Tweaks to extractor and template

Author: julianxcarter

src/extractors/CSVAdverseEventExtractor.js

@@ -1,6 +1,6 @@
 const path = require('path');
 const { CSVModule } = require('../modules');
-const { generatemCODEResources } = require('../templates');
+const { generateMcodeResources } = require('../templates');
 const { Extractor } = require('./Extractor');
 const logger = require('../helpers/logger');
 const { formatDateTime } = require('../helpers/dateUtils');
@@ -21,21 +21,21 @@ function formatData(adverseEventData) {
       id: adverseEventId,
       subjectId: mrn,
       code: adverseEventCode,
-      system: adverseEventCodeSystem,
+      system: !adverseEventCodeSystem ? 'http://snomed.info/sct' : adverseEventCodeSystem,
       display: adverseEventDisplayText,
       suspectedCauseId,
       suspectedCauseType,
       seriousnessCode: seriousness,
-      seriousnessCodeSystem,
+      seriousnessCodeSystem: !seriousnessCodeSystem ? 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness' : seriousnessCodeSystem,
       seriousnessDisplayText,
       categoryCode: category,
-      categoryCodeSystem,
+      categoryCodeSystem: !categoryCodeSystem ? 'http://terminology.hl7.org/CodeSystem/adverse-event-category' : categoryCodeSystem,
       categoryDisplayText,
       severity,
-      actuality,
+      actuality: !actuality ? 'actual' : actuality,
       studyId,
       effectiveDateTime: formatDateTime(effectiveDate),
-      recordedDateTime: formatDateTime(recordedDate),
+      recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),
     };
   });
 }
@@ -55,7 +55,7 @@ class CSVAdverseEventExtractor extends Extractor {
     const adverseEventData = await this.getAdverseEventData(mrn);
     const formattedData = formatData(adverseEventData);
 
-    return generatemCODEResources('AdverseEvent', formattedData);
+    return generateMcodeResources('AdverseEvent', formattedData);
   }
 }
 

src/extractors/index.js

@@ -1,5 +1,5 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
-const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor')
+const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor');
 const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
 const { CSVCancerRelatedMedicationExtractor } = require('./CSVCancerRelatedMedicationExtractor');
 const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');

src/templates/AdverseEventTemplate.js

@@ -1,19 +1,11 @@
 const { coding, reference } = require('./snippets');
-const { ifAllArgsObj, ifSomeArgsObj } = require('../helpers/templateUtils');
+const { ifAllArgsObj, ifSomeArgsObj, ifAllArgs } = require('../helpers/templateUtils');
 
-function eventTemplate({ eventCode, eventSystem, eventDisplay }) {
-  let codeSystem = eventSystem;
-  if (!codeSystem) {
-    codeSystem = 'http://snomed.info/sct';
-  }
+function eventTemplate(eventCoding) {
   return {
     event: {
       coding: [
-        coding({
-          code: eventCode,
-          system: codeSystem,
-          display: eventDisplay,
-        }),
+        coding(eventCoding),
       ],
     },
   };
@@ -31,67 +23,50 @@ function suspectedCauseTemplate({ suspectedCauseId, suspectedCauseType }) {
 }
 
 
-function seriousnessTemplate({ seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText }) {
-  let codeSystem = seriousnessCodeSystem;
-  if (!codeSystem) {
-    codeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness';
-  }
+function seriousnessTemplate(seriousnessCoding) {
   return {
     seriousness: {
       coding: [
-        coding({
-          code: seriousnessCode,
-          system: codeSystem,
-          display: seriousnessDisplayText,
-        }),
+        coding(seriousnessCoding),
       ],
     },
   };
 }
 
-function categoryTemplate({ categoryCode, categoryCodeSystem, categoryDisplayText }) {
-  let codeSystem = categoryCodeSystem;
-  if (!codeSystem) {
-    codeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category';
-  }
+function categoryTemplate(categoryCoding) {
   return {
-    category: {
+    category: [{
       coding: [
-        coding({
-          code: categoryCode,
-          system: codeSystem,
-          display: categoryDisplayText,
-        }),
+        coding(categoryCoding),
       ],
-    },
+    }],
   };
 }
 
-function severityTemplate({ severityCode }) {
+function severityTemplate(severityCode) {
   return {
     severity: {
       coding: [
         coding({
           code: severityCode,
+          system: 'http://terminology.hl7.org/CodeSystem/adverse-event-severity',
         }),
       ],
     },
   };
 }
 
-function actualityTemplate({ actuality }) {
-  let actualityCode = actuality;
-  if (!actualityCode) {
-    actualityCode = 'https://www.hl7.org/fhir/valueset-adverse-event-actuality.html';
-  }
+function studyTemplate(studyId) {
   return {
-    actuality: {
-      coding: [
-        coding({
-          code: actualityCode,
-        }),
-      ],
-    },
+    study: [
+      reference({ id: studyId, resourceType: 'ResearchStudy' }),
+    ],
+  };
+}
+
+function recordedDateTemplate(recordedDateTime) {
+  return {
+    recordedDate: recordedDateTime,
   };
 }
 
@@ -108,14 +83,14 @@ function adverseEventTemplate({
     id,
     subject: reference({ id: subjectId, resourceType: 'Patient' }),
     ...ifSomeArgsObj(eventTemplate)({ code, system, display }),
-    ...ifAllArgsObj(suspectedCauseTemplate)({ id: suspectedCauseId, resourceType: suspectedCauseType }),
-    ...ifSomeArgsObj(seriousnessTemplate)({ seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText }),
-    ...ifSomeArgsObj(categoryTemplate)({ categoryCode, categoryCodeSystem, categoryDisplayText }),
-    ...ifAllArgsObj(severityTemplate)({ severity }),
-    ...actualityTemplate(actuality),
-    study: reference({ id: studyId, resourceType: 'ResearchStudy' }),
+    ...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),
+    ...ifSomeArgsObj(seriousnessTemplate)({ code: seriousnessCode, system: seriousnessCodeSystem, display: seriousnessDisplayText }),
+    ...ifSomeArgsObj(categoryTemplate)({ code: categoryCode, system: categoryCodeSystem, display: categoryDisplayText }),
+    ...ifAllArgs(severityTemplate)(severity),
+    actuality,
+    ...ifAllArgs(studyTemplate)(studyId),
     date: effectiveDateTime,
-    recordedDate: recordedDateTime,
+    ...ifAllArgs(recordedDateTemplate)(recordedDateTime),
   };
 }