Merge branch 'master' into master-release

opensrp · Oct 13, 2023 · 6d7f341 · 6d7f341
2 parents 658f9c4 + 633b482
commit 6d7f341
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diff --git a/.github/actions/commonSetup/action.yml b/.github/actions/commonSetup/action.yml
@@ -15,6 +15,8 @@ runs:
     - name: "Setup Gradle"
       uses: gradle/gradle-build-action@v2
       with:
+        # See https://github.com/marketplace/actions/gradle-build-action#enable-dependency-graph-generation-for-a-workflow
+        dependency-graph: generate-and-submit
         # Limit the size of the cache entry.
         # These directories contain instrumented/transformed dependency jars which can be reconstructed relatively quickly.
         gradle-home-cache-excludes: |

diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -0,0 +1,17 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+
+updates:
+  - package-ecosystem: gradle
+    directory: /
+    schedule:
+      interval: weekly
+      day: monday
+      time: "04:00"
+
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+      day: monday
+      time: "04:00"
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -33,7 +33,7 @@ jobs:
   # Build will compile APK, test APK and run tests, lint, etc.
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04-64core
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

diff --git a/.github/workflows/codeql.yaml b/.github/workflows/codeql.yaml
@@ -0,0 +1,51 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "master" ]
+  schedule:
+    - cron: '32 13 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-22.04-64core
+    timeout-minutes: 60
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Switch to Java 17 from Eclipse Temurin distro
+      uses: actions/setup-java@v3
+      with:
+        java-version: 17
+        distribution: temurin
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+
+    # TODO: use Autobuild instead of ./gradlew after https://github.com/github/codeql-action/issues/1417 is fixed
+    # - name: Autobuild
+    #   uses: github/codeql-action/autobuild@v2
+    - name: Build with Gradle
+      run: ./gradlew --scan --full-stacktrace -Dorg.gradle.dependency.verification=off compileDebugAndroidTestSources
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Android FHIR SDK
 
-[![master](https://github.com/google/android-fhir/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/google/android-fhir/actions/workflows/build.yml) [![master](https://storage.googleapis.com/android-fhir-build-badges/build.svg)](https://storage.googleapis.com/android-fhir-build-badges/build.html) [![codecov](https://codecov.io/gh/google/android-fhir/branch/master/graph/badge.svg?token=PDSC4WRDTQ)](https://codecov.io/gh/google/android-fhir/branch/master) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://chat.fhir.org/#narrow/stream/276344-android)
+[![master](https://github.com/google/android-fhir/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/google/android-fhir/actions/workflows/build.yml) [![codecov](https://codecov.io/gh/google/android-fhir/branch/master/graph/badge.svg?token=PDSC4WRDTQ)](https://codecov.io/gh/google/android-fhir/branch/master) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://chat.fhir.org/#narrow/stream/276344-android)
 
 The Android FHIR SDK is a set of Kotlin libraries for building offline-capable, mobile-first
 healthcare applications using the [HL7® FHIR® standard](https://www.hl7.org/fhir/) on Android. It
@@ -15,7 +15,7 @@ The SDK contains the following libraries:
 | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- |----------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Data Capture Library | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/data-capture/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:data-capture) | [code](https://github.com/google/android-fhir/tree/master/datacapture)| [wiki](https://github.com/google/android-fhir/wiki/Structured-Data-Capture-Library) | Android 7.0 (API level 24) | Collect, validate, and process healthcare data on Android                                                                                                  |
 | FHIR Engine Library  | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/engine/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:engine)             | [code](https://github.com/google/android-fhir/tree/master/engine)     | [wiki](https://github.com/google/android-fhir/wiki/FHIR-Engine-Library)             | Android 7.0 (API level 24) | Store and manage FHIR resources locally on Android and synchronize with FHIR server                                                                        |
-| Workflow Library     | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/workflow/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:workflow)         | [code](https://github.com/google/android-fhir/tree/master/workflow)   | [wiki](https://github.com/google/android-fhir/wiki/Workflow-Library)                | Android 8.0 (API level 26) | Provide decision support and analytics in clinical workflow on Android including implementation of specific FHIR operations ($measure_evaluate and $apply) |
+| Workflow Library     | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/workflow/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:workflow)         | [code](https://github.com/google/android-fhir/tree/master/workflow)   | [wiki](https://github.com/google/android-fhir/wiki/Workflow-Library)                | Android 7.0 (API level 24) | Provide decision support and analytics in clinical workflow on Android including implementation of specific FHIR operations ($measure_evaluate and $apply) |
 
 ## Demo apps
 
@@ -38,7 +38,7 @@ To contribute to the project, please see [Contributing](https://github.com/googl
 
 You can create a [GitHub issue](https://github.com/google/android-fhir/issues) for bugs and feature requests.
 
-In case you find any security bug, please do NOT create a Github issue. Instead, email us at <android-fhir-sdk-feedback@google.com>.
+In case you find any security bug, please do NOT create a GitHub issue. Instead, email us at <android-fhir-sdk-feedback@google.com>.
 
 If you want to provide any feedback or discuss use cases you can: 
 * email us at <android-fhir-sdk-feedback@google.com>

diff --git a/buildSrc/build.gradle.kts b/buildSrc/build.gradle.kts
@@ -11,13 +11,13 @@ repositories {
 dependencies {
   implementation("com.diffplug.spotless:spotless-plugin-gradle:6.21.0")
 
-  implementation("com.android.tools.build:gradle:8.1.1")
+  implementation("com.android.tools.build:gradle:8.1.2")
 
   implementation("app.cash.licensee:licensee-gradle-plugin:1.3.0")
   implementation("com.osacky.flank.gradle:fladle:0.17.4")
 
   implementation("com.spotify.ruler:ruler-gradle-plugin:1.2.1")
 
-  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
+  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.8.0")
   implementation("com.squareup:kotlinpoet:1.12.0")
 }
diff --git a/buildSrc/src/main/kotlin/Dependencies.kt b/buildSrc/src/main/kotlin/Dependencies.kt
@@ -17,22 +17,6 @@
 import org.gradle.api.artifacts.Configuration
 import org.gradle.kotlin.dsl.exclude
 
-/*
- * 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.
- */
-
 object Dependencies {
 
   object Androidx {
@@ -50,22 +34,11 @@ object Dependencies {
   }
 
   object Cql {
-    const val openCdsGroup = "org.opencds.cqf.cql"
-    const val translatorGroup = "info.cqframework"
-
-    const val engine = "$openCdsGroup:engine:${Versions.Cql.engine}"
-    const val engineJackson = "$openCdsGroup:engine.jackson:${Versions.Cql.engine}"
-
-    const val evaluator = "$openCdsGroup:evaluator:${Versions.Cql.evaluator}"
-    const val evaluatorBuilder = "$openCdsGroup:evaluator.builder:${Versions.Cql.evaluator}"
-    const val evaluatorDagger = "$openCdsGroup:evaluator.dagger:${Versions.Cql.evaluator}"
-    const val evaluatorPlanDef = "$openCdsGroup:evaluator.plandefinition:${Versions.Cql.evaluator}"
-    const val translatorCqlToElm = "$translatorGroup:cql-to-elm:${Versions.Cql.translator}"
-    const val translatorElm = "$translatorGroup:elm:${Versions.Cql.translator}"
-    const val translatorModel = "$translatorGroup:model:${Versions.Cql.translator}"
-
-    const val translatorElmJackson = "$translatorGroup:elm-jackson:${Versions.Cql.translator}"
-    const val translatorModelJackson = "$translatorGroup:model-jackson:${Versions.Cql.translator}"
+    const val evaluator = "org.opencds.cqf.fhir:cqf-fhir-cr:${Versions.Cql.clinicalReasoning}"
+    const val evaluatorFhirJackson =
+      "org.opencds.cqf.fhir:cqf-fhir-jackson:${Versions.Cql.clinicalReasoning}"
+    const val evaluatorFhirUtilities =
+      "org.opencds.cqf.fhir:cqf-fhir-utility:${Versions.Cql.clinicalReasoning}"
   }
 
   object Glide {
@@ -100,10 +73,7 @@ object Dependencies {
     const val fhirCoreConvertors =
       "ca.uhn.hapi.fhir:org.hl7.fhir.convertors:${Versions.hapiFhirCore}"
 
-    // Runtime dependency that is required to run FhirPath (also requires minSDK of 26).
-    // Version 3.0 uses java.lang.System.Logger, which is not available on Android
-    // Replace for Guava when this PR gets merged: https://github.com/hapifhir/hapi-fhir/pull/3977
-    const val caffeine = "com.github.ben-manes.caffeine:caffeine:${Versions.caffeine}"
+    const val guavaCaching = "ca.uhn.hapi.fhir:hapi-fhir-caching-guava:${Versions.hapiFhir}"
   }
 
   object Jackson {
@@ -115,7 +85,7 @@ object Dependencies {
 
     const val annotations = "$coreGroup:jackson-annotations:${Versions.jackson}"
     const val bom = "$mainGroup:jackson-bom:${Versions.jackson}"
-    const val core = "$coreGroup:jackson-core:${Versions.jackson}"
+    const val core = "$coreGroup:jackson-core:${Versions.jacksonCore}"
     const val databind = "$coreGroup:jackson-databind:${Versions.jackson}"
     const val dataformatXml = "$dataformatGroup:jackson-dataformat-xml:${Versions.jackson}"
     const val jaxbAnnotations = "$moduleGroup:jackson-module-jaxb-annotations:${Versions.jackson}"
@@ -175,6 +145,9 @@ object Dependencies {
     "$androidFhirGroup:$androidFhirEngineModule:${Versions.androidFhirEngine}"
   const val androidFhirKnowledge = "$androidFhirGroup:knowledge:${Versions.androidFhirKnowledge}"
 
+  const val apacheCommonsCompress =
+    "org.apache.commons:commons-compress:${Versions.apacheCommonsCompress}"
+
   const val desugarJdkLibs = "com.android.tools:desugar_jdk_libs:${Versions.desugarJdkLibs}"
   const val fhirUcum = "org.fhir:ucum:${Versions.fhirUcum}"
   const val gson = "com.google.code.gson:gson:${Versions.gson}"
@@ -242,9 +215,7 @@ object Dependencies {
     }
 
     object Cql {
-      const val engine = "2.4.0"
-      const val evaluator = "2.4.0"
-      const val translator = "2.4.0"
+      const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
     }
 
     object Glide {
@@ -256,28 +227,28 @@ object Dependencies {
       const val stdlib = "1.8.20"
     }
 
-    const val androidFhirCommon = "0.1.0-alpha04"
-    const val androidFhirEngine = "0.1.0-beta03"
+    const val androidFhirCommon = "0.1.0-alpha05"
+    const val androidFhirEngine = "0.1.0-beta04"
     const val androidFhirKnowledge = "0.1.0-alpha01"
+    const val apacheCommonsCompress = "1.21"
     const val desugarJdkLibs = "2.0.3"
     const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"
     const val gson = "2.9.1"
-    const val guava = "28.2-android"
-
-    // Hapi FHIR and HL7 Core Components are interlinked.
-    // Newer versions of HapiFhir don't work on Android due to the use of Caffeine 3+
-    // Wait for this to release (6.3): https://github.com/hapifhir/hapi-fhir/pull/4196
-    const val hapiFhir = "6.0.1"
+    const val guava = "32.1.2-android"
 
-    // Newer versions don't work on Android due to Apache Commons Codec:
-    // Wait for this fix: https://github.com/hapifhir/org.hl7.fhir.core/issues/1046
-    const val hapiFhirCore = "5.6.36"
+    const val hapiFhir = "6.8.0"
+    const val hapiFhirCore = "6.0.22"
 
     const val http = "4.11.0"
-    // Maximum version that supports Android API Level 24:
+
+    // 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"
+
     const val jsonToolsPatch = "1.13"
     const val jsonAssert = "1.5.1"
     const val material = "1.9.0"
@@ -321,15 +292,26 @@ object Dependencies {
     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")
+  }
+
+  fun Configuration.forceGuava() {
+    // Removes caffeine
+    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+
+    resolutionStrategy {
+      force(guava)
+      force(HapiFhir.guavaCaching)
+    }
   }
 
   fun Configuration.forceHapiVersion() {
     // Removes newer versions of caffeine and manually imports 2.9
     // Removes newer versions of hapi and keeps on 6.0.1
     // (newer versions don't work on Android)
     resolutionStrategy {
-      force(HapiFhir.caffeine)
-
       force(HapiFhir.fhirBase)
       force(HapiFhir.fhirClient)
       force(HapiFhir.fhirCoreConvertors)

diff --git a/buildSrc/src/main/kotlin/FirebaseTestLabConfig.kt b/buildSrc/src/main/kotlin/FirebaseTestLabConfig.kt
@@ -30,24 +30,23 @@ fun Project.configureFirebaseTestLabForLibraries() {
       mapOf(
         "coverage" to "true",
         "coverageFilePath" to "/sdcard/Download/",
-        "clearPackageData" to "true"
-      )
+        "clearPackageData" to "true",
+      ),
     )
-    flakyTestAttempts.set(3)
     devices.set(
       listOf(
         mapOf(
           "model" to "Nexus6P",
           "version" to
             "${project.extensions.getByType(LibraryExtension::class.java).defaultConfig.minSdk}",
-          "locale" to "en_US"
+          "locale" to "en_US",
         ),
         mapOf(
-          "model" to "panther",
+          "model" to "MediumPhone.arm",
           "version" to "${project.extensions.getByType(LibraryExtension::class.java).compileSdk}",
-          "locale" to "en_US"
+          "locale" to "en_US",
         ),
-      )
+      ),
     )
   }
 }
@@ -61,19 +60,17 @@ fun Project.configureFirebaseTestLabForMicroBenchmark() {
       mapOf(
         "additionalTestOutputDir" to "/sdcard/Download",
         "no-isolated-storage" to "true",
-        "clearPackageData" to "true"
-      )
+        "clearPackageData" to "true",
+      ),
     )
-    // some of the benchmark tests get timed-out in the default 15m
-    testTimeout.set("45m")
     devices.set(
       listOf(
         mapOf(
           "model" to "panther",
           "version" to "${project.extensions.getByType(LibraryExtension::class.java).compileSdk}",
-          "locale" to "en_US"
+          "locale" to "en_US",
         ),
-      )
+      ),
     )
   }
 }
@@ -83,17 +80,19 @@ private fun FlankGradleExtension.commonConfigurationForFirebaseTestLab(project:
   debugApk.set(
     project.provider {
       "${project.rootDir}/demo/build/outputs/apk/androidTest/debug/demo-debug-androidTest.apk"
-    }
+    },
   )
   useOrchestrator.set(true)
-  maxTestShards.set(20)
+  flakyTestAttempts.set(1)
+  maxTestShards.set(10)
+  testTimeout.set("45m")
   directoriesToPull.set(listOf("/sdcard/Download"))
   resultsBucket.set("android-fhir-build-artifacts")
   resultsDir.set(
     if (project.providers.environmentVariable("KOKORO_BUILD_ARTIFACTS_SUBDIR").isPresent) {
       "${System.getenv("KOKORO_BUILD_ARTIFACTS_SUBDIR")}/firebase/${project.name}"
     } else {
       "${project.name}-${UUID.randomUUID()}"
-    }
+    },
   )
 }