CQL combo 2.0.0 Upgrade - Full PD$apply implementation

buildSrc/build.gradle.kts

@@ -17,8 +17,8 @@ dependencies {
 
   implementation("com.spotify.ruler:ruler-gradle-plugin:1.2.1")
 
-  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:5.4.0")
+  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
   implementation("com.squareup:kotlinpoet:1.9.0")
-  implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.6.10")
+  implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.6.21")
   implementation("org.jetbrains.dokka:dokka-gradle-plugin:1.6.10")
 }

buildSrc/src/main/kotlin/Dependencies.kt

@@ -31,16 +31,36 @@ object Dependencies {
   }
 
   object Cql {
-    const val evaluator = "org.opencds.cqf.cql:evaluator:${Versions.Cql.evaluator}"
-    const val evaluatorBuilder = "org.opencds.cqf.cql:evaluator.builder:${Versions.Cql.evaluator}"
-    const val evaluatorDagger = "org.opencds.cqf.cql:evaluator.dagger:${Versions.Cql.evaluator}"
-    const val evaluatorPlanDef =
-      "org.opencds.cqf.cql:evaluator.plandefinition:${Versions.Cql.evaluator}"
+    const val openCdsGroup = "org.opencds.cqf.cql"
+    const val translatorGroup = "info.cqframework"
+
+    // Remove this after this issue has been fixed:
+    // https://github.com/cqframework/clinical_quality_language/issues/799
+    const val antlr4Runtime = "org.antlr:antlr4-runtime:${Versions.Cql.antlr}"
+
+    const val engine = "$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}"
   }
 
   object HapiFhir {
     const val structuresR4 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${Versions.hapiFhir}"
     const val validation = "ca.uhn.hapi.fhir:hapi-fhir-validation:${Versions.hapiFhir}"
+
+    // 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}"
   }
 
   object Jackson {
@@ -49,13 +69,6 @@ object Dependencies {
     const val databind = "com.fasterxml.jackson.core:jackson-databind:${Versions.jackson}"
   }
 
-  object JavaJsonTools {
-    const val jacksonCoreUtils =
-      "com.github.java-json-tools:jackson-coreutils:${Versions.JavaJsonTools.jacksonCoreUtils}"
-    const val msgSimple =
-      "com.github.java-json-tools:msg-simple:${Versions.JavaJsonTools.msgSimple}"
-  }
-
   object Kotlin {
     const val kotlinCoroutinesAndroid =
       "org.jetbrains.kotlinx:kotlinx-coroutines-android:${Versions.Kotlin.kotlinCoroutinesCore}"
@@ -64,7 +77,7 @@ object Dependencies {
     const val kotlinTestJunit = "org.jetbrains.kotlin:kotlin-test-junit:${Versions.Kotlin.stdlib}"
     const val kotlinCoroutinesTest =
       "org.jetbrains.kotlinx:kotlinx-coroutines-test:${Versions.Kotlin.kotlinCoroutinesCore}"
-    const val stdlib = "org.jetbrains.kotlin:kotlin-stdlib-jdk7:${Versions.Kotlin.stdlib}"
+    const val stdlib = "org.jetbrains.kotlin:kotlin-stdlib:${Versions.Kotlin.stdlib}"
   }
 
   object Lifecycle {
@@ -109,13 +122,13 @@ object Dependencies {
   const val guava = "com.google.guava:guava:${Versions.guava}"
   const val httpInterceptor = "com.squareup.okhttp3:logging-interceptor:${Versions.http}"
   const val http = "com.squareup.okhttp3:okhttp:${Versions.http}"
-  const val stax = "javax.xml.stream:stax-api:${Versions.stax}"
+
   const val jsonToolsPatch = "com.github.java-json-tools:json-patch:${Versions.jsonToolsPatch}"
   const val kotlinPoet = "com.squareup:kotlinpoet:${Versions.kotlinPoet}"
   const val material = "com.google.android.material:material:${Versions.material}"
   const val sqlcipher = "net.zetetic:android-database-sqlcipher:${Versions.sqlcipher}"
   const val timber = "com.jakewharton.timber:timber:${Versions.timber}"
-  const val woodstox = "org.codehaus.woodstox:woodstox-core-asl:${Versions.woodstox}"
+  const val woodstox = "com.fasterxml.woodstox:woodstox-core:${Versions.woodstox}"
   const val xerces = "xerces:xercesImpl:${Versions.xerces}"
 
   // Dependencies for testing go here
@@ -137,11 +150,16 @@ object Dependencies {
   }
 
   const val androidJunitRunner = "androidx.test.runner.AndroidJUnitRunner"
+  // Makes Json assertions where the order of elements, tabs/whitespaces are not important.
+  const val jsonAssert = "org.skyscreamer:jsonassert:${Versions.jsonAssert}"
   const val junit = "junit:junit:${Versions.junit}"
   const val mockitoKotlin = "org.mockito.kotlin:mockito-kotlin:${Versions.mockitoKotlin}"
   const val mockitoInline = "org.mockito:mockito-inline:${Versions.mockitoInline}"
   const val robolectric = "org.robolectric:robolectric:${Versions.robolectric}"
+  const val slf4j = "org.slf4j:slf4j-android:${Versions.slf4j}"
   const val truth = "com.google.truth:truth:${Versions.truth}"
+  // Makes XML assertions where the order of elements, tabs/whitespaces are not important.
+  const val xmlUnit = "org.xmlunit:xmlunit-core:${Versions.xmlUnit}"
 
   object Versions {
     object Androidx {
@@ -160,12 +178,10 @@ object Dependencies {
     }
 
     object Cql {
-      const val evaluator = "1.4.2"
-    }
-
-    object JavaJsonTools {
-      const val jacksonCoreUtils = "2.0"
-      const val msgSimple = "1.2"
+      const val antlr = "4.10.1"
+      const val engine = "2.1.0"
+      const val evaluator = "2.1.0"
+      const val translator = "2.2.0"
     }
 
     object Kotlin {
@@ -175,24 +191,24 @@ object Dependencies {
 
     const val androidFhirCommon = "0.1.0-alpha03"
     const val desugarJdkLibs = "1.1.5"
+    const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"
     const val guava = "28.2-android"
     const val hapiFhir = "6.0.1"
     const val http = "4.9.1"
-    // TODO: The next release of HAPI FHIR will hopefully have
-    // https://github.com/hapifhir/hapi-fhir/pull/3043 merged in. If it does, when we update, we
-    // should remove any excludes directives for "net.sf.saxon" across our build.gradle files.
     const val jackson = "2.12.2"
     const val jsonToolsPatch = "1.13"
+    const val jsonAssert = "1.5.1"
     const val kotlinPoet = "1.9.0"
     const val material = "1.6.0"
     const val retrofit = "2.7.2"
-    const val stax = "1.0-2"
+    const val slf4j = "1.7.36"
     const val sqlcipher = "4.5.0"
     const val timber = "5.0.1"
     const val truth = "1.0.1"
-    const val woodstox = "4.4.1"
-    const val xerces = "2.11.0"
+    const val woodstox = "6.2.7"
+    const val xerces = "2.12.2"
+    const val xmlUnit = "2.9.0"
 
     // Test dependencies
 

buildSrc/src/main/kotlin/Java.kt

@@ -0,0 +1,39 @@
+/*
+ * 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.
+ */
+
+import org.gradle.api.JavaVersion
+
+/*
+ * 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 Java {
+  val sourceCompatibility = JavaVersion.VERSION_1_8
+  val targetCompatibility = JavaVersion.VERSION_1_8
+  val kotlinJvmTarget = JavaVersion.VERSION_1_8
+}

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Google LLC
+ * 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.
@@ -41,10 +41,6 @@ fun Project.configureLicensee() {
     allowDependency("xpp3", "xpp3_xpath", "1.1.4c") {
       because("Custom license, essentially BSD-5. https://fedoraproject.org/wiki/Licensing/xpp")
     }
-    allowDependency("xpp3", "xpp3", "1.1.4c") {
-      because("Custom license, essentially BSD-5. https://fedoraproject.org/wiki/Licensing/xpp")
-    }
-
     // json-patch and its transitive deps
     allowDependency("com.github.java-json-tools", "btf", "1.3") {
       because("Dual-licensed under Apache. https://github.com/java-json-tools/btf")
@@ -64,11 +60,18 @@ fun Project.configureLicensee() {
       because("Custom license, essentially BSD-3. https://www.zetetic.net/sqlcipher/license/")
     }
 
-    // JAXB https://github.com/eclipse-ee4j/jaxb-ri
+    // Jakarta XML Binding API
     allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "2.3.3") {
       because("BSD 3-clause.")
     }
 
+    // Jakarta Activation API 2.1 Specification
+    allowDependency("jakarta.activation", "jakarta.activation-api", "1.2.2") {
+      because(
+        "Licensed under Eclipse Distribution License 1.0. http://www.eclipse.org/org/documents/edl-v10.php"
+      )
+    }
+
     // Javax Annotation API
     allowDependency("javax.annotation", "javax.annotation-api", "1.3.2") {
       because("Dual-licensed under CDDL 1.1 and GPL v2 with classpath exception.")
@@ -79,16 +82,27 @@ fun Project.configureLicensee() {
       because("Dual-licensed under CDDL 1.0 and GPL v3.")
     }
 
-    // ANTLR 4
-    allowDependency("org.antlr", "antlr4-runtime", "4.9.1") {
+    // xml-commons
+    allowDependency("xml-apis", "xml-apis", "1.4.01") {
+      because("Licensed under Mozilla Public License Version 2.0. http://www.mozilla.org/MPL/2.0/")
+    }
+
+    // The XSLT and XQuery Processor
+    allowDependency("net.sf.saxon", "Saxon-HE", "9.8.0-15") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
 
-    // JSON-P https://javaee.github.io/jsonp/
-    allowDependency("org.glassfish", "javax.json", "1.1.4") {
-      because(
-        "Dual-licensed under CDDL 1.1 and GPL v2 with classpath exception. https://oss.oracle.com/licenses/CDDL+GPL-1.1"
-      )
+    // ANTLR 4
+    allowDependency("org.antlr", "antlr-runtime", "3.5.3") {
+      because("BSD 3-clause. http://www.antlr.org/license.html")
+    }
+    // ANTLR 4
+    allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
+      because("BSD 3-clause. http://www.antlr.org/license.html")
+    }
+    // ANTLR 4
+    allowDependency("org.antlr", "antlr4", "4.10.1") {
+      because("BSD 3-clause. http://www.antlr.org/license.html")
     }
 
     // Utilities
@@ -135,27 +149,6 @@ fun Project.configureLicensee() {
     // Vision Common
     // https://developers.google.com/android/reference/com/google/mlkit/vision/common/package-summary
     allowDependency("com.google.mlkit", "vision-internal-vkp", "18.0.0") { because("") }
-
-    // Eclipse persistence
-    allowDependency("org.eclipse.persistence", "org.eclipse.persistence.asm", "2.7.7") {
-      because(
-        "Temporary dependency. Will be removed in https://github.com/cqframework/clinical_quality_language/pull/752"
-      )
-    }
-
-    // Eclipse persistence
-    allowDependency("org.eclipse.persistence", "org.eclipse.persistence.core", "2.7.7") {
-      because(
-        "Temporary dependency. Will be removed in https://github.com/cqframework/clinical_quality_language/pull/752"
-      )
-    }
-
-    // Eclipse persistence
-    allowDependency("org.eclipse.persistence", "org.eclipse.persistence.moxy", "2.7.7") {
-      because(
-        "Temporary dependency. Will be removed in https://github.com/cqframework/clinical_quality_language/pull/752"
-      )
-    }
   }
 }
 

catalog/build.gradle.kts

@@ -31,15 +31,11 @@ android {
     // Flag to enable support for the new language APIs
     // See https://developer.android.com/studio/write/java8-support
     isCoreLibraryDesugaringEnabled = true
-    // Sets Java compatibility to Java 8
-    // See https://developer.android.com/studio/write/java8-support
-    sourceCompatibility = JavaVersion.VERSION_1_8
-    targetCompatibility = JavaVersion.VERSION_1_8
-  }
-  kotlinOptions {
-    // See https://developer.android.com/studio/write/java8-support
-    jvmTarget = "1.8"
+
+    sourceCompatibility = Java.sourceCompatibility
+    targetCompatibility = Java.targetCompatibility
   }
+  kotlinOptions { jvmTarget = Java.kotlinJvmTarget.toString() }
 }
 
 dependencies {

codelabs/datacapture/app/build.gradle.kts

@@ -23,11 +23,11 @@ android {
         }
     }
     compileOptions {
-        sourceCompatibility = JavaVersion.VERSION_1_8
-        targetCompatibility = JavaVersion.VERSION_1_8
+        sourceCompatibility = Java.sourceCompatibility
+        targetCompatibility = Java.targetCompatibility
     }
     kotlinOptions {
-        jvmTarget = "1.8"
+        jvmTarget = Java.kotlinJvmTarget.toString()
     }
 }
 

common/build.gradle.kts

@@ -17,10 +17,10 @@ android {
     targetSdk = Sdk.targetSdk
   }
   compileOptions {
-    sourceCompatibility = JavaVersion.VERSION_1_8
-    targetCompatibility = JavaVersion.VERSION_1_8
+    sourceCompatibility = Java.sourceCompatibility
+    targetCompatibility = Java.targetCompatibility
   }
-  kotlinOptions { jvmTarget = JavaVersion.VERSION_1_8.toString() }
+  kotlinOptions { jvmTarget = Java.kotlinJvmTarget.toString() }
   configureJacocoTestOptions()
 }
 

common/src/test/java/com/google/android/fhir/MoreTypesTest.kt

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Google LLC
+ * 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.

common/src/test/java/com/google/android/fhir/UnitConverterTest.kt

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Google LLC
+ * 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.

contrib/barcode/build.gradle.kts

@@ -29,18 +29,10 @@ android {
     }
   }
   compileOptions {
-    // Flag to enable support for the new language APIs
-    // See https://developer.android.com/studio/write/java8-support
-    isCoreLibraryDesugaringEnabled = false
-    // Sets Java compatibility to Java 8
-    // See https://developer.android.com/studio/write/java8-support
-    sourceCompatibility = JavaVersion.VERSION_1_8
-    targetCompatibility = JavaVersion.VERSION_1_8
-  }
-  kotlinOptions {
-    // See https://developer.android.com/studio/write/java8-support
-    jvmTarget = JavaVersion.VERSION_1_8.toString()
+    sourceCompatibility = Java.sourceCompatibility
+    targetCompatibility = Java.targetCompatibility
   }
+  kotlinOptions { jvmTarget = Java.kotlinJvmTarget.toString() }
   packagingOptions { resources.excludes.addAll(listOf("META-INF/INDEX.LIST")) }
   configureJacocoTestOptions()
 

contrib/barcode/src/test/java/com/google/android/fhir/datacapture/contrib/views/barcode/mlkit/md/UtilsTest.kt

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Google LLC
+ * 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.

contrib/barcode/src/test/java/com/google/android/fhir/datacapture/contrib/views/barcode/mlkit/md/camera/GraphicOverlayTest.kt

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021 Google LLC
+ * 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.