Merge pull request #87 from mcode/add-trial-research-system

Added optional trialResearchSystem column to ClinicalTrialInformationExtractor

Author: dmendelowitz

src/extractors/CSVClinicalTrialInformationExtractor.js

@@ -27,6 +27,8 @@ class CSVClinicalTrialInformationExtractor extends Extractor {
   joinClinicalTrialData(patientId, clinicalTrialData) {
     logger.debug('Reformatting clinical trial data from CSV into template format');
     const { trialSubjectID, enrollmentStatus, trialResearchID, trialStatus } = clinicalTrialData;
+    // since trialResearchSystem is optional, check for blank value and replace with default value
+    const trialResearchSystem = (clinicalTrialData.trialResearchSystem === '') ? 'http://example.com/clinicaltrialids' : clinicalTrialData.trialResearchSystem;
     const { clinicalSiteID } = this;
 
     if (!(patientId && clinicalSiteID && trialSubjectID && enrollmentStatus && trialResearchID && trialStatus)) {
@@ -40,11 +42,13 @@ class CSVClinicalTrialInformationExtractor extends Extractor {
         trialSubjectID,
         trialResearchID,
         patientId,
+        trialResearchSystem,
       },
       formattedDataStudy: {
         trialStatus,
         trialResearchID,
         clinicalSiteID,
+        trialResearchSystem,
       },
     };
   }

src/templates/ResearchStudyTemplate.js

@@ -14,9 +14,9 @@ function siteTemplate(clinicalSiteID) {
   };
 }
 
-function researchStudyIdentifierTemplate(trialResearchID) {
+function researchStudyIdentifierTemplate(trialResearchID, trialResearchSystem) {
   return identifierArr({
-    system: 'http://example.com/clinicaltrialids',
+    system: trialResearchSystem,
     type: {
       text: 'Clinical Trial Research ID',
     },
@@ -26,7 +26,9 @@ function researchStudyIdentifierTemplate(trialResearchID) {
 
 
 // Based on https://www.hl7.org/fhir/researchstudy.html
-function researchStudyTemplate({ id, trialStatus, trialResearchID, clinicalSiteID }) {
+function researchStudyTemplate({
+  id, trialStatus, trialResearchID, clinicalSiteID, trialResearchSystem,
+}) {
   if (!(id && trialStatus && trialResearchID && clinicalSiteID)) {
     throw Error('Trying to render a ResearchStudyTemplate, but a required argument is missing; ensure that id, trialStatus, trialResearchID, clinicalSiteID are all present');
   }
@@ -36,7 +38,7 @@ function researchStudyTemplate({ id, trialStatus, trialResearchID, clinicalSiteI
     id,
     status: trialStatus,
     ...siteTemplate(clinicalSiteID),
-    ...researchStudyIdentifierTemplate(trialResearchID),
+    ...researchStudyIdentifierTemplate(trialResearchID, trialResearchSystem),
   };
 }
 

src/templates/ResearchSubjectTemplate.js

@@ -37,7 +37,7 @@ function researchSubjectTemplate({
   trialSubjectID,
   trialResearchID,
   patientId,
-  trialResearchSystem = 'http://example.com/clinicaltrialids',
+  trialResearchSystem,
 }) {
   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');

test/extractors/CSVClinicalTrialInformationExtractor.test.js

@@ -37,6 +37,7 @@ describe('CSVClinicalTrialInformationExtractor', () => {
         const clonedData = _.cloneDeep(firstClinicalTrialInfoResponse);
         expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, clonedData)).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));
       });
@@ -51,11 +52,13 @@ describe('CSVClinicalTrialInformationExtractor', () => {
           trialSubjectID: firstClinicalTrialInfoResponse.trialSubjectID,
           trialResearchID: firstClinicalTrialInfoResponse.trialResearchID,
           patientId: MOCK_PATIENT_MRN,
+          trialResearchSystem: firstClinicalTrialInfoResponse.trialResearchSystem,
         },
         formattedDataStudy: {
           trialStatus: firstClinicalTrialInfoResponse.trialStatus,
           trialResearchID: firstClinicalTrialInfoResponse.trialResearchID,
           clinicalSiteID: MOCK_CLINICAL_SITE_ID,
+          trialResearchSystem: firstClinicalTrialInfoResponse.trialResearchSystem,
         },
       });
     });

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

@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:d528f1b04f5d3588ef80ca680fbc0f82b93e7c05eb08d293f698c7b075fc0b25",
+      "fullUrl": "urn:uuid:f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
       "resource": {
         "resourceType": "ResearchSubject",
-        "id": "d528f1b04f5d3588ef80ca680fbc0f82b93e7c05eb08d293f698c7b075fc0b25",
+        "id": "f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
         "identifier": [
           {
             "system": "http://example.com/clinicaltrialsubjectids",
@@ -17,18 +17,18 @@
         "status": "example-enrollment-status",
         "study": {
           "identifier": {
-            "system": "http://example.com/clinicaltrialids",
+            "system": "example-system",
             "value": "example-researchId"
           }
         },
         "individual": { "reference": "urn:uuid:EXAMPLE-MRN", "type": "Patient" }
       }
     },
     {
-      "fullUrl": "urn:uuid:1b04fc751b08fd0e0b89293a0ccb61e931e6eeed87d88100fb0c3b15d0cf7fbb",
+      "fullUrl": "urn:uuid:b245aa8a67b5f67263f5a688813c435ccfb364e0f7865885c512e3a5ca3c9093",
       "resource": {
         "resourceType": "ResearchStudy",
-        "id": "1b04fc751b08fd0e0b89293a0ccb61e931e6eeed87d88100fb0c3b15d0cf7fbb",
+        "id": "b245aa8a67b5f67263f5a688813c435ccfb364e0f7865885c512e3a5ca3c9093",
         "status": "example-trialStatus",
         "site": [
           {
@@ -41,7 +41,7 @@
         ],
         "identifier": [
           {
-            "system": "http://example.com/clinicaltrialids",
+            "system": "example-system",
             "type": { "text": "Clinical Trial Research ID" },
             "value": "example-researchId"
           }

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

@@ -4,6 +4,7 @@
     "trialSubjectID": "example-subjectId",
     "enrollmentStatus": "example-enrollment-status",
     "trialResearchID": "example-researchId",
-    "trialStatus": "example-trialStatus"
+    "trialStatus": "example-trialStatus",
+    "trialResearchSystem":"example-system"
   }
 ]

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

@@ -1,4 +1,4 @@
-mrn,trialSubjectID,enrollmentStatus,trialResearchID,trialStatus
-123,subjectId-1,potential-candidate,researchId-1,approved
-456,subjectId-2,on-study-intervention,researchId-1,completed
-789,subjectId-3,on-study-observation,researchId-2,active
+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,

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

@@ -14,7 +14,7 @@
   "identifier": [
     {
       "value": "AFT1235",
-      "system": "http://example.com/clinicaltrialids",
+      "system": "example-system",
       "type": {
         "text": "Clinical Trial Research ID"
       }

test/templates/researchStudy.test.js

@@ -7,6 +7,7 @@ const VALID_DATA = {
   trialStatus: 'active',
   trialResearchID: 'AFT1235',
   clinicalSiteID: 'EXAMPLE_SITE_ID',
+  trialResearchSystem: 'example-system',
 };
 
 const INVALID_DATA = {