Merge pull request #101 from mcode/adverse-event-uses-study-context

Use ResearchStudy id from context in AdverseEvent search

Author: julianxcarter

src/extractors/FHIRAdverseEventExtractor.js

@@ -1,4 +1,6 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
+const { getResearchStudiesFromContext } = require('../helpers/contextUtils');
+const logger = require('../helpers/logger');
 
 const BASE_STUDY = ''; // No base study specified
 
@@ -12,14 +14,28 @@ class FHIRAdverseEventExtractor extends BaseFHIRExtractor {
   // In addition to default parametrization, add study if specified
   async parametrizeArgsForFHIRModule({ context }) {
     const paramsWithID = await super.parametrizeArgsForFHIRModule({ context });
+    let allResearchStudyResources = [];
+    try {
+      allResearchStudyResources = getResearchStudiesFromContext(context);
+    } catch (e) {
+      logger.error(e.message);
+      logger.debug(e.stack);
+    }
+
     // The patient is referenced in the 'subject' field of an AdverseEvent
     paramsWithID.subject = paramsWithID.patient;
     delete paramsWithID.patient;
-    // Only add study to parameters if it has been specified
-    return {
+
+    // If there are research study resources, create a parameters object for each call to be made
+    const newStudyIds = allResearchStudyResources.map((rs) => rs.id).join(',');
+    const studyIdsForCurrentPatient = `${this.study}${this.study && newStudyIds ? ',' : ''}${newStudyIds}`;
+
+    // Only add study to parameters if it has been specified or was included from context
+    const obj = {
       ...paramsWithID,
-      ...(this.study && { study: this.study }),
+      ...(studyIdsForCurrentPatient && { study: studyIdsForCurrentPatient }),
     };
+    return obj;
   }
 }
 

src/helpers/contextUtils.js

@@ -62,9 +62,20 @@ function getEncountersFromContext(context) {
   return encounterResourcesInContext;
 }
 
+function getResearchStudiesFromContext(context) {
+  logger.debug('Getting ResearchStudy resources from context');
+  const researchStudyResourcesInContext = getBundleResourcesByType(context, 'ResearchStudy', {}, false);
+  if (researchStudyResourcesInContext.length === 0) {
+    throw Error('Could not find any ResearchStudy resources in context; ensure that a ClinicalTrialInformationExtractor or ResearchStudyExtractor is used earlier in your extraction configuration');
+  }
+  logger.debug(`ResearchStudy resources found in context. Found ${researchStudyResourcesInContext.length} ResearchStudy resources.`);
+  return researchStudyResourcesInContext;
+}
+
 module.exports = {
   getConditionEntriesFromContext,
   getConditionsFromContext,
   getEncountersFromContext,
   getPatientFromContext,
+  getResearchStudiesFromContext,
 };

test/extractors/FHIRAdverseEventExtractor.test.js

@@ -15,6 +15,28 @@ const MOCK_CONTEXT = {
     },
   ],
 };
+const researchStudyResource = {
+  resourceType: 'ResearchStudy',
+  id: 'ResearchStudyExample01',
+};
+const MOCK_CONTEXT_WITH_RESEARCH_STUDY = {
+  resourceType: 'Bundle',
+  type: 'collection',
+  entry: [
+    {
+      fullUrl: 'context-url-1',
+      resource: { resourceType: 'Patient', id: MOCK_MRN },
+    },
+    {
+      fullUrl: 'context-url-2',
+      resource: researchStudyResource,
+    },
+    {
+      fullUrl: 'context-url-3',
+      resource: { ...researchStudyResource, id: 'ResearchStudyExample02' },
+    },
+  ],
+};
 
 // Construct extractor and create spies for mocking responses
 const extractor = new FHIRAdverseEventExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
@@ -40,6 +62,12 @@ describe('FHIRAdverseEventExtractor', () => {
       expect(params).not.toHaveProperty('study');
     });
 
+    test('should add study id for all ResearchStudy resources that are in context', async () => {
+      const params = await extractor.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT_WITH_RESEARCH_STUDY });
+      expect(params).toHaveProperty('study');
+      expect(params.study).toEqual(`${researchStudyResource.id},ResearchStudyExample02`);
+    });
+
     describe('pass in optional study parameter', () => {
       test('should add study when set to param values', async () => {
         const params = await extractorWithStudy.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
@@ -51,6 +79,12 @@ describe('FHIRAdverseEventExtractor', () => {
         const params = await extractorWithStudy.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
         expect(params).not.toHaveProperty('patient');
       });
+
+      test('should add study from study parameter and from context', async () => {
+        const params = await extractorWithStudy.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT_WITH_RESEARCH_STUDY });
+        expect(params).toHaveProperty('study');
+        expect(params.study).toEqual(`${extractorWithStudy.study},${researchStudyResource.id},ResearchStudyExample02`);
+      });
     });
   });
 });

test/helpers/contextUtils.test.js

@@ -1,6 +1,10 @@
-const { getConditionEntriesFromContext, getConditionsFromContext, getEncountersFromContext, getPatientFromContext } = require('../../src/helpers/contextUtils');
-
-const MOCK_PATIENT_MRN = '123';
+const {
+  getConditionEntriesFromContext,
+  getConditionsFromContext,
+  getEncountersFromContext,
+  getPatientFromContext,
+  getResearchStudiesFromContext,
+} = require('../../src/helpers/contextUtils');
 
 describe('getPatientFromContext', () => {
   const patientResource = {
@@ -124,7 +128,39 @@ describe('getEncountersFromContext', () => {
   });
 
   test('Should throw an error if there are no encounters in context', () => {
-    expect(() => getEncountersFromContext(MOCK_PATIENT_MRN, {}))
+    expect(() => getEncountersFromContext({}))
       .toThrow('Could not find any encounter resources in context; ensure that an EncounterExtractor is used earlier in your extraction configuration');
   });
 });
+
+describe('getResearchStudyFromContext', () => {
+  const researchStudyResource = {
+    resourceType: 'ResearchStudy',
+    id: 'ResearchStudyExample01',
+  };
+  const researchStudyContext = {
+    resourceType: 'Bundle',
+    type: 'collection',
+    entry: [
+      {
+        fullUrl: 'context-url-1',
+        resource: researchStudyResource,
+      },
+      {
+        fullUrl: 'context-url-2',
+        resource: { ...researchStudyResource, id: 'ResearchStudyExample02' },
+      },
+    ],
+  };
+
+  test('Should return all ResearchStudy resources in context', () => {
+    const researchStudyResources = getResearchStudiesFromContext(researchStudyContext);
+    expect(researchStudyResources).toHaveLength(2);
+    expect(researchStudyResources[0]).toEqual(researchStudyResource);
+  });
+
+  test('Should throw an error if there are no research studies in context', () => {
+    expect(() => getResearchStudiesFromContext({}))
+      .toThrow('Could not find any ResearchStudy resources in context; ensure that a ClinicalTrialInformationExtractor or ResearchStudyExtractor is used earlier in your extraction configuration');
+  });
+});