Ig manager integration with the workflow library (#1854)

* Integrate IgManager

* Address review comments

* Address review comments

* Address review comments

* Address review comments

* Workaround #1920 : lookup by id in IgManager

* Address review comments

* Make implementationGuide field in the db optional, remove the concept of the "default ig" and use `null` instead

benchmark/build.gradle.kts

@@ -87,6 +87,7 @@ dependencies {
  androidTestImplementation(Dependencies.truth)
 
  androidTestImplementation(project(":engine"))
+ androidTestImplementation(project(":implementationguide"))
  androidTestImplementation(project(":workflow"))
  androidTestImplementation(project(":workflow-testing"))
 }

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/G_CqlEvaluatorBenchmark.kt

@@ -16,18 +16,22 @@
 
 package com.google.android.fhir.benchmark
 
+import android.content.Context
 import androidx.benchmark.junit4.BenchmarkRule
 import androidx.benchmark.junit4.measureRepeated
 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.FhirEngineProvider
-import com.google.android.fhir.workflow.FhirOperator
+import com.google.android.fhir.implementationguide.IgManager
+import com.google.android.fhir.workflow.FhirOperatorBuilder
 import com.google.common.truth.Truth.assertThat
+import java.io.File
 import java.io.InputStream
 import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.r4.model.Bundle
+import org.hl7.fhir.r4.model.Library
 import org.hl7.fhir.r4.model.Parameters
 import org.junit.Rule
 import org.junit.Test
@@ -48,20 +52,30 @@ class G_CqlEvaluatorBenchmark {
  val fhirOperator = runWithTimingDisabled {
  val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
  val jsonParser = fhirContext.newJsonParser()
+ val context: Context = ApplicationProvider.getApplicationContext()
 
  val patientImmunizationHistory =
  jsonParser.parseResource(open("/immunity-check/ImmunizationHistory.json")) as Bundle
  val fhirEngine = FhirEngineProvider.getInstance(ApplicationProvider.getApplicationContext())
+ val igManager = IgManager.createInMemory(context)
+ val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Library
 
  runBlocking {
  for (entry in patientImmunizationHistory.entry) {
  fhirEngine.create(entry.resource)
  }
+ igManager.install(
+ File(context.filesDir, lib.name).apply {
+ writeText(jsonParser.encodeResourceToString(lib))
+ }
+ )
  }
 
- val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Bundle
-
- FhirOperator(fhirContext, fhirEngine).also { it.loadLibs(lib) }
+ FhirOperatorBuilder(context)
+ .withFhirContext(fhirContext)
+ .withFhirEngine(fhirEngine)
+ .withIgManager(igManager)
+ .build()
  }
 
  val results =

implementationguide/build.gradle.kts

@@ -25,9 +25,9 @@ android {
  }
 
  sourceSets {
- getByName("androidTest").apply { resources.setSrcDirs(listOf("sampledata")) }
+ getByName("androidTest").apply { resources.setSrcDirs(listOf("testdata")) }
 
- getByName("test").apply { resources.setSrcDirs(listOf("sampledata")) }
+ getByName("test").apply { resources.setSrcDirs(listOf("testdata")) }
  }
 
  buildTypes {

implementationguide/src/main/java/com/google/android/fhir/implementationguide/IgManager.kt

@@ -24,25 +24,27 @@ import com.google.android.fhir.implementationguide.db.impl.entities.ResourceMeta
 import com.google.android.fhir.implementationguide.db.impl.entities.toEntity
 import java.io.File
 import java.io.FileInputStream
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.withContext
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.MetadataResource
 import org.hl7.fhir.r4.model.Resource
 import org.hl7.fhir.r4.model.ResourceType
 import timber.log.Timber
 
 /** Responsible for importing, accessing and deleting Implementation Guides. */
-class IgManager internal constructor(igDatabase: ImplementationGuideDatabase) {
+class IgManager internal constructor(private val igDatabase: ImplementationGuideDatabase) {
 
  private val igDao = igDatabase.implementationGuideDao()
  private val jsonParser = FhirContext.forR4().newJsonParser()
 
  /**
- * * Checks if the [igDependencies] are present in DB. If necessary, downloads the dependencies
- * from NPM and imports data from the package manager (populates the metadata of the FHIR
- * Resorces)
+ * * Checks if the [implementationGuides] 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)
  */
- suspend fun install(vararg igDependencies: ImplementationGuide) {
- TODO("not implemented yet")
+ suspend fun install(vararg implementationGuides: ImplementationGuide) {
+ TODO("[1937]Not implemented yet ")
  }
 
  /**
@@ -68,20 +70,22 @@ class IgManager internal constructor(igDatabase: ImplementationGuideDatabase) {
 
  /** Imports the IG from the provided [file] to the default dependency. */
  suspend fun install(file: File) {
- TODO("not implemented yet")
+ importFile(null, file)
  }
 
  /** Loads resources from IGs listed in dependencies. */
  suspend fun loadResources(
  resourceType: String,
  url: String? = null,
+ id: String? = null,
  name: String? = null,
  version: String? = null,
  ): Iterable<IBaseResource> {
  val resType = ResourceType.fromCode(resourceType)
  val resourceEntities =
  when {
  url != null -> listOfNotNull(igDao.getResourceWithUrl(url))
+ id != null -> listOfNotNull(igDao.getResourceWithUrlLike("%$id"))
  name != null && version != null ->
  listOfNotNull(igDao.getResourcesWithNameAndVersion(resType, name, version))
  name != null -> igDao.getResourcesWithName(resType, name)
@@ -94,12 +98,28 @@ class IgManager internal constructor(igDatabase: ImplementationGuideDatabase) {
  suspend fun delete(vararg igDependencies: ImplementationGuide) {
  igDependencies.forEach { igDependency ->
  val igEntity = igDao.getImplementationGuide(igDependency.packageId, igDependency.version)
- igDao.deleteImplementationGuide(igEntity)
- igEntity.rootDirectory.deleteRecursively()
+ if (igEntity != null) {
+ igDao.deleteImplementationGuide(igEntity)
+ igEntity.rootDirectory.deleteRecursively()
+ }
+ }
+ }
+
+ 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 -> importResource(igId, resource, file)
  }
  }
 
- private suspend fun importResource(igId: Long, resource: Resource, file: File) {
+ private suspend fun importResource(igId: Long?, resource: Resource, file: File) {
  val metadataResource = resource as? MetadataResource
  val res =
  ResourceMetadataEntity(
@@ -117,6 +137,10 @@ class IgManager internal constructor(igDatabase: ImplementationGuideDatabase) {
  return jsonParser.parseResource(FileInputStream(resourceEntity.resourceFile))
  }
 
+ fun close() {
+ igDatabase.close()
+ }
+
  companion object {
  private const val DB_NAME = "implementationguide.db"
 

implementationguide/src/main/java/com/google/android/fhir/implementationguide/db/impl/dao/ImplementationGuideDao.kt

@@ -33,7 +33,7 @@ abstract class ImplementationGuideDao {
 
  @Transaction
  internal open suspend fun insertResource(
- implementationGuideId: Long,
+ implementationGuideId: Long?,
  resource: ResourceMetadataEntity,
  ) {
 
@@ -47,14 +47,16 @@ abstract class ImplementationGuideDao {
  // exception if they
  // are different.
  val resourceMetadataId = resourceMetadata?.resourceMetadataId ?: insert(resource)
- insert(ImplementationGuideResourceMetadataEntity(implementationGuideId, resourceMetadataId))
+ insert(ImplementationGuideResourceMetadataEntity(0, implementationGuideId, resourceMetadataId))
  }
 
  @Transaction
  internal open suspend fun deleteImplementationGuide(name: String, version: String) {
  val igEntity = getImplementationGuide(name, version)
- deleteImplementationGuide(igEntity)
- deleteOrphanedResources()
+ if (igEntity != null) {
+ deleteImplementationGuide(igEntity)
+ deleteOrphanedResources()
+ }
  }
 
  @Query(
@@ -71,7 +73,7 @@ abstract class ImplementationGuideDao {
  internal abstract suspend fun getImplementationGuide(
  packageId: String,
  version: String?,
- ): ImplementationGuideEntity
+ ): ImplementationGuideEntity?
 
  @Query("SELECT * from ResourceMetadataEntity")
  internal abstract suspend fun getResources(): List<ResourceMetadataEntity>
@@ -85,6 +87,11 @@ abstract class ImplementationGuideDao {
  internal abstract suspend fun getResourceWithUrl(
  url: String,
  ): ResourceMetadataEntity?
+ // Remove after https://github.com/google/android-fhir/issues/1920
+ @Query("SELECT * from ResourceMetadataEntity WHERE url LIKE :urlPart")
+ internal abstract suspend fun getResourceWithUrlLike(
+ urlPart: String,
+ ): ResourceMetadataEntity?
 
  @Query(
  "SELECT * from ResourceMetadataEntity WHERE resourceType = :resourceType AND name = :name"

implementationguide/src/main/java/com/google/android/fhir/implementationguide/db/impl/entities/ImplementationGuideResourceMetadataEntity.kt

@@ -21,12 +21,17 @@ import androidx.room.Entity
 import androidx.room.ForeignKey
 import androidx.room.Index
 import androidx.room.Junction
+import androidx.room.PrimaryKey
 import androidx.room.Relation
 
 /** Connects [ImplementationGuideEntity] to [ResourceMetadataEntity]. */
 @Entity(
- primaryKeys = ["implementationGuideId", "resourceMetadataId"],
- indices = [Index(value = ["implementationGuideId"]), Index(value = ["resourceMetadataId"])],
+ indices =
+ [
+ Index(value = ["implementationGuideId"]),
+ Index(value = ["resourceMetadataId"]),
+ Index(value = ["implementationGuideId", "resourceMetadataId"], unique = true)
+ ],
  foreignKeys =
  [
  ForeignKey(
@@ -44,7 +49,8 @@ import androidx.room.Relation
  ]
 )
 internal data class ImplementationGuideResourceMetadataEntity(
- val implementationGuideId: Long,
+ @PrimaryKey(autoGenerate = true) val id: Long,
+ val implementationGuideId: Long?,
  val resourceMetadataId: Long,
 )
 
@@ -55,5 +61,5 @@ internal data class ImplementationGuideWithResources(
  entityColumn = "resourceMetadataId",
  associateBy = Junction(ImplementationGuideResourceMetadataEntity::class)
  )
- val resources: List<ResourceMetadataEntity>
+ val resources: List<ResourceMetadataEntity>,
 )

implementationguide/src/main/java/com/google/android/fhir/implementationguide/db/impl/entities/ResourceMetadataEntity.kt

@@ -37,8 +37,8 @@ internal data class ResourceMetadataEntity(
  @PrimaryKey(autoGenerate = true) val resourceMetadataId: Long,
  val resourceType: ResourceType,
  val url: String?,
- val version: String?,
  val name: String?,
+ val version: String?,
  /** Location of the JSON file with a full Resource. */
  val resourceFile: File,
 )

implementationguide/src/test/java/com/google/android/fhir/implementationguide/IgManagerTest.kt

@@ -47,16 +47,16 @@ internal class IgManagerTest {
  @Test
  fun `importing IG creates entries in DB`() = runTest {
  igManager.install(implementationGuide, dataFolder)
+ val implementationGuideId =
+ igDb
+ .implementationGuideDao()
+ .getImplementationGuide("anc-cds", "0.3.0")!!
+ .implementationGuideId
 
  assertThat(
  igDb
  .implementationGuideDao()
- .getImplementationGuidesWithResources(
- igDb
- .implementationGuideDao()
- .getImplementationGuide("anc-cds", "0.3.0")
- .implementationGuideId
- )
+ .getImplementationGuidesWithResources(implementationGuideId)
  ?.resources
  )
  .hasSize(6)

workflow-testing/src/main/resources/plan-definition/med-request/med_request_careplan.json

@@ -3,6 +3,9 @@
  "contained": [ {
  "resourceType": "RequestGroup",
  "id": "MedRequest-Example",
+ "instantiatesCanonical":[
+ "http:https://localhost/PlanDefinition/MedRequest-Example"
+ ],
  "status": "draft",
  "intent": "proposal",
  "subject": {
@@ -24,6 +27,9 @@
  "reference": "Patient/Patient-Example"
  }
  } ],
+ "instantiatesCanonical": [
+ "http:https://localhost/PlanDefinition/MedRequest-Example"
+ ],
  "status": "draft",
  "intent": "proposal",
  "subject": {

workflow-testing/src/main/resources/plan-definition/med-request/med_request_plan_definition.json

@@ -17,6 +17,7 @@
  "resource": {
  "resourceType" : "PlanDefinition",
  "id" : "MedRequest-Example",
+ "url" : "http:https://localhost/PlanDefinition/MedRequest-Example",
  "title" : "This example illustrates a medication request",
  "status" : "active",
  "action" : [{

workflow/build.gradle.kts

@@ -25,6 +25,12 @@ android {
  testInstrumentationRunnerArguments["package"] = "com.google.android.fhir.workflow"
  }
 
+ sourceSets {
+ getByName("androidTest").apply { resources.setSrcDirs(listOf("sampledata")) }
+
+ getByName("test").apply { resources.setSrcDirs(listOf("sampledata")) }
+ }
+
  // Added this for fixing out of memory issue in running test cases
  tasks.withType<Test>().configureEach {
  maxParallelForks = (Runtime.getRuntime().availableProcessors() - 1).takeIf { it > 0 } ?: 1
@@ -110,6 +116,7 @@ dependencies {
  implementation(Dependencies.Cql.translatorElmJackson) // Necessary to import XML/JSON CQL Libs
  implementation(Dependencies.Cql.translatorModel) // Overrides HAPI's old versions
  implementation(Dependencies.Cql.translatorModelJackson) // Necessary to import XML/JSON ModelInfos
+ implementation(Dependencies.timber)
 
  // Forces the most recent version of jackson, ignoring what dependencies use.
  // Remove these lines when HAPI 6.4 becomes available.
@@ -131,6 +138,7 @@ dependencies {
  implementation(Dependencies.Kotlin.stdlib)
  implementation(Dependencies.xerces)
  implementation(project(":engine"))
+ implementation(project(":implementationguide"))
 
  testImplementation(Dependencies.AndroidxTest.core)
  testImplementation(Dependencies.jsonAssert)