Participation Extension added

docs/ctc-adverse-event.csv

@@ -1,4 +1,4 @@
-mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventCodeVersion,adverseEventDisplayText,adverseEventText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade,expectation,resolvedDate,seriousnessOutcome
-mrn-full-example,example-id-1,event-code,code-system,code-version,code-display,event-text,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,id,1994-12-09,1994-12-09,1,expectation-code,YYYY-MM-DD,seriousness-outcome-code
-mrn-two-category-example,example-id-2,event-code,code-system,code-version,code-display,event-text,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,id,1994-12-09,1994-12-09,1,expectation-code,YYYY-MM-DD,seriousness-outcome-code
-mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,1994-12-09,,1,,,,,
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventCodeVersion,adverseEventDisplayText,adverseEventText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade,expectation,resolvedDate,seriousnessOutcome,actor,functionCode
+mrn-full-example,example-id-1,event-code,code-system,code-version,code-display,event-text,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,id,1994-12-09,1994-12-09,1,expectation-code,YYYY-MM-DD,seriousness-outcome-code,practitioner-id,function-code
+mrn-two-category-example,example-id-2,event-code,code-system,code-version,code-display,event-text,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,id,1994-12-09,1994-12-09,1,expectation-code,YYYY-MM-DD,seriousness-outcome-code,practitioner-id,
+mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,1994-12-09,,1,,,,,,

src/extractors/CSVCTCAdverseEventExtractor.js

@@ -34,10 +34,14 @@ function formatData(adverseEventData, patientId) {
       expectation,
       resolveddate: resolvedDate,
       seriousnessoutcome: seriousnessOutcome,
+      actor,
+      functioncode: functionCode,
     } = data;
 
     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.');
+    } else if (functionCode && !actor) {
+      throw new Error('The adverse event is missing an expected attribute. Adverse event actor is a required element when a functionCode value is included.');
     }
 
     const categoryCodes = category.split('|');
@@ -90,6 +94,16 @@ function formatData(adverseEventData, patientId) {
           'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
         ),
       },
+      actor,
+      functionCode: !functionCode ? null : {
+        code: functionCode,
+        system: 'http://terminology.hl7.org/CodeSystem/v3-ParticipationType',
+        display: getDisplayFromConcept(
+          path.resolve(__dirname, '..', 'helpers', 'valueSets', 'adverse-event-participant-function-value-set.json'),
+          functionCode,
+          'http://terminology.hl7.org/CodeSystem/v3-ParticipationType',
+        ),
+      },
     };
   });
 }

src/helpers/valueSets/adverse-event-participant-function-value-set.json

@@ -0,0 +1,67 @@
+{
+  "resourceType": "ValueSet",
+  "id": "adverse-event-participant-function-value-set",
+  "text": {
+    "status": "extensions",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><ul><li>Include these codes as defined in <a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html\"><code>http://terminology.hl7.org/CodeSystem/v3-ParticipationType</code></a><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td><a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html#v3-ParticipationType-INF\">INF</a></td><td>Informant</td><td>A source of reported information (e.g., a next of kin who answers questions about the patient's history). For history questions, the patient is logically an informant, yet the informant of history questions is implicitly the subject.</td></tr><tr><td><a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html#v3-ParticipationType-PART\">PART</a></td><td>Participation</td><td>Indicates that the target of the participation is involved in some manner in the act, but does not qualify how.</td></tr><tr><td><a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html#v3-ParticipationType-WIT\">WIT</a></td><td>Witness</td><td>Only with service events. A person witnessing the action happening without doing anything. A witness is not necessarily aware, much less approves of anything stated in the service event. Example for a witness is students watching an operation or an advanced directive witness.</td></tr><tr><td><a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html#v3-ParticipationType-AUT\">AUT</a></td><td>Author (originator)</td><td>**Definition:** A party that originates the Act and therefore has responsibility for the information given in the Act and ownership of this Act.<br/><br/>**Example:** the report writer, the person writing the act definition, the guideline author, the placer of an order, the EKG cart (device) creating a report etc. Every Act should have an author. Authorship is regardless of mood always actual authorship.<br/><br/>Examples of such policies might include:<br/><br/> *  The author and anyone they explicitly delegate may update the report;<br/> *  All administrators within the same clinic may cancel and reschedule appointments created by other administrators within that clinic;<br/><br/>A party that is neither an author nor a party who is extended authorship maintenance rights by policy, may only amend, reverse, override, replace, or follow up in other ways on this Act, whereby the Act remains intact and is linked to another Act authored by that other party.</td></tr><tr><td><a href=\"http://terminology.hl7.org/2.1.0/CodeSystem-v3-ParticipationType.html#v3-ParticipationType-AUTHEN\">AUTHEN</a></td><td>Authenticator</td><td>A verifier who attests to the accuracy of an act, but who does not have privileges to legally authenticate the act. An example would be a resident physician who sees a patient and dictates a note, then later signs it. Their signature constitutes an authentication.</td></tr></table></li></ul></div>"
+  },
+  "url": "http://hl7.org/fhir/us/ctcae/ValueSet/adverse-event-participant-function-value-set",
+  "version": "0.0.1",
+  "name": "AdverseEventParticipantFunctionVS",
+  "title": "Adverse Event Participant Function",
+  "status": "active",
+  "date": "2021-12-03T16:46:43+00:00",
+  "publisher": "HL7 International Clinical Interoperability Council",
+  "contact": [
+    {
+      "name": "HL7 International Clinical Interoperability Council",
+      "telecom": [
+        {
+          "system": "url",
+          "value": "http://www.mcodeinitiative.org"
+        }
+      ]
+    }
+  ],
+  "description": "This value set includes codes that describe the type of involvement of the actor in the adverse event",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "urn:iso:std:iso:3166",
+          "code": "US",
+          "display": "United States of America"
+        }
+      ]
+    }
+  ],
+  "compose": {
+    "include": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+        "concept": [
+          {
+            "code": "INF",
+            "display": "Informant"
+          },
+          {
+            "code": "PART",
+            "display": "Participation"
+          },
+          {
+            "code": "WIT",
+            "display": "Witness"
+          },
+          {
+            "code": "AUT",
+            "display": "Author (originator)"
+          },
+          {
+            "code": "AUTHEN",
+            "display": "Authenticator"
+          }
+        ]
+      }
+    ]
+  }
+}

src/templates/CTCAdverseEventTemplate.js

@@ -102,13 +102,47 @@ function seriousnessOutcomeTemplate(seriousnessOutcome) {
   };
 }
 
+function participantFunctionTemplate(functionCode) {
+  return {
+    url: 'function',
+    valueCodeableConcept: {
+      coding: [
+        coding(functionCode),
+      ],
+    },
+  };
+}
+
+function participantActorTemplate(actor) {
+  return {
+    url: 'actor',
+    valueReference: {
+      ...reference({ id: actor }),
+    },
+  };
+}
+
+function participantTemplate(actor, functionCode) {
+  return {
+    url: 'http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-participant',
+    ...extensionArr(
+      functionCode ? participantFunctionTemplate(functionCode) : null,
+      participantActorTemplate(actor),
+    ),
+  };
+}
+
 
 function CTCAdverseEventTemplate({
   id, subjectId, code, system, version, display, text, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
-  studyId, effectiveDateTime, recordedDateTime, grade, resolvedDate, expectation, seriousnessOutcome,
+  studyId, effectiveDateTime, recordedDateTime, grade, resolvedDate, expectation, seriousnessOutcome, actor, functionCode,
 }) {
   if (!(subjectId && code && system && effectiveDateTime && grade)) {
-    throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code, system, grade, and effectiveDateTime are all present');
+    throw Error('Trying to render an AdverseEventTemplate, but a required argument is missing; ensure that subjectId, code, system, grade, and effectiveDateTime are all present');
+  }
+
+  if (functionCode && !actor) {
+    throw Error('Trying to render an AdverseEventTemplate, but a required argument is missing; actor is a required value when functionCode is included');
   }
 
   return {
@@ -119,6 +153,7 @@ function CTCAdverseEventTemplate({
       resolvedDate ? resolvedDateTemplate(resolvedDate) : null,
       expectation ? expectationTemplate(expectation) : null,
       seriousnessOutcome ? seriousnessOutcomeTemplate(seriousnessOutcome) : null,
+      actor ? participantTemplate(actor, functionCode) : null,
     ),
     subject: reference({ id: subjectId, resourceType: 'Patient' }),
     ...ifSomeArgs(eventTemplate)({ code, system, version, display }, text),

test/extractors/CSVCTCAdverseEventextractor.test.js

@@ -36,6 +36,7 @@ describe('CSVCTCAdverseEventExtractor', () => {
     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 expectedActorErrorString = 'The adverse event is missing an expected attribute. Adverse event actor is a required element when a functionCode value is included.';
       const localData = _.cloneDeep(exampleCTCCSVAdverseEventModuleResponse);
       const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
@@ -60,6 +61,15 @@ describe('CSVCTCAdverseEventExtractor', () => {
       localData[0].categorydisplaytext = 'Product Use Error|';
       expect(formatData(localData, patientId)).toEqual(expect.anything());
 
+      // Test that deleting the actor value but leaving functionCode will throw an error
+      delete localData[0].actor;
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedActorErrorString));
+
+      // Test that deleting the functionCode value works fine
+      localData[0].actor = 'practitioner-id';
+      delete localData[0].functioncode;
+      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));

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

@@ -47,6 +47,29 @@
                 }
               ]
             }
+          },
+          {
+            "url": "http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-participant",
+            "extension": [
+              {
+                "url": "function",
+                "valueCodeableConcept": {
+                  "coding": [
+                    {
+                      "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+                      "code": "INF",
+                      "display": "Informant"
+                    }
+                  ]
+                }
+              },
+              {
+                "url": "actor",
+                "valueReference": {
+                    "reference": "urn:uuid:practitioner-id"
+                }
+              }
+            ]
           }
         ],
         "subject": {

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

@@ -21,6 +21,8 @@
     "grade": "1",
     "resolveddate": "2021-12-01",
     "seriousnessoutcome": "C113380",
-    "expectation": "C41333"
+    "expectation": "C41333",
+    "actor": "practitioner-id",
+    "functioncode": "INF"
   }
 ]

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

@@ -1,4 +1,4 @@
-mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventCodeVersion,adverseEventDisplayText,adverseEventText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade,expectation,resolvedDate,seriousnessOutcome
-123,adverseEventId-1,10012174,http://terminology.hl7.org/CodeSystem/MDRAE,20.0,Dehydration,DHN IV given,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,researchId-1,12-09-1994,12-09-1994,1,C41333,2021-12-01,C113380
-456,adverseEventId-2,C143283,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl,20.0,Anemia,AIHA NGTD,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|,researchId-2,12-10-1995,12-10-1995,2,C41333,2020-10-02,C113380
-789,adverseEventId-3,150003,,,,,,,,,,product-use-error,,,,12-09-1994,,3,,,
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventCodeVersion,adverseEventDisplayText,adverseEventText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade,expectation,resolvedDate,seriousnessOutcome,actor,functionCode
+123,adverseEventId-1,10012174,http://terminology.hl7.org/CodeSystem/MDRAE,20.0,Dehydration,DHN IV given,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,researchId-1,12-09-1994,12-09-1994,1,C41333,2021-12-01,C113380,practitioner-1,PART
+456,adverseEventId-2,C143283,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl,20.0,Anemia,AIHA NGTD,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|,researchId-2,12-10-1995,12-10-1995,2,C41333,2020-10-02,C113380,practitioner-2,
+789,adverseEventId-3,150003,,,,,,,,,,product-use-error,,,,12-09-1994,,3,,,,,

test/templates/ctcAdverseEvent.test.js

@@ -33,6 +33,12 @@ const VALID_DATA = {
     system: 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
     display: 'Expected Adverse Event',
   },
+  actor: 'practitioner-id',
+  functionCode: {
+    code: 'PART',
+    system: 'http://terminology.hl7.org/CodeSystem/v3-ParticipationType',
+    display: 'Participation',
+  },
 };
 
 const MINIMAL_DATA = {
@@ -90,13 +96,20 @@ const INVALID_DATA = {
     system: 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
     display: 'Expected Adverse Event',
   },
+  actor: 'practitioner-id',
+  functionCode: {
+    code: 'PART',
+    system: 'http://terminology.hl7.org/CodeSystem/v3-ParticipationType',
+    display: 'Participation',
+  },
 };
 
 describe('test Adverse Event template', () => {
   test('valid data passed into template should generate FHIR resource', () => {
     const generatedAdverseEvent = CTCAdverseEventTemplate(VALID_DATA);
 
     expect(generatedAdverseEvent).toEqual(maximalValidExampleAdverseEvent);
+
     expect(isValidFHIR(generatedAdverseEvent)).toBeTruthy();
   });
 
@@ -137,4 +150,9 @@ describe('test Adverse Event template', () => {
   test('invalid data should throw an error', () => {
     expect(() => CTCAdverseEventTemplate(INVALID_DATA)).toThrow(Error);
   });
+
+  test('Otherwise valid data including the functionCode but not an actor should throw an error', () => {
+    delete VALID_DATA.actor;
+    expect(() => CTCAdverseEventTemplate(VALID_DATA)).toThrow(Error);
+  });
 });

test/templates/fixtures/maximal-ctc-adverse-event-resource.json

@@ -45,6 +45,29 @@
           }
         ]
       }
+    },
+    {
+      "url": "http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-participant",
+      "extension": [
+        {
+          "url": "function",
+          "valueCodeableConcept": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+                "code": "PART",
+                "display": "Participation"
+              }
+            ]
+          }
+        },
+        {
+          "url": "actor",
+          "valueReference": {
+              "reference": "urn:uuid:practitioner-id"
+          }
+        }
+      ]
     }
   ],
   "event": {