Merge pull request #84 from mcode/add-identifier-system

Add identifier helper and update ResearchSubject template

Author: Dtphelan1

src/helpers/fhirUtils.js

@@ -95,6 +95,13 @@ function mapFHIRVersions(resource, currentVersion, targetVersion) {
   return resource;
 }
 
+function firstIdentifierEntry(resource) {
+  if (resource.identifier && resource.identifier.length > 0) {
+    return resource.identifier[0];
+  }
+  return null;
+}
+
 // Utility function to get the resources of a type from our bundle
 // Optionally get only the first resource of that type via 'first' parameter
 const getBundleResourcesByType = (bundle, type, context = {}, first = false) => {
@@ -158,10 +165,12 @@ const logOperationOutcomeInfo = (operationOutcome) => {
 
 const isValidFHIR = (resource) => validator.validate('FHIR', resource);
 
+
 module.exports = {
   allResourcesInBundle,
   determineVersion,
   firstEntryInBundle,
+  firstIdentifierEntry,
   firstResourceInBundle,
   getBundleEntriesByResourceType,
   getBundleResourcesByType,

src/index.js

@@ -42,6 +42,7 @@ const { getEthnicityDisplay,
 const {
   allResourcesInBundle,
   firstEntryInBundle,
+  firstIdentifierEntry,
   firstResourceInBundle,
   getBundleEntriesByResourceType,
   getBundleResourcesByType,
@@ -104,6 +105,7 @@ module.exports = {
   // FHIR and resource helpers
   allResourcesInBundle,
   firstEntryInBundle,
+  firstIdentifierEntry,
   firstResourceInBundle,
   formatDate,
   formatDateTime,

src/templates/ResearchSubjectTemplate.js

@@ -1,10 +1,10 @@
 const { reference, identifier, identifierArr } = require('./snippets');
 
-function studyTemplate(trialResearchID) {
+function studyTemplate(trialResearchID, trialResearchSystem) {
   return {
     study: {
       ...identifier({
-        system: 'http://example.com/clinicaltrialids',
+        system: trialResearchSystem,
         value: trialResearchID,
       }),
     },
@@ -37,6 +37,7 @@ function researchSubjectTemplate({
   trialSubjectID,
   trialResearchID,
   patientId,
+  trialResearchSystem = 'http://example.com/clinicaltrialids',
 }) {
   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');
@@ -46,7 +47,7 @@ function researchSubjectTemplate({
     resourceType: 'ResearchSubject',
     id,
     status: enrollmentStatus,
-    ...studyTemplate(trialResearchID),
+    ...studyTemplate(trialResearchID, trialResearchSystem),
     ...individualTemplate(patientId),
     ...researchSubjectIdentifiersTemplate(trialSubjectID),
   };

test/helpers/fhirUtils.test.js

@@ -2,6 +2,7 @@ const {
   getQuantityUnit,
   isBundleEmpty,
   firstEntryInBundle,
+  firstIdentifierEntry,
   firstResourceInBundle,
   allResourcesInBundle,
   quantityCodeToUnitLookup,
@@ -43,8 +44,8 @@ describe('isBundleEmpty', () => {
 
 describe('firstEntryInBundle', () => {
   test('Empty bundle should return undefined', () => {
+    expect(firstEntryInBundle(emptyBundle)).toBeUndefined();
   });
-  expect(firstEntryInBundle(emptyBundle)).toBeUndefined();
 
   test('Bundles with entries should always return the first', () => {
     expect(firstEntryInBundle(bundleWithOneEntry))
@@ -54,6 +55,28 @@ describe('firstEntryInBundle', () => {
   });
 });
 
+describe('firstIdentifierEntry', () => {
+  test('Resource with no identifier returns null', () => {
+    expect(firstIdentifierEntry({})).toBeNull();
+  });
+
+  test('Resource with identifier gives first value', () => {
+    const id1 = {
+      system: 'example',
+      value: 'example-value',
+    };
+    const id2 = {
+      system: 'example2',
+      value: 'example-value2',
+    };
+    const resourceWithIdentifier = {
+      identifier: [id1, id2],
+    };
+
+    expect(firstIdentifierEntry(resourceWithIdentifier)).toEqual(id1);
+  });
+});
+
 describe('firstResourceInBundle', () => {
   test('Empty bundle should throw an error', () => {
     expect(() => firstResourceInBundle(emptyBundle))