Merge branch 'master' of github.com:google/android-fhir into 2075-x-f…

…hir-query-support-for-variable

.github/actions/commonSetup/action.yml

@@ -8,9 +8,6 @@ runs:
       with:
         distribution: temurin
         java-version: "17"
-    - name: Make files executable
-      shell: bash
-      run: chmod +x ./gradlew
 
     - name: "Setup Gradle"
       uses: gradle/gradle-build-action@v2

.github/workflows/build.yml

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-name: "GitHub Actions: Build"
+name: "Build"
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 # events for the `master` branch
@@ -22,49 +22,65 @@ on:
     tags:
       build*
   pull_request:
+    # The branches below must be a subset of the branches above
     branches: [ master ]
+  schedule:
+    # Run once a week (even if no new code or PRs) to detect random regressions
+    - cron: '12 13 * * 2'
+
 env:
   # Allow precise monitoring of the save/restore of Gradle User Home by `gradle-build-action`
   # See https://github.com/marketplace/actions/gradle-build-action?version=v2.1.1#cache-debugging-and-analysis
   GRADLE_BUILD_ACTION_CACHE_DEBUG_ENABLED: true
   GRADLE_BUILD_ACTION_CACHE_KEY_PREFIX: "fhir" # change this to invalidate cache
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+
+concurrency:
+  # github.head_ref uniquely identifies Pull Requests (but is not available when building branches like main or master)
+  # github.ref is the fallback used when building for workflows triggered by push
+  # Note that || are fallback values (not "concatenations")
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true # Use e.g. ${{ github.ref != 'refs/heads/main' }} (or master, until #2180) to only cancel for PRs not on branch
+
+  # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # Build will compile APK, test APK and run tests, lint, etc.
   build:
+    runs-on: ubuntu-22.04-8core
+    timeout-minutes: 60
+    permissions:
+      actions: read
+      contents: read
 
-    runs-on: ubuntu-22.04-64core
+    strategy:
+      fail-fast: false
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      - name: Cancel previous
-        uses: styfle/cancel-workflow-action@0.7.0
-        with:
-          access_token: ${{ github.token }}
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout Repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # Fetch origin/master for spotless ratchet to work
           # https://github.com/diffplug/spotless/issues/1242
           fetch-depth: 0
+
       - name: Setup machine
         uses: ./.github/actions/commonSetup
 
       - name: Spotless check
-        run: ./gradlew spotlessCheck --scan --stacktrace
+        run: ./gradlew spotlessCheck --scan --full-stacktrace
 
-      - name: Build with Gradle
-        run: ./gradlew build --scan --stacktrace
+      - name: Build (full) with Gradle
+        run: ./gradlew build --scan --full-stacktrace
 
       - name: Check with Gradle
-        run: ./gradlew check --scan --stacktrace
+        run: ./gradlew check --scan --full-stacktrace
 
       - name: Release artifacts to local repo
         run: ./gradlew publishReleasePublicationToCIRepository --scan
       - name: Upload maven repo
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: maven-repository
           path: build/ci-repo
@@ -76,7 +92,7 @@ jobs:
       # Upload the build dir for all the modules for diagnosis
       - name: Upload build dir
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: build
           path: build.zip

.github/workflows/codeql.yaml

@@ -1,5 +1,24 @@
+# Copyright 2020 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.
+
 name: "CodeQL"
 
+# NB: This GitHub Action for https://codeql.github.com seems to be
+# a bit "special"; it does not appear to be (easily) possible to just
+# integrate and run this as part of the main build.yaml action; see
+# https://github.com/google/android-fhir/issues/2310.
+
 on:
   push:
     branches: [ "master" ]
@@ -9,10 +28,14 @@ on:
   schedule:
     - cron: '32 13 * * 2'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref || || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   analyze:
     name: Analyze
-    runs-on: ubuntu-22.04-64core
+    runs-on: ubuntu-22.04-8core
     timeout-minutes: 60
     permissions:
       actions: read
@@ -26,7 +49,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Switch to Java 17 from Eclipse Temurin distro
       uses: actions/setup-java@v3

.github/workflows/runFlank.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+#
+# Copyright 2022 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.
+#
+
+# Fail on any error.
+set -e
+
+lib_names=("workflow:benchmark" "engine:benchmark" "datacapture" "engine" "knowledge" "workflow")
+firebase_pids=()
+
+for lib_name in "${lib_names[@]}"; do
+  ./gradlew :$lib_name:runFlank --scan --stacktrace &
+  firebase_pids+=("$!")
+done
+
+for firebase_pid in ${firebase_pids[*]}; do
+    wait $firebase_pid
+done

buildSrc/build.gradle.kts

@@ -9,15 +9,15 @@ repositories {
 }
 
 dependencies {
-  implementation("com.diffplug.spotless:spotless-plugin-gradle:6.21.0")
+  implementation("com.diffplug.spotless:spotless-plugin-gradle:6.22.0")
 
-  implementation("com.android.tools.build:gradle:8.1.2")
+  implementation("com.android.tools.build:gradle:8.1.4")
 
-  implementation("app.cash.licensee:licensee-gradle-plugin:1.3.0")
+  implementation("app.cash.licensee:licensee-gradle-plugin:1.8.0")
   implementation("com.osacky.flank.gradle:fladle:0.17.4")
 
-  implementation("com.spotify.ruler:ruler-gradle-plugin:1.2.1")
+  implementation("com.spotify.ruler:ruler-gradle-plugin:1.4.0")
 
   implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.8.0")
-  implementation("com.squareup:kotlinpoet:1.12.0")
+  implementation("com.squareup:kotlinpoet:1.14.2")
 }

buildSrc/src/main/kotlin/Dependencies.kt

@@ -41,10 +41,6 @@ object Dependencies {
       "org.opencds.cqf.fhir:cqf-fhir-utility:${Versions.Cql.clinicalReasoning}"
   }
 
-  object Glide {
-    const val glide = "com.github.bumptech.glide:glide:${Versions.Glide.glide}"
-  }
-
   object HapiFhir {
     const val fhirBase = "ca.uhn.hapi.fhir:hapi-fhir-base:${Versions.hapiFhir}"
     const val fhirClient = "ca.uhn.hapi.fhir:hapi-fhir-client:${Versions.hapiFhir}"
@@ -218,18 +214,14 @@ object Dependencies {
       const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
     }
 
-    object Glide {
-      const val glide = "4.14.2"
-    }
-
     object Kotlin {
       const val kotlinCoroutinesCore = "1.7.2"
       const val stdlib = "1.8.20"
     }
 
     const val androidFhirCommon = "0.1.0-alpha05"
-    const val androidFhirEngine = "0.1.0-beta04"
-    const val androidFhirKnowledge = "0.1.0-alpha01"
+    const val androidFhirEngine = "0.1.0-beta05"
+    const val androidFhirKnowledge = "0.1.0-alpha03"
     const val apacheCommonsCompress = "1.21"
     const val desugarJdkLibs = "2.0.3"
     const val caffeine = "2.9.1"

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -22,6 +22,8 @@ fun Project.configureLicensee() {
   apply(plugin = "app.cash.licensee")
   configure<app.cash.licensee.LicenseeExtension> {
     allow("Apache-2.0")
+    allow("BSD-2-Clause")
+    allow("BSD-3-Clause")
     allow("MIT")
 
     ignoreDependencies("com.ibm.icu", "icu4j") {

buildSrc/src/main/kotlin/Releases.kt

@@ -48,7 +48,7 @@ object Releases {
 
   object Engine : LibraryArtifact {
     override val artifactId = "engine"
-    override val version = "0.1.0-beta04"
+    override val version = "0.1.0-beta05"
     override val name = "Android FHIR Engine Library"
   }
 
@@ -60,7 +60,7 @@ object Releases {
 
   object Workflow : LibraryArtifact {
     override val artifactId = "workflow"
-    override val version = "0.1.0-alpha03"
+    override val version = "0.1.0-alpha04"
     override val name = "Android FHIR Workflow Library"
   }
 
@@ -74,7 +74,7 @@ object Releases {
 
   object Knowledge : LibraryArtifact {
     override val artifactId = "knowledge"
-    override val version = "0.1.0-alpha02"
+    override val version = "0.1.0-alpha03"
     override val name = "Android FHIR Knowledge Manager Library"
   }
 

codelabs/datacapture/app/build.gradle.kts

@@ -4,12 +4,13 @@ plugins {
 }
 
 android {
-    compileSdk = 31
+    namespace = "com.google.codelab.sdclibrary"
+    compileSdk = 34
 
     defaultConfig {
         applicationId = "com.google.android.fhir.codelabs.datacapture"
         minSdk = 24
-        targetSdk = 31
+        targetSdk = 34
         versionCode = 1
         versionName = "1.0"
 
@@ -22,24 +23,30 @@ android {
             proguardFiles(getDefaultProguardFile("proguard-android-optimize.txt"), "proguard-rules.pro")
         }
     }
-    compileOptions {
-        sourceCompatibility = JavaVersion.VERSION_1_8
-        targetCompatibility = JavaVersion.VERSION_1_8
+    buildFeatures {
+        buildConfig = true
+        viewBinding = true
     }
-    kotlinOptions {
-        jvmTarget = "1.8"
+    compileOptions {
+        // Flag to enable support for the new language APIs
+        // See https://developer.android.com/studio/write/java8-support
+        isCoreLibraryDesugaringEnabled = true
     }
+
+    packaging { resources.excludes.addAll(listOf("META-INF/ASL-2.0.txt", "META-INF/LGPL-3.0.txt")) }
+    kotlin { jvmToolchain(11) }
 }
 
 dependencies {
-    implementation("androidx.core:core-ktx:1.7.0")
-    implementation("androidx.appcompat:appcompat:1.4.0")
-    implementation("com.google.android.material:material:1.4.0")
-    implementation("androidx.constraintlayout:constraintlayout:2.1.2")
-
-    testImplementation("junit:junit:4.+")
-    androidTestImplementation("androidx.test.ext:junit:1.1.3")
-    androidTestImplementation("androidx.test.espresso:espresso-core:3.4.0")
+    coreLibraryDesugaring("com.android.tools:desugar_jdk_libs:2.0.3")
+    implementation("androidx.core:core-ktx:1.12.0")
+    implementation("androidx.appcompat:appcompat:1.6.1")
+    implementation("com.google.android.material:material:1.10.0")
+    implementation("androidx.constraintlayout:constraintlayout:2.1.4")
+
+    testImplementation("junit:junit:4.13.2")
+    androidTestImplementation("androidx.test.ext:junit:1.1.5")
+    androidTestImplementation("androidx.test.espresso:espresso-core:3.5.1")
 
     // 3 Add dependencies for Structured Data Capture Library and Fragment KTX
 }

codelabs/datacapture/build.gradle.kts

@@ -6,8 +6,8 @@ buildscript {
         gradlePluginPortal()
     }
     dependencies {
-        classpath("com.android.tools.build:gradle:7.0.4")
-        classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:1.6.10")
+        classpath("com.android.tools.build:gradle:8.1.2")
+        classpath("org.jetbrains.kotlin:kotlin-gradle-plugin:1.8.20")
 
         // NOTE: Do not place your application dependencies here; they belong
         // in the individual module build.gradle.kts files

codelabs/datacapture/gradle.properties

@@ -15,7 +15,5 @@ org.gradle.jvmargs=-Xmx2048m -Dfile.encoding=UTF-8
 # Android operating system, and which are packaged with your app"s APK
 # https://developer.android.com/topic/libraries/support-library/androidx-rn
 android.useAndroidX=true
-# Automatically convert third-party libraries to use AndroidX
-android.enableJetifier=true
 # Kotlin code style for this project: "official" or "obsolete":
-kotlin.code.style=official
+kotlin.code.style=official

codelabs/datacapture/gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
-#Fri Jan 28 09:30:50 GMT 2022
 distributionBase=GRADLE_USER_HOME
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.0.2-bin.zip
 distributionPath=wrapper/dists
-zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.0-bin.zip
 zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists