not-evaluated status parsing

Author: julianxcarter

src/extractors/CSVCancerDiseaseStatusExtractor.js

@@ -23,7 +23,7 @@ class CSVCancerDiseaseStatusExtractor {
     const evidenceDelimiter = '|';
     return arrOfDiseaseStatusData.map((record) => ({
       status: record.observationStatus || 'final',
-      value: {
+      value: record.observationStatus === 'not-evaluated' ? null : {
         code: record.diseaseStatusCode,
         system: 'http://snomed.info/sct',
         display: record.diseaseStatusText ? record.diseaseStatusText : getDiseaseStatusDisplay(record.diseaseStatusCode, this.implementation),

src/templates/CancerDiseaseStatusTemplate.js

@@ -1,4 +1,4 @@
-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 +23,11 @@ function subjectTemplate({ subject }) {
   };
 }
 
+function valueTemplate(valueObj) {
+  if (valueObj === null) return { valueCodeableConcept: extensionArr(dataAbsentReasonExtension('not-asked')) };
+  return valueX(valueObj, 'valueCodeableConcept');
+}
+
 function cancerDiseaseStatusTemplate({
   id,
   status,
@@ -32,7 +37,7 @@ function cancerDiseaseStatusTemplate({
   value,
   evidence,
 }) {
-  if (!(id && status && effectiveDateTime && condition && subject && value)) {
+  if (!id || !status || !effectiveDateTime || !condition || !subject || (!value && status !== 'not-evaluated')) {
     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');
   }
 
@@ -45,7 +50,7 @@ function cancerDiseaseStatusTemplate({
       ],
     },
     ...extensionArr(...evidenceTemplate({ evidence })),
-    status,
+    status: status === 'not-evaluated' ? 'final' : status,
     category: [
       {
         coding: [
@@ -70,7 +75,7 @@ function cancerDiseaseStatusTemplate({
     effectiveDateTime,
     ...focusTemplate({ condition }),
     ...subjectTemplate({ subject }),
-    ...valueX(value, 'valueCodeableConcept'),
+    ...valueTemplate(value),
   };
 }
 

test/templates/cancerDiseaseStatus.test.js

@@ -44,12 +44,8 @@ describe('test CancerDiseaseStatus template', () => {
     const MINIMAL_DATA = {
       // Minimal amount of data to be accepted, evidence is excluded
       id: 'CancerDiseaseStatus-fixture',
-      status: 'final',
-      value: {
-        code: '385633008',
-        system: 'http://snomed.info/sct',
-        display: 'Improving',
-      },
+      status: 'not-evaluated',
+      value: null,
       subject: {
         id: '123-example-patient',
         name: 'Mr. Patient Example',

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"
         }
       ]
     }