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julianxcarterjulianxcarter
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Typo fixes + id field change in extractor
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-15
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‎docs/adverse-event.csv

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
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,12-09-1994,12-09-1994
3-
mrn-two-category-example,example-id-1,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,12-09-1994,12-09-1994
4-
mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,12-09-1994,
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
3+
mrn-two-category-example,example-id-1,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
4+
mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,

‎src/extractors/CSVAdverseEventExtractor.js

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -23,20 +23,20 @@ function formatData(adverseEventData) {
2323
const categoryDisplays = categoryDisplayText.split('|');
2424

2525
if (!(categoryCodes.length === categorySystems.length && categoryCodes.length === categoryDisplays.length)) {
26-
throw new Error('A category atrribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.');
26+
throw new Error('A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.');
2727
}
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2929

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return {
31-
id: adverseEventId,
31+
...(adverseEventId && { id: adverseEventId }),
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subjectId: mrn,
3333
code: adverseEventCode,
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system: !adverseEventCodeSystem ? 'http://snomed.info/sct' : adverseEventCodeSystem,
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display: adverseEventDisplayText,
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suspectedCauseId,
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suspectedCauseType,
3838
seriousnessCode: seriousness,
39-
seriousnessCodeSystem,
39+
seriousnessCodeSystem: !seriousnessCodeSystem ? 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness' : seriousnessCodeSystem,
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seriousnessDisplayText,
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category: categoryCodes.map((categoryCode, index) => {
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if (!categoryCode) return null;

‎src/templates/AdverseEventTemplate.js

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ function seriousnessTemplate(seriousnessCoding) {
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return {
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seriousness: {
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coding: [
30-
coding({ system: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness', ...seriousnessCoding }),
30+
coding(seriousnessCoding),
3131
],
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},
3333
};

‎test/extractors/CSVAdverseEventExtractor.test.js

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ describe('CSVAdverseEventExtractor', () => {
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describe('formatData', () => {
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test('should join data appropriately and throw errors when missing required properties', () => {
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const expectedErrorString = 'The adverse event is missing an expected attribute. Adverse event code, mrn, and effective date are all required.';
37-
const expectedCategoryErrorString = 'A category atrribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.';
37+
const expectedCategoryErrorString = 'A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.';
3838
const localData = _.cloneDeep(exampleCSVAdverseEventModuleResponse);
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// Test that valid maximal data works fine

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/adverse-event-seriousness",
35-
"code": "Serious",
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"code": "serious",
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"display": "Serious"
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}
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]

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
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"adverseEventDisplayText": "Anxiety disorder of childhood OR adolescence",
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"suspectedCauseId": "procedure-id",
99
"suspectedCauseType": "Procedure",
10-
"seriousness": "Serious",
10+
"seriousness": "serious",
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"seriousnessCodeSystem": "http://terminology.hl7.org/CodeSystem/adverse-event-seriousness",
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"seriousnessDisplayText": "Serious",
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"category": "product-use-error",

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
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
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+
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
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
44
789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,

‎test/templates/adverseEvent.test.js

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ const VALID_DATA = {
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display: 'Anxiety disorder of childhood OR adolescence',
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suspectedCauseId: 'procedure-id',
1414
suspectedCauseType: 'Procedure',
15-
seriousnessCode: 'Serious',
15+
seriousnessCode: 'serious',
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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' }],
@@ -55,7 +55,7 @@ const INVALID_DATA = {
5555
display: 'Anxiety disorder of childhood OR adolescence',
5656
suspectedCauseId: 'procedure-id',
5757
suspectedCauseType: 'Procedure',
58-
seriousnessCode: 'Serious',
58+
seriousnessCode: 'serious',
5959
seriousnessCodeSystem: 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness',
6060
seriousnessDisplayText: 'Serious',
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category: [{ code: 'product-use-error', system: 'http://terminology.hl7.org/CodeSystem/adverse-event-category' }],

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
"coding": [
2727
{
2828
"system": "http://terminology.hl7.org/CodeSystem/adverse-event-seriousness",
29-
"code": "Serious",
29+
"code": "serious",
3030
"display": "Serious"
3131
}
3232
]

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