Merge pull request #202 from mcode/add_search_parameters

Add search parameters
mcode · Nov 27, 2023 · 47078f6 · 47078f6
2 parents 939155f + 0c09fd7
commit 47078f6
Show file tree

Hide file tree

Showing 20 changed files with 53 additions and 193 deletions.
diff --git a/.eslintrc.json b/.eslintrc.json
@@ -21,6 +21,6 @@
         "object-curly-newline": ["error", {
             "ObjectPattern": { "minProperties": 5 }
         }],
-        "no-underscore-dangle":  ["error", { "allow": ["__get__", "__set__"] }]
+        "no-underscore-dangle":  ["error", { "allow": ["__get__", "__set__","_include"] }]
     }
 }
diff --git a/src/extractors/BaseFHIRExtractor.js b/src/extractors/BaseFHIRExtractor.js
@@ -5,11 +5,14 @@ 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 +24,8 @@ 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 */
 

diff --git a/src/extractors/FHIRAdverseEventExtractor.js b/src/extractors/FHIRAdverseEventExtractor.js
@@ -5,8 +5,10 @@ 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;
   }

diff --git a/src/extractors/FHIRAllergyIntoleranceExtractor.js b/src/extractors/FHIRAllergyIntoleranceExtractor.js
@@ -1,21 +1,10 @@
 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,
-    };
   }
 }
 

diff --git a/src/extractors/FHIRConditionExtractor.js b/src/extractors/FHIRConditionExtractor.js
@@ -1,21 +1,9 @@
 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,
-    };
   }
 }
 

diff --git a/src/extractors/FHIRDocumentReferenceExtractor.js b/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';
   }
 }

diff --git a/src/extractors/FHIREncounterExtractor.js b/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';
   }
 }

diff --git a/src/extractors/FHIRMedicationOrderExtractor.js b/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';
   }
 }

diff --git a/src/extractors/FHIRMedicationRequestExtractor.js b/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, 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 }),
-    };
   }
 }
 

diff --git a/src/extractors/FHIRMedicationStatementExtractor.js b/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';
   }
 }

diff --git a/src/extractors/FHIRObservationExtractor.js b/src/extractors/FHIRObservationExtractor.js
@@ -1,21 +1,9 @@
 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, 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,
-    };
   }
 }
 

diff --git a/src/extractors/FHIRPatientExtractor.js b/src/extractors/FHIRPatientExtractor.js
@@ -2,8 +2,10 @@ 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;
   }

diff --git a/src/extractors/FHIRProcedureExtractor.js b/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';
   }
 }

diff --git a/src/helpers/patientUtils.js b/src/helpers/patientUtils.js
@@ -87,7 +87,7 @@ function maskPatientData(bundle, mask, maskAll = false) {
   // get Patient resource from bundle
   const patient = fhirpath.evaluate(
     bundle,
-    'Bundle.entry.where(resource.resourceType=\'Patient\').resource,first()',
+    'Bundle.entry.where(resource.resourceType=\'Patient\').resource.first()',
   )[0];
 
   const validFields = [

diff --git a/src/helpers/schemas/config.schema.json b/src/helpers/schemas/config.schema.json
@@ -156,6 +156,10 @@
           "title": "Type",
           "type": "string"
         },
+        "searchParameters": {
+          "title": "Search Parameters",
+          "type": "object"
+        },
         "mask": {
           "title": "Masked Fields",
           "oneOf": [

diff --git a/test/extractors/BaseFHIRExtractor.test.js b/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 = {
@@ -21,7 +24,7 @@ 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
@@ -30,7 +33,10 @@ const moduleRequestHeadersSpy = jest.spyOn(baseFHIRModule, 'updateRequestHeaders
 
 // Ensure that data is returned for condition
 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 +53,12 @@ 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 () => {

diff --git a/test/extractors/FHIRAllergyIntoleranceExtractor.test.js b/test/extractors/FHIRAllergyIntoleranceExtractor.test.js
@@ -1,45 +1,14 @@
-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);
-    });
   });
 });
diff --git a/test/extractors/FHIRConditionExtractor.test.js b/test/extractors/FHIRConditionExtractor.test.js
@@ -1,37 +1,15 @@
-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);
-    });
   });
 });