Merge pull request #86 from mcode/cds-data-absent-reason

Parsing of 'not evaluated' status value in CDS extractor

Author: julianxcarter

src/extractors/CSVCancerDiseaseStatusExtractor.js

@@ -16,7 +16,7 @@ class CSVCancerDiseaseStatusExtractor {
     logger.debug('Reformatting disease status data from CSV into template format');
     // Check the shape of the data
     arrOfDiseaseStatusData.forEach((record) => {
-      if (!(record.mrn && record.conditionId && record.diseaseStatusCode && record.dateOfObservation)) {
+      if (!record.mrn || !record.conditionId || !record.diseaseStatusCode || !record.dateOfObservation) {
         throw new Error('DiseaseStatusData missing an expected property: mrn, conditionId, diseaseStatusCode, and dateOfObservation are required.');
       }
     });

src/templates/CancerDiseaseStatusTemplate.js

@@ -1,4 +1,10 @@
-const { coding, extensionArr, reference, valueX } = require('./snippets');
+const {
+  coding,
+  extensionArr,
+  reference,
+  valueX,
+  dataAbsentReasonExtension,
+} = require('./snippets');
 
 function evidenceTemplate({ evidence }) {
   if (!evidence || evidence.length === 0) return [];
@@ -23,6 +29,11 @@ function subjectTemplate({ subject }) {
   };
 }
 
+function valueTemplate({ code, display, system }) {
+  if (code === '709137006') return { valueCodeableConcept: extensionArr(dataAbsentReasonExtension('not-asked')) };
+  return valueX({ code, display, system }, 'valueCodeableConcept');
+}
+
 function cancerDiseaseStatusTemplate({
   id,
   status,
@@ -32,7 +43,7 @@ function cancerDiseaseStatusTemplate({
   value,
   evidence,
 }) {
-  if (!(id && status && effectiveDateTime && condition && subject && value)) {
+  if (!id || !status || !effectiveDateTime || !condition || !subject || !value) {
     throw Error('Trying to render a CancerDiseaseStatusTemplate, but a required argument is missing; ensure that id, status, effectiveDateTime, condition, subject, and value are all present');
   }
 
@@ -70,7 +81,7 @@ function cancerDiseaseStatusTemplate({
     effectiveDateTime,
     ...focusTemplate({ condition }),
     ...subjectTemplate({ subject }),
-    ...valueX(value, 'valueCodeableConcept'),
+    ...valueTemplate(value),
   };
 }
 

test/templates/cancerDiseaseStatus.test.js

@@ -46,9 +46,9 @@ describe('test CancerDiseaseStatus template', () => {
       id: 'CancerDiseaseStatus-fixture',
       status: 'final',
       value: {
-        code: '385633008',
+        code: '709137006',
         system: 'http://snomed.info/sct',
-        display: 'Improving',
+        display: 'not evaluated',
       },
       subject: {
         id: '123-example-patient',

test/templates/fixtures/minimal-disease-status-resource.json

@@ -41,11 +41,10 @@
     },
     "effectiveDateTime" : "1994-12-09T09:07:00Z",
     "valueCodeableConcept": {
-      "coding": [
+      "extension": [
         {
-          "system": "http://snomed.info/sct",
-          "code": "385633008",
-          "display": "Improving"
+          "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+          "valueCode": "not-asked"
         }
       ]
     }