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Workflow Library: Implementing Library.evaluate and first androidTest…
… suite (#1326) * Operator.evaluateLibrary function Generalization of FhirEngineRetrieveProvider * Fixes from spotlessApply * Moving COVID tests to its own directory. * Removing redundant (contextPath != "id") * Using Truth library and clearing up the logs * BugFix on assetPath and Organization ID * Fixing the JSON structure of the test to become a Bundle instead of a Composite. * Updating LibraryEvaluate Tests to the new FhirEngineProviderTestRule * Update workflow/src/main/java/com/google/android/fhir/workflow/FhirOperator.kt Improving documentation as suggested by the reviewer. Co-authored-by: Jing Tang <[email protected]> * Adding a new line before the function definition. * Adding a new line before the function for consistency. * deleting unnecessary test files * Simplifying Test Case * Removing new line * Fixing Documentation of evaluateLibrary * Improving the explanation of the test case for Library Evaluate * Improving documentation of the Library Evaluate test case by describing the CQLEvaluator steps being tested * Running spotless check * update to trigger github actions after OutOfMemory exception * removing spaces to pass spotless * Improving documentation * Use a cached version of R4 Co-authored-by: Jing Tang <[email protected]>
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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 androidx.test.ext.junit.runners.AndroidJUnit4 | ||
| import ca.uhn.fhir.context.FhirContext | ||
| import ca.uhn.fhir.context.FhirVersionEnum | ||
| import com.google.android.fhir.FhirEngine | ||
| import com.google.android.fhir.FhirEngineProvider | ||
| import com.google.android.fhir.testing.FhirEngineProviderTestRule | ||
| import com.google.common.truth.Truth.assertThat | ||
| import java.io.InputStream | ||
| import kotlinx.coroutines.runBlocking | ||
| import org.hl7.fhir.r4.model.Bundle | ||
| import org.hl7.fhir.r4.model.Parameters | ||
| import org.junit.Before | ||
| import org.junit.Rule | ||
| import org.junit.Test | ||
| import org.junit.runner.RunWith | ||
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| @RunWith(AndroidJUnit4::class) | ||
| class FhirOperatorLibraryEvaluateTest { | ||
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| @get:Rule val fhirEngineProviderRule = FhirEngineProviderTestRule() | ||
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| private lateinit var fhirEngine: FhirEngine | ||
| private lateinit var fhirOperator: FhirOperator | ||
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| private val fhirContext = FhirContext.forCached(FhirVersionEnum.R4) | ||
| private val jsonParser = fhirContext.newJsonParser() | ||
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| private fun open(asset: String): InputStream? { | ||
| return javaClass.getResourceAsStream(asset) | ||
| } | ||
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| private fun load(asset: String): Bundle { | ||
| return jsonParser.parseResource(open(asset)) as Bundle | ||
| } | ||
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| @Before | ||
| fun setUp() = runBlocking { | ||
| fhirEngine = FhirEngineProvider.getInstance(ApplicationProvider.getApplicationContext()) | ||
| fhirOperator = FhirOperator(fhirContext, fhirEngine) | ||
| } | ||
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| /** | ||
| * Evaluates a compiled CQL that was exported to Jxson and included inside a FHIRLibrary Json. The | ||
| * compiled CQL file is encoded in Base64 and placed inside the JSON Library. The expression | ||
| * `CompletedImmunization` simply checks if a vaccination protocol has been finished as below. | ||
| * | ||
| * This test requires the CQLEvaluator to | ||
| * 1. load the patient using a `FhirEngineRetrieveProvider`, | ||
| * 2. load the Immunization records of that patient, | ||
| * 3. load the CQL Library using a `FhirEngineLibraryContentProvider` | ||
| * 4. evaluate if the immunization record presents a Protocol where the number of doses taken | ||
| * matches the number of required doses or if the number of required doses is null. | ||
| * | ||
| * ``` | ||
| * library ImmunityCheck version '1.0.0' | ||
| * | ||
| * using FHIR version '4.0.0' | ||
| * include "FHIRHelpers" version '4.0.0' called FHIRHelpers | ||
| * context Immunization | ||
| * | ||
| * define "CompletedImmunization": | ||
| * exists(GetFinalDose) or exists(GetSingleDose) | ||
| * | ||
| * define "GetFinalDose": | ||
| * [Immunization] I | ||
| * where exists(I.protocolApplied) | ||
| * and I.protocolApplied.doseNumber.value = I.protocolApplied.seriesDoses.value | ||
| * | ||
| * define "GetSingleDose": | ||
| * [Immunization] I | ||
| * where exists(I.protocolApplied) | ||
| * and exists(I.protocolApplied.doseNumber.value) | ||
| * and not exists(I.protocolApplied.seriesDoses.value) | ||
| * ``` | ||
| */ | ||
| @Test | ||
| fun evaluateImmunityCheck() = runBlocking { | ||
| // Load patient | ||
| val patientImmunizationHistory = load("/immunity-check/ImmunizationHistory.json") | ||
| for (entry in patientImmunizationHistory.entry) { | ||
| fhirEngine.create(entry.resource) | ||
| } | ||
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| // Load Library that checks if Patient has taken a vaccine | ||
| fhirOperator.loadLibs(load("/immunity-check/ImmunityCheck.json")) | ||
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| // Evaluates a specific Patient | ||
| val results = | ||
| fhirOperator.evaluateLibrary( | ||
| "http://localhost/Library/ImmunityCheck|1.0.0", | ||
| "d4d35004-24f8-40e4-8084-1ad75924514f", | ||
| setOf("CompletedImmunization") | ||
| ) as | ||
| Parameters | ||
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| assertThat(results.getParameterBool("CompletedImmunization")).isTrue() | ||
| } | ||
| } |
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