Upgrade sdk libraries to latest versions

.github/workflows/apk-release.yml

@@ -40,10 +40,10 @@ jobs:
         with:
           fetch-depth: 2
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew

.github/workflows/ci.yml

@@ -29,10 +29,10 @@ jobs:
         with:
           fetch-depth: 2
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
@@ -101,10 +101,10 @@ jobs:
         with:
           fetch-depth: 2
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
@@ -172,10 +172,10 @@ jobs:
         with:
           fetch-depth: 2
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
@@ -221,9 +221,10 @@ jobs:
           force-avd-creation: true
           emulator-options: -no-snapshot-save -no-window -gpu swiftshader_indirect -noaudio -no-boot-anim -camera-back none
           disable-animations: true
-          script: ./gradlew -PlocalPropertiesFile=local.properties :quest:clean && ./gradlew -PlocalPropertiesFile=local.properties :quest:assembleOpensrpDebugAndroidTest --stacktrace && /Users/runner/Library/Android/sdk/platform-tools/adb install quest/build/outputs/apk/androidTest/opensrp/debug/quest-opensrp-debug-androidTest.apk && ./gradlew -PlocalPropertiesFile=local.properties :quest:assembleOpensrpDebug --stacktrace && /Users/runner/Library/Android/sdk/platform-tools/adb install quest/build/outputs/apk/opensrp/debug/quest-opensrp-debug.apk && /Users/runner/Library/Android/sdk/platform-tools/adb shell am instrument -w -e notPackage org.smartregister.fhircore.quest.performance -e coverage "true" org.smartregister.opensrp.test/org.smartregister.fhircore.quest.QuestTestRunner && /Users/runner/Library/Android/sdk/platform-tools/adb shell run-as org.smartregister.opensrp cat "/data/data/org.smartregister.opensrp/files/coverage.ec" > quest/coverage.ec && ./gradlew -PlocalPropertiesFile=local.properties :quest:fhircoreJacocoReport --stacktrace
+          script: ./gradlew clean  -PlocalPropertiesFile=local.properties :quest:fhircoreJacocoReport --stacktrace -Pandroid.testInstrumentationRunnerArguments.notPackage=org.smartregister.fhircore.quest.performance
+          # ./gradlew -PlocalPropertiesFile=local.properties :quest:clean && ./gradlew -PlocalPropertiesFile=local.properties :quest:assembleOpensrpDebugAndroidTest --stacktrace && /Users/runner/Library/Android/sdk/platform-tools/adb install quest/build/outputs/apk/androidTest/opensrp/debug/quest-opensrp-debug-androidTest.apk && ./gradlew -PlocalPropertiesFile=local.properties :quest:assembleOpensrpDebug --stacktrace && /Users/runner/Library/Android/sdk/platform-tools/adb install quest/build/outputs/apk/opensrp/debug/quest-opensrp-debug.apk && /Users/runner/Library/Android/sdk/platform-tools/adb shell am instrument -w -e package org.smartregister.fhircore.quest.ui.profile -e coverage "true" org.smartregister.opensrp.test/org.smartregister.fhircore.quest.QuestTestRunner && /Users/runner/Library/Android/sdk/platform-tools/adb shell run-as org.smartregister.opensrp cat "/data/user/0/org.smartregister.opensrp/files/coverage.ec" > quest/coverage.ec && ./gradlew -PlocalPropertiesFile=local.properties :quest:fhircoreJacocoReport --stacktrace
 
       - name: Upload Quest module test coverage report to Codecov
         if: matrix.api-level == 30 # Only upload coverage on API level 30
         working-directory: android
-        run:  bash <(curl -s https://codecov.io/bash) -F quest -f "quest/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"
+        run:  bash <(curl -s https://codecov.io/bash) -F quest -f "quest/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"

.github/workflows/docs.yml

@@ -40,10 +40,10 @@ jobs:
       - name: Checkout 🛎️
         uses: actions/checkout@v2.3.1
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew

.github/workflows/performance-tests.yml

@@ -27,10 +27,10 @@ jobs:
         with:
           fetch-depth: 2
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
@@ -80,4 +80,4 @@ jobs:
 
       - name: Check performance results
         working-directory: android
-        run: ./gradlew :quest:evaluatePerformanceBenchmarkResults --stacktrace
+        run: ./gradlew :quest:evaluatePerformanceBenchmarkResults --stacktrace

.github/workflows/sonarqube.yml

@@ -20,10 +20,10 @@ jobs:
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
 
       - name: Cache SonarQube packages
         uses: actions/cache@v1

android/build.gradle.kts

@@ -11,14 +11,14 @@ buildscript {
   }
 
   dependencies {
-    classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:1.8.10")
-    classpath("org.jetbrains.kotlin:kotlin-serialization:1.8.10")
+    classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:1.8.20")
+    classpath("org.jetbrains.kotlin:kotlin-serialization:1.8.20")
     classpath("com.google.dagger:hilt-android-gradle-plugin:2.45")
     classpath("androidx.navigation:navigation-safe-args-gradle-plugin:2.5.3")
     classpath("com.diffplug.spotless:spotless-plugin-gradle:6.19.0")
     classpath("gradle.plugin.org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.12.0")
     classpath("de.mannodermaus.gradle.plugins:android-junit5:1.8.2.1")
-    classpath("com.android.tools.build:gradle:7.1.3")
+    classpath("com.android.tools.build:gradle:8.0.2")
     classpath("org.jetbrains.dokka:dokka-base:1.8.20")
     classpath("org.owasp:dependency-check-gradle:8.2.1")
   }
@@ -93,16 +93,17 @@ subprojects {
     resolutionStrategy {
       eachDependency {
         when (requested.group) {
-          "org.jacoco" -> useVersion("0.8.7")
+          "org.jacoco" -> useVersion("0.8.11")
         }
       }
+      force("com.google.guava:guava:32.1.2-android")
     }
   }
 
-  tasks.withType<Test> {
+ tasks.withType<Test> {
     configure<JacocoTaskExtension> {
       isIncludeNoLocationClasses = true
-      excludes = listOf("jdk.internal.*")
+      excludes = listOf("jdk.internal.*", "**org.hl7*")
     }
   }
 }

android/engine/build.gradle.kts

@@ -19,9 +19,10 @@ plugins {
 android {
   compileSdk = 34
 
+  namespace = "org.smartregister.fhircore.engine"
+
   defaultConfig {
     minSdk = 26
-    targetSdk = 34
     testInstrumentationRunner = "org.smartregister.fhircore.engine.EngineTestRunner"
     consumerProguardFiles("consumer-rules.pro")
     buildConfigField(
@@ -32,7 +33,7 @@ android {
   }
 
   buildTypes {
-    getByName("debug") { isTestCoverageEnabled = true }
+    getByName("debug") { enableUnitTestCoverage = true }
 
     create("debugNonProxy") {
       initWith(getByName("debug"))
@@ -50,21 +51,22 @@ android {
   }
   compileOptions {
     isCoreLibraryDesugaringEnabled = true
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
+    sourceCompatibility = JavaVersion.VERSION_17
+    targetCompatibility = JavaVersion.VERSION_17
   }
   kotlinOptions {
-    jvmTarget = JavaVersion.VERSION_11.toString()
+    jvmTarget = JavaVersion.VERSION_17.toString()
     freeCompilerArgs = listOf("-Xjvm-default=all-compatibility")
   }
   buildFeatures {
     compose = true
     viewBinding = true
     dataBinding = true
+    buildConfig = true
   }
-  composeOptions { kotlinCompilerExtensionVersion = "1.4.3" }
+  composeOptions { kotlinCompilerExtensionVersion = "1.4.6" }
 
-  packagingOptions {
+  packaging {
     resources.excludes.addAll(
       listOf(
         "license.html",
@@ -98,7 +100,7 @@ android {
     }
   }
 
-  testCoverage { jacocoVersion = "0.8.7" }
+  testCoverage { jacocoVersion = "0.8.11" }
 }
 
 tasks.withType<Test> {
@@ -135,34 +137,20 @@ dependencies {
   implementation(libs.compressor)
   implementation(libs.xercesImpl)
   implementation(libs.msg.simple)
-  implementation(libs.cqf.cql.engine)
-  implementation(libs.cql.engine.jackson)
   implementation(libs.dagger.hilt.android)
   implementation(libs.hilt.work)
   implementation(libs.slf4j.nop)
-  implementation(libs.cqf.cql.evaluator) {
-    exclude(group = "com.github.ben-manes.caffeine")
-    exclude(group = "ca.uhn.hapi.fhir")
-  }
-  implementation(libs.cql.evaluator.builder) {
-    exclude(group = "com.github.ben-manes.caffeine")
-    exclude(group = "ca.uhn.hapi.fhir")
-  }
-  implementation(libs.cql.evaluator.plandefinition) {
-    exclude(group = "com.github.ben-manes.caffeine")
-    exclude(group = "ca.uhn.hapi.fhir")
-  }
-  implementation(libs.cql.evaluator.dagger) {
-    exclude(group = "com.github.ben-manes.caffeine")
-    exclude(group = "ca.uhn.hapi.fhir")
+  api("org.opencds.cqf.fhir:cqf-fhir-cr:3.0.0-PRE9") {
+    exclude(group = "org.codelibs", module = "xpp3")
+    exclude(group = "org.slf4j", module = "jcl-over-slf4j")
   }
 
   // Shared dependencies
   api(libs.glide)
-  api(libs.knowledger)
+  api(libs.knowledge) { exclude(group = "org.slf4j", module = "jcl-over-slf4j") }
   api(libs.p2p.lib)
   api(libs.jjwt)
-  api(libs.fhir.common.utils)
+  api(libs.fhir.common.utils) { exclude(group = "org.slf4j", module = "jcl-over-slf4j") }
   api(libs.lifecycle.livedata.ktx)
   api(libs.lifecycle.viewmodel.ktx)
   api(libs.ui)
@@ -181,15 +169,12 @@ dependencies {
   api(libs.paging.compose)
   api(libs.activity.compose)
   api(libs.kotlinx.serialization.json)
-  api(libs.accompanist.flowlayout)
-  api(libs.accompanist.placeholder)
   api(libs.work.runtime.ktx)
   api(libs.prettytime)
   api(libs.kotlinx.coroutines.core)
   api(libs.kotlinx.coroutines.android)
   api(libs.kotlin.reflect)
   api(libs.stax.api)
-  api(libs.caffeine)
   api(libs.gson)
   api(libs.timber)
   api(libs.retrofit)
@@ -207,13 +192,14 @@ dependencies {
     isTransitive = true
     exclude(group = "ca.uhn.hapi.fhir")
     exclude(group = "com.google.android.fhir", module = "engine")
+    exclude(group = "com.google.android.fhir", module = "common")
+    exclude(group = "org.slf4j", module = "jcl-over-slf4j")
   }
   api(libs.workflow) {
     isTransitive = true
     exclude(group = "xerces")
     exclude(group = "com.github.java-json-tools")
     exclude(group = "org.codehaus.woodstox")
-    exclude(group = "ca.uhn.hapi.fhir")
     exclude(group = "com.google.android.fhir", module = "common")
     exclude(group = "com.google.android.fhir", module = "engine")
     exclude(group = "com.github.ben-manes.caffeine")

android/engine/src/main/AndroidManifest.xml

@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android"
-    xmlns:tools="http://schemas.android.com/tools"
-    package="org.smartregister.fhircore.engine">
+    xmlns:tools="http://schemas.android.com/tools">
 
     <uses-permission android:name="android.permission.INTERNET" />
     <uses-permission android:name="android.permission.ACCESS_NETWORK_STATE" />

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

@@ -18,6 +18,7 @@ package org.smartregister.fhircore.engine.configuration
 
 import android.content.Context
 import android.database.SQLException
+import android.os.Process
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.db.ResourceNotFoundException
 import com.google.android.fhir.get
@@ -84,6 +85,12 @@ constructor(
   private val supportedFileExtensions = listOf("json", "properties")
   private var _isNonProxy = BuildConfig.IS_NON_PROXY_APK
 
+  init {
+    Thread.setDefaultUncaughtExceptionHandler { thread, throwable ->
+      Process.killProcess(Process.myPid())
+    }
+  }
+
   /**
    * Retrieve configuration for the provided [ConfigType]. The JSON retrieved from [configsJsonMap]
    * can be directly converted to a FHIR resource or hard coded custom model. The filtering assumes
@@ -545,7 +552,7 @@ constructor(
   suspend fun create(vararg resources: Resource) {
     return withContext(dispatcherProvider.io()) {
       resources.onEach { it.generateMissingId() }
-      fhirEngine.createRemote(*resources)
+      fhirEngine.create(*resources, isLocalOnly = true)
     }
   }
 

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/DefaultRepository.kt

@@ -160,7 +160,7 @@ constructor(
   suspend fun createRemote(addResourceTags: Boolean = true, vararg resource: Resource) {
     return withContext(dispatcherProvider.io()) {
       preProcessResources(addResourceTags, *resource)
-      fhirEngine.createRemote(*resource)
+      fhirEngine.create(*resource, isLocalOnly = true)
     }
   }
 

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

@@ -65,6 +65,15 @@ class CoreModule {
 
   @Singleton
   @Provides
-  fun provideFhirOperator(fhirEngine: FhirEngine): FhirOperator =
-    FhirOperator(fhirContext = FhirContext.forCached(FhirVersionEnum.R4), fhirEngine = fhirEngine)
+  fun provideFhirOperator(
+    @ApplicationContext context: Context,
+    fhirContext: FhirContext,
+    fhirEngine: FhirEngine,
+    knowledgeManager: KnowledgeManager,
+  ): FhirOperator =
+    FhirOperator.Builder(context)
+      .fhirEngine(fhirEngine)
+      .fhirContext(fhirContext)
+      .knowledgeManager(knowledgeManager)
+      .build()
 }