Migrate FHIR SDK

android/engine/build.gradle.kts

@@ -166,7 +166,6 @@ dependencies {
   api(libs.fhir.common.utils) { exclude(group = "org.slf4j", module = "jcl-over-slf4j") }
   api(libs.runtime.livedata)
   api(libs.foundation)
-  api(libs.fhir.common.utils)
   api(libs.kotlinx.serialization.json)
   api(libs.work.runtime.ktx)
   api(libs.prettytime)
@@ -210,7 +209,6 @@ dependencies {
   }
   api(libs.fhir.engine) {
     isTransitive = true
-    exclude(group = "com.google.android.fhir", module = "common")
     exclude(group = "com.github.ben-manes.caffeine")
   }
 

android/engine/src/main/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistry.kt

@@ -19,15 +19,13 @@
 import android.content.Context
 import android.database.SQLException
 import ca.uhn.fhir.context.ConfigurationException
-import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.parser.DataFormatException
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.db.ResourceNotFoundException
 import com.google.android.fhir.get
 import com.google.android.fhir.knowledge.KnowledgeManager
 import com.google.android.fhir.sync.download.ResourceSearchParams
 import dagger.hilt.android.qualifiers.ApplicationContext
-import java.io.File
 import java.io.FileNotFoundException
 import java.io.InputStreamReader
 import java.net.UnknownHostException
@@ -36,6 +34,8 @@
 import java.util.ResourceBundle
 import javax.inject.Inject
 import javax.inject.Singleton
+import kotlinx.coroutines.sync.Mutex
+import kotlinx.coroutines.sync.withLock
 import kotlinx.coroutines.withContext
 import kotlinx.serialization.json.Json
 import okhttp3.RequestBody.Companion.toRequestBody
@@ -60,6 +60,7 @@
 import org.smartregister.fhircore.engine.di.NetworkModule
 import org.smartregister.fhircore.engine.domain.model.MultiSelectViewAction
 import org.smartregister.fhircore.engine.util.DispatcherProvider
+import org.smartregister.fhircore.engine.util.KnowledgeManagerUtil
 import org.smartregister.fhircore.engine.util.SharedPreferenceKey
 import org.smartregister.fhircore.engine.util.SharedPreferencesHelper
 import org.smartregister.fhircore.engine.util.extension.camelCase
@@ -71,7 +72,6 @@
 import org.smartregister.fhircore.engine.util.extension.fileExtension
 import org.smartregister.fhircore.engine.util.extension.generateMissingId
 import org.smartregister.fhircore.engine.util.extension.interpolate
-import org.smartregister.fhircore.engine.util.extension.referenceValue
 import org.smartregister.fhircore.engine.util.extension.retrieveCompositionSections
 import org.smartregister.fhircore.engine.util.extension.retrieveRelatedEntitySyncLocationState
 import org.smartregister.fhircore.engine.util.extension.searchCompositionByIdentifier
@@ -100,8 +100,7 @@
   val localizationHelper: LocalizationHelper by lazy { LocalizationHelper(this) }
   private val supportedFileExtensions = listOf("json", "properties")
   private var _isNonProxy = BuildConfig.IS_NON_PROXY_APK
-  private val fhirContext = FhirContext.forR4Cached()
-  private val authConfiguration = configService.provideAuthConfiguration()
+  private val mutex = Mutex()
 
   /**
    * Retrieve configuration for the provided [ConfigType]. The JSON retrieved from [configsJsonMap]
@@ -409,6 +408,7 @@
    */
   @Throws(UnknownHostException::class, HttpException::class)
   suspend fun fetchNonWorkflowConfigResources() {
+    Timber.d("Triggered fetching application configurations remotely")
     configCacheMap.clear()
     sharedPreferencesHelper.read(SharedPreferenceKey.APP_ID.name, null)?.let { appId ->
       val parsedAppId = appId.substringBefore(TYPE_REFERENCE_DELIMITER).trim()
@@ -433,7 +433,11 @@
 
               chunkedResourceIdList.forEach { sectionComponents ->
                 Timber.d(
-                  "Fetching config resource ${entry.key}: with ids ${sectionComponents.joinToString(",")}",
+                  "Fetching config resource ${entry.key}: with ids ${
+                                        sectionComponents.joinToString(
+                                            ",",
+                                        )
+                                    }",
                 )
                 fetchResources(
                   resourceType = entry.key,
@@ -449,7 +453,7 @@
         // Save composition after fetching all the referenced section resources
         addOrUpdate(compositionResource)
 
-        Timber.d("Done fetching application configurations remotely")
+        Timber.d("Done saving composition resource")
       }
     }
   }
@@ -573,7 +577,7 @@
           if (bundleEntryComponent.resource != null) {
             addOrUpdate(bundleEntryComponent.resource)
             Timber.d(
-              "Fetched and processed resources ${bundleEntryComponent.resource.resourceType}/${bundleEntryComponent.resource.id}",
+              "Fetched and processed resources ${bundleEntryComponent.resource.resourceType}/${bundleEntryComponent.resource.idPart}",
             )
           }
         }
@@ -596,46 +600,29 @@
       }
 
       /**
-       * Knowledge manager [MetadataResource]s install Here we install all resources types of
+       * Knowledge manager [MetadataResource]s install. Here we install all resources types of
        * [MetadataResource] as per FHIR Spec.This supports future use cases as well
        */
       try {
-        if (resource is MetadataResource && resource.name != null) {
-          knowledgeManager.install(
-            writeToFile(resource.overwriteCanonicalURL()),
-          )
+        if (resource is MetadataResource) {
+          mutex.withLock {
+            knowledgeManager.install(
+              KnowledgeManagerUtil.writeToFile(
+                context = context,
+                configService = configService,
+                metadataResource = resource,
+                subFilePath =
+                  "${KnowledgeManagerUtil.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER}/${resource.resourceType}/${resource.idElement.idPart}.json",
+              ),
+            )
+          }
         }
       } catch (exception: Exception) {
         Timber.e(exception)
       }
     }
   }
 
-  private fun MetadataResource.overwriteCanonicalURL() =
-    this.apply {
-      url =
-        url
-          ?: """${authConfiguration.fhirServerBaseUrl.trimEnd { it == '/' }}/${this.referenceValue()}"""
-    }
-
-  fun writeToFile(resource: Resource): File {
-    val fileName =
-      if (resource is MetadataResource && resource.name != null) {
-        resource.name
-      } else {
-        resource.idElement.idPart
-      }
-
-    return File(
-        context.filesDir,
-        "$KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER/${resource.resourceType}/$fileName.json",
-      )
-      .apply {
-        this.parentFile?.mkdirs()
-        writeText(fhirContext.newJsonParser().encodeResourceToString(resource))
-      }
-  }
-
   /**
    * Using this [FhirEngine] and [DispatcherProvider], for all passed resources, make sure they all
    * have IDs or generate if they don't, then pass them to create.
@@ -818,7 +805,6 @@
     const val PAGINATION_NEXT = "next"
     const val RESOURCES_PATH = "resources/"
     const val SYNC_LOCATION_IDS = "_syncLocations"
-    const val KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER = "km"
 
     /**
      * The list of resources whose types can be synced down as part of the Composition configs.

android/engine/src/main/java/org/smartregister/fhircore/engine/di/CoreModule.kt

@@ -30,42 +30,71 @@ import dagger.hilt.components.SingletonComponent
 import java.io.File
 import java.io.FileInputStream
 import javax.inject.Singleton
+import kotlinx.coroutines.DelicateCoroutinesApi
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.GlobalScope
+import kotlinx.coroutines.launch
+import kotlinx.coroutines.withContext
 import org.hl7.fhir.r4.context.SimpleWorkerContext
 import org.hl7.fhir.r4.model.Parameters
 import org.hl7.fhir.r4.model.Resource
 import org.hl7.fhir.r4.utils.FHIRPathEngine
-import org.smartregister.fhircore.engine.configuration.ConfigurationRegistry
+import org.smartregister.fhircore.engine.util.KnowledgeManagerUtil
 import org.smartregister.fhircore.engine.util.helper.TransformSupportServices
+import timber.log.Timber
 
 @InstallIn(SingletonComponent::class)
 @Module
 class CoreModule {
 
+  @OptIn(DelicateCoroutinesApi::class)
   @Singleton
   @Provides
   fun provideWorkerContextProvider(@ApplicationContext context: Context): SimpleWorkerContext =
     SimpleWorkerContext().apply {
-      setExpansionProfile(Parameters())
-      isCanRunWithoutTerminology = true
-      context.filesDir
-        .resolve(ConfigurationRegistry.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER)
-        .list()
-        ?.forEach { resourceFolder ->
+      GlobalScope.launch {
+        withContext(Dispatchers.IO) {
+          setExpansionProfile(Parameters())
+          isCanRunWithoutTerminology = true
           context.filesDir
-            .resolve("${ConfigurationRegistry.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER}/$resourceFolder")
+            .resolve(KnowledgeManagerUtil.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER)
             .list()
-            ?.forEach { file ->
-              cacheResource(
-                FhirContext.forR4Cached()
-                  .newJsonParser()
-                  .parseResource(
-                    FileInputStream(
-                      File(context.filesDir.resolve("km/$resourceFolder/$file").toString()),
-                    ),
-                  ) as Resource,
-              )
+            ?.forEach { resourceFolder ->
+              context.filesDir
+                .resolve(
+                  "${KnowledgeManagerUtil.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER}/$resourceFolder",
+                )
+                .list()
+                ?.forEach { file ->
+                  try {
+                    cacheResource(
+                      FhirContext.forR4Cached()
+                        .newJsonParser()
+                        .parseResource(
+                          FileInputStream(
+                            File(
+                              context.filesDir
+                                .resolve(
+                                  "${KnowledgeManagerUtil.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER}/$resourceFolder/$file",
+                                )
+                                .toString(),
+                            ),
+                          ),
+                        ) as Resource,
+                    )
+                  } catch (e: Exception) {
+                    Timber.e(
+                      "EXCEPTION PROCESSING ${context.filesDir
+                                                .resolve(
+                                                    "${KnowledgeManagerUtil.KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER}/$resourceFolder/$file",
+                                                )}",
+                    )
+                    Timber.e(e)
+                  }
+                }
             }
         }
+      }
     }
 
   @Singleton

android/engine/src/main/java/org/smartregister/fhircore/engine/sync/AppSyncWorker.kt

@@ -24,6 +24,8 @@
 import com.google.android.fhir.sync.ConflictResolver
 import com.google.android.fhir.sync.DownloadWorkManager
 import com.google.android.fhir.sync.FhirSyncWorker
+import com.google.android.fhir.sync.upload.HttpCreateMethod
+import com.google.android.fhir.sync.upload.HttpUpdateMethod
 import com.google.android.fhir.sync.upload.UploadStrategy
 import dagger.assisted.Assisted
 import dagger.assisted.AssistedInject
@@ -50,5 +52,11 @@
 
   override fun getFhirEngine(): FhirEngine = openSrpFhirEngine
 
-  override fun getUploadStrategy(): UploadStrategy = UploadStrategy.AllChangesSquashedBundlePut
+  override fun getUploadStrategy(): UploadStrategy =
+    UploadStrategy.forBundleRequest(
+      methodForCreate = HttpCreateMethod.PUT,
+      methodForUpdate = HttpUpdateMethod.PATCH,
+      squash = true,
+      bundleSize = 500,
+    )
 }

android/engine/src/main/java/org/smartregister/fhircore/engine/util/KnowledgeManagerUtil.kt

@@ -0,0 +1,70 @@
+/*
+ * Copyright 2021-2024 Ona Systems, Inc
+ *
+ * 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.
+ */
+
+package org.smartregister.fhircore.engine.util
+
+import android.content.Context
+import ca.uhn.fhir.context.FhirContext
+import java.io.File
+import org.hl7.fhir.r4.model.MetadataResource
+import org.smartregister.fhircore.engine.configuration.app.AuthConfiguration
+import org.smartregister.fhircore.engine.configuration.app.ConfigService
+import org.smartregister.fhircore.engine.util.extension.referenceValue
+
+object KnowledgeManagerUtil {
+  const val KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER = "km"
+  private val fhirContext = FhirContext.forR4Cached()
+
+  /**
+   * Util method that creates a physical file and writes the Metadata FHIR resource content to it.
+   * Note the filepath provided is appended to the apps private directory as returned by
+   * Context.filesDir
+   *
+   * @param subFilePath the path of the file but within the apps private directory
+   *   {Context.filesDir}
+   * @param metadataResource the actual FHIR Resource of type MetadataResource
+   * @param configService the configuration service
+   * @param context the application context
+   * @return File the file object after creating and writing
+   */
+  fun writeToFile(
+    subFilePath: String,
+    metadataResource: MetadataResource,
+    configService: ConfigService,
+    context: Context,
+  ): File =
+    context
+      .createFileInPrivateDirectory(subFilePath)
+      .also { it.parentFile?.mkdirs() }
+      .apply {
+        writeText(
+          fhirContext
+            .newJsonParser()
+            .encodeResourceToString(
+              metadataResource.overwriteCanonicalURL(configService.provideAuthConfiguration()),
+            ),
+        )
+      }
+
+  private fun Context.createFileInPrivateDirectory(filePath: String) = File(this.filesDir, filePath)
+
+  private fun MetadataResource.overwriteCanonicalURL(authConfiguration: AuthConfiguration) =
+    this.apply {
+      url =
+        url
+          ?: """${authConfiguration.fhirServerBaseUrl.trimEnd { it == '/' }}/${this.referenceValue()}"""
+    }
+}