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