Add util function for getting encounters from context. Add FHIREncounterExtractor

Author: jafeltra

src/client/MCODEClient.js

@@ -14,6 +14,7 @@ const {
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
+  FHIREncounterExtractor,
   FHIRMedicationOrderExtractor,
   FHIRMedicationRequestExtractor,
   FHIRMedicationStatementExtractor,
@@ -40,6 +41,7 @@ class MCODEClient extends BaseClient {
       FHIRAllergyIntoleranceExtractor,
       FHIRConditionExtractor,
       FHIRDocumentReferenceExtractor,
+      FHIREncounterExtractor,
       FHIRMedicationOrderExtractor,
       FHIRMedicationRequestExtractor,
       FHIRMedicationStatementExtractor,

src/extractors/FHIREncounterExtractor.js

@@ -0,0 +1,12 @@
+const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
+
+class FHIREncounterExtractor extends BaseFHIRExtractor {
+  constructor({ baseFhirUrl, requestHeaders, version }) {
+    super({ baseFhirUrl, requestHeaders, version });
+    this.resourceType = 'Encounter';
+  }
+}
+
+module.exports = {
+  FHIREncounterExtractor,
+};

src/extractors/index.js

@@ -14,6 +14,7 @@ const { FHIRAdverseEventExtractor } = require('./FHIRAdverseEventExtractor');
 const { FHIRAllergyIntoleranceExtractor } = require('./FHIRAllergyIntoleranceExtractor');
 const { FHIRConditionExtractor } = require('./FHIRConditionExtractor');
 const { FHIRDocumentReferenceExtractor } = require('./FHIRDocumentReferenceExtractor');
+const { FHIREncounterExtractor } = require('./FHIREncounterExtractor');
 const { FHIRMedicationOrderExtractor } = require('./FHIRMedicationOrderExtractor');
 const { FHIRMedicationRequestExtractor } = require('./FHIRMedicationRequestExtractor');
 const { FHIRMedicationStatementExtractor } = require('./FHIRMedicationStatementExtractor');
@@ -40,6 +41,7 @@ module.exports = {
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
+  FHIREncounterExtractor,
   FHIRMedicationOrderExtractor,
   FHIRMedicationRequestExtractor,
   FHIRMedicationStatementExtractor,

src/helpers/contextUtils.js

@@ -21,7 +21,23 @@ function getConditionEntriesFromContext(mrn, context) {
   return conditionsInContext;
 }
 
+/**
+* Parses context for Encounter resources
+* @param {Object} context - Context object consisting of a FHIR Bundle
+* @return {Array} All the encounter resources found in context
+*/
+function getEncountersFromContext(context) {
+  logger.debug('Getting encounter resources from context');
+  const encountersInContext = getBundleResourcesByType(context, 'Encounter');
+  if (encountersInContext.length === 0) {
+    throw Error('Could not find any encounter resources in context; ensure that an EncounterExtractor is used earlier in your extraction configuration');
+  }
+  logger.debug(`Condition resources found in context. Found ${encountersInContext.length} condition resources.`);
+  return encountersInContext;
+}
+
 module.exports = {
   getConditionEntriesFromContext,
+  getEncountersFromContext,
   getPatientFromContext,
 };

src/index.js

@@ -25,6 +25,7 @@ const {
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
+  FHIREncounterExtractor,
   FHIRMedicationOrderExtractor,
   FHIRMedicationRequestExtractor,
   FHIRMedicationStatementExtractor,
@@ -62,7 +63,7 @@ const {
 } = require('./helpers/conditionUtils');
 const { getDiseaseStatusCode, getDiseaseStatusEvidenceCode, mEpochToDate } = require('./helpers/diseaseStatusUtils');
 const { formatDate, formatDateTime } = require('./helpers/dateUtils');
-const { getConditionEntriesFromContext, getPatientFromContext } = require('./helpers/contextUtils');
+const { getConditionEntriesFromContext, getEncountersFromContext, getPatientFromContext } = require('./helpers/contextUtils');
 
 module.exports = {
   // CLI Related utilities
@@ -91,6 +92,7 @@ module.exports = {
   FHIRAllergyIntoleranceExtractor,
   FHIRConditionExtractor,
   FHIRDocumentReferenceExtractor,
+  FHIREncounterExtractor,
   FHIRMedicationOrderExtractor,
   FHIRMedicationRequestExtractor,
   FHIRMedicationStatementExtractor,
@@ -130,5 +132,6 @@ module.exports = {
   mEpochToDate,
   // Context operations
   getConditionEntriesFromContext,
+  getEncountersFromContext,
   getPatientFromContext,
 };

test/extractors/FHIREncounterExtractor.test.js

@@ -0,0 +1,11 @@
+const { FHIREncounterExtractor } = require('../../src/extractors/FHIREncounterExtractor.js');
+
+const MOCK_URL = 'http://example.com';
+const MOCK_HEADERS = {};
+
+const extractor = new FHIREncounterExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
+describe('FHIREncounterExtractor', () => {
+  test('Constructor sets resourceType as Encounter', () => {
+    expect(extractor.resourceType).toEqual('Encounter');
+  });
+});

test/helpers/contextUtils.test.js

@@ -1,4 +1,4 @@
-const { getConditionEntriesFromContext, getPatientFromContext } = require('../../src/helpers/contextUtils');
+const { getConditionEntriesFromContext, getEncountersFromContext, getPatientFromContext } = require('../../src/helpers/contextUtils');
 
 const MOCK_PATIENT_MRN = '123';
 
@@ -61,3 +61,35 @@ describe('getConditionFromContext', () => {
       .toThrow('Could not find any conditions in context; ensure that a ConditionExtractor is used earlier in your extraction configuration');
   });
 });
+
+describe('getEncountersFromContext', () => {
+  const encounterResource = {
+    resourceType: 'Encounter',
+    id: 'EncounterExample01',
+  };
+  const encounterContext = {
+    resourceType: 'Bundle',
+    type: 'collection',
+    entry: [
+      {
+        fullUrl: 'context-url-1',
+        resource: encounterResource,
+      },
+      {
+        fullUrl: 'context-url-2',
+        resource: { ...encounterResource, id: 'EncounterExample02' },
+      },
+    ],
+  };
+
+  test('Should return all Encounter resources in context', () => {
+    const encounters = getEncountersFromContext(encounterContext);
+    expect(encounters).toHaveLength(2);
+    expect(encounters[0]).toEqual(encounterResource);
+  });
+
+  test('Should throw an error if there are no encounters in context', () => {
+    expect(() => getEncountersFromContext(MOCK_PATIENT_MRN, {}))
+      .toThrow('Could not find any encounter resources in context; ensure that an EncounterExtractor is used earlier in your extraction configuration');
+  });
+});