diff --git a/docs/CSV_Templates.xlsx b/docs/CSV_Templates.xlsx index bee42813..e350d737 100755 Binary files a/docs/CSV_Templates.xlsx and b/docs/CSV_Templates.xlsx differ diff --git a/docs/ctc-adverse-event.csv b/docs/ctc-adverse-event.csv index 90d4b8a5..e2357065 100644 --- a/docs/ctc-adverse-event.csv +++ b/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 diff --git a/src/extractors/CSVCTCAdverseEventExtractor.js b/src/extractors/CSVCTCAdverseEventExtractor.js index ac4642cd..e99b4fdb 100644 --- a/src/extractors/CSVCTCAdverseEventExtractor.js +++ b/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), diff --git a/src/templates/CTCAdverseEventTemplate.js b/src/templates/CTCAdverseEventTemplate.js index 3a25b26f..082fa8b0 100644 --- a/src/templates/CTCAdverseEventTemplate.js +++ b/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), diff --git a/test/extractors/fixtures/csv-ctc-adverse-event-bundle.json b/test/extractors/fixtures/csv-ctc-adverse-event-bundle.json index 8a129919..cac09cd3 100644 --- a/test/extractors/fixtures/csv-ctc-adverse-event-bundle.json +++ b/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": [ { diff --git a/test/extractors/fixtures/csv-ctc-adverse-event-module-response.json b/test/extractors/fixtures/csv-ctc-adverse-event-module-response.json index 25f1f9d3..8c2b868c 100644 --- a/test/extractors/fixtures/csv-ctc-adverse-event-module-response.json +++ b/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", diff --git a/test/sample-client-data/ctc-adverse-event-information.csv b/test/sample-client-data/ctc-adverse-event-information.csv index e4f74c95..aed2d5a3 100644 --- a/test/sample-client-data/ctc-adverse-event-information.csv +++ b/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 \ No newline at end of file +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 \ No newline at end of file diff --git a/test/templates/ctcAdverseEvent.test.js b/test/templates/ctcAdverseEvent.test.js index ed0d323a..19608cbc 100644 --- a/test/templates/ctcAdverseEvent.test.js +++ b/test/templates/ctcAdverseEvent.test.js @@ -16,8 +16,6 @@ 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', @@ -25,12 +23,11 @@ const VALID_DATA = { }; 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' }, }; diff --git a/test/templates/fixtures/maximal-ctc-adverse-event-resource.json b/test/templates/fixtures/maximal-ctc-adverse-event-resource.json index a285da94..81acb308 100644 --- a/test/templates/fixtures/maximal-ctc-adverse-event-resource.json +++ b/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": [ {