expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, firstClinicalTrialInfoResponse)).toEqual({
+      expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(firstClinicalTrialInfoResponse, patientId)).toEqual({
         formattedDataSubject: {
           enrollmentStatus: firstClinicalTrialInfoResponse.enrollmentStatus,
           trialSubjectID: firstClinicalTrialInfoResponse.trialSubjectID,
           trialResearchID: firstClinicalTrialInfoResponse.trialResearchID,
-          patientId: MOCK_PATIENT_MRN,
+          patientId,
           trialResearchSystem: firstClinicalTrialInfoResponse.trialResearchSystem,
         },
         formattedDataStudy: {
@@ -67,36 +64,9 @@ describe('CSVClinicalTrialInformationExtractor', () => {
     });
   });
 
-  describe('getPatientId', () => {
-    test('should return patient id when patient resource in context', () => {
-      const contextPatient = {
-        resourceType: 'Patient',
-        id: 'context-patient-id',
-      };
-      const contextBundle = {
-        resourceType: 'Bundle',
-        type: 'collection',
-        entry: [
-          {
-            fullUrl: 'context-url',
-            resource: contextPatient,
-          },
-        ],
-      };
-
-      const patientId = getPatientId(contextBundle);
-      expect(patientId).toEqual(contextPatient.id);
-    });
-
-    test('getPatientId should return undefined when no patient resource in context', () => {
-      const patientId = getPatientId({});
-      expect(patientId).toBeUndefined();
-    });
-  });
-
   describe('get', () => {
     test('should return a bundle with the correct resources', async () => {
-      const data = await csvClinicalTrialInformationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvClinicalTrialInformationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');

test/extractors/fixtures/csv-clinical-trial-information-bundle.json

@@ -3,14 +3,16 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
+      "fullUrl": "urn:uuid:a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
       "resource": {
         "resourceType": "ResearchSubject",
-        "id": "f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
+        "id": "a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
         "identifier": [
           {
             "system": "http://example.com/clinicaltrialsubjectids",
-            "type": { "text": "Clinical Trial Subject ID" },
+            "type": {
+              "text": "Clinical Trial Subject ID"
+            },
             "value": "example-subjectId"
           }
         ],
@@ -21,7 +23,10 @@
             "value": "example-researchId"
           }
         },
-        "individual": { "reference": "urn:uuid:EXAMPLE-MRN", "type": "Patient" }
+        "individual": {
+          "reference": "urn:uuid:mrn-1",
+          "type": "Patient"
+        }
       }
     },
     {
@@ -42,7 +47,9 @@
         "identifier": [
           {
             "system": "example-system",
-            "type": { "text": "Clinical Trial Research ID" },
+            "type": {
+              "text": "Clinical Trial Research ID"
+            },
             "value": "example-researchId"
           }
         ]