CTC Adverse Event Grade Extension

config/csv.config.example.json

@@ -89,6 +89,13 @@
       "constructorArgs": {
         "filePath": "./test/sample-client-data/adverse-event-information.csv"
       }
+    },
+    {
+      "label": "ctcAdverseEvent",
+      "type": "CSVCTCAdverseEventExtractor",
+      "constructorArgs": {
+        "filePath": "./test/sample-client-data/ctc-adverse-event-information.csv"
+      }
     }
   ]
-}
+}

docs/ctc-adverse-event.csv

@@ -1,4 +1,4 @@
-mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
-mrn-full-example,example-id-1,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,mild,actual,id,1994-12-09,1994-12-09
-mrn-two-category-example,example-id-2,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code|category-code,code-system|code-system,category-display|category-display,mild,actual,id,1994-12-09,1994-12-09
-mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
+mrn-full-example,example-id-1,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,mild,actual,id,1994-12-09,1994-12-09,1,
+mrn-two-category-example,example-id-2,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code|category-code,code-system|code-system,category-display|category-display,mild,actual,id,1994-12-09,1994-12-09,3
+mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,,1

src/extractors/CSVCTCAdverseEventExtractor.js

@@ -3,6 +3,7 @@ const { generateMcodeResources } = require('../templates');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { getPatientFromContext } = require('../helpers/contextUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
+const { ctcAEGradeCodeToTextLookup } = require('../helpers/lookups/ctcAdverseEventLookup');
 const logger = require('../helpers/logger');
 
 // Formats data to be passed into template-friendly format
@@ -27,10 +28,11 @@ function formatData(adverseEventData, patientId) {
       studyid: studyId,
       effectivedate: effectiveDate,
       recordeddate: recordedDate,
+      grade,
     } = data;
 
-    if (!(adverseEventCode && effectiveDate)) {
-      throw new Error('The adverse event is missing an expected attribute. Adverse event code and effective date are all required.');
+    if (!(adverseEventCode && effectiveDate && grade)) {
+      throw new Error('The adverse event is missing an expected attribute. Adverse event code, effective date, and grade are all required.');
     }
 
     const categoryCodes = category.split('|');
@@ -64,6 +66,7 @@ function formatData(adverseEventData, patientId) {
       studyId,
       effectiveDateTime: formatDateTime(effectiveDate),
       recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),
+      grade: { code: grade, display: ctcAEGradeCodeToTextLookup[grade] },
     };
   });
 }

src/helpers/lookups/ctcAdverseEventLookup.js

@@ -0,0 +1,17 @@
+const { createInvertedLookup, createLowercaseLookup } = require('../lookupUtils');
+
+const ctcAEGradeTextToCodeLookup = {
+  'Absent Adverse Event': '0',
+  'Mild Adverse Event': '1',
+  'Moderate Adverse Event': '2',
+  'Severe Adverse Event': '3',
+  'Life Threatening or Disabling Adverse Event': '4',
+  'Death Related to Adverse Event': '5',
+};
+
+const ctcAEGradeCodeToTextLookup = createInvertedLookup(ctcAEGradeTextToCodeLookup);
+
+module.exports = {
+  ctcAEGradeCodeToTextLookup: createLowercaseLookup(ctcAEGradeCodeToTextLookup),
+  ctcAEGradeTextToCodeLookup: createLowercaseLookup(ctcAEGradeTextToCodeLookup),
+};

src/templates/CTCAdverseEventTemplate.js

@@ -1,4 +1,4 @@
-const { coding, reference } = require('./snippets');
+const { coding, reference, extensionArr } = require('./snippets');
 const { ifAllArgsObj, ifSomeArgsObj, ifAllArgs, ifSomeArgsArr } = require('../helpers/templateUtils');
 
 function eventTemplate(eventCoding) {
@@ -72,17 +72,29 @@ function recordedDateTemplate(recordedDateTime) {
   };
 }
 
+function gradeTemplate(grade) {
+  return {
+    url: 'http://hl7.org/fhir/us/ctcae/StructureDefinition/ctcae-grade',
+    valueCodeableConcept: {
+      coding: [
+        coding({ ...grade, system: 'http://hl7.org/fhir/us/ctcae/CodeSystem/ctcae-grade-code-system' }),
+      ],
+    },
+  };
+}
+
 function CTCAdverseEventTemplate({
   id, subjectId, code, system, display, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
-  severity, actuality, studyId, effectiveDateTime, recordedDateTime,
+  severity, actuality, studyId, effectiveDateTime, recordedDateTime, grade,
 }) {
-  if (!(subjectId && code && system && effectiveDateTime && actuality)) {
-    throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code, system, actuality, and effectiveDateTime are all present');
+  if (!(subjectId && code && system && effectiveDateTime && actuality && grade)) {
+    throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code, system, actuality, grade, and effectiveDateTime are all present');
   }
 
   return {
     resourceType: 'AdverseEvent',
     id,
+    ...extensionArr(gradeTemplate(grade)),
     subject: reference({ id: subjectId, resourceType: 'Patient' }),
     ...ifSomeArgsObj(eventTemplate)({ code, system, display }),
     ...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),

test/extractors/CSVCTCAdverseEventextractor.test.js

@@ -0,0 +1,101 @@
+const path = require('path');
+const rewire = require('rewire');
+const _ = require('lodash');
+const { CSVCTCAdverseEventExtractor } = require('../../src/extractors');
+const exampleCTCCSVAdverseEventModuleResponse = require('./fixtures/csv-ctc-adverse-event-module-response.json');
+const exampleCTCCSVAdverseEventBundle = require('./fixtures/csv-ctc-adverse-event-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
+
+// Constants for tests
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response and context-with-patient 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
+const csvCTCAdverseEventExtractor = new CSVCTCAdverseEventExtractor({
+  filePath: MOCK_CSV_PATH,
+});
+
+// Destructure all modules
+const { csvModule } = csvCTCAdverseEventExtractor;
+
+// Spy on csvModule
+const csvModuleSpy = jest.spyOn(csvModule, 'get');
+
+// Creating an example bundle with two medication statements
+const exampleEntry = exampleCTCCSVAdverseEventModuleResponse[0];
+const expandedExampleBundle = _.cloneDeep(exampleCTCCSVAdverseEventBundle);
+expandedExampleBundle.entry.push(exampleCTCCSVAdverseEventBundle.entry[0]);
+
+// Rewired extractor for helper tests
+const CSVCTCAdverseEventExtractorRewired = rewire('../../src/extractors/CSVCTCAdverseEventExtractor.js');
+
+describe('CSVCTCAdverseEventExtractor', () => {
+  describe('formatData', () => {
+    const formatData = CSVCTCAdverseEventExtractorRewired.__get__('formatData');
+    test('should join data appropriately and throw errors when missing required properties', () => {
+      const expectedErrorString = 'The adverse event is missing an expected attribute. Adverse event code, effective date, and grade are all required.';
+      const expectedCategoryErrorString = 'A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.';
+      const localData = _.cloneDeep(exampleCTCCSVAdverseEventModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
+      // Test that valid maximal data works fine
+      expect(formatData(exampleCTCCSVAdverseEventModuleResponse, patientId)).toEqual(expect.anything());
+
+      // Test that deleting an optional value works fine
+      delete localData[0].actuality;
+      expect(formatData(exampleCTCCSVAdverseEventModuleResponse, patientId)).toEqual(expect.anything());
+
+      // Test that adding another category but not adding a corresponding categoryCodeSystem throws an error
+      localData[0].category = 'product-use-error|product-problem';
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedCategoryErrorString));
+
+      // Test that adding another category but adding a corresponding categoryCodeSystem and categoryDisplayText works fine
+      localData[0].categorycodesystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct';
+      localData[0].categorydisplaytext = 'Product Use Error|Product Problem';
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
+
+      // Test that adding another category but including syntax for default categoryCodeSystem and categoryDisplayText values works fine
+      localData[0].categorycodesystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|';
+      localData[0].categorydisplaytext = 'Product Use Error|';
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
+
+      // Test that deleting a mandatory value throws an error
+      delete localData[0].grade;
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedErrorString));
+    });
+  });
+
+  describe('get', () => {
+    test('should return bundle with a CTCAdverseEvent resource', async () => {
+      csvModuleSpy.mockReturnValue(exampleCTCCSVAdverseEventModuleResponse);
+      const data = await csvCTCAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
+      expect(data.resourceType).toEqual('Bundle');
+      expect(data.type).toEqual('collection');
+      expect(data.entry).toBeDefined();
+      expect(data.entry.length).toEqual(1);
+      expect(data.entry).toEqual(exampleCTCCSVAdverseEventBundle.entry);
+    });
+
+    test('should return empty bundle when no data available from module', async () => {
+      csvModuleSpy.mockReturnValue([]);
+      const data = await csvCTCAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
+      expect(data.resourceType).toEqual('Bundle');
+      expect(data.type).toEqual('collection');
+      expect(data.entry).toBeDefined();
+      expect(data.entry.length).toEqual(0);
+    });
+
+    test('get() should return an array of 2 when two adverse event resources are tied to a single patient', async () => {
+      exampleCTCCSVAdverseEventModuleResponse.push(exampleEntry);
+      csvModuleSpy.mockReturnValue(exampleCTCCSVAdverseEventModuleResponse);
+      const data = await csvCTCAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
+
+      expect(data.resourceType).toEqual('Bundle');
+      expect(data.type).toEqual('collection');
+      expect(data.entry).toBeDefined();
+      expect(data.entry.length).toEqual(2);
+      expect(data).toEqual(expandedExampleBundle);
+    });
+  });
+});

test/extractors/fixtures/csv-ctc-adverse-event-bundle.json

@@ -0,0 +1,85 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:adverseEventId-1",
+      "resource": {
+        "resourceType": "AdverseEvent",
+        "id": "adverseEventId-1",
+        "extension" : [
+          {
+            "url" : "http://hl7.org/fhir/us/ctcae/StructureDefinition/ctcae-grade",
+            "valueCodeableConcept" : {
+              "coding" : [
+                {
+                  "system" : "http://hl7.org/fhir/us/ctcae/CodeSystem/ctcae-grade-code-system",
+                  "code" : "1",
+                  "display" : "Mild Adverse Event"
+                }
+              ]
+            }
+          }
+        ],
+        "subject": {
+          "reference": "urn:uuid:mrn-1",
+          "type": "Patient"
+        },
+        "event": {
+          "coding": [
+            {
+              "system": "code-system",
+              "code": "109006",
+              "display": "Anxiety disorder of childhood OR adolescence"
+            }
+          ]
+        },
+        "suspectEntity": [
+          {
+            "instance": {
+              "reference": "urn:uuid:procedure-id",
+              "type": "Procedure"
+            }
+          }
+        ],
+        "seriousness": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/adverse-event-seriousness",
+              "code": "serious",
+              "display": "Serious"
+            }
+          ]
+        },
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/adverse-event-category",
+                "code": "product-use-error",
+                "display": "Product Use Error"
+              }
+            ]
+          }
+        ],
+        "severity": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/adverse-event-severity",
+              "code": "severe"
+            }
+          ]
+        },
+        "actuality": "actual",
+        "study": [
+          {
+            "reference": "urn:uuid:researchId-1",
+            "type": "ResearchStudy"
+          }
+        ],
+        "date": "1994-12-09",
+        "recordedDate": "1994-12-09"
+      }
+    }
+  ]
+}

test/extractors/fixtures/csv-ctc-adverse-event-module-response.json

@@ -0,0 +1,23 @@
+[
+  {
+    "mrn": "mrn-1",
+    "adverseeventid": "adverseEventId-1",
+    "adverseeventcode": "109006",
+    "adverseeventcodesystem": "code-system",
+    "adverseeventdisplaytext": "Anxiety disorder of childhood OR adolescence",
+    "suspectedcauseid": "procedure-id",
+    "suspectedcausetype": "Procedure",
+    "seriousness": "serious",
+    "seriousnesscodesystem": "http://terminology.hl7.org/CodeSystem/adverse-event-seriousness",
+    "seriousnessdisplaytext": "Serious",
+    "category": "product-use-error",
+    "categorycodesystem": "http://terminology.hl7.org/CodeSystem/adverse-event-category",
+    "categorydisplaytext": "Product Use Error",
+    "severity": "severe",
+    "actuality": "actual",
+    "studyid": "researchId-1",
+    "effectivedate": "12-09-1994",
+    "recordeddate": "12-09-1994",
+    "grade": "1"
+  }
+]

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

@@ -1,4 +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|product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct|http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Use Error|Product Quality|Wrong Rate,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|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|,Product Quality|,mild,potential,researchId-2,12-10-1995,12-10-1995
-789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
+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|product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct|http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Use Error|Product Quality|Wrong Rate,severe,actual,researchId-1,12-09-1994,12-09-1994,1
+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|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|,Product Quality|,mild,potential,researchId-2,12-10-1995,12-10-1995,2
+789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,,3