Adding searchParameters to fhir extractor construction args to allow …

…for customizing the searches to servers to scope results. This will allow us to target specific Resources as best we can depending on the fhir server being accessed.

src/extractors/BaseFHIRExtractor.js

@@ -5,11 +5,12 @@ const { getPatientFromContext } = require('../helpers/contextUtils');
 const logger = require('../helpers/logger');
 
 class BaseFHIRExtractor extends Extractor {
-  constructor({ baseFhirUrl, requestHeaders, version, resourceType }) {
+  constructor({ baseFhirUrl, requestHeaders, version, resourceType, searchParameters={} }) {
     super();
     this.resourceType = resourceType;
     this.version = version;
     this.baseFHIRModule = new BaseFHIRModule(baseFhirUrl, requestHeaders);
+    this.searchParameters = searchParameters;
   }
 
   updateRequestHeaders(newHeaders) {
@@ -21,7 +22,8 @@ class BaseFHIRExtractor extends Extractor {
   // NOTE: Async because other extractors that extend this may need to make async lookups in the future
   async parametrizeArgsForFHIRModule({ context }) {
     const patient = getPatientFromContext(context);
-    return { patient: patient.id };
+
+    return { ...this.searchParameters, patient: patient.id };
   }
   /* eslint-enable class-methods-use-this */
 

src/extractors/FHIRAdverseEventExtractor.js

@@ -5,8 +5,8 @@ const logger = require('../helpers/logger');
 const BASE_STUDY = ''; // No base study specified
 
 class FHIRAdverseEventExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, study }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, study, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version,searchParameters });
     this.resourceType = 'AdverseEvent';
     this.study = study || BASE_STUDY;
   }

src/extractors/FHIRAllergyIntoleranceExtractor.js

@@ -3,20 +3,11 @@ const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 const BASE_CLINICAL_STATUS = 'active';
 
 class FHIRAllergyIntoleranceExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, clinicalStatus }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version,searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version,searchParameters });
     this.resourceType = 'AllergyIntolerance';
-    this.clinicalStatus = clinicalStatus || BASE_CLINICAL_STATUS;
   }
 
-  // In addition to default parametrization, add clinical status
-  async parametrizeArgsForFHIRModule({ context }) {
-    const paramsWithID = await super.parametrizeArgsForFHIRModule({ context });
-    return {
-      ...paramsWithID,
-      'clinical-status': this.clinicalStatus,
-    };
-  }
 }
 
 module.exports = {

src/extractors/FHIRConditionExtractor.js

@@ -1,22 +1,11 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
-const BASE_CATEGORIES = 'problem-list-item';
-
 class FHIRConditionExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, category }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters}) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'Condition';
-    this.category = category || BASE_CATEGORIES;
   }
 
-  // In addition to default parametrization, add category
-  async parametrizeArgsForFHIRModule({ context }) {
-    const paramsWithID = await super.parametrizeArgsForFHIRModule({ context });
-    return {
-      ...paramsWithID,
-      category: this.category,
-    };
-  }
 }
 
 module.exports = {

src/extractors/FHIRDocumentReferenceExtractor.js

@@ -1,8 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
 class FHIRDocumentReferenceExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version,searchParameters });
     this.resourceType = 'DocumentReference';
   }
 }

src/extractors/FHIREncounterExtractor.js

@@ -1,8 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
 class FHIREncounterExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'Encounter';
   }
 }

src/extractors/FHIRMedicationOrderExtractor.js

@@ -1,8 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
 class FHIRMedicationOrderExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'MedicationOrder';
   }
 }

src/extractors/FHIRMedicationRequestExtractor.js

@@ -1,22 +1,9 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
-const BASE_STATUSES = ''; // No status specified, returns all statuses (on-hold, completed, stopped, active)
-
 class FHIRMedicationRequestExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, status }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, status, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'MedicationRequest';
-    this.status = status || BASE_STATUSES;
-  }
-
-  // In addition to default parametrization, add status if specified
-  async parametrizeArgsForFHIRModule({ context }) {
-    const paramsWithID = await super.parametrizeArgsForFHIRModule({ context });
-    // Only add status to parameters if it has been specified
-    return {
-      ...paramsWithID,
-      ...(this.status && { status: this.status }),
-    };
   }
 }
 

src/extractors/FHIRMedicationStatementExtractor.js

@@ -1,8 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
 class FHIRMedicationStatementExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'MedicationStatement';
   }
 }

src/extractors/FHIRObservationExtractor.js

@@ -1,22 +1,11 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
-const BASE_CATEGORIES = 'laboratory,vital-signs,social-history,LDA,core-characteristics';
-
 class FHIRObservationExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, category }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, category, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'Observation';
-    this.category = category || BASE_CATEGORIES;
   }
 
-  // In addition to default parametrization, add category
-  async parametrizeArgsForFHIRModule({ context }) {
-    const paramsWithID = await super.parametrizeArgsForFHIRModule({ context });
-    return {
-      ...paramsWithID,
-      category: this.category,
-    };
-  }
 }
 
 module.exports = {

src/extractors/FHIRPatientExtractor.js

@@ -2,8 +2,8 @@ const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 const { maskPatientData } = require('../helpers/patientUtils.js');
 
 class FHIRPatientExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version, mask = [] }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, mask = [], searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'Patient';
     this.mask = mask;
   }

src/extractors/FHIRProcedureExtractor.js

@@ -1,8 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 
 class FHIRProcedureExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
-    super({ baseFhirUrl, requestHeaders, version });
+  constructor({ baseFhirUrl, requestHeaders, version, searchParameters }) {
+    super({ baseFhirUrl, requestHeaders, version, searchParameters });
     this.resourceType = 'Procedure';
   }
 }

src/helpers/schemas/config.schema.json

@@ -41,6 +41,10 @@
           "title": "Request Headers",
           "type": "object"
         },
+        "queryParameters": {
+          "title": "Query Parameters",
+          "type": "object"
+        },
         "csvParse" : {
           "title": "CSV Parse",
           "type": "object",

test/extractors/BaseFHIRExtractor.test.js

@@ -8,6 +8,9 @@ const MOCK_URL = 'http://localhost';
 const MOCK_REQUEST_HEADERS = {
   Accept: 'application/json',
 };
+const MOCK_SEARCH_PARAMS = {"_include": "Condition::subject",
+                            "category" : "problem-list-item",
+                            "status" : "final"}
 const MOCK_RESOURCE_TYPE = 'Condition';
 const MOCK_PATIENT_MRN = 'EXAMPLE-MRN';
 const MOCK_CONTEXT = {
@@ -21,16 +24,20 @@ const MOCK_CONTEXT = {
 };
 
 // Create extractor and destructure to mock responses on modules
-const baseFHIRExtractor = new BaseFHIRExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_REQUEST_HEADERS, resourceType: MOCK_RESOURCE_TYPE });
+const baseFHIRExtractor = new BaseFHIRExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_REQUEST_HEADERS, resourceType: MOCK_RESOURCE_TYPE , searchParameters: MOCK_SEARCH_PARAMS});
 const { baseFHIRModule } = baseFHIRExtractor;
 
 // Spies for mocking
 const baseFHIRModuleSearchSpy = jest.spyOn(baseFHIRModule, 'search');
 const moduleRequestHeadersSpy = jest.spyOn(baseFHIRModule, 'updateRequestHeaders');
 
 // Ensure that data is returned for condition
+debugger
 when(baseFHIRModuleSearchSpy)
-  .calledWith('Condition', { patient: examplePatientBundle.entry[0].resource.id })
+  .calledWith('Condition', { patient: examplePatientBundle.entry[0].resource.id, 
+                            _include: MOCK_SEARCH_PARAMS._include, 
+                             category: MOCK_SEARCH_PARAMS.category,
+                             status: MOCK_SEARCH_PARAMS.status })
   .mockReturnValue(exampleConditionBundle);
 
 // Tests
@@ -47,6 +54,13 @@ describe('BaseFhirExtractor', () => {
     expect(baseFHIRModuleSearchSpy).not.toHaveBeenCalled();
     expect(paramsBasedOnContext).toHaveProperty('patient');
     expect(paramsBasedOnContext.patient).toEqual(MOCK_CONTEXT.entry[0].resource.id);
+    expect(paramsBasedOnContext).toHaveProperty("_include");
+    expect(paramsBasedOnContext._include).toEqual(MOCK_SEARCH_PARAMS._include);
+    expect(paramsBasedOnContext).toHaveProperty("category");
+    expect(paramsBasedOnContext.category).toEqual(MOCK_SEARCH_PARAMS.category);
+    expect(paramsBasedOnContext).toHaveProperty("status");
+    expect(paramsBasedOnContext.status).toEqual(MOCK_SEARCH_PARAMS.status);
+
   });
 
   test('parametrizeArgsForFHIRModule throws an error if context has no relevant ID', async () => {
@@ -56,6 +70,7 @@ describe('BaseFhirExtractor', () => {
   });
 
   test('get should return a condition resource', async () => {
+    debugger
     const data = await baseFHIRExtractor.get({ context: MOCK_CONTEXT });
     expect(data.resourceType).toEqual('Bundle');
     expect(data.entry).toBeDefined();

test/extractors/FHIRAllergyIntoleranceExtractor.test.js

@@ -1,45 +1,15 @@
-const rewire = require('rewire');
 const { FHIRAllergyIntoleranceExtractor } = require('../../src/extractors/FHIRAllergyIntoleranceExtractor.js');
-
-const FHIRAllergyIntoleranceExtractorRewired = rewire('../../src/extractors/FHIRAllergyIntoleranceExtractor.js');
 const MOCK_URL = 'http://example.com';
 const MOCK_HEADERS = {};
-const MOCK_MRN = '123456789';
-const MOCK_CLINICAL_STATUS = 'status1,status2';
-const MOCK_CONTEXT = {
-  resourceType: 'Bundle',
-  entry: [
-    {
-      fullUrl: 'context-url',
-      resource: { resourceType: 'Patient', id: MOCK_MRN },
-    },
-  ],
-};
 
 const extractor = new FHIRAllergyIntoleranceExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
-const extractorWithClinicalStatus = new FHIRAllergyIntoleranceExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS, clinicalStatus: MOCK_CLINICAL_STATUS });
-const baseClinicalStatus = FHIRAllergyIntoleranceExtractorRewired.__get__('BASE_CLINICAL_STATUS');
 
 describe('FHIRAllergyIntoleranceExtractor', () => {
   describe('Constructor', () => {
     test('sets resourceType as AllergyIntolerance', () => {
       expect(extractor.resourceType).toEqual('AllergyIntolerance');
     });
 
-    test('sets clinical status based on BASE_CLINICAL_STATUS', () => {
-      expect(extractor.clinicalStatus).toEqual(baseClinicalStatus);
-    });
-
-    test('sets clinical status if provided', () => {
-      expect(extractorWithClinicalStatus.clinicalStatus).toEqual(MOCK_CLINICAL_STATUS);
-    });
   });
 
-  describe('parametrizeArgsForFHIRModule', () => {
-    test('should add category to param values', async () => {
-      const params = await extractor.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
-      expect(params).toHaveProperty('clinical-status');
-      expect(params['clinical-status']).toEqual(baseClinicalStatus);
-    });
-  });
 });

test/extractors/FHIRConditionExtractor.test.js

@@ -1,37 +1,16 @@
-const rewire = require('rewire');
 const { FHIRConditionExtractor } = require('../../src/extractors/FHIRConditionExtractor.js');
-const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
-const FHIRConditionExtractorRewired = rewire('../../src/extractors/FHIRConditionExtractor');
 const MOCK_URL = 'http://example.com';
 const MOCK_HEADERS = {};
-const MOCK_CATEGORIES = 'category1,category2';
+
 
 
 const extractor = new FHIRConditionExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
-const extractorWithCategories = new FHIRConditionExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS, category: MOCK_CATEGORIES });
-const baseCategories = FHIRConditionExtractorRewired.__get__('BASE_CATEGORIES');
 
 describe('FHIRConditionExtractor', () => {
   describe('Constructor', () => {
     test('sets resourceType to Condition', () => {
       expect(extractor.resourceType).toEqual('Condition');
     });
-
-    test('sets category based on BASE_CATEGORIES if not provided', () => {
-      expect(extractor.category).toEqual(baseCategories);
-    });
-
-    test('sets category if provided', () => {
-      expect(extractorWithCategories.category).toEqual(MOCK_CATEGORIES);
-    });
-  });
-
-  describe('parametrizeArgsForFHIRModule', () => {
-    test('should add category to param values', async () => {
-      const params = await extractor.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
-      expect(params).toHaveProperty('category');
-      expect(params.category).toEqual(baseCategories);
-    });
   });
 });

test/extractors/FHIRMedicationRequestExtractor.test.js

@@ -1,49 +1,14 @@
-const rewire = require('rewire');
 const { FHIRMedicationRequestExtractor } = require('../../src/extractors/FHIRMedicationRequestExtractor.js');
 
-const FHIRMedicationRequestExtractorRewired = rewire('../../src/extractors/FHIRMedicationRequestExtractor.js');
 const MOCK_URL = 'http://example.com';
 const MOCK_HEADERS = {};
-const MOCK_MRN = '123456789';
-const MOCK_STATUSES = 'status1,status2';
-const MOCK_CONTEXT = {
-  resourceType: 'Bundle',
-  entry: [
-    {
-      fullUrl: 'context-url',
-      resource: { resourceType: 'Patient', id: MOCK_MRN },
-    },
-  ],
-};
-
 // Construct extractor and create spies for mocking responses
 const extractor = new FHIRMedicationRequestExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
-const extractorWithStatuses = new FHIRMedicationRequestExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS, status: MOCK_STATUSES });
-const baseStatuses = FHIRMedicationRequestExtractorRewired.__get__('BASE_STATUSES');
 
 describe('FHIRMedicationRequestExtractor', () => {
   describe('Constructor', () => {
     test('sets resourceType as MedicationRequest', () => {
       expect(extractor.resourceType).toEqual('MedicationRequest');
     });
-    test('sets status based on BASE_STATUS if not provided', () => {
-      expect(extractor.status).toEqual(baseStatuses);
-    });
-    test('sets status if provided', () => {
-      expect(extractorWithStatuses.status).toEqual(MOCK_STATUSES);
-    });
-  });
-
-  describe('parametrizeArgsForFHIRModule', () => {
-    test('should not add status when not set to param values', async () => {
-      const params = await extractor.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
-      expect(params).not.toHaveProperty('status');
-    });
-
-    test('should add status when set to param values', async () => {
-      const params = await extractorWithStatuses.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
-      expect(params).toHaveProperty('status');
-      expect(params.status).toEqual(extractorWithStatuses.status);
-    });
   });
 });