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Add test cases for FhirOperator.kt (#1290)
* - Add test cases for FhirOperator.kt * - connectedCheck * - Ignore FhirOperatorPopulationTest * - Add min-max heap size in gradle for test cases * - Update gradle * - Update gradle * Update ci-gradle.properties * Create blank.yml * Delete blank.yml * Update ci-gradle.properties * - Testing commit * - Testing commit changes reverted * Increase heap size to 4GB * - Revert changes * - Modify build.gradle.kts * - Modify build.gradle.kts * - Add some more assertions to validate generated MeasureReport resource * - Resolved requested changes * - Resolved requested changes * - Resolve requested changes * - Added a comment to trigger CI workflow. Co-authored-by: Ephraim Kigamba <[email protected]> Co-authored-by: Ephraim Kigamba <[email protected]> Co-authored-by: Francis Odhiambo Otieno <[email protected]>
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28 changes: 28 additions & 0 deletions
28
workflow/src/test/java/com/google/android/fhir/workflow/DateUtils.kt
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| /* | ||
| * Copyright 2021 Google LLC | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package com.google.android.fhir.workflow | ||
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| import java.time.LocalDate | ||
| import org.hl7.fhir.r4.model.DateType | ||
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| val DateType.toLocalDate: LocalDate | ||
| get() = | ||
| LocalDate.of( | ||
| year, | ||
| month + 1, | ||
| day, | ||
| ) |
139 changes: 139 additions & 0 deletions
139
workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorPopulationTest.kt
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| /* | ||
| * Copyright 2021 Google LLC | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package com.google.android.fhir.workflow | ||
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| import androidx.test.core.app.ApplicationProvider | ||
| import ca.uhn.fhir.context.FhirContext | ||
| import com.google.android.fhir.FhirEngineProvider | ||
| import com.google.common.truth.Truth.assertThat | ||
| import java.util.Date | ||
| import kotlinx.coroutines.runBlocking | ||
| import org.hl7.fhir.r4.model.Bundle | ||
| import org.hl7.fhir.r4.model.DateType | ||
| import org.hl7.fhir.r4.model.Library | ||
| import org.hl7.fhir.r4.model.MeasureReport | ||
| import org.hl7.fhir.r4.model.Resource | ||
| import org.hl7.fhir.r4.model.ResourceType | ||
| import org.junit.Before | ||
| import org.junit.Test | ||
| import org.junit.runner.RunWith | ||
| import org.robolectric.RobolectricTestRunner | ||
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| @RunWith(RobolectricTestRunner::class) | ||
| class FhirOperatorPopulationTest { | ||
| private val fhirEngine = | ||
| FhirEngineProvider.getInstance(ApplicationProvider.getApplicationContext()) | ||
| private val fhirContext = FhirContext.forR4() | ||
| private val jsonParser = fhirContext.newJsonParser() | ||
| private val xmlParser = fhirContext.newXmlParser() | ||
| private val fhirOperator = FhirOperator(fhirContext, fhirEngine) | ||
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| @Before | ||
| fun setUp() = runBlocking { | ||
| loadBundle("/ANCIND01-bundle.json") | ||
| loadBundle("/tests-Reportable-bundle.json") | ||
| loadBundle("/tests-NotReportable-bundle.json") | ||
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| // TODO Fix the FHIRHelpers library | ||
| // loadBundle("/RuleFilters-1.0.0-bundle.json") | ||
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| loadFile("/first-contact/01-registration/patient-charity-otala-1.json") | ||
| loadFile("/first-contact/02-enrollment/careplan-charity-otala-1-pregnancy-plan.xml") | ||
| loadFile("/first-contact/02-enrollment/episodeofcare-charity-otala-1-pregnancy-episode.xml") | ||
| loadFile("/first-contact/03-contact/encounter-anc-encounter-charity-otala-1.xml") | ||
| } | ||
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| @Test | ||
| fun evaluatePopulationMeasure() = runBlocking { | ||
| val measureReport = | ||
| fhirOperator.evaluateMeasure( | ||
| measureUrl = "http://fhir.org/guides/who/anc-cds/Measure/ANCIND01", | ||
| start = "2019-01-01", | ||
| end = "2021-12-31", | ||
| reportType = "population", | ||
| subject = null, | ||
| practitioner = "jane", | ||
| lastReceivedOn = null | ||
| ) | ||
| val measureReportJSON = | ||
| FhirContext.forR4().newJsonParser().encodeResourceToString(measureReport) | ||
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| assertThat(MeasureReport.MeasureReportStatus.COMPLETE).isEqualTo(measureReport.status) | ||
| assertThat(MeasureReport.MeasureReportType.SUMMARY).isEqualTo(measureReport.type) | ||
| assertThat("2019-01-01").isEqualTo(DateType(measureReport.period.start).toLocalDate.toString()) | ||
| assertThat("2021-12-31").isEqualTo(DateType(measureReport.period.end).toLocalDate.toString()) | ||
| assertThat(DateType(Date()).toLocalDate).isEqualTo(DateType(measureReport.date).toLocalDate) | ||
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| assertThat(measureReportJSON).isNotNull() | ||
| assertThat(measureReport).isNotNull() | ||
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| assertThat(measureReport.extension[0].value.toString()) | ||
| .isEqualTo( | ||
| "Percentage of pregnant women with first ANC contact in the first trimester (before 12 weeks of gestation)" | ||
| ) | ||
| assertThat(measureReport.extension[0].url) | ||
| .isEqualTo( | ||
| "http://hl7.org/fhir/5.0/StructureDefinition/extension-MeasureReport.population.description" | ||
| ) | ||
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| assertThat(measureReport.measure.toString()) | ||
| .isEqualTo("http://fhir.org/guides/who/anc-cds/Measure/ANCIND01") | ||
| assertThat(measureReport.improvementNotation.coding[0].system) | ||
| .isEqualTo("http://terminology.hl7.org/CodeSystem/measure-improvement-notation") | ||
| assertThat(measureReport.improvementNotation.coding[0].code.toString()).isEqualTo("increase") | ||
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| val population = measureReport.group[0].population | ||
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| assertThat(population[0].id).isEqualTo("initial-population") | ||
| assertThat(population[0].code.coding[0].code.toString()).isEqualTo("initial-population") | ||
| assertThat(population[0].code.coding[0].system) | ||
| .isEqualTo("http://terminology.hl7.org/CodeSystem/measure-population") | ||
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| assertThat(population[1].id).isEqualTo("denominator") | ||
| assertThat(population[1].code.coding[0].code.toString()).isEqualTo("denominator") | ||
| assertThat(population[1].code.coding[0].system) | ||
| .isEqualTo("http://terminology.hl7.org/CodeSystem/measure-population") | ||
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| assertThat(population[2].id).isEqualTo("numerator") | ||
| assertThat(population[2].code.coding[0].code.toString()).isEqualTo("numerator") | ||
| assertThat(population[2].code.coding[0].system) | ||
| .isEqualTo("http://terminology.hl7.org/CodeSystem/measure-population") | ||
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| assertThat(measureReport.type.display).isEqualTo("Summary") | ||
| } | ||
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| private suspend fun loadFile(path: String) { | ||
| if (path.endsWith(suffix = ".xml")) { | ||
| val resource = xmlParser.parseResource(javaClass.getResourceAsStream(path)) as Resource | ||
| fhirEngine.create(resource) | ||
| } else if (path.endsWith(".json")) { | ||
| val resource = jsonParser.parseResource(javaClass.getResourceAsStream(path)) as Resource | ||
| fhirEngine.create(resource) | ||
| } | ||
| } | ||
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| private suspend fun loadBundle(path: String) { | ||
| val bundle = jsonParser.parseResource(javaClass.getResourceAsStream(path)) as Bundle | ||
| for (entry in bundle.entry) { | ||
| when (entry.resource.resourceType) { | ||
| ResourceType.Library -> fhirOperator.loadLib(entry.resource as Library) | ||
| ResourceType.Bundle -> Unit | ||
| else -> fhirEngine.create(entry.resource) | ||
| } | ||
| } | ||
| } | ||
| } |
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