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fix: fix stu3 schema for Bundle & AllergyIntolerance (#65)
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@carvantes
carvantes committed Mar 25, 2021
1 parent 5a87d2b commit 87857d1
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28 changes: 12 additions & 16 deletions src/router/validation/jsonSchemaValidator.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -38,26 +38,22 @@ describe('Validating V3 resources', () => {
await expect(validatorV3.validate(validV3Account)).resolves.toEqual(undefined);
});

// TODO: Validator does not validate v3 Bundles correctly
test.skip('No error when validating valid v3 Bundle', async () => {
const bundle = {
resourceType: 'Bundle',
type: 'transaction',
entry: [
{
resource: {
resourceType: 'Patient',
name: [{ family: 'Smith', given: ['John'] }],
gender: 'male',
},
request: { method: 'POST', url: 'Patient' },
},
],
};
test('No error when validating valid v3 Bundle', async () => {
// example Bundle from https://www.hl7.org/fhir/stu3/bundle-transaction.json.html
// eslint-disable-next-line prettier/prettier
const bundle = {"resourceType":"Bundle","id":"bundle-transaction","meta":{"lastUpdated":"2014-08-18T01:43:30Z"},"type":"transaction","entry":[{"fullUrl":"urn:uuid:61ebe359-bfdc-4613-8bf2-c5e300945f0a","resource":{"resourceType":"Patient","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"},"active":true,"name":[{"use":"official","family":"Chalmers","given":["Peter","James"]}],"gender":"male","birthDate":"1974-12-25"},"request":{"method":"POST","url":"Patient"}},{"fullUrl":"urn:uuid:88f151c0-a954-468a-88bd-5ae15c08e059","resource":{"resourceType":"Patient","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"},"active":true,"name":[{"use":"official","family":"Chalmers","given":["Peter","James"]}],"gender":"male","birthDate":"1974-12-25"},"request":{"method":"POST","url":"Patient","ifNoneExist":"identifier=234234"}},{"fullUrl":"http://example.org/fhir/Patient/123","resource":{"resourceType":"Patient","id":"123","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"},"active":true,"name":[{"use":"official","family":"Chalmers","given":["Peter","James"]}],"gender":"male","birthDate":"1974-12-25"},"request":{"method":"PUT","url":"Patient/123"}},{"fullUrl":"urn:uuid:74891afc-ed52-42a2-bcd7-f13d9b60f096","resource":{"resourceType":"Patient","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"},"active":true,"name":[{"use":"official","family":"Chalmers","given":["Peter","James"]}],"gender":"male","birthDate":"1974-12-25"},"request":{"method":"PUT","url":"Patient?identifier=234234"}},{"fullUrl":"http://example.org/fhir/Patient/123a","resource":{"resourceType":"Patient","id":"123a","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"},"active":true,"name":[{"use":"official","family":"Chalmers","given":["Peter","James"]}],"gender":"male","birthDate":"1974-12-25"},"request":{"method":"PUT","url":"Patient/123a","ifMatch":"W/\"2\""}},{"request":{"method":"DELETE","url":"Patient/234"}},{"request":{"method":"DELETE","url":"Patient?identifier=123456"}},{"fullUrl":"urn:uuid:79378cb8-8f58-48e8-a5e8-60ac2755b674","resource":{"resourceType":"Parameters","parameter":[{"name":"coding","valueCoding":{"system":"http://loinc.org","code":"1963-8"}}]},"request":{"method":"POST","url":"ValueSet/$lookup"}},{"request":{"method":"GET","url":"Patient?name=peter"}},{"request":{"method":"GET","url":"Patient/12334","ifNoneMatch":"W/\"4\"","ifModifiedSince":"2015-08-31T08:14:33+10:00"}}]}

await expect(validatorV3.validate(bundle)).resolves.toEqual(undefined);
});

test('valid AllergyIntolerance', async () => {
// example AllergyIntolerance from http://hl7.org/fhir/STU3/allergyintolerance-example.json.html
// eslint-disable-next-line prettier/prettier
const allergyIntolerance = {"resourceType":"AllergyIntolerance","id":"example","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>identifier</b>: 49476534</p><p><b>clinicalStatus</b>: active</p><p><b>verificationStatus</b>: confirmed</p><p><b>type</b>: allergy</p><p><b>category</b>: food</p><p><b>criticality</b>: high</p><p><b>code</b>: Cashew nuts <span>(Details : {SNOMED CT code '227493005' = 'Cashew nuts', given as 'Cashew nuts'})</span></p><p><b>patient</b>: <a>Patient/example</a></p><p><b>onset</b>: 01/01/2004</p><p><b>assertedDate</b>: 09/10/2014 2:58:00 PM</p><p><b>recorder</b>: <a>Practitioner/example</a></p><p><b>asserter</b>: <a>Patient/example</a></p><p><b>lastOccurrence</b>: 01/06/2012</p><p><b>note</b>: The criticality is high becasue of the observed anaphylactic reaction when challenged with cashew extract.</p><blockquote><p><b>reaction</b></p><p><b>substance</b>: cashew nut allergenic extract Injectable Product <span>(Details : {RxNorm code '1160593' = '1160593', given as 'cashew nut allergenic extract Injectable Product'})</span></p><p><b>manifestation</b>: Anaphylactic reaction <span>(Details : {SNOMED CT code '39579001' = 'Anaphylaxis', given as 'Anaphylactic reaction'})</span></p><p><b>description</b>: Challenge Protocol. Severe reaction to subcutaneous cashew extract. Epinephrine administered</p><p><b>onset</b>: 12/06/2012</p><p><b>severity</b>: severe</p><p><b>exposureRoute</b>: Subcutaneous route <span>(Details : {SNOMED CT code '34206005' = 'Subcutaneous route', given as 'Subcutaneous route'})</span></p></blockquote><blockquote><p><b>reaction</b></p><p><b>manifestation</b>: Urticaria <span>(Details : {SNOMED CT code '64305001' = 'Urticaria', given as 'Urticaria'})</span></p><p><b>onset</b>: 01/01/2004</p><p><b>severity</b>: moderate</p><p><b>note</b>: The patient reports that the onset of urticaria was within 15 minutes of eating cashews.</p></blockquote></div>"},"identifier":[{"system":"http://acme.com/ids/patients/risks","value":"49476534"}],"clinicalStatus":"active","verificationStatus":"confirmed","type":"allergy","category":["food"],"criticality":"high","code":{"coding":[{"system":"http://snomed.info/sct","code":"227493005","display":"Cashew nuts"}]},"patient":{"reference":"Patient/example"},"onsetDateTime":"2004","assertedDate":"2014-10-09T14:58:00+11:00","recorder":{"reference":"Practitioner/example"},"asserter":{"reference":"Patient/example"},"lastOccurrence":"2012-06","note":[{"text":"The criticality is high becasue of the observed anaphylactic reaction when challenged with cashew extract."}],"reaction":[{"substance":{"coding":[{"system":"http://www.nlm.nih.gov/research/umls/rxnorm","code":"1160593","display":"cashew nut allergenic extract Injectable Product"}]},"manifestation":[{"coding":[{"system":"http://snomed.info/sct","code":"39579001","display":"Anaphylactic reaction"}]}],"description":"Challenge Protocol. Severe reaction to subcutaneous cashew extract. Epinephrine administered","onset":"2012-06-12","severity":"severe","exposureRoute":{"coding":[{"system":"http://snomed.info/sct","code":"34206005","display":"Subcutaneous route"}]}},{"manifestation":[{"coding":[{"system":"http://snomed.info/sct","code":"64305001","display":"Urticaria"}]}],"onset":"2004","severity":"moderate","note":[{"text":"The patient reports that the onset of urticaria was within 15 minutes of eating cashews."}]}]}

await expect(validatorV3.validate(allergyIntolerance)).resolves.toEqual(undefined);
});

test('Show error when validating invalid resource', async () => {
await expect(validatorV3.validate(invalidPatient)).rejects.toThrowError(
new InvalidResourceError(
Expand Down
31 changes: 14 additions & 17 deletions src/router/validation/schemas/fhir.schema.v3.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4793,15 +4793,14 @@
},
"category": {
"description": "Category of the identified substance.",
"enum": [
"food",
"medication",
"environment",
"biologic"
],
"type": "array",
"items": {
"type": "string"
"enum": [
"food",
"medication",
"environment",
"biologic"
]
}
},
"_category": {
Expand Down Expand Up @@ -24749,6 +24748,13 @@
{
"description": "This special resource type is used to represent an operation request and response (operations.html). It has no other use, and there is no RESTful endpoint associated with it.",
"properties": {
"resourceType": {
"description": "This is a Parameters resource",
"type": "string",
"enum": [
"Parameters"
]
},
"parameter": {
"description": "A parameter passed to or received from the operation.",
"type": "array",
Expand Down Expand Up @@ -36585,9 +36591,6 @@
{
"$ref": "#/definitions/DocumentReference"
},
{
"$ref": "#/definitions/DomainResource"
},
{
"$ref": "#/definitions/EligibilityRequest"
},
Expand Down Expand Up @@ -36714,9 +36717,6 @@
{
"$ref": "#/definitions/Parameters"
},
{
"$ref": "#/definitions/Parameters"
},
{
"$ref": "#/definitions/Patient"
},
Expand Down Expand Up @@ -36774,9 +36774,6 @@
{
"$ref": "#/definitions/ResearchSubject"
},
{
"$ref": "#/definitions/Resource"
},
{
"$ref": "#/definitions/RiskAssessment"
},
Expand Down Expand Up @@ -36834,4 +36831,4 @@
]
}
}
}
}

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