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

CHANGELOG.md

@@ -5,6 +5,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.0] - 2024-xx-xx
+
+### Changed
+- Upgrade to latest Android FHIR SDK version includes
+    1. an upgrade to the HAPI FHIR libraries used to process StructureMaps. In the previous libraries `$this.id` returned `[ResourceType]/[ID #]`, the new libraries return `[ID #]`. Therefore, any existing StructureMaps that call `$this.id` will need to replace that with `$this.type().name + '/' + $this.id` to have the equivalent output.
+    2. changes to Measure evaluation that requires all Measure JSON files to be rebuilt.
+    3. change to some [MetadataResources](https://hl7.org/fhir/R5/metadataresource.html) that requires they are referenced by URL and not ID. Any existing content that referes to StructureMaps by ID must be updated to refer to it by URL. If we are not storing a URL for it, we will need to add that. E.g. `Library.url`, `Plandefinition.url` because the `FhirOperator` API uses that field to uniquely identify/retrieve the Metadata resource.
+    4. for CQL evaluation, the context is referred to using `%subject` and not `$this`. The latter is reserved for FHIRPath expressions while the  former is used for CQL expressions to refer to the primary subject of the expression e.g. patient.
+
 ## [0.2.4] - 2023-06-24
 ### Added
 - Insights feature to show stats on any _Unsynced_ Resources on the device

android/build.gradle.kts

@@ -6,22 +6,23 @@ import org.jetbrains.dokka.base.DokkaBaseConfiguration
 // Top-level build file where you can add configuration options common to all sub-projects/modules.
 buildscript {
   dependencies {
-    classpath("de.mannodermaus.gradle.plugins:android-junit5:1.8.2.1")
-    classpath("com.android.tools.build:gradle:7.1.3")
-    classpath("org.jetbrains.dokka:dokka-base:1.8.20")
+    classpath(libs.kotlin.gradle.plugin)
+    classpath(libs.coveralls.gradle.plugin)
+    classpath(libs.gradle)
+    classpath(libs.dokka.base)
   }
 }
 
-@Suppress("DSL_SCOPE_VIOLATION")
 plugins {
-  id("com.github.kt3k.coveralls") version "2.12.0"
-  id("org.jetbrains.kotlin.jvm") version "1.8.10"
+  alias(libs.plugins.org.jetbrains.kotlin.jvm)
+  alias(libs.plugins.kt3k.coveralls)
   alias(libs.plugins.kotlin.serialization)
   alias(libs.plugins.dagger.hilt.android) apply false
   alias(libs.plugins.androidx.navigation.safeargs) apply false
   alias(libs.plugins.org.jetbrains.dokka)
   alias(libs.plugins.org.owasp.dependencycheck)
-  alias(libs.plugins.com.diffplug.spotless)
+  alias(libs.plugins.com.diffplug.spotless) apply false
+  alias(libs.plugins.android.junit5) apply false
 
 }
 
@@ -36,6 +37,7 @@ tasks.dokkaHtmlMultiModule {
 
 allprojects {
   repositories {
+    gradlePluginPortal()
     mavenLocal()
     google()
     mavenCentral()
@@ -89,16 +91,16 @@ subprojects {
     resolutionStrategy {
       eachDependency {
         when (requested.group) {
-          "org.jacoco" -> useVersion("0.8.7")
+          "org.jacoco" -> useVersion("0.8.11")
         }
       }
     }
   }
 
-  tasks.withType<Test> {
+ tasks.withType<Test> {
     configure<JacocoTaskExtension> {
       isIncludeNoLocationClasses = true
-      excludes = listOf("jdk.internal.*")
+      excludes = listOf("jdk.internal.*", "**org.hl7*")
     }
   }
 }

android/buildSrc/build.gradle.kts

@@ -0,0 +1,9 @@
+plugins {
+    `kotlin-dsl`
+}
+
+repositories {
+    google()
+    gradlePluginPortal()
+    mavenCentral()
+}

android/buildSrc/src/main/kotlin/Dependencies.kt

@@ -0,0 +1,144 @@
+/*
+ * Copyright 2023-2024 Google LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * 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.
+ */
+
+import org.gradle.api.artifacts.Configuration
+import org.gradle.api.artifacts.DependencyConstraint
+import org.gradle.kotlin.dsl.exclude
+
+object Dependencies {
+
+  object HapiFhir {
+    const val fhirBaseModule = "ca.uhn.hapi.fhir:hapi-fhir-base"
+    const val fhirClientModule = "ca.uhn.hapi.fhir:hapi-fhir-client"
+    const val structuresDstu2Module = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2"
+    const val structuresDstu3Module = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3"
+    const val structuresR4Module = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4"
+    const val structuresR4bModule = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4b"
+    const val structuresR5Module = "ca.uhn.hapi.fhir:hapi-fhir-structures-r5"
+
+    const val validationModule = "ca.uhn.hapi.fhir:hapi-fhir-validation"
+    const val validationDstu3Module = "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3"
+    const val validationR4Module = "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4"
+    const val validationR5Module = "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5"
+
+    const val fhirCoreDstu2Module = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2"
+    const val fhirCoreDstu2016Module = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may"
+    const val fhirCoreDstu3Module = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3"
+    const val fhirCoreR4Module = "ca.uhn.hapi.fhir:org.hl7.fhir.r4"
+    const val fhirCoreR4bModule = "ca.uhn.hapi.fhir:org.hl7.fhir.r4b"
+    const val fhirCoreR5Module = "ca.uhn.hapi.fhir:org.hl7.fhir.r5"
+    const val fhirCoreUtilsModule = "ca.uhn.hapi.fhir:org.hl7.fhir.utilities"
+    const val fhirCoreConvertorsModule = "ca.uhn.hapi.fhir:org.hl7.fhir.convertors"
+
+    const val guavaCachingModule = "ca.uhn.hapi.fhir:hapi-fhir-caching-guava"
+
+    const val fhirBase = "$fhirBaseModule:${Versions.hapiFhir}"
+    const val fhirClient = "$fhirClientModule:${Versions.hapiFhir}"
+    const val structuresDstu2 = "$structuresDstu2Module:${Versions.hapiFhir}"
+    const val structuresDstu3 = "$structuresDstu3Module:${Versions.hapiFhir}"
+    const val structuresR4 = "$structuresR4Module:${Versions.hapiFhir}"
+    const val structuresR4b = "$structuresR4bModule:${Versions.hapiFhir}"
+    const val structuresR5 = "$structuresR5Module:${Versions.hapiFhir}"
+
+    const val validation = "$validationModule:${Versions.hapiFhir}"
+    const val validationDstu3 = "$validationDstu3Module:${Versions.hapiFhir}"
+    const val validationR4 = "$validationR4Module:${Versions.hapiFhir}"
+    const val validationR5 = "$validationR5Module:${Versions.hapiFhir}"
+
+    const val fhirCoreDstu2 = "$fhirCoreDstu2Module:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu2016 = "$fhirCoreDstu2016Module:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu3 = "$fhirCoreDstu3Module:${Versions.hapiFhirCore}"
+    const val fhirCoreR4 = "$fhirCoreR4Module:${Versions.hapiFhirCore}"
+    const val fhirCoreR4b = "$fhirCoreR4bModule:${Versions.hapiFhirCore}"
+    const val fhirCoreR5 = "$fhirCoreR5Module:${Versions.hapiFhirCore}"
+    const val fhirCoreUtils = "$fhirCoreUtilsModule:${Versions.hapiFhirCore}"
+    const val fhirCoreConvertors = "$fhirCoreConvertorsModule:${Versions.hapiFhirCore}"
+
+    const val guavaCaching = "$guavaCachingModule:${Versions.hapiFhir}"
+  }
+
+  object Jackson {
+    private const val mainGroup = "com.fasterxml.jackson"
+    private const val coreGroup = "$mainGroup.core"
+    private const val dataformatGroup = "$mainGroup.dataformat"
+    private const val datatypeGroup = "$mainGroup.datatype"
+    private const val moduleGroup = "$mainGroup.module"
+
+    const val annotationsBase = "$coreGroup:jackson-annotations:${Versions.jackson}"
+    const val bomBase = "$mainGroup:jackson-bom:${Versions.jackson}"
+    const val coreBase = "$coreGroup:jackson-core:${Versions.jacksonCore}"
+    const val databindBase = "$coreGroup:jackson-databind:${Versions.jackson}"
+    const val dataformatXmlBase = "$dataformatGroup:jackson-dataformat-xml:${Versions.jackson}"
+    const val jaxbAnnotationsBase =
+      "$moduleGroup:jackson-module-jaxb-annotations:${Versions.jackson}"
+    const val jsr310Base = "$datatypeGroup:jackson-datatype-jsr310:${Versions.jackson}"
+  }
+
+  object Versions {
+    const val hapiFhir = "6.8.0"
+    const val hapiFhirCore = "6.0.22"
+
+    // Maximum Jackson libraries (excluding core) version that supports Android API Level 24:
+    // https://github.com/FasterXML/jackson-databind/issues/3658
+    const val jackson = "2.13.5"
+
+    // Maximum Jackson Core library version that supports Android API Level 24:
+    const val jacksonCore = "2.15.2"
+  }
+
+  fun Configuration.removeIncompatibleDependencies() {
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(module = "xmlpull")
+    exclude(module = "javax.json")
+    exclude(module = "jcl-over-slf4j")
+    exclude(group = "org.apache.httpcomponents")
+    exclude(group = "org.antlr", module = "antlr4")
+    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
+    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+  }
+
+  fun hapiFhirConstraints(): Map<String, DependencyConstraint.() -> Unit> {
+    return mutableMapOf<String, DependencyConstraint.() -> Unit>(
+      HapiFhir.fhirBaseModule to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.fhirClientModule to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.fhirCoreConvertorsModule to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreDstu2Module to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreDstu2016Module to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreDstu3Module to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreR4Module to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreR4bModule to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreR5Module to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.fhirCoreUtilsModule to { version { strictly(Versions.hapiFhirCore) } },
+      HapiFhir.structuresDstu2Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.structuresDstu3Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.structuresR4Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.structuresR5Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.validationModule to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.validationDstu3Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.validationR4Module to { version { strictly(Versions.hapiFhir) } },
+      HapiFhir.validationR5Module to { version { strictly(Versions.hapiFhir) } },
+              Jackson.annotationsBase to { version { strictly(Versions.jackson) } },
+      Jackson.bomBase to { version { strictly(Versions.jackson) } },
+      Jackson.coreBase to { version { strictly(Versions.jacksonCore) } },
+      Jackson.databindBase to { version { strictly(Versions.jackson) } },
+      Jackson.jaxbAnnotationsBase to { version { strictly(Versions.jackson) } },
+      Jackson.jsr310Base to { version { strictly(Versions.jackson) } },
+      Jackson.dataformatXmlBase to { version { strictly(Versions.jackson) } },
+    )
+  }
+}