Support for new simple extensions added to the CTC AE Extractor

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
-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,
-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|category-code,code-system|code-system,category-display|category-display,id,1994-12-09,1994-12-09,3
-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
+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,,,,,

src/extractors/CSVCTCAdverseEventExtractor.js

@@ -1,8 +1,10 @@
+const path = require('path');
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { getPatientFromContext } = require('../helpers/contextUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
+const { getDisplayFromConcept } = require('../helpers/valueSetUtils');
 const { ctcAEGradeCodeToTextLookup } = require('../helpers/lookups/ctcAdverseEventLookup');
 const logger = require('../helpers/logger');
 
@@ -29,6 +31,9 @@ function formatData(adverseEventData, patientId) {
       effectivedate: effectiveDate,
       recordeddate: recordedDate,
       grade,
+      expectation,
+      resolveddate: resolvedDate,
+      seriousnessoutcome: seriousnessOutcome,
     } = data;
 
     if (!(adverseEventCode && effectiveDate && grade)) {
@@ -43,7 +48,6 @@ function formatData(adverseEventData, patientId) {
       throw new Error('A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.');
     }
 
-
     return {
       ...(adverseEventId && { id: adverseEventId }),
       subjectId: patientId,
@@ -67,6 +71,25 @@ function formatData(adverseEventData, patientId) {
       effectiveDateTime: formatDateTime(effectiveDate),
       recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),
       grade: { code: grade, display: ctcAEGradeCodeToTextLookup[grade] },
+      resolvedDate: !resolvedDate ? null : formatDateTime(resolvedDate),
+      expectation: !expectation ? null : {
+        code: expectation,
+        system: 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
+        display: getDisplayFromConcept(
+          path.resolve(__dirname, '..', 'helpers', 'valueSets', 'adverse-event-expectation-value-set.json'),
+          expectation,
+          'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
+        ),
+      },
+      seriousnessOutcome: !seriousnessOutcome ? null : {
+        code: seriousnessOutcome,
+        system: 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
+        display: getDisplayFromConcept(
+          path.resolve(__dirname, '..', 'helpers', 'valueSets', 'adverse-event-seriousness-outcome-value-set.json'),
+          seriousnessOutcome,
+          'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl',
+        ),
+      },
     };
   });
 }

src/helpers/valueSetUtils.js

@@ -35,6 +35,37 @@ function loadVs(absoluteFilepath, typeOfVS) {
   }
 }
 
+function getConceptFromVSExpansion(valueSet, code, codeSystem) {
+  if (!code || !codeSystem || !valueSet) return undefined;
+  return valueSet.expansion.contains.find((containsItem) => containsItem
+      && containsItem.system
+      && code === containsItem.code
+      && codeSystem === containsItem.system);
+}
+
+function getConceptFromVSCompose(valueSet, code, codeSystem) {
+  if (!code || !codeSystem || !valueSet) return undefined;
+  const includeItem = valueSet.compose.include.find((item) => item
+      && item.system
+      && item.system === codeSystem
+      && item.concept);
+  if (!includeItem) return undefined;
+  return includeItem.concept.find((concept) => concept.code === code);
+}
+
+function getDisplayFromConcept(pathToValueSet, code, codeSystem) {
+  if (!code || !codeSystem || !pathToValueSet) return undefined;
+  const valueSet = loadVs(pathToValueSet, vsTypes.json);
+  let concept;
+  if (valueSet.expansion) {
+    // If valueSet has expansion, we only need to check these codes
+    concept = getConceptFromVSExpansion(valueSet, code, codeSystem);
+    return (concept && concept.display) ? concept.display : undefined;
+  }
+  concept = getConceptFromVSCompose(valueSet, code, codeSystem);
+  return (concept && concept.display) ? concept.display : undefined;
+}
+
 /**
  * Check if code is in value set
  * @param {string} code value to look for in a valueset
@@ -43,22 +74,21 @@ function loadVs(absoluteFilepath, typeOfVS) {
  * @param {string} typeOfVS the file type of the value set to be searched
  * @return {boolean} true if condition is in valueSet's compose block or expansion block
  */
-const checkCodeInVs = (code, codeSystem, valueSetFilePath, typeOfVS = vsTypes.json) => {
+const checkCodeInVs = (
+  code,
+  codeSystem,
+  valueSetFilePath,
+  typeOfVS = vsTypes.json,
+) => {
   const valueSet = loadVs(valueSetFilePath, typeOfVS);
   let inVSExpansion = false;
   let inVSCompose = false;
   if (valueSet.expansion) {
     // If valueSet has expansion, we only need to check these codes
-    inVSExpansion = valueSet.expansion.contains.some((containsItem) => {
-      if (!code || !codeSystem || !containsItem || !containsItem.system) return false;
-      return code === containsItem.code && codeSystem === containsItem.system;
-    });
+    inVSExpansion = (getConceptFromVSExpansion(valueSet, code, codeSystem) !== undefined);
   } else {
     // Checks if code is in any of the valueSet.compose.include arrays
-    inVSCompose = valueSet.compose.include.some((includeItem) => {
-      if (!code || !codeSystem || !includeItem || !includeItem.system || !includeItem.concept) return false;
-      return includeItem.system === codeSystem && includeItem.concept.map((concept) => concept.code).includes(code);
-    });
+    inVSCompose = (getConceptFromVSCompose(valueSet, code, codeSystem) !== undefined);
   }
   return inVSCompose || inVSExpansion;
 };
@@ -68,4 +98,7 @@ module.exports = {
   loadJsonVs,
   loadVs,
   checkCodeInVs,
+  getDisplayFromConcept,
+  getConceptFromVSCompose,
+  getConceptFromVSExpansion,
 };

src/helpers/valueSets/adverse-event-expectation-value-set.json

@@ -0,0 +1,55 @@
+{
+  "resourceType": "ValueSet",
+  "id": "adverse-event-expectation-value-set",
+  "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><ul><li>Include these codes as defined in <code>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl</code><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td>C41333</td><td>Expected Adverse Event</td></tr><tr><td>C41334</td><td>Unexpected Adverse Event</td></tr></table></li></ul></div>"
+  },
+  "url": "http://hl7.org/fhir/us/ctcae/ValueSet/adverse-event-expectation-value-set",
+  "version": "0.0.1",
+  "name": "AdverseEventExpectationVS",
+  "title": "Adverse Event Expectation Value Set",
+  "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": "An expected adverse event is one whose nature and severity have been previously observed, identified in nature, severity, or frequency, and documented in the investigator brochure, investigational plan, protocol, current consent form, scientific publication, or in other relevant and reliable document. An unexpected adverse event is one that has not been previously observed, whether or not the event was anticipated because of the pharmacologic properties of the study agent or the nature of the medical procedure. This includes events that are more serious than expected or occur more frequently than expected, particularly, any adverse experience, the nature, severity or frequency of which is not consistent with the product label, or with the current investigator brochure for investigational agent; or with the risk information described in the investigational plan or protocol or consent form (NCI Thesaurus).",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "urn:iso:std:iso:3166",
+          "code": "US",
+          "display": "United States of America"
+        }
+      ]
+    }
+  ],
+  "compose": {
+    "include": [
+      {
+        "system": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
+        "concept": [
+          {
+            "code": "C41333",
+            "display": "Expected Adverse Event"
+          },
+          {
+            "code": "C41334",
+            "display": "Unexpected Adverse Event"
+          }
+        ]
+      }
+    ]
+  }
+}

src/helpers/valueSets/adverse-event-seriousness-outcome-value-set.json

@@ -0,0 +1,70 @@
+{
+  "resourceType": "ValueSet",
+  "id": "adverse-event-seriousness-outcome-value-set",
+  "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><ul><li>Include these codes as defined in <code>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl</code><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td>C84266</td><td>Life Threatening Adverse Event</td></tr><tr><td>C48275</td><td>Death Related to Adverse Event</td></tr><tr><td>C113380</td><td>Disabling Adverse Event</td></tr><tr><td>C83052</td><td>Adverse Event associated with Hospitalization</td></tr><tr><td>C2849</td><td>Congenital Abnormality</td></tr><tr><td>C52668</td><td>Intervention Required</td></tr></table></li></ul></div>"
+  },
+  "url": "http://hl7.org/fhir/us/ctcae/ValueSet/adverse-event-seriousness-outcome-value-set",
+  "version": "0.0.1",
+  "name": "AdverseEventSeriousnessOutcomeVS",
+  "title": "Adverse Event Seriousness Outcome Value Set",
+  "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": "The outcome of a serious adverse event",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "urn:iso:std:iso:3166",
+          "code": "US",
+          "display": "United States of America"
+        }
+      ]
+    }
+  ],
+  "compose": {
+    "include": [
+      {
+        "system": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
+        "concept": [
+          {
+            "code": "C84266",
+            "display": "Life Threatening Adverse Event"
+          },
+          {
+            "code": "C48275",
+            "display": "Death Related to Adverse Event"
+          },
+          {
+            "code": "C113380",
+            "display": "Disabling Adverse Event"
+          },
+          {
+            "code": "C83052",
+            "display": "Adverse Event associated with Hospitalization"
+          },
+          {
+            "code": "C2849",
+            "display": "Congenital Abnormality"
+          },
+          {
+            "code": "C52668",
+            "display": "Intervention Required"
+          }
+        ]
+      }
+    ]
+  }}

src/templates/CTCAdverseEventTemplate.js

@@ -1,4 +1,4 @@
-const { coding, reference, extensionArr } = require('./snippets');
+const { coding, reference, extensionArr, valueX } = require('./snippets');
 const {
   ifAllArgsObj, ifSomeArgsObj, ifAllArgs, ifSomeArgs, ifSomeArgsArr,
 } = require('../helpers/templateUtils');
@@ -73,9 +73,39 @@ function gradeTemplate(grade) {
   };
 }
 
+function resolvedDateTemplate(resolvedDate) {
+  return {
+    url: 'http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-resolved-date',
+    ...valueX(resolvedDate, 'valueDateTime'),
+  };
+}
+
+function expectationTemplate(expectation) {
+  return {
+    url: 'http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-expectation',
+    valueCodeableConcept: {
+      coding: [
+        coding(expectation),
+      ],
+    },
+  };
+}
+
+function seriousnessOutcomeTemplate(seriousnessOutcome) {
+  return {
+    url: 'http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-seriousness-outcome',
+    valueCodeableConcept: {
+      coding: [
+        coding(seriousnessOutcome),
+      ],
+    },
+  };
+}
+
+
 function CTCAdverseEventTemplate({
   id, subjectId, code, system, version, display, text, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
-  studyId, effectiveDateTime, recordedDateTime, grade,
+  studyId, effectiveDateTime, recordedDateTime, grade, resolvedDate, expectation, seriousnessOutcome,
 }) {
   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');
@@ -84,7 +114,12 @@ function CTCAdverseEventTemplate({
   return {
     resourceType: 'AdverseEvent',
     id,
-    ...extensionArr(gradeTemplate(grade)),
+    ...extensionArr(
+      gradeTemplate(grade),
+      resolvedDate ? resolvedDateTemplate(resolvedDate) : null,
+      expectation ? expectationTemplate(expectation) : null,
+      seriousnessOutcome ? seriousnessOutcomeTemplate(seriousnessOutcome) : null,
+    ),
     subject: reference({ id: subjectId, resourceType: 'Patient' }),
     ...ifSomeArgs(eventTemplate)({ code, system, version, display }, text),
     ...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),

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

@@ -19,6 +19,34 @@
                 }
               ]
             }
+          },
+          {
+            "url": "http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-resolved-date",
+            "valueDateTime": "2021-12-01"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-expectation",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
+                  "code": "C41333",
+                  "display": "Expected Adverse Event"
+                }
+              ]
+            }
+          },
+          {
+            "url": "http://hl7.org/fhir/us/ctcae/StructureDefinition/adverse-event-seriousness-outcome",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
+                  "code": "C113380",
+                  "display": "Disabling Adverse Event"
+                }
+              ]
+            }
           }
         ],
         "subject": {

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

@@ -18,6 +18,9 @@
     "studyid": "researchId-1",
     "effectivedate": "12-09-1994",
     "recordeddate": "12-09-1994",
-    "grade": "1"
+    "grade": "1",
+    "resolveddate": "2021-12-01",
+    "seriousnessoutcome": "C113380",
+    "expectation": "C41333"
   }
 ]