Merge pull request #77 from mcode/fhir-adverse-event-extractor

FHIR Extractor for Adverse Events

Author: mickohanlon23

src/client/MCODEClient.js

@@ -9,6 +9,7 @@ const {
   CSVProcedureExtractor,
   CSVStagingExtractor,
   CSVTreatmentPlanChangeExtractor,
+  FHIRAdverseEventExtractor,
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
@@ -33,6 +34,7 @@ class MCODEClient extends BaseClient {
       CSVProcedureExtractor,
       CSVStagingExtractor,
       CSVTreatmentPlanChangeExtractor,
+      FHIRAdverseEventExtractor,
       FHIRAllergyIntoleranceExtractor,
       FHIRConditionExtractor,
       FHIRDocumentReferenceExtractor,

src/extractors/FHIRAdverseEventExtractor.js

@@ -0,0 +1,28 @@
+const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
+
+const BASE_STUDY = ''; // No base study specified
+
+class FHIRAdverseEventExtractor extends BaseFHIRExtractor {
+  constructor({ baseFhirUrl, requestHeaders, version, study }) {
+    super({ baseFhirUrl, requestHeaders, version });
+    this.resourceType = 'AdverseEvent';
+    this.study = study || BASE_STUDY;
+  }
+
+  // In addition to default parametrization, add study if specified
+  async parametrizeArgsForFHIRModule({ mrn, context }) {
+    const paramsWithID = await super.parametrizeArgsForFHIRModule({ mrn, context });
+    // 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 {
+      ...paramsWithID,
+      ...(this.study && { study: this.study }),
+    };
+  }
+}
+
+module.exports = {
+  FHIRAdverseEventExtractor,
+};

src/extractors/index.js

@@ -9,6 +9,7 @@ const { CSVProcedureExtractor } = require('./CSVProcedureExtractor');
 const { CSVStagingExtractor } = require('./CSVStagingExtractor');
 const { CSVTreatmentPlanChangeExtractor } = require('./CSVTreatmentPlanChangeExtractor');
 const { Extractor } = require('./Extractor');
+const { FHIRAdverseEventExtractor } = require('./FHIRAdverseEventExtractor');
 const { FHIRAllergyIntoleranceExtractor } = require('./FHIRAllergyIntoleranceExtractor');
 const { FHIRConditionExtractor } = require('./FHIRConditionExtractor');
 const { FHIRDocumentReferenceExtractor } = require('./FHIRDocumentReferenceExtractor');
@@ -33,6 +34,7 @@ module.exports = {
   CSVStagingExtractor,
   CSVTreatmentPlanChangeExtractor,
   Extractor,
+  FHIRAdverseEventExtractor,
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,

src/index.js

@@ -20,6 +20,7 @@ const {
   CSVStagingExtractor,
   CSVTreatmentPlanChangeExtractor,
   Extractor,
+  FHIRAdverseEventExtractor,
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
@@ -83,6 +84,7 @@ module.exports = {
   CSVStagingExtractor,
   CSVTreatmentPlanChangeExtractor,
   Extractor,
+  FHIRAdverseEventExtractor,
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,

test/extractors/FHIRAdverseEventExtractor.test.js

@@ -0,0 +1,62 @@
+const rewire = require('rewire');
+const { FHIRAdverseEventExtractor } = require('../../src/extractors/FHIRAdverseEventExtractor');
+const examplePatientBundle = require('./fixtures/patient-bundle.json');
+
+const FHIRAdverseEventExtractorRewired = rewire('../../src/extractors/FHIRAdverseEventExtractor.js');
+const MOCK_URL = 'http://example.com';
+const MOCK_HEADERS = {};
+const MOCK_MRN = '123456789';
+const MOCK_STUDIES = 'study1,study2';
+
+// Construct extractor and create sppies for mocking responses
+const extractor = new FHIRAdverseEventExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
+const extractorWithStudy = new FHIRAdverseEventExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS, study: MOCK_STUDIES });
+const baseStudy = FHIRAdverseEventExtractorRewired.__get__('BASE_STUDY');
+
+describe('FHIRAdverseEventExtractor', () => {
+  describe('Constructor', () => {
+    test('Constructor sets resourceType as AdverseEvent', () => {
+      expect(extractor.resourceType).toEqual('AdverseEvent');
+    });
+    test('sets study based on BASE_STUDY if not provided', () => {
+      expect(extractor.study).toEqual(baseStudy);
+    });
+    test('sets study if provided', () => {
+      expect(extractorWithStudy.study).toEqual(MOCK_STUDIES);
+    });
+  });
+
+  describe('parametrizeArgsForFHIRModule', () => {
+    test('should not add study when not set to param values', async () => {
+      // Create spy
+      const { baseFHIRModule } = extractor;
+      const baseFHIRModuleSearchSpy = jest.spyOn(baseFHIRModule, 'search');
+      baseFHIRModuleSearchSpy
+        .mockReturnValue(examplePatientBundle);
+
+      const params = await extractor.parametrizeArgsForFHIRModule({ mrn: MOCK_MRN });
+      expect(params).not.toHaveProperty('study');
+    });
+
+    describe('pass in optional study parameter', () => {
+      beforeEach(() => {
+        // Create spy
+        const { baseFHIRModule } = extractorWithStudy;
+        const baseFHIRModuleSearchSpy = jest.spyOn(baseFHIRModule, 'search');
+        baseFHIRModuleSearchSpy
+          .mockReturnValue(examplePatientBundle);
+      });
+
+      test('should add study when set to param values', async () => {
+        const params = await extractorWithStudy.parametrizeArgsForFHIRModule({ mrn: MOCK_MRN });
+        expect(params).toHaveProperty('study');
+        expect(params.study).toEqual(extractorWithStudy.study);
+      });
+
+      test('should delete patient after its value is moved to subject', async () => {
+        const params = await extractorWithStudy.parametrizeArgsForFHIRModule({ mrn: MOCK_MRN });
+        expect(params).not.toHaveProperty('patient');
+      });
+    });
+  });
+});

test/sample-client-data/adverse-event-information.csv

@@ -0,0 +1,4 @@
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
+123,adverseEventId-1,109006,code-system,Anxiety disorder of childhood OR adolescence,procedure-id,Procedure,Serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Serious,product-use-error,http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Use Error,severe,actual,researchId-1,12-09-1994,12-09-1994
+456,adverseEventId-2,134006,http://snomed.info/sct,Decreased hair growth,medicationId-1,Medication,Non-serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Non-serious,product-quality,http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Quality,mild,potential,researchId-2,12-10-1995,12-10-1995
+789,adverseEventId-3,150003,,,,,,,,,,,,,,12-09-1994,