Removing severity and fixing actuality to 'actual'

docs/ctc-adverse-event.csv

@@ -1,4 +1,4 @@
-mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
-mrn-full-example,example-id-1,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,mild,actual,id,1994-12-09,1994-12-09,1,
-mrn-two-category-example,example-id-2,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code|category-code,code-system|code-system,category-display|category-display,mild,actual,id,1994-12-09,1994-12-09,3
-mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,,1
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade
+mrn-full-example,example-id-1,event-code,code-system,code-display,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-display,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

src/extractors/CSVCTCAdverseEventExtractor.js

@@ -23,8 +23,6 @@ function formatData(adverseEventData, patientId) {
       category,
       categorycodesystem: categoryCodeSystem,
       categorydisplaytext: categoryDisplayText,
-      severity,
-      actuality,
       studyid: studyId,
       effectivedate: effectiveDate,
       recordeddate: recordedDate,
@@ -61,8 +59,6 @@ function formatData(adverseEventData, patientId) {
         if (categoryDisplays[index]) categoryCoding.display = categoryDisplays[index];
         return categoryCoding;
       }),
-      severity,
-      actuality: !actuality ? 'actual' : actuality,
       studyId,
       effectiveDateTime: formatDateTime(effectiveDate),
       recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),

src/templates/CTCAdverseEventTemplate.js

@@ -45,19 +45,6 @@ function categoryArrayTemplate(categoryArr) {
   return { category };
 }
 
-function severityTemplate(severityCode) {
-  return {
-    severity: {
-      coding: [
-        coding({
-          code: severityCode,
-          system: 'http://terminology.hl7.org/CodeSystem/adverse-event-severity',
-        }),
-      ],
-    },
-  };
-}
-
 function studyTemplate(studyId) {
   return {
     study: [
@@ -85,9 +72,9 @@ function gradeTemplate(grade) {
 
 function CTCAdverseEventTemplate({
   id, subjectId, code, system, display, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
-  severity, actuality, studyId, effectiveDateTime, recordedDateTime, grade,
+  studyId, effectiveDateTime, recordedDateTime, grade,
 }) {
-  if (!(subjectId && code && system && effectiveDateTime && actuality && grade)) {
+  if (!(subjectId && code && system && effectiveDateTime && grade)) {
     throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code, system, actuality, grade, and effectiveDateTime are all present');
   }
 
@@ -100,8 +87,7 @@ function CTCAdverseEventTemplate({
     ...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),
     ...ifSomeArgsObj(seriousnessTemplate)({ code: seriousnessCode, system: seriousnessCodeSystem, display: seriousnessDisplayText }),
     ...ifSomeArgsArr(categoryArrayTemplate)(category),
-    ...ifAllArgs(severityTemplate)(severity),
-    actuality,
+    actuality: 'actual',
     ...ifAllArgs(studyTemplate)(studyId),
     date: effectiveDateTime,
     ...ifAllArgs(recordedDateTemplate)(recordedDateTime),

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

@@ -62,14 +62,6 @@
             ]
           }
         ],
-        "severity": {
-          "coding": [
-            {
-              "system": "http://terminology.hl7.org/CodeSystem/adverse-event-severity",
-              "code": "severe"
-            }
-          ]
-        },
         "actuality": "actual",
         "study": [
           {

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

@@ -13,8 +13,6 @@
     "category": "product-use-error",
     "categorycodesystem": "http://terminology.hl7.org/CodeSystem/adverse-event-category",
     "categorydisplaytext": "Product Use Error",
-    "severity": "severe",
-    "actuality": "actual",
     "studyid": "researchId-1",
     "effectivedate": "12-09-1994",
     "recordeddate": "12-09-1994",

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

@@ -1,4 +1,4 @@
-mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
-123,adverseEventId-1,109006,code-system,Anxiety disorder of childhood OR adolescence,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,severe,actual,researchId-1,12-09-1994,12-09-1994,1
-456,adverseEventId-2,134006,http://snomed.info/sct,Decreased hair growth,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|,mild,potential,researchId-2,12-10-1995,12-10-1995,2
-789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,,3
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade
+123,adverseEventId-1,109006,code-system,Anxiety disorder of childhood OR adolescence,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
+456,adverseEventId-2,134006,http://snomed.info/sct,Decreased hair growth,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
+789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,12-09-1994,,3

test/templates/ctcAdverseEvent.test.js

@@ -16,21 +16,18 @@ const VALID_DATA = {
   seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
   seriousnessDisplayText: 'Serious',
   category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category', display: 'Product Use Error' }],
-  severity: 'severe',
-  actuality: 'actual',
   studyId: 'researchId-1',
   effectiveDateTime: '1994-12-09',
   recordedDateTime: '1994-12-09',
   grade: { code: '2', display: 'Moderate Adverse Event' },
 };
 
 const MINIMAL_DATA = {
-  // Only include 'id', 'subjectId', 'code', 'system', 'actuality', 'grade', and 'effectiveDateTime' fields which are required
+  // Only include 'id', 'subjectId', 'code', 'system', 'grade', and 'effectiveDateTime' fields which are required
   subjectId: 'mrn-1',
   code: '109006',
   system: 'code-system',
   effectiveDateTime: '1994-12-09',
-  actuality: 'actual',
   id: 'adverseEventId-1',
   grade: { code: '2', display: 'Moderate Adverse Event' },
   display: null,
@@ -40,19 +37,17 @@ const MINIMAL_DATA = {
   seriousnessCodeSystem: null,
   seriousnessDisplayText: null,
   category: [null],
-  severity: null,
   studyId: null,
   recordedDateTime: null,
 };
 
 
 const INVALID_DATA = {
-  // Omitting 'subjectId', 'code', 'system', 'actuality', and 'effectiveDateTime' fields which are required
+  // Omitting 'subjectId', 'code', 'system', and 'effectiveDateTime' fields which are required
   subjectId: null,
   code: null,
   system: null,
   effectiveDateTime: null,
-  actuality: null,
   grade: null,
   id: 'adverseEventId-1',
   display: 'Anxiety disorder of childhood OR adolescence',
@@ -62,7 +57,6 @@ const INVALID_DATA = {
   seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
   seriousnessDisplayText: 'Serious',
   category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category' }],
-  severity: 'severe',
   studyId: 'researchId-1',
   recordedDateTime: '1994-12-09',
 };
@@ -92,7 +86,6 @@ describe('test Adverse Event template', () => {
       seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
       seriousnessDisplayText: 'Serious',
       category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category' }],
-      severity: 'severe',
       studyId: 'researchId-1',
       recordedDateTime: '1994-12-09',
     };
@@ -102,7 +95,6 @@ describe('test Adverse Event template', () => {
       code: '109006',
       system: 'code-system',
       effectiveDateTime: '1994-12-09',
-      actuality: 'actual',
       grade: { code: '2', display: 'Moderate Adverse Event' },
     };
 

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

@@ -56,14 +56,6 @@
       ]
     }
   ],
-  "severity": {
-    "coding": [
-      {
-        "system": "http://terminology.hl7.org/CodeSystem/adverse-event-severity",
-        "code": "severe"
-      }
-    ]
-  },
   "actuality": "actual",
   "study": [
     {