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* Removes outdated antlr dependency fix of 2.4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:https://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:https://www.antlr.org/license.html")
  }
- // ANTLR 4
- allowDependency("org.antlr", "antlr4", "4.10.1") {
- because("BSD 3-clause. http:https://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
  }
  }
  }