Bump CQL Translator/Evaluator to 2.4 (#1771)

* Migrating CQL Evaluator and its dependencies to 2.4 to fix #1733

* Evaluator 2.4's generate care plan returns an IBaseResource to prepare for R5.

* Migrates to evaluator 2.4

* Removes outdated antlr dependency fix of 2.4

* Forces Jackson 2.14.1 due to a dependency bug when using Gradle and the 2.13.4.1 version FasterXML/jackson-databind#3627

* Forces Jackson 2.14.1 due to a dependency bug when using Gradle and the 2.13.4.1 version FasterXML/jackson-databind#3627

* Fixing tests to match CQL-Evaluator's tests

* Spotless apply

* Force version of caffeine

* Forces HAPI and FHIR CORE to earlier versions due to hapifhir/org.hl7.fhir.core#1046

* deleting non existant r4b

* Fixing imports of the Benchmark module

* Moving common blocks to Dependencies.

* spotless apply

benchmark/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceHapiVersion
+import Dependencies.removeIncompatibleDependencies
+
 plugins {
   id(Plugins.BuildPlugins.androidLib)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -67,15 +70,8 @@ android {
 
 configurations {
   all {
-    exclude(module = "xpp3")
-    exclude(module = "xpp3_min")
-    exclude(module = "xmlpull")
-    exclude(module = "javax.json")
-    exclude(module = "jcl-over-slf4j")
-    exclude(group = "org.apache.httpcomponents")
-    // Remove this after this issue has been fixed:
-    // https://github.com/cqframework/clinical_quality_language/issues/799
-    exclude(module = "antlr4")
+    removeIncompatibleDependencies()
+    forceHapiVersion()
   }
 }
 

buildSrc/src/main/kotlin/Dependencies.kt

@@ -1,3 +1,22 @@
+/*
+ * 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.artifacts.Configuration
+import org.gradle.kotlin.dsl.exclude
+
 /*
  * Copyright 2022 Google LLC
  *
@@ -34,10 +53,6 @@ object Dependencies {
     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}"
 
@@ -54,8 +69,32 @@ object Dependencies {
   }
 
   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}"
+    const val structuresDstu2 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:${Versions.hapiFhir}"
+    const val structuresDstu3 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:${Versions.hapiFhir}"
     const val structuresR4 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${Versions.hapiFhir}"
+    const val structuresR4b = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4b:${Versions.hapiFhir}"
+    const val structuresR5 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r5:${Versions.hapiFhir}"
+
     const val validation = "ca.uhn.hapi.fhir:hapi-fhir-validation:${Versions.hapiFhir}"
+    const val validationDstu3 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:${Versions.hapiFhir}"
+    const val validationR4 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:${Versions.hapiFhir}"
+    const val validationR5 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5:${Versions.hapiFhir}"
+
+    const val fhirCoreDstu2 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu2016 =
+      "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu3 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:${Versions.hapiFhirCore}"
+    const val fhirCoreR4 = "ca.uhn.hapi.fhir:org.hl7.fhir.r4:${Versions.hapiFhirCore}"
+    const val fhirCoreR4b = "ca.uhn.hapi.fhir:org.hl7.fhir.r4b:${Versions.hapiFhirCore}"
+    const val fhirCoreR5 = "ca.uhn.hapi.fhir:org.hl7.fhir.r5:${Versions.hapiFhirCore}"
+    const val fhirCoreUtils = "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:${Versions.hapiFhirCore}"
+    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
@@ -64,9 +103,19 @@ object Dependencies {
   }
 
   object Jackson {
-    const val annotations = "com.fasterxml.jackson.core:jackson-annotations:${Versions.jackson}"
-    const val core = "com.fasterxml.jackson.core:jackson-core:${Versions.jackson}"
-    const val databind = "com.fasterxml.jackson.core:jackson-databind:${Versions.jackson}"
+    const val mainGroup = "com.fasterxml.jackson"
+    const val coreGroup = "$mainGroup.core"
+    const val dataformatGroup = "$mainGroup.dataformat"
+    const val datatypeGroup = "$mainGroup.datatype"
+    const val moduleGroup = "$mainGroup.module"
+
+    const val annotations = "$coreGroup:jackson-annotations:${Versions.jackson}"
+    const val bom = "$mainGroup:jackson-bom:${Versions.jackson}"
+    const val core = "$coreGroup:jackson-core:${Versions.jackson}"
+    const val databind = "$coreGroup:jackson-databind:${Versions.jackson}"
+    const val dataformatXml = "$dataformatGroup:jackson-dataformat-xml:${Versions.jackson}"
+    const val jaxbAnnotations = "$moduleGroup:jackson-module-jaxb-annotations:${Versions.jackson}"
+    const val jsr310 = "$datatypeGroup:jackson-datatype-jsr310:${Versions.jackson}"
   }
 
   object Kotlin {
@@ -188,9 +237,9 @@ object Dependencies {
 
     object Cql {
       const val antlr = "4.10.1"
-      const val engine = "2.1.0"
-      const val evaluator = "2.1.0"
-      const val translator = "2.2.0"
+      const val engine = "2.4.0"
+      const val evaluator = "2.4.0"
+      const val translator = "2.4.0"
     }
 
     object Kotlin {
@@ -204,9 +253,17 @@ object Dependencies {
     const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"
     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"
+    // 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 http = "4.9.1"
-    const val jackson = "2.12.2"
+    const val jackson = "2.14.1"
     const val jsonToolsPatch = "1.13"
     const val jsonAssert = "1.5.1"
     const val kotlinPoet = "1.9.0"
@@ -245,4 +302,45 @@ object Dependencies {
       const val objectDetectionCustom = "16.3.1"
     }
   }
+
+  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")
+  }
+
+  fun Configuration.forceHapiVersion() {
+    // Removes newer versions of caffeine and manually imports 2.9
+    // Removes newer versions of hapi and keeps on 6.0.1
+    // Removes newer versions of HL7 core and keeps it on 5.6.36
+    // (newer versions don't work on Android)
+    resolutionStrategy {
+      force(HapiFhir.caffeine)
+
+      force(HapiFhir.fhirBase)
+      force(HapiFhir.fhirClient)
+      force(HapiFhir.fhirCoreConvertors)
+
+      force(HapiFhir.fhirCoreDstu2)
+      force(HapiFhir.fhirCoreDstu2016)
+      force(HapiFhir.fhirCoreDstu3)
+      force(HapiFhir.fhirCoreR4)
+      force(HapiFhir.fhirCoreR4b)
+      force(HapiFhir.fhirCoreR5)
+      force(HapiFhir.fhirCoreUtils)
+
+      force(HapiFhir.structuresDstu2)
+      force(HapiFhir.structuresDstu3)
+      force(HapiFhir.structuresR4)
+      force(HapiFhir.structuresR5)
+
+      force(HapiFhir.validation)
+      force(HapiFhir.validationDstu3)
+      force(HapiFhir.validationR4)
+      force(HapiFhir.validationR5)
+    }
+  }
 }

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -100,10 +100,6 @@ fun Project.configureLicensee() {
     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
     // https://developers.google.com/android/reference/com/google/android/gms/common/package-summary

workflow-testing/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceHapiVersion
+import Dependencies.removeIncompatibleDependencies
+
 plugins {
   id(Plugins.BuildPlugins.androidLib)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -18,6 +21,13 @@ android {
   kotlinOptions { jvmTarget = Java.kotlinJvmTarget.toString() }
 }
 
+configurations {
+  all {
+    removeIncompatibleDependencies()
+    forceHapiVersion()
+  }
+}
+
 dependencies {
   compileOnly(Dependencies.Cql.engine)
   compileOnly(Dependencies.Cql.evaluator)
@@ -28,6 +38,16 @@ dependencies {
   compileOnly(Dependencies.Cql.translatorElm)
   compileOnly(Dependencies.Cql.translatorModel)
 
+  // Forces the most recent version of jackson, ignoring what dependencies use.
+  // Remove these lines when HAPI 6.4 becomes available.
+  compileOnly(Dependencies.Jackson.annotations)
+  compileOnly(Dependencies.Jackson.bom)
+  compileOnly(Dependencies.Jackson.core)
+  compileOnly(Dependencies.Jackson.databind)
+  compileOnly(Dependencies.Jackson.dataformatXml)
+  compileOnly(Dependencies.Jackson.jaxbAnnotations)
+  compileOnly(Dependencies.Jackson.jsr310)
+
   compileOnly(Dependencies.junit)
   compileOnly(Dependencies.jsonAssert)
   compileOnly(Dependencies.woodstox)

workflow-testing/src/main/java/com/google/android/fhir/workflow/testing/PlanDefinition.kt

@@ -21,7 +21,6 @@ import ca.uhn.fhir.context.FhirVersionEnum
 import org.hl7.fhir.instance.model.api.IBaseBundle
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.Bundle
-import org.hl7.fhir.r4.model.CarePlan
 import org.hl7.fhir.r4.model.Coding
 import org.hl7.fhir.r4.model.Endpoint
 import org.hl7.fhir.r4.model.IdType
@@ -49,7 +48,7 @@ import org.opencds.cqf.cql.evaluator.fhir.adapter.r4.AdapterFactory
 import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal
 import org.opencds.cqf.cql.evaluator.library.CqlFhirParametersConverter
 import org.opencds.cqf.cql.evaluator.library.LibraryProcessor
-import org.opencds.cqf.cql.evaluator.plandefinition.r4.OperationParametersParser
+import org.opencds.cqf.cql.evaluator.plandefinition.OperationParametersParser
 import org.opencds.cqf.cql.evaluator.plandefinition.r4.PlanDefinitionProcessor
 import org.skyscreamer.jsonassert.JSONAssert
 
@@ -218,7 +217,7 @@ object PlanDefinition : Loadable() {
     }
   }
 
-  class GeneratedCarePlan(val carePlan: CarePlan) {
+  class GeneratedCarePlan(val carePlan: IBaseResource) {
     fun isEqualsTo(expectedCarePlanAssetName: String) {
       try {
         JSONAssert.assertEquals(
@@ -229,6 +228,9 @@ object PlanDefinition : Loadable() {
       } catch (e: JSONException) {
         e.printStackTrace()
         fail("Unable to compare Jsons: " + e.message)
+      } catch (e: AssertionError) {
+        println("Actual: " + jsonParser.encodeResourceToString(carePlan))
+        throw e
       }
     }
   }