Merge pull request #197 from mcode/research-subject-period

Adding Period to ResearchSubjects in CSVClinicalTrialInformationExtractor

src/extractors/CSVClinicalTrialInformationExtractor.js

@@ -4,6 +4,7 @@ const { firstEntryInBundle, getEmptyBundle } = require('../helpers/fhirUtils');
 const { getPatientFromContext } = require('../helpers/contextUtils');
 const { generateMcodeResources } = require('../templates');
 const logger = require('../helpers/logger');
+const { formatDateTime } = require('../helpers/dateUtils');
 const { CSVClinicalTrialInformationSchema } = require('../helpers/schemas/csv');
 
 
@@ -25,6 +26,8 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
       trialresearchid: trialResearchID,
       trialstatus: trialStatus,
       trialresearchsystem: trialResearchSystem,
+      startdate: startDate,
+      enddate: endDate,
     } = clinicalTrialData;
     const { clinicalSiteID, clinicalSiteSystem } = this;
 
@@ -40,6 +43,8 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
         trialResearchID,
         patientId,
         trialResearchSystem,
+        startDate: !startDate ? null : formatDateTime(startDate),
+        endDate: !endDate ? null : formatDateTime(endDate),
       },
       formattedDataStudy: {
         trialStatus,

src/helpers/schemas/csv.js

@@ -54,6 +54,8 @@ const CSVClinicalTrialInformationSchema = {
     { name: 'trialResearchID', required: true },
     { name: 'trialStatus', required: true },
     { name: 'trialResearchSystem' },
+    { name: 'startDate' },
+    { name: 'endDate' },
   ],
 };
 

src/templates/EncounterTemplate.js

@@ -1,14 +1,5 @@
-const { ifAllArgsObj } = require('../helpers/templateUtils');
-const { coding, reference } = require('./snippets');
-
-function periodTemplate({ startDate, endDate }) {
-  return {
-    period: {
-      start: startDate,
-      end: endDate,
-    },
-  };
-}
+const { ifAllArgsObj, ifSomeArgsObj } = require('../helpers/templateUtils');
+const { coding, reference, periodTemplate } = require('./snippets');
 
 function classTemplate({ classCode, classSystem }) {
   return {
@@ -42,7 +33,7 @@ function encounterTemplate({
     ...classTemplate({ classCode, classSystem }),
     ...subjectTemplate({ subject }),
     ...ifAllArgsObj(typeTemplate)({ typeCode, typeSystem }),
-    ...ifAllArgsObj(periodTemplate)({ startDate, endDate }),
+    ...ifSomeArgsObj(periodTemplate)({ startDate, endDate }),
   };
 }
 

src/templates/ResearchSubjectTemplate.js

@@ -1,4 +1,5 @@
-const { reference, identifier, identifierArr } = require('./snippets');
+const { reference, identifier, identifierArr, periodTemplate } = require('./snippets');
+const { ifSomeArgsObj } = require('../helpers/templateUtils');
 
 function studyTemplate(trialResearchID, trialResearchSystem) {
   return {
@@ -38,6 +39,8 @@ function researchSubjectTemplate({
   trialResearchID,
   patientId,
   trialResearchSystem,
+  startDate,
+  endDate,
 }) {
   if (!(id && enrollmentStatus && trialSubjectID && trialResearchID && patientId)) {
     throw Error('Trying to render a ResearchStudyTemplate, but a required argument is missing; ensure that id, trialStatus, trialResearchID, clinicalSiteID are all present');
@@ -50,6 +53,7 @@ function researchSubjectTemplate({
     ...studyTemplate(trialResearchID, trialResearchSystem),
     ...individualTemplate(patientId),
     ...researchSubjectIdentifiersTemplate(trialSubjectID),
+    ...ifSomeArgsObj(periodTemplate)({ startDate, endDate }),
   };
 }
 

src/templates/snippets/index.js

@@ -10,6 +10,7 @@ const { stagingMethodTemplate } = require('./cancerStaging');
 const { medicationTemplate } = require('./medication');
 const { subjectTemplate } = require('./subject');
 const { treatmentReasonTemplate } = require('./treatmentReason');
+const { periodTemplate } = require('./period');
 
 module.exports = {
   bodySiteTemplate,
@@ -22,6 +23,7 @@ module.exports = {
   medicationTemplate,
   meta,
   narrative,
+  periodTemplate,
   reference,
   stagingMethodTemplate,
   subjectTemplate,

src/templates/snippets/period.js

@@ -0,0 +1,12 @@
+function periodTemplate({ startDate, endDate }) {
+  return {
+    period: {
+      ...(startDate && { start: startDate }),
+      ...(endDate && { end: endDate }),
+    },
+  };
+}
+
+module.exports = {
+  periodTemplate,
+};

test/extractors/CSVClinicalTrialInformationExtractor.test.js

@@ -40,6 +40,8 @@ describe('CSVClinicalTrialInformationExtractor', () => {
         expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toEqual(expect.anything());
         if (key === 'patientId') return; // MRN is optional
         if (key === 'trialresearchsystem') return; // trialResearchSystem is optional
+        if (key === 'startdate') return; // startDate is optional
+        if (key === 'enddate') return; // endDate is optional
         delete clonedData[key];
         expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
@@ -52,6 +54,8 @@ describe('CSVClinicalTrialInformationExtractor', () => {
           trialResearchID: firstClinicalTrialInfoResponse.trialresearchid,
           patientId,
           trialResearchSystem: firstClinicalTrialInfoResponse.trialresearchsystem,
+          startDate: firstClinicalTrialInfoResponse.startdate,
+          endDate: firstClinicalTrialInfoResponse.enddate,
         },
         formattedDataStudy: {
           trialStatus: firstClinicalTrialInfoResponse.trialstatus,

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

@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
+      "fullUrl": "urn:uuid:aea78e13731d4b105b3a731a48ce77602f159d46299bb02aaaf80e49530115bd",
       "resource": {
         "resourceType": "ResearchSubject",
-        "id": "a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
+        "id": "aea78e13731d4b105b3a731a48ce77602f159d46299bb02aaaf80e49530115bd",
         "identifier": [
           {
             "system": "http://example.com/clinicaltrialsubjectids",
@@ -26,6 +26,10 @@
         "individual": {
           "reference": "urn:uuid:mrn-1",
           "type": "Patient"
+        },
+        "period": {
+          "start": "2020-01-01",
+          "end": "2021-01-01"
         }
       }
     },

test/extractors/fixtures/csv-clinical-trial-information-module-response.json

@@ -5,6 +5,8 @@
     "enrollmentstatus": "example-enrollment-status",
     "trialresearchid": "example-researchId",
     "trialstatus": "example-trialStatus",
-    "trialresearchsystem":"example-system"
+    "trialresearchsystem":"example-system",
+    "startdate": "2020-01-01",
+    "enddate": "2021-01-01"
   }
 ]

test/sample-client-data/clinical-trial-information.csv

@@ -1,4 +1,4 @@
-mrn,trialSubjectID,enrollmentStatus,trialResearchID,trialStatus,trialResearchSystem
-123,subjectId-1,potential-candidate,researchId-1,approved,system-1
-456,subjectId-2,on-study-intervention,researchId-1,completed,system-2
-789,subjectId-3,on-study-observation,researchId-2,active,
+mrn,trialSubjectID,enrollmentStatus,trialResearchID,trialStatus,trialResearchSystem,startDate,endDate
+123,subjectId-1,potential-candidate,researchId-1,approved,system-1,2020-01-01,2021-01-03
+456,subjectId-2,on-study-intervention,researchId-1,completed,system-2,2023-05-03,
+789,subjectId-3,on-study-observation,researchId-2,active,,,

test/templates/fixtures/research-subject-resource.json

@@ -16,5 +16,9 @@
   },
   "individual": {
     "reference": "urn:uuid:mCODEPatient1"
+  },
+  "period": {
+    "start": "2020-01-01",
+    "end": "2021-01-01"
   }
 }

test/templates/researchSubject.test.js

@@ -8,6 +8,8 @@ const VALID_DATA = {
   trialSubjectID: 'trial-123',
   trialResearchID: 'rs1',
   patientId: 'mCODEPatient1',
+  startDate: '2020-01-01',
+  endDate: '2021-01-01',
 };
 
 const INVALID_DATA = {
@@ -16,6 +18,8 @@ const INVALID_DATA = {
   trialResearchID: 'rs1',
   patientId: 'mCODEPatient1',
   trialSubjectID: null,
+  startDate: '2020-01-01',
+  endDate: '2021-01-01',
 };
 
 describe('test ResearchSubject template', () => {
@@ -25,6 +29,8 @@ describe('test ResearchSubject template', () => {
     expect(generatedResearchSubject.id).toEqual(validResearchSubject.id);
     expect(generatedResearchSubject.trialStatus).toEqual(validResearchSubject.trialStatus);
     expect(generatedResearchSubject.trialResearchID).toEqual(validResearchSubject.trialResearchID);
+    expect(generatedResearchSubject.period.start).toEqual(validResearchSubject.period.start);
+    expect(generatedResearchSubject.period.end).toEqual(validResearchSubject.period.end);
     expect(isValidFHIR(generatedResearchSubject)).toBeTruthy();
   });