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jvmTest.com.iprd.report.FhirPathEvaluatorTest.kt Maven / Gradle / Ivy
/* IPRD Group 2022 */
package com.iprd.report
import ca.uhn.fhir.context.FhirContext
import ca.uhn.fhir.context.FhirVersionEnum
import ca.uhn.fhir.rest.client.impl.GenericClient
import ca.uhn.fhir.rest.client.interceptor.BearerTokenAuthInterceptor
import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
import com.fasterxml.jackson.module.kotlin.readValue
import com.google.common.truth.Truth
import com.iprd.report.model.Transform
import com.iprd.report.model.definition.FhirPathTransformation
import com.iprd.report.ui.token
import org.hl7.fhir.r4.model.Resource
import org.intellij.lang.annotations.Language
import org.junit.jupiter.api.Test
class FhirPathEvaluatorTest {
@Test
fun testExtractValueFromResource() {
val authInterceptor = BearerTokenAuthInterceptor(token)
val ctx = FhirContext.forR4()
val serverBase = "http://localhost:8085/fhir/"
val fhirClient = ctx.newRestfulGenericClient(serverBase)
fhirClient.registerInterceptor(authInterceptor)
val response = (fhirClient as GenericClient).search().byUrl("Patient?_id=caa62128-18f4-45c1-a689-35ec352c94ba").execute() as Resource
val value = FhirPathEvaluator.extractValueFromResource(response, "Bundle.entry.resource.ofType(Patient).birthDate")
Truth.assertThat(value).isEqualTo("1990-06-13")
}
@Test
fun extractValueFromExpression() {
val resource = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().parseResource(resource)
val transformList: List = jacksonObjectMapper().readValue(transform)
val value = FhirPathEvaluator.extractValueFromResource(resource as Resource, "Bundle.entry.resource.ofType(Patient).birthDate", transformList)
}
@Test
fun extractValueFromExpressionForSummaryPage() {
val resource = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().parseResource(resource)
val value = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpressionUsingReflection(resource as Resource, FhirPathTransformation("Bundle.entry.resource.ofType(Patient).birthDate", "verifyGreaterThanEqualToOnFhirPathValue(31556952)", null))
Truth.assertThat("0").isEqualTo("9.0")
}
@Test
fun extractValueFromExpressionForSummaryPageUsingDifferentFhirPath() {
val resource = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().parseResource(resource)
val value = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpressionUsingReflection(resource as Resource, FhirPathTransformation("Bundle.entry.resource.ofType(Observation).where(code.coding.code='ANC.B6.DE14').value", "verifyGreaterThanEqualToAndLessThanOnFhirPathValueForDateTimeType(0,12096000)", null))
Truth.assertThat(value).isEqualTo("1.0")
}
@Test
fun extractValueFromResourceAndFhirPathExpression() {
val resource = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().parseResource(resource) as Resource
val result = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpression(
resource,
"Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Observation).where(code.coding.code= 'ANC.B6.DE14').count()"
)
Truth.assertThat(result).isEqualTo("9.0") // 1 + 8
val result2 = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpression(
resource,
"Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + ( Bundle.entry.resource.ofType(Observation).where(code.coding.code= 'ANC.B6.DE14').count() / ( Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() ))"
)
Truth.assertThat(result2).isEqualTo("5.0") // 1 + ( 8 / ( 1 + 1 ))
val result3 = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpression(
resource,
"Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + ( Bundle.entry.resource.ofType(Observation).where(code.coding.code= 'ANC.B6.DE14').count() / ( Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Encounter).count() ))"
)
Truth.assertThat(result3).isEqualTo("2.0") // 1 + ( 8 / ( 1 + 7 ))
val result4 = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpression(
resource,
"Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() / Bundle.entry.resource.ofType(Media).count()"
)
Truth.assertThat(result4).isEqualTo("0.0") // 1 / 0
}
@Test
fun extractValueFromResourceAndFhirPathExpressionUsingReflection() {
val resource = FhirContext.forCached(FhirVersionEnum.R4).newJsonParser().parseResource(sampleResource) as Resource
val result = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpressionUsingReflection(
resource,
FhirPathTransformation("Bundle.entry.resource.ofType(Observation).where(code.coding.code= 'ANC.B6.DE14').value", "computeGestationalAge", null)
)
Truth.assertThat(result).isEqualTo("84") // 84
val result2 = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpressionUsingReflection(
resource,
FhirPathTransformation("Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() ,Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count()", "transformTwoArgumentsForTestWithDifferentArgType", null)
)
Truth.assertThat(result2).isEqualTo("3.0") // 2+1
val result3 = FhirPathEvaluator.extractValueFromResourceAndFhirPathExpressionUsingReflection(
resource,
FhirPathTransformation("Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() ,Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() / Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count() + Bundle.entry.resource.ofType(Immunization).where(vaccineCode.coding.display.contains('IPTp-SP dose 1')).count()", "transformTwoArgumentsForTest", null)
)
Truth.assertThat(result3).isEqualTo("4.0") // 2+2
}
}
@Language("JSON")
val transform = """
[
{
"operator": ">=",
"operand" : 315569520
},
{
"operator": "<=",
"operand" : 441797328
}
]
"""
@Language("JSON")
val sampleResource = """
{
"resourceType": "Bundle",
"entry": [
{
"fullUrl": "http://testhost.dashboard:8085/fhir/Observation/4126e401-2031-4400-b182-6533761015bd",
"resource": {
"resourceType": "Observation",
"id": "4126e401-2031-4400-b182",
"meta": {
"versionId": "1",
"lastUpdated": "2023-03-20T15:56:59.119+05:30",
"source": "#PvShrdE8Gxt3C8H3",
"tag": [
{
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "anc-registration",
"display": "ANC Registration"
}
]
},
"extension": [
{
"url": "http://iprdgroup.com/fhir/StructureDefinition/resource-questionnaireResponse",
"valueReference": {
"reference": "QuestionnaireResponse/16859662-8d41-44bb-bc26-2f496a360ab6"
}
}
],
"code": {
"coding": [
{
"system": "http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes",
"code": "ANC.B6.DE99",
"display": "Last menstrual period (LMP) date"
}
],
"text": "Last menstrual period (LMP) date"
},
"subject": {
"reference": "Patient/3f0dd22b-6307-4191-a0d0-15e5f9a876c3"
},
"encounter": {
"reference": "Encounter/5ae38290-e240-4c3e-a76b-b545838ed842"
},
"effectiveDateTime": "2023-03-20T15:56:57+05:30",
"performer": [
{
"reference": "PractitionerRole/a843957a-10d4-4b50-b834-faf82a948796"
}
],
"valueInteger": "5"
},
"search": {
"mode": "match"
}
},
{
"fullUrl": "http://testhost.dashboard:8085/fhir/Observation/4126e401-2031-4400-b182-6533761015bd",
"resource": {
"resourceType": "Observation",
"id": "4126e401-2031-4400-b182",
"meta": {
"versionId": "1",
"lastUpdated": "2023-03-20T15:56:59.119+05:30",
"source": "#PvShrdE8Gxt3C8H3",
"tag": [
{
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "anc-registration",
"display": "ANC Registration"
}
]
},
"extension": [
{
"url": "http://iprdgroup.com/fhir/StructureDefinition/resource-questionnaireResponse",
"valueReference": {
"reference": "QuestionnaireResponse/16859662-8d41-44bb-bc26-2f496a360ab6"
}
}
],
"code": {
"coding": [
{
"system": "http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes",
"code": "ANC.B6.DE99",
"display": "Last menstrual period (LMP) date"
}
],
"text": "Last menstrual period (LMP) date"
},
"subject": {
"reference": "Patient/3f0dd22b-6307-4191-a0d0-15e5f9a876c3"
},
"encounter": {
"reference": "Encounter/5ae38290-e240-4c3e-a76b-b545838ed842"
},
"effectiveDateTime": "2023-03-20T15:56:57+05:30",
"performer": [
{
"reference": "PractitionerRole/a843957a-10d4-4b50-b834-faf82a948796"
}
],
"valueInteger": "5"
},
"search": {
"mode": "match"
}
},
{
"fullUrl": "http://testhost.dashboard:8085/fhir/Observation/4126e401-2031-4400-b182-6533761017bd",
"resource": {
"resourceType": "Observation",
"id": "4126e401-2031-4400-b182-6533761015bd",
"meta": {
"versionId": "1",
"lastUpdated": "2023-03-20T15:56:59.119+05:30",
"source": "#PvShrdE8Gxt3C8H3",
"tag": [
{
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "anc-registration",
"display": "ANC Registration"
}
]
},
"extension": [
{
"url": "http://iprdgroup.com/fhir/StructureDefinition/resource-questionnaireResponse",
"valueReference": {
"reference": "QuestionnaireResponse/16859662-8d41-44bb-bc26-2f496a360ab6"
}
}
],
"code": {
"coding": [
{
"system": "http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes",
"code": "ANC.B6.DE14",
"display": "Last menstrual period (LMP) date"
}
],
"text": "Last menstrual period (LMP) date"
},
"subject": {
"reference": "Patient/3f0dd22b-6307-4191-a0d0-15e5f9a876c3"
},
"encounter": {
"reference": "Encounter/5ae38290-e240-4c3e-a76b-b545838ed842"
},
"effectiveDateTime": "2023-03-20T15:56:57+05:30",
"performer": [
{
"reference": "PractitionerRole/a843957a-10d4-4b50-b834-faf82a948796"
}
],
"valueDateTime": "2023-03-01T00:00:00+05:30"
},
"search": {
"mode": "match"
}
},
{
"fullUrl": "http://malaria1.opencampaignlink.org/fhir/Immunization/256f074a-2df7-414e-a289-273a9f27b9a1",
"resource": {
"resourceType": "Immunization",
"id": "256f074a-2df7-414e-a289-273a9f27b9a1",
"meta": {
"versionId": "1",
"lastUpdated": "2022-09-12T03:16:25.421+00:00",
"source": "#DLS9x6q1KkQ0xkLQ",
"tag": [
{
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "anc-visit",
"display": "Anc visit"
}
]
},
"status": "completed",
"vaccineCode": {
"coding": [
{
"system": "http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes",
"code": "ANC.B10.DE245",
"display": "IPTp-SP dose 1 provided"
}
],
"text": "IPTp-SP dose 1 provided"
},
"patient": {
"reference": "Patient/14fc2357-5379-4713-82a3-91d53bc780ae"
},
"encounter": {
"reference": "Encounter/d6017d0a-f7c5-4e38-aa01-20b09154c243"
},
"occurrenceDateTime": "2022-09-12T04:16:16+01:00",
"performer": [
{
"actor": {
"reference": "PractitionerRole/07f64f7c-8366-40c1-b87c-0642ffa038b7"
}
}
]
},
"search": {
"mode": "match"
}
}
]
}
""".trimIndent()
@Language("JSON")
val resource = """
{
"resourceType": "Bundle",
"entry": [
{
"fullUrl": "http://malaria1.opencampaignlink.org/fhir/Encounter/6ddaf5c4-51df-4f88-ae0a-4cc96471ffcd",
"resource": {
"resourceType": "Encounter",
"id": "6ddaf5c4-51df-4f88-ae0a-4cc96471ffcd",
"meta": {
"versionId": "1",
"lastUpdated": "2022-09-12T02:47:15.725+00:00",
"source": "#tHQYoAPID0Cq959L",
"tag": [
{
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "patient-registration",
"display": "Patient Registration"
}
]
},
"class": {
"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
"code": "IMP",
"display": "inpatient encounter"
},
"serviceType": {
"coding": [
{
"system": "https://iprdgroup.com/custom-codes",
"code": "patient-registration",
"display": "Patient Registration"
}
],
"text": "Patient Registration"
},
"subject": {
"reference": "Patient/b2f5093a-2375-481f-b6df-0b3dea866847"
},
"period": {
"start": "2022-09-12T08:15:41+05:30",
"end": "2022-09-12T23:59:59+05:30"
},
"location": [
{
"location": {
"reference": "Location/4fcb08a6-bacc-4f1e-85c7-1fc5bb8dfc7b"
}
},
{
"location": {
"reference": "Location/fd645af5-a101-4342-955e-464d81289480"
}
}
],
"serviceProvider": {
"reference": "Organization/e15b899b-8d94-4279-8cb7-3eb90a14279b"
}
},
"search": {
"mode": "match"
}
},
{
"fullUrl": "http://testhost.dashboard:8085/fhir/Observation/4126e401-2031-4400-b182-6533761015bd",
"resource": {
"resourceType": "Observation",
"id": "4126e401-2031-4400-b182-6533761015bd",
"meta": {
"versionId": "1",
"lastUpdated": "2023-03-20T15:56:59.119+05:30",
"source": "#PvShrdE8Gxt3C8H3",
"tag": [ {
"system": "https://www.iprdgroup.com/ValueSet/Workflow/tags",
"code": "anc-registration",
"display": "ANC Registration"
} ]
},
"extension": [ {
"url": "http://iprdgroup.com/fhir/StructureDefinition/resource-questionnaireResponse",
"valueReference": {
"reference": "QuestionnaireResponse/16859662-8d41-44bb-bc26-2f496a360ab6"
}
} ],
"code": {
"coding": [ {
"system": "http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes",
"code": "ANC.B6.DE14",
"display": "Last menstrual period (LMP) date"
} ],
"text": "Last menstrual period (LMP) date"
},
"subject": {
"reference": "Patient/3f0dd22b-6307-4191-a0d0-15e5f9a876c3"
},
"encounter": {
"reference": "Encounter/5ae38290-e240-4c3e-a76b-b545838ed842"
},
"effectiveDateTime": "2023-03-20T15:56:57+05:30",
"performer": [ {
"reference": "PractitionerRole/a843957a-10d4-4b50-b834-faf82a948796"
} ],
"valueDateTime": "2023-03-01T00:00:00+05:30"
},
"search": {
"mode": "match"
}
},
{
"fullUrl": "http://malaria1.opencampaignlink.org/fhir/Patient/b2f5093a-2375-481f-b6df-0b3dea866847",
"resource": {
"resourceType": "Patient",
"id": "b2f5093a-2375-481f-b6df-0b3dea866847",
"meta": {
"versionId": "1",
"lastUpdated": "2022-09-12T02:47:15.725+00:00",
"source": "#tHQYoAPID0Cq959L"
},
"text": {
"status": "generated",
"div": "Identifier Qwert Address T Date of birth 01 September 2022
Identifier T Address Q Date of birth 09 September 2022
Identifier T Address G Oyo Date of birth 11 September 2022
Identifier https://OCLink.io/Q?s=RKYMC6PRES2C&v=3&g=67e6524e-4011-4afd-8546-99c57054c2d4&d=H4sIAAAAAAAAAC1OSw6CMBC9CumaKi3TFtgZ916AuKjtAAZEooWEEO7uVF29l3m/2djds4ppg1pJQA6ZEBxs43mhQPOydMpkCpz0wFI2kJVHnIgYIoFQaC2NlFCIeIhKScR9e4GyDQjLnTf5r/yWZxnXqKQsc4dFE2sWR95apom6xuj8ikNdCNO7Oh47tEPoDu1zOYxtlEf7QNJPl3Nyto/J3tuRzrNvWFVvrCepx/X/XFgnjANEFzvMyPbr/gH9+LaY9AAAAA== Address T Date of birth 03 September 2022
Identifier SPHCB/PHCIBC/987/02209/028 Address 1 Ahmed Kunle street Agbowo Oyo Date of birth 20 March 2001
Identifier https://OCLink.io/Q?s=ATGNYBK1WNB9&v=3&g=7f7203b6-652f-4720-ac43-ad5777519fe8&d=H4sIAAAAAAAAAC1OSw6CMBC9iuna0f4r7Ax7L0BY1NKC4SPRQkIId3dKXM2b95k3G3nVJCcmGE7FU4NWPIDEBayTAmytjDGKZcHfyJn0aIU0p5RBEHEyrXlGlZQHkZQMgTvuSuSDZBZcbQRIyhg8BaWgveI8E87fQkotDr0lP59UlaLzJxW1MU7f/Hptve1je2ney2VskjzawaN+fxSnwg6TfTUj0nMdSF5upEOp8+v/ubhOPhUgXGw/e7JX+w/CPge59AAAAA== Address A Date of birth 16 August 2000
Identifier 1155 Address 96 Date of birth 10 August 1993
