From 603792f4e865ba3c736565d40672eda3a587ad97 Mon Sep 17 00:00:00 2001 From: Jing Tang Date: Fri, 2 Aug 2024 12:42:01 +0100 Subject: [PATCH] Rename install API to index for file in knowledge manager (#2634) * Rename install to index for file * Revert workflow unit tests since they use published knowledge manager * Remove extra dependency in workflow build file * Address review comments * Fix smart immunizations test * Update knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt Co-authored-by: aditya-07 * Update knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt Co-authored-by: aditya-07 * Run spotless --------- Co-authored-by: aditya-07 --- .../fhir/knowledge/KnowledgeManager.kt | 187 +++++++++++------- .../db/entities/ImplementationGuideEntity.kt | 7 +- .../fhir/knowledge/KnowledgeManagerTest.kt | 63 +++--- .../care_plan.json | 12 +- .../med-request/med_request_careplan.json | 10 +- .../benchmark/F_CqlEvaluatorBenchmark.kt | 2 +- workflow/build.gradle.kts | 12 +- .../CarePlan/CarePlan.json | 10 +- .../FhirOperatorLibraryEvaluateTest.kt | 8 +- .../workflow/SmartImmunizationAndroidTest.kt | 4 +- .../FhirOperatorLibraryEvaluateJavaTest.kt | 8 +- .../android/fhir/workflow/FhirOperatorTest.kt | 6 +- .../fhir/workflow/SmartImmunizationTest.kt | 4 +- 13 files changed, 194 insertions(+), 139 deletions(-) diff --git a/knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt b/knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt index e319fa79c9..3a3a956c6f 100644 --- a/knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt +++ b/knowledge/src/main/java/com/google/android/fhir/knowledge/KnowledgeManager.kt @@ -21,22 +21,19 @@ import androidx.room.Room import ca.uhn.fhir.context.FhirContext import ca.uhn.fhir.parser.IParser import com.google.android.fhir.knowledge.db.KnowledgeDatabase +import com.google.android.fhir.knowledge.db.entities.ImplementationGuideEntity import com.google.android.fhir.knowledge.db.entities.ResourceMetadataEntity -import com.google.android.fhir.knowledge.db.entities.toEntity import com.google.android.fhir.knowledge.files.NpmFileManager import com.google.android.fhir.knowledge.npm.NpmPackageDownloader import com.google.android.fhir.knowledge.npm.OkHttpNpmPackageDownloader import java.io.File import java.io.FileInputStream -import java.io.FileOutputStream import kotlinx.coroutines.Dispatchers import kotlinx.coroutines.withContext import org.hl7.fhir.instance.model.api.IBaseResource import org.hl7.fhir.r4.context.IWorkerContext import org.hl7.fhir.r4.context.SimpleWorkerContext -import org.hl7.fhir.r4.model.IdType import org.hl7.fhir.r4.model.MetadataResource -import org.hl7.fhir.r4.model.Resource import org.hl7.fhir.r4.model.ResourceType import org.hl7.fhir.utilities.npm.NpmPackage import timber.log.Timber @@ -46,9 +43,20 @@ import timber.log.Timber * individually as JSON files or from FHIR NPM packages. * * Coordinates the management of knowledge artifacts by using the three following components: - * - database: indexing knowledge artifacts stored in the local file system, - * - file manager: managing files containing the knowledge artifacts, and - * - NPM downloader: downloading from an NPM package server the knowledge artifacts. + * - knowledgeDatabase: indexing knowledge artifacts stored in the local file system, + * - npmFileManager: managing files containing the knowledge artifacts, and + * - npmPackageDownloader: downloading the knowledge artifacts from an NPM package server . + * + * Knowledge artifacts are scoped by the application. Multiple applications using the knowledge + * manager will not share the same sets of knowledge artifacts. + * + * See [Clinical Reasoning](https://hl7.org/fhir/R4/clinicalreasoning-module.html) for the formal + * definition of knowledge artifacts. In this implementation, however, knowledge artifacts are + * represented as [MetadataResource]s. + * + * **Note** that the list of resources implementing the [MetadataResource] class differs from the + * list of resources implementing the + * [MetadataResource interface](https://www.hl7.org/fhir/R5/metadataresource.html) in FHIR R5. */ class KnowledgeManager internal constructor( @@ -60,9 +68,11 @@ internal constructor( private val knowledgeDao = knowledgeDatabase.knowledgeDao() /** - * Checks if the [fhirNpmPackages] are present in DB. If necessary, downloads the dependencies - * from NPM and imports data from the package manager (populates the metadata of the FHIR - * Resources). + * Downloads and installs the [fhirNpmPackages] from the NPM package server with transitive + * dependencies. The NPM packages will be unzipped to a directory managed by the knowledge + * manager. The resources will be indexed in the database for future retrieval. + * + * FHIR NPM packages already present in the database will be skipped. */ suspend fun install(vararg fhirNpmPackages: FhirNpmPackage) { fhirNpmPackages @@ -81,7 +91,7 @@ internal constructor( try { val localFhirNpmPackageMetadata = npmFileManager.getLocalFhirNpmPackageMetadata(it.name, it.version) - install(it, localFhirNpmPackageMetadata.rootDirectory) + import(it, localFhirNpmPackageMetadata.rootDirectory) install(*localFhirNpmPackageMetadata.dependencies.toTypedArray()) } catch (e: Exception) { Timber.w("Unable to install package ${it.name} ${it.version}") @@ -90,35 +100,70 @@ internal constructor( } /** - * Checks if the [fhirNpmPackage] is present in DB. If necessary, populates the database with the - * metadata of FHIR Resource from the provided [rootDirectory]. + * Imports the content of the [fhirNpmPackage] from the provided [rootDirectory] by indexing the + * metadata of the FHIR resources for future retrieval. + * + * FHIR NPM packages already present in the database will be skipped. */ - suspend fun install(fhirNpmPackage: FhirNpmPackage, rootDirectory: File) { + suspend fun import(fhirNpmPackage: FhirNpmPackage, rootDirectory: File) { // TODO(ktarasenko) copy files to the safe space? - val igId = knowledgeDao.insert(fhirNpmPackage.toEntity(rootDirectory)) - rootDirectory.listFiles()?.sorted()?.forEach { file -> - try { - val resource = jsonParser.parseResource(FileInputStream(file)) - if (resource is Resource) { - val newId = indexResourceFile(igId, resource, file) - resource.setId(IdType(resource.resourceType.name, newId)) - - // Overrides the Id in the file - FileOutputStream(file).use { - it.write(jsonParser.encodeResourceToString(resource).toByteArray()) - } - } else { - Timber.d("Unable to import file: %file") - } - } catch (exception: Exception) { - Timber.d(exception, "Unable to import file: %file") - } + val implementationGuideId = + knowledgeDao.insert( + ImplementationGuideEntity( + 0L, + fhirNpmPackage.canonical ?: "", + fhirNpmPackage.name, + fhirNpmPackage.version, + rootDirectory, + ), + ) + val files = rootDirectory.listFiles() ?: return + files.sorted().forEach { file -> + // Ignore files that are not meta resources instead of throwing exceptions since unzipped + // NPM package might contain other types of files e.g. package.json. + val resource = readMetadataResourceOrNull(file) ?: return@forEach + knowledgeDao.insertResource( + implementationGuideId, + ResourceMetadataEntity( + 0, + resource.resourceType, + resource.url, + resource.name, + resource.version, + file, + ), + ) } } - /** Imports the Knowledge Artifact from the provided [file] to the default dependency. */ - suspend fun install(file: File) { - importFile(null, file) + /** + * Indexes a knowledge artifact as a JSON object in the provided [file]. + * + * This creates a record of the knowledge artifact's metadata and the file's location. When the + * knowledge artifact is requested, knowledge manager will load the content of the file, + * deserialize it and return the resulting FHIR resource. + * + * This operation does not make a copy of the knowledge artifact, nor does it checksum the content + * of the file. Therefore, it cannot be guaranteed that subsequent retrievals of the knowledge + * artifact will produce the same result. Applications using this function must be aware of the + * risk of the content of the file being modified or corrupt, potentially resulting in incorrect + * or inaccurate result of decision support or measure evaluation. + * + * Use this API for knowledge artifacts in immutable files (e.g. in the app's `assets` folder). + */ + suspend fun index(file: File) { + val resource = readMetadataResourceOrThrow(file) + knowledgeDao.insertResource( + null, + ResourceMetadataEntity( + 0L, + resource.resourceType, + resource.url, + resource.name, + resource.version, + file, + ), + ) } /** Loads resources from IGs listed in dependencies. */ @@ -141,7 +186,7 @@ internal constructor( name != null -> knowledgeDao.getResourcesWithName(resType, name) else -> knowledgeDao.getResources(resType) } - return resourceEntities.map { loadResource(it) } + return resourceEntities.map { readMetadataResourceOrThrow(it.resourceFile)!! } } /** Deletes Implementation Guide, cleans up files. */ @@ -155,43 +200,6 @@ internal constructor( } } - private suspend fun importFile(igId: Long?, file: File) { - val resource = - withContext(Dispatchers.IO) { - try { - FileInputStream(file).use(jsonParser::parseResource) - } catch (exception: Exception) { - Timber.d(exception, "Unable to import file: $file. Parsing to FhirResource failed.") - } - } - when (resource) { - is Resource -> { - val newId = indexResourceFile(igId, resource, file) - resource.setId(IdType(resource.resourceType.name, newId)) - - // Overrides the Id in the file - FileOutputStream(file).use { - it.write(jsonParser.encodeResourceToString(resource).toByteArray()) - } - } - } - } - - private suspend fun indexResourceFile(igId: Long?, resource: Resource, file: File): Long { - val metadataResource = resource as? MetadataResource - val res = - ResourceMetadataEntity( - 0L, - resource.resourceType, - metadataResource?.url, - metadataResource?.name, - metadataResource?.version, - file, - ) - - return knowledgeDao.insertResource(igId, res) - } - /** * Loads and initializes a worker context with the specified npm packages. * @@ -220,8 +228,37 @@ internal constructor( } } - private fun loadResource(resourceEntity: ResourceMetadataEntity): IBaseResource { - return jsonParser.parseResource(FileInputStream(resourceEntity.resourceFile)) + /** + * Parses and returns the content of a file containing a FHIR resource in JSON, or null if the + * file does not contain a FHIR resource. + */ + private suspend fun readResourceOrNull(file: File): IBaseResource? = + withContext(Dispatchers.IO) { + try { + FileInputStream(file).use(jsonParser::parseResource) + } catch (e: Exception) { + Timber.e(e, "Unable to load resource from $file") + null + } + } + + /** + * Parses and returns the content of a file containing a FHIR metadata resource in JSON, or null + * if the file does not contain a FHIR metadata resource. + */ + private suspend fun readMetadataResourceOrNull(file: File) = + readResourceOrNull(file) as? MetadataResource + + /** + * Parses and returns the content of a file containing a FHIR metadata resource in JSON, or throws + * an exception if the file does not contain a FHIR metadata resource. + */ + private suspend fun readMetadataResourceOrThrow(file: File): MetadataResource { + val resource = readResourceOrNull(file)!! + check(resource is MetadataResource) { + "Resource ${resource.idElement} is not a MetadataResource" + } + return resource } companion object { diff --git a/knowledge/src/main/java/com/google/android/fhir/knowledge/db/entities/ImplementationGuideEntity.kt b/knowledge/src/main/java/com/google/android/fhir/knowledge/db/entities/ImplementationGuideEntity.kt index 8d2a1804e0..91e53a6d82 100644 --- a/knowledge/src/main/java/com/google/android/fhir/knowledge/db/entities/ImplementationGuideEntity.kt +++ b/knowledge/src/main/java/com/google/android/fhir/knowledge/db/entities/ImplementationGuideEntity.kt @@ -1,5 +1,5 @@ /* - * Copyright 2022-2023 Google LLC + * Copyright 2022-2024 Google LLC * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -19,7 +19,6 @@ package com.google.android.fhir.knowledge.db.entities import androidx.room.Entity import androidx.room.Index import androidx.room.PrimaryKey -import com.google.android.fhir.knowledge.FhirNpmPackage import java.io.File /** @@ -45,7 +44,3 @@ internal data class ImplementationGuideEntity( /** Directory where the Implementation Guide files are stored */ val rootDirectory: File, ) - -internal fun FhirNpmPackage.toEntity(rootFolder: File): ImplementationGuideEntity { - return ImplementationGuideEntity(0L, canonical ?: "", name, version, rootFolder) -} diff --git a/knowledge/src/test/java/com/google/android/fhir/knowledge/KnowledgeManagerTest.kt b/knowledge/src/test/java/com/google/android/fhir/knowledge/KnowledgeManagerTest.kt index abef67cbee..48cdefd60f 100644 --- a/knowledge/src/test/java/com/google/android/fhir/knowledge/KnowledgeManagerTest.kt +++ b/knowledge/src/test/java/com/google/android/fhir/knowledge/KnowledgeManagerTest.kt @@ -25,11 +25,14 @@ import com.google.android.fhir.knowledge.db.KnowledgeDatabase import com.google.android.fhir.knowledge.files.NpmFileManager import com.google.common.truth.Truth.assertThat import java.io.File +import kotlinx.coroutines.runBlocking import kotlinx.coroutines.test.runTest +import org.hl7.fhir.r4.model.BaseResource import org.hl7.fhir.r4.model.Library -import org.hl7.fhir.r4.model.MetadataResource +import org.hl7.fhir.r4.model.Patient import org.hl7.fhir.r4.model.PlanDefinition import org.junit.After +import org.junit.Assert.assertThrows import org.junit.Test import org.junit.runner.RunWith import org.robolectric.RobolectricTestRunner @@ -65,7 +68,7 @@ internal class KnowledgeManagerTest { @Test fun `importing IG creates entries in DB`() = runTest { - knowledgeManager.install(fhirNpmPackage, dataFolder) + knowledgeManager.import(fhirNpmPackage, dataFolder) val implementationGuideId = knowledgeDb.knowledgeDao().getImplementationGuide("anc-cds", "0.3.0")!!.implementationGuideId @@ -81,9 +84,10 @@ internal class KnowledgeManagerTest { @Test fun `deleting IG deletes files and DB entries`() = runTest { val igRoot = File(dataFolder.parentFile, "anc-cds.copy") + igRoot.deleteRecursively() igRoot.deleteOnExit() dataFolder.copyRecursively(igRoot) - knowledgeManager.install(fhirNpmPackage, igRoot) + knowledgeManager.import(fhirNpmPackage, igRoot) knowledgeManager.delete(fhirNpmPackage) @@ -93,7 +97,7 @@ internal class KnowledgeManagerTest { @Test fun `imported entries are readable`() = runTest { - knowledgeManager.install(fhirNpmPackage, dataFolder) + knowledgeManager.import(fhirNpmPackage, dataFolder) assertThat(knowledgeManager.loadResources(resourceType = "Library", name = "WHOCommon")) .isNotNull() @@ -112,7 +116,16 @@ internal class KnowledgeManagerTest { } @Test - fun `inserting a library of a different version creates new entry`() = runTest { + fun `indexing non metadata resource should throw an exception`() { + val patient = Patient().apply { id = "Patient/defaultA-A.1.0.0" } + + assertThrows(IllegalStateException::class.java) { + runBlocking { knowledgeManager.index(writeToFile(patient)) } + } + } + + @Test + fun `should index a library of a different version`() = runTest { val libraryAOld = Library().apply { id = "Library/defaultA-A.1.0.0" @@ -128,8 +141,8 @@ internal class KnowledgeManagerTest { version = "A.1.0.1" } - knowledgeManager.install(writeToFile(libraryAOld)) - knowledgeManager.install(writeToFile(libraryANew)) + knowledgeManager.index(writeToFile(libraryAOld)) + knowledgeManager.index(writeToFile(libraryANew)) val resources = knowledgeDb.knowledgeDao().getResources() assertThat(resources).hasSize(2) @@ -137,14 +150,14 @@ internal class KnowledgeManagerTest { val resourceA100 = knowledgeManager .loadResources(resourceType = "Library", name = "defaultA", version = "A.1.0.0") - .single() - assertThat(resourceA100.idElement.toString()).isEqualTo("Library/1") + .single() as Library + assertThat(resourceA100.version).isEqualTo("A.1.0.0") val resourceA101 = knowledgeManager .loadResources(resourceType = "Library", name = "defaultA", version = "A.1.0.1") - .single() - assertThat(resourceA101.idElement.toString()).isEqualTo("Library/2") + .single() as Library + assertThat(resourceA101.version.toString()).isEqualTo("A.1.0.1") } fun `installing from npmPackageManager`() = runTest { @@ -182,19 +195,20 @@ internal class KnowledgeManagerTest { url = commonUrl } - knowledgeManager.install(writeToFile(libraryWithSameUrl)) - knowledgeManager.install(writeToFile(planDefinitionWithSameUrl)) + knowledgeManager.index(writeToFile(libraryWithSameUrl)) + knowledgeManager.index(writeToFile(planDefinitionWithSameUrl)) val resources = knowledgeDb.knowledgeDao().getResources() assertThat(resources).hasSize(2) val libraryLoadedByUrl = - knowledgeManager.loadResources(resourceType = "Library", url = commonUrl).single() - assertThat(libraryLoadedByUrl.idElement.toString()).isEqualTo("Library/1") + knowledgeManager.loadResources(resourceType = "Library", url = commonUrl).single() as Library + assertThat(libraryLoadedByUrl.name.toString()).isEqualTo("LibraryName") val planDefinitionLoadedByUrl = knowledgeManager.loadResources(resourceType = "PlanDefinition", url = commonUrl).single() - assertThat(planDefinitionLoadedByUrl.idElement.toString()).isEqualTo("PlanDefinition/2") + as PlanDefinition + assertThat(planDefinitionLoadedByUrl.name.toString()).isEqualTo("PlanDefinitionName") } @Test @@ -215,25 +229,26 @@ internal class KnowledgeManagerTest { version = "0" } - knowledgeManager.install(writeToFile(libraryWithSameUrl)) - knowledgeManager.install(writeToFile(planDefinitionWithSameUrl)) + knowledgeManager.index(writeToFile(libraryWithSameUrl)) + knowledgeManager.index(writeToFile(planDefinitionWithSameUrl)) val resources = knowledgeDb.knowledgeDao().getResources() assertThat(resources).hasSize(2) val libraryLoadedByUrl = - knowledgeManager.loadResources(resourceType = "Library", url = commonUrl).single() - assertThat(libraryLoadedByUrl.idElement.toString()).isEqualTo("Library/1") + knowledgeManager.loadResources(resourceType = "Library", url = commonUrl).single() as Library + assertThat(libraryLoadedByUrl.name.toString()).isEqualTo("LibraryName") val planDefinitionLoadedByUrl = knowledgeManager.loadResources(resourceType = "PlanDefinition", url = commonUrl).single() - assertThat(planDefinitionLoadedByUrl.idElement.toString()).isEqualTo("PlanDefinition/2") + as PlanDefinition + assertThat(planDefinitionLoadedByUrl.name.toString()).isEqualTo("PlanDefinitionName") } - private fun writeToFile(metadataResource: MetadataResource): File { - return File(context.filesDir, metadataResource.id).apply { + private fun writeToFile(resource: BaseResource): File { + return File(context.filesDir, resource.id).apply { this.parentFile?.mkdirs() - writeText(jsonParser.encodeResourceToString(metadataResource)) + writeText(jsonParser.encodeResourceToString(resource)) } } } diff --git a/workflow-testing/src/main/resources/plan-definition/cql-applicability-condition/care_plan.json b/workflow-testing/src/main/resources/plan-definition/cql-applicability-condition/care_plan.json index 131bb2fc7d..3779b876d0 100644 --- a/workflow-testing/src/main/resources/plan-definition/cql-applicability-condition/care_plan.json +++ b/workflow-testing/src/main/resources/plan-definition/cql-applicability-condition/care_plan.json @@ -1,9 +1,9 @@ { "resourceType": "CarePlan", - "id": "17", + "id": "Plan-Definition-Example", "contained": [ { "resourceType": "RequestGroup", - "id": "17", + "id": "Plan-Definition-Example", "instantiatesCanonical": [ "http://example.com/PlanDefinition/Plan-Definition-Example" ], "status": "draft", "intent": "proposal", @@ -20,15 +20,15 @@ } } ], "resource": { - "reference": "Task/16" + "reference": "Task/Activity-Example" } } ] }, { "resourceType": "Task", - "id": "16", + "id": "Activity-Example", "instantiatesCanonical": "http://example.com/ActivityDefinition/Activity-Example", "basedOn": [ { - "reference": "RequestGroup/17" + "reference": "RequestGroup/Plan-Definition-Example" } ], "status": "draft", "intent": "proposal", @@ -45,7 +45,7 @@ }, "activity": [ { "reference": { - "reference": "#RequestGroup/17" + "reference": "#RequestGroup/Plan-Definition-Example" } } ] } \ No newline at end of file diff --git a/workflow-testing/src/main/resources/plan-definition/med-request/med_request_careplan.json b/workflow-testing/src/main/resources/plan-definition/med-request/med_request_careplan.json index 8e7b401c7b..f152723d04 100644 --- a/workflow-testing/src/main/resources/plan-definition/med-request/med_request_careplan.json +++ b/workflow-testing/src/main/resources/plan-definition/med-request/med_request_careplan.json @@ -1,10 +1,10 @@ { "resourceType": "CarePlan", - "id": "17", + "id": "MedRequest-Example", "contained": [ { "resourceType": "RequestGroup", - "id": "17", + "id": "MedRequest-Example", "instantiatesCanonical": [ "http://localhost/PlanDefinition/MedRequest-Example" ], @@ -18,14 +18,14 @@ "id": "medication-action-1", "title": "Administer Medication 1", "resource": { - "reference": "medication-action-1-16" + "reference": "medication-action-1-MedicationRequest-1" } } ] }, { "resourceType": "MedicationRequest", - "id": "medication-action-1-16", + "id": "medication-action-1-MedicationRequest-1", "status": "draft", "intent": "order", "medicationCodeableConcept": { @@ -50,7 +50,7 @@ "activity": [ { "reference": { - "reference": "#RequestGroup/17" + "reference": "#RequestGroup/MedRequest-Example" } } ] diff --git a/workflow/benchmark/src/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt b/workflow/benchmark/src/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt index dc63e1fc5c..4c3d40fbe1 100644 --- a/workflow/benchmark/src/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt +++ b/workflow/benchmark/src/androidTest/java/com/google/android/fhir/workflow/benchmark/F_CqlEvaluatorBenchmark.kt @@ -68,7 +68,7 @@ class F_CqlEvaluatorBenchmark { for (entry in patientImmunizationHistory.entry) { fhirEngine.create(entry.resource) } - knowledgeManager.install( + knowledgeManager.index( File(context.filesDir, lib.name).apply { writeText(jsonParser.encodeResourceToString(lib)) }, diff --git a/workflow/build.gradle.kts b/workflow/build.gradle.kts index 83e5d49f56..3d2696e944 100644 --- a/workflow/build.gradle.kts +++ b/workflow/build.gradle.kts @@ -114,8 +114,18 @@ dependencies { testImplementation(libs.androidx.test.core) testImplementation(libs.junit) testImplementation(libs.truth) - testImplementation(project(mapOf("path" to ":knowledge"))) testImplementation(project(":workflow-testing")) + testImplementation(project(":knowledge")) + + configurations.all { + if (name.contains("test", ignoreCase = true)) { + resolutionStrategy.dependencySubstitution { + // To test the workflow library against the latest Knowledge Manager APIs, substitute the + // dependency on the released Knowledge Manager library with the current build. + substitute(module(Dependencies.androidFhirKnowledge)).using(project(":knowledge")) + } + } + } constraints { Dependencies.hapiFhirConstraints().forEach { (libName, constraints) -> diff --git a/workflow/sampledata/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/CarePlan/CarePlan.json b/workflow/sampledata/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/CarePlan/CarePlan.json index 8996cb92fc..50b5053423 100644 --- a/workflow/sampledata/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/CarePlan/CarePlan.json +++ b/workflow/sampledata/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/CarePlan/CarePlan.json @@ -1,10 +1,10 @@ { "resourceType": "CarePlan", - "id": "26", + "id": "IMMZD2DTMeasles", "contained": [ { "resourceType": "RequestGroup", - "id": "26", + "id": "IMMZD2DTMeasles", "instantiatesCanonical": [ "http://fhir.org/guides/who/smart-immunization/PlanDefinition/IMMZD2DTMeasles|0.1.0" ], @@ -28,14 +28,14 @@ } ], "resource": { - "reference": "MedicationRequest/1" + "reference": "MedicationRequest/IMMZD2DTMeaslesMR" } } ] }, { "resourceType": "MedicationRequest", - "id": "1", + "id": "IMMZD2DTMeaslesMR", "meta": { "profile": [ "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-immunizationrequest" @@ -77,7 +77,7 @@ "activity": [ { "reference": { - "reference": "#RequestGroup/26" + "reference": "#RequestGroup/IMMZD2DTMeasles" } } ] diff --git a/workflow/src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt b/workflow/src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt index 345bc28049..f42ecfb020 100644 --- a/workflow/src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt +++ b/workflow/src/androidTest/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateTest.kt @@ -121,7 +121,7 @@ class FhirOperatorLibraryEvaluateTest { } // Load Library that checks if Patient has taken a vaccine - knowledgeManager.install(copy("/immunity-check/ImmunityCheck.json")) + knowledgeManager.index(copy("/immunity-check/ImmunityCheck.json")) // Evaluates a specific Patient val results = @@ -142,8 +142,8 @@ class FhirOperatorLibraryEvaluateTest { } // Load Library that checks if Patient has taken a vaccine - knowledgeManager.install(copy("/immunity-check/ImmunityCheck.json")) - knowledgeManager.install(copy("/immunity-check/FhirHelpers.json")) + knowledgeManager.index(copy("/immunity-check/ImmunityCheck.json")) + knowledgeManager.index(copy("/immunity-check/FhirHelpers.json")) val location = """ @@ -185,7 +185,7 @@ class FhirOperatorLibraryEvaluateTest { } // Load Library that checks if Patient has taken a vaccine - knowledgeManager.install(copy("/immunity-check/ImmunityCheck.json")) + knowledgeManager.index(copy("/immunity-check/ImmunityCheck.json")) // Evaluates a specific Patient val results = diff --git a/workflow/src/androidTest/java/com/google/android/fhir/workflow/SmartImmunizationAndroidTest.kt b/workflow/src/androidTest/java/com/google/android/fhir/workflow/SmartImmunizationAndroidTest.kt index 32f88a275a..f562b3ae13 100644 --- a/workflow/src/androidTest/java/com/google/android/fhir/workflow/SmartImmunizationAndroidTest.kt +++ b/workflow/src/androidTest/java/com/google/android/fhir/workflow/SmartImmunizationAndroidTest.kt @@ -116,7 +116,7 @@ class SmartImmunizationAndroidTest { moveAllIGResourcesIntoFilesDir("smart-imm") - knowledgeManager.install( + knowledgeManager.import( FhirNpmPackage( "who.fhir.immunization", "1.0.0", @@ -136,8 +136,6 @@ class SmartImmunizationAndroidTest { ) .single() - assertThat(planDef.idElement.idPart).isEqualTo("26") - val patient = load( "/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/Patient/Patient-IMMZ-Patient-NoVaxeninfant-f.json", diff --git a/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt b/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt index be66a40615..96e6982b9d 100644 --- a/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt +++ b/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorLibraryEvaluateJavaTest.kt @@ -110,8 +110,8 @@ class FhirOperatorLibraryEvaluateJavaTest { } // Load Library that checks if Patient has taken a vaccine - knowledgeManager.install(writeToFile(load("/immunity-check/ImmunityCheck.json") as Library)) - knowledgeManager.install(writeToFile(load("/immunity-check/FhirHelpers.json") as Library)) + knowledgeManager.index(writeToFile(load("/immunity-check/ImmunityCheck.json") as Library)) + knowledgeManager.index(writeToFile(load("/immunity-check/FhirHelpers.json") as Library)) // Evaluates a specific Patient val results = @@ -137,7 +137,7 @@ class FhirOperatorLibraryEvaluateJavaTest { val library = CqlBuilder.assembleFhirLib(cql, null, null, "TestGetName", "1.0.0") - knowledgeManager.install(writeToFile(library)) + knowledgeManager.index(writeToFile(library)) // Evaluates expression without any extra data val results = @@ -162,7 +162,7 @@ class FhirOperatorLibraryEvaluateJavaTest { val library = CqlBuilder.assembleFhirLib(cql, null, null, "TestSumWithParams", "1.0.0") - knowledgeManager.install(writeToFile(library)) + knowledgeManager.index(writeToFile(library)) val params = Parameters().apply { diff --git a/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorTest.kt b/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorTest.kt index 287faceef8..f9b4ff4ff2 100644 --- a/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorTest.kt +++ b/workflow/src/test/java/com/google/android/fhir/workflow/FhirOperatorTest.kt @@ -61,7 +61,7 @@ class FhirOperatorTest { // Installing ANC CDS to the IGManager val rootDirectory = File(javaClass.getResource("/anc-cds")!!.file) - knowledgeManager.install( + knowledgeManager.import( FhirNpmPackage( "com.google.android.fhir", "1.0.0", @@ -281,7 +281,9 @@ class FhirOperatorTest { } private suspend fun installToIgManager(resource: Resource) { - knowledgeManager.install(writeToFile(resource)) + try { + knowledgeManager.index(writeToFile(resource)) + } catch (_: Exception) {} } private fun writeToFile(resource: Resource): File { diff --git a/workflow/src/test/java/com/google/android/fhir/workflow/SmartImmunizationTest.kt b/workflow/src/test/java/com/google/android/fhir/workflow/SmartImmunizationTest.kt index 85d46f13d2..cdfde7e17f 100644 --- a/workflow/src/test/java/com/google/android/fhir/workflow/SmartImmunizationTest.kt +++ b/workflow/src/test/java/com/google/android/fhir/workflow/SmartImmunizationTest.kt @@ -63,7 +63,7 @@ class SmartImmunizationTest { // Installing SmartImmunizations IG into the IGManager val rootDirectory = File(javaClass.getResource("/smart-imm/ig/")!!.file) - knowledgeManager.install( + knowledgeManager.import( FhirNpmPackage( "who.fhir.immunization", "1.0.0", @@ -83,8 +83,6 @@ class SmartImmunizationTest { ) .firstOrNull() - assertThat(planDef?.idElement?.idPart).isEqualTo("26") - loader.loadFile( "/smart-imm/tests/IMMZ-Patient-NoVaxeninfant-f/Patient/Patient-IMMZ-Patient-NoVaxeninfant-f.json", ::importToFhirEngine,