Fix all tests here

Author: Dtphelan1

src/extractors/CSVTreatmentPlanChangeExtractor.js

@@ -3,6 +3,7 @@ const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { formatDate } = require('../helpers/dateUtils');
 const { generateMcodeResources } = require('../templates');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
+const { getPatientFromContext } = require('../helpers/contextUtils');
 const logger = require('../helpers/logger');
 const { CSVTreatmentPlanChangeSchema } = require('../helpers/schemas/csv');
 
@@ -15,7 +16,7 @@ function formatData(tpcData, patientId) {
     return [];
   }
 
-  // Newly combined data has mrn and list of reviews to map to an extension
+  // Newly combined data has subjectId and list of reviews to map to an extension
   const combinedFormat = { subjectId: patientId, reviews: [] };
 
   // If there are multiple entries, combine them into one object with multiple reviews
@@ -75,15 +76,16 @@ class CSVTreatmentPlanChangeExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn, fromDate, toDate);
   }
 
-  async get({ mrn, fromDate, toDate }) {
+  async get({ mrn, context, fromDate, toDate }) {
     const tpcData = await this.getTPCData(mrn, fromDate, toDate);
     if (tpcData.length === 0) {
       logger.warn('No treatment plan change data found for patient');
       return getEmptyBundle();
     }
+    const patientId = getPatientFromContext(context).id;
 
     // Reformat data
-    const formattedData = formatData(tpcData);
+    const formattedData = formatData(tpcData, patientId);
 
     // Fill templates
     return generateMcodeResources('CarePlanWithReview', formattedData);

test/cli/fixtures/example-patient.csv

@@ -0,0 +1,4 @@
+mrn,familyName,givenName,gender,birthsex,dateOfBirth,race,ethnicity,language,addressLine,city,state,zip
+123,Doe,Jane,female,F,1980-01-01,2028-9,2186-5,en,2 West Side Rd,Malden,MA,02148
+456,Doe,John,male,M,1970-01-01,2106-3,2186-5,en-US,3 East Side Rd,Brooklyn,NY,11201
+789,Doe,Jimmy,other,UNK,1980-03-01,ASKU,2186-5,ar,,,,90001

test/cli/mcodeExtraction.test.js

@@ -46,6 +46,13 @@ describe('mcodeExtraction', () => {
     it('should succeed in extraction when CSV files do not have data for all patients', async () => {
       const testConfig = {
         extractors: [
+          {
+            label: 'patients',
+            type: 'CSVPatientExtractor',
+            constructorArgs: {
+              filePath: path.join(__dirname, './fixtures/example-patient.csv'),
+            },
+          },
           {
             label: 'condition',
             type: 'CSVConditionExtractor',

test/extractors/CSVStagingExtractor.test.js

@@ -4,9 +4,11 @@ const _ = require('lodash');
 const { CSVStagingExtractor } = require('../../src/extractors');
 const exampleStagingModuleResponse = require('./fixtures/csv-staging-module-response.json');
 const exampleCSVStagingBundle = require('./fixtures/csv-staging-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'pat-mrn-1'; // linked to values in example-module-response above
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
 
 // Instantiate module with parameters
@@ -17,16 +19,17 @@ const { csvModule } = csvStagingExtractor;
 
 // Spy on csvModule
 const csvModuleSpy = jest.spyOn(csvModule, 'get');
-
 const formatTNMCategoryData = rewire('../../src/extractors/CSVStagingExtractor.js').__get__('formatTNMCategoryData');
 
 describe('CSVStagingExtractor', () => {
   describe('formatTNMCategoryData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'Staging data is missing an expected property: mrn, conditionId, effectiveDate are required.';
+      const expectedErrorString = 'Staging data is missing an expected property: conditionId, effectiveDate are required.';
       const localData = _.cloneDeep(exampleStagingModuleResponse[0]);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
       // Test that valid data works fine
-      expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
+      expect(formatTNMCategoryData(localData, patientId)).toEqual(expect.anything());
 
       // Test all optional properties can be empty without issue
       localData.t = '';
@@ -41,7 +44,7 @@ describe('CSVStagingExtractor', () => {
       expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
 
       // Removing each required property should throw an error
-      const requiredKeys = ['mrn', 'conditionId', 'effectiveDate'];
+      const requiredKeys = ['conditionId', 'effectiveDate'];
       requiredKeys.forEach((key) => {
         const clonedData = _.cloneDeep(localData);
         clonedData[key] = '';
@@ -53,7 +56,7 @@ describe('CSVStagingExtractor', () => {
   describe('get', () => {
     test('should return bundle with Observation', async () => {
       csvModuleSpy.mockReturnValue(exampleStagingModuleResponse);
-      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -63,7 +66,7 @@ describe('CSVStagingExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();

test/extractors/CSVTreatmentPlanChangeExtractor.test.js

@@ -4,18 +4,23 @@ const _ = require('lodash');
 const { CSVTreatmentPlanChangeExtractor } = require('../../src/extractors');
 const exampleCSVTPCModuleResponse = require('./fixtures/csv-treatment-plan-change-module-response.json');
 const exampleCSVTPCBundle = require('./fixtures/csv-treatment-plan-change-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
-const MOCK_MRN = 'mrn-1';
+// Constants for tests
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv');
+
+// Instantiate module with parameters
 const csvTPCExtractor = new CSVTreatmentPlanChangeExtractor({
   filePath: MOCK_CSV_PATH,
 });
 
+// Destructure all modules
 const { csvModule } = csvTPCExtractor;
 
 // Spy on csvModule
 const csvModuleSpy = jest.spyOn(csvModule, 'get');
-
 const formatData = rewire('../../src/extractors/CSVTreatmentPlanChangeExtractor.js').__get__('formatData');
 
 describe('CSVTreatmentPlanChangeExtractor', () => {
@@ -33,19 +38,21 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
         mrn: 'id',
       },
     ];
+    const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'Treatment Plan Change Data missing an expected property: mrn, dateOfCarePlan, changed are required';
+      const expectedErrorString = 'Treatment Plan Change Data missing an expected property: dateOfCarePlan, changed are required';
 
       // formatData on example data should not throw error when changed is false
-      expect(() => formatData(exampleData)).not.toThrowError();
+      expect(() => formatData(exampleData, patientId)).not.toThrowError();
 
       // Test required properties throw error
-      Object.keys(exampleData[0]).forEach((key) => {
+      const requiredKeys = ['dateOfCarePlan', 'changed'];
+      requiredKeys.forEach((key) => {
         const clonedData = _.cloneDeep(exampleData);
 
         delete clonedData[0][key];
-        expect(() => formatData(clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => formatData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
     });
 
@@ -54,17 +61,17 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
 
       // error should get throw when changed flag is true and there is no reasonCode provided
       exampleData[0].changed = 'true';
-      expect(() => formatData(exampleData)).toThrow(new Error(expectedErrorString));
+      expect(() => formatData(exampleData, patientId)).toThrow(new Error(expectedErrorString));
 
       // No error should be throw when reasonCode is provided
       exampleData[0].reasonCode = 'example code';
-      expect(() => formatData(exampleData)).not.toThrowError();
+      expect(() => formatData(exampleData, patientId)).not.toThrowError();
     });
 
     test('should join multiple entries into one', () => {
       const expectedFormattedData = [
         {
-          mrn: 'mrn-1',
+          subjectId: 'mrn-1',
           reviews: [
             {
               effectiveDate: '2020-04-15',
@@ -81,14 +88,14 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
         },
       ];
 
-      expect(formatData(exampleCSVTPCModuleResponse)).toEqual(expectedFormattedData);
+      expect(formatData(exampleCSVTPCModuleResponse, patientId)).toEqual(expectedFormattedData);
     });
   });
 
   describe('get', () => {
     test('should return bundle with CarePlan', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVTPCModuleResponse);
-      const data = await csvTPCExtractor.get({ mrn: MOCK_MRN });
+      const data = await csvTPCExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
@@ -98,7 +105,7 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
 
     test('should return empty bundle with no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvTPCExtractor.get({ mrn: MOCK_MRN });
+      const data = await csvTPCExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');

test/extractors/fixtures/csv-staging-bundle.json

@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+      "fullUrl": "urn:uuid:626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
       "resource": {
         "resourceType": "Observation",
-        "id": "ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+        "id": "626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-primary-tumor-category"
@@ -32,7 +32,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -61,10 +61,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+      "fullUrl": "urn:uuid:66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
       "resource": {
         "resourceType": "Observation",
-        "id": "88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+        "id": "66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-distant-metastases-category"
@@ -90,7 +90,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -119,10 +119,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+      "fullUrl": "urn:uuid:4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
       "resource": {
         "resourceType": "Observation",
-        "id": "1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+        "id": "4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-regional-nodes-category"
@@ -148,7 +148,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -177,10 +177,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:23564150098c6afeb2abc712086a21ead2e9bd308929f9d290988c6921ac841b",
+      "fullUrl": "urn:uuid:8fca0c2922335ea3c92022b4b2d4de17ba0645ce72d884b1e1c71a757c300a10",
       "resource": {
         "resourceType": "Observation",
-        "id": "23564150098c6afeb2abc712086a21ead2e9bd308929f9d290988c6921ac841b",
+        "id": "8fca0c2922335ea3c92022b4b2d4de17ba0645ce72d884b1e1c71a757c300a10",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-stage-group"
@@ -214,7 +214,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "effectiveDateTime": "2020-01-01",
@@ -234,15 +234,15 @@
         ],
         "hasMember": [
           {
-            "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+            "reference": "urn:uuid:626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
             "type": "Observation"
           },
           {
-            "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+            "reference": "urn:uuid:66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
             "type": "Observation"
           },
           {
-            "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+            "reference": "urn:uuid:4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
             "type": "Observation"
           }
         ]

test/extractors/fixtures/csv-staging-module-response.json

@@ -1,6 +1,6 @@
 [
   {
-    "mrn": "pat-mrn-1",
+    "mrn": "mrn-1",
     "conditionId": "cond-1",
     "stageGroup": "3C",
     "t": "cT3",