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Merge pull request #166 from mcode/remove-ae-fields
Removing severity and fixing actuality to 'actual'
2 parents 6ac5f70 + 91396c1 commit d8465ab

9 files changed

+13
-57
lines changed

‎docs/CSV_Templates.xlsx

-77.6 KB
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‎docs/ctc-adverse-event.csv

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
2-
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,
3-
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
4-
mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,,1
1+
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade
2+
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,
3+
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
4+
mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,1994-12-09,,1

‎src/extractors/CSVCTCAdverseEventExtractor.js

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,6 @@ function formatData(adverseEventData, patientId) {
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category,
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categorycodesystem: categoryCodeSystem,
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categorydisplaytext: categoryDisplayText,
26-
severity,
27-
actuality,
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studyid: studyId,
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effectivedate: effectiveDate,
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recordeddate: recordedDate,
@@ -61,8 +59,6 @@ function formatData(adverseEventData, patientId) {
6159
if (categoryDisplays[index]) categoryCoding.display = categoryDisplays[index];
6260
return categoryCoding;
6361
}),
64-
severity,
65-
actuality: !actuality ? 'actual' : actuality,
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studyId,
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effectiveDateTime: formatDateTime(effectiveDate),
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recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),

‎src/templates/CTCAdverseEventTemplate.js

Lines changed: 3 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -45,19 +45,6 @@ function categoryArrayTemplate(categoryArr) {
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return { category };
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}
4747

48-
function severityTemplate(severityCode) {
49-
return {
50-
severity: {
51-
coding: [
52-
coding({
53-
code: severityCode,
54-
system: 'http://terminology.hl7.org/CodeSystem/adverse-event-severity',
55-
}),
56-
],
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},
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};
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}
60-
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function studyTemplate(studyId) {
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return {
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study: [
@@ -85,9 +72,9 @@ function gradeTemplate(grade) {
8572

8673
function CTCAdverseEventTemplate({
8774
id, subjectId, code, system, display, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
88-
severity, actuality, studyId, effectiveDateTime, recordedDateTime, grade,
75+
studyId, effectiveDateTime, recordedDateTime, grade,
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}) {
90-
if (!(subjectId && code && system && effectiveDateTime && actuality && grade)) {
77+
if (!(subjectId && code && system && effectiveDateTime && grade)) {
9178
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');
9279
}
9380

@@ -100,8 +87,7 @@ function CTCAdverseEventTemplate({
10087
...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),
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...ifSomeArgsObj(seriousnessTemplate)({ code: seriousnessCode, system: seriousnessCodeSystem, display: seriousnessDisplayText }),
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...ifSomeArgsArr(categoryArrayTemplate)(category),
103-
...ifAllArgs(severityTemplate)(severity),
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actuality,
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actuality: 'actual',
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...ifAllArgs(studyTemplate)(studyId),
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date: effectiveDateTime,
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...ifAllArgs(recordedDateTemplate)(recordedDateTime),

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

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@@ -62,14 +62,6 @@
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]
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}
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],
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"severity": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/adverse-event-severity",
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"code": "severe"
70-
}
71-
]
72-
},
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"actuality": "actual",
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"study": [
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{

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

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@@ -13,8 +13,6 @@
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"category": "product-use-error",
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"categorycodesystem": "http://terminology.hl7.org/CodeSystem/adverse-event-category",
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"categorydisplaytext": "Product Use Error",
16-
"severity": "severe",
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"actuality": "actual",
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"studyid": "researchId-1",
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"effectivedate": "12-09-1994",
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"recordeddate": "12-09-1994",

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

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@@ -1,4 +1,4 @@
1-
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate,grade
2-
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
3-
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
4-
789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,,3
1+
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,studyId,effectiveDate,recordedDate,grade
2+
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
3+
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
4+
789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,12-09-1994,,3

‎test/templates/ctcAdverseEvent.test.js

Lines changed: 2 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -16,21 +16,18 @@ const VALID_DATA = {
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seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
1717
seriousnessDisplayText: 'Serious',
1818
category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category', display: 'Product Use Error' }],
19-
severity: 'severe',
20-
actuality: 'actual',
2119
studyId: 'researchId-1',
2220
effectiveDateTime: '1994-12-09',
2321
recordedDateTime: '1994-12-09',
2422
grade: { code: '2', display: 'Moderate Adverse Event' },
2523
};
2624

2725
const MINIMAL_DATA = {
28-
// Only include 'id', 'subjectId', 'code', 'system', 'actuality', 'grade', and 'effectiveDateTime' fields which are required
26+
// Only include 'id', 'subjectId', 'code', 'system', 'grade', and 'effectiveDateTime' fields which are required
2927
subjectId: 'mrn-1',
3028
code: '109006',
3129
system: 'code-system',
3230
effectiveDateTime: '1994-12-09',
33-
actuality: 'actual',
3431
id: 'adverseEventId-1',
3532
grade: { code: '2', display: 'Moderate Adverse Event' },
3633
display: null,
@@ -40,19 +37,17 @@ const MINIMAL_DATA = {
4037
seriousnessCodeSystem: null,
4138
seriousnessDisplayText: null,
4239
category: [null],
43-
severity: null,
4440
studyId: null,
4541
recordedDateTime: null,
4642
};
4743

4844

4945
const INVALID_DATA = {
50-
// Omitting 'subjectId', 'code', 'system', 'actuality', and 'effectiveDateTime' fields which are required
46+
// Omitting 'subjectId', 'code', 'system', and 'effectiveDateTime' fields which are required
5147
subjectId: null,
5248
code: null,
5349
system: null,
5450
effectiveDateTime: null,
55-
actuality: null,
5651
grade: null,
5752
id: 'adverseEventId-1',
5853
display: 'Anxiety disorder of childhood OR adolescence',
@@ -62,7 +57,6 @@ const INVALID_DATA = {
6257
seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
6358
seriousnessDisplayText: 'Serious',
6459
category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category' }],
65-
severity: 'severe',
6660
studyId: 'researchId-1',
6761
recordedDateTime: '1994-12-09',
6862
};
@@ -92,7 +86,6 @@ describe('test Adverse Event template', () => {
9286
seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
9387
seriousnessDisplayText: 'Serious',
9488
category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category' }],
95-
severity: 'severe',
9689
studyId: 'researchId-1',
9790
recordedDateTime: '1994-12-09',
9891
};
@@ -102,7 +95,6 @@ describe('test Adverse Event template', () => {
10295
code: '109006',
10396
system: 'code-system',
10497
effectiveDateTime: '1994-12-09',
105-
actuality: 'actual',
10698
grade: { code: '2', display: 'Moderate Adverse Event' },
10799
};
108100

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

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@@ -56,14 +56,6 @@
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]
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}
5858
],
59-
"severity": {
60-
"coding": [
61-
{
62-
"system": "http://terminology.hl7.org/CodeSystem/adverse-event-severity",
63-
"code": "severe"
64-
}
65-
]
66-
},
6759
"actuality": "actual",
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"study": [
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{

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