Migrates Workflow to CQL Evaluator 3.0.0-PRE9-SNAPSHOT (#2259)

* Updates dependencies

* Updates test cases

* Removes moxy and antlr from dependencies.

* Migrates the workflow to the new API

* Migrates workflow testing to the new API

* Fixes workflow benchmark module

* Fixes workflow benchmark module

* Adds contents.txt file to all test repos so it can be loaded on androidTest

* Normalizes path before trying to open files

* Uses contents.txt when running tests on Android

* Spotless

* Updating Json and XML comparisons to pass when elements are just out of order.

* Ignores testANCDT17 for now

buildSrc/src/main/kotlin/Dependencies.kt

@@ -34,22 +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 {
@@ -84,10 +73,6 @@ 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}"
  }
 
@@ -230,9 +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 {
@@ -245,7 +228,7 @@ object Dependencies {
  }
 
  const val androidFhirCommon = "0.1.0-alpha05"
- const val androidFhirEngine = "0.1.0-beta03"
+ 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"
@@ -309,6 +292,8 @@ 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() {

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -42,10 +42,6 @@ fun Project.configureLicensee() {
  allowDependency("org.javassist", "javassist", "3.29.0-GA") {
  because("Multi-licensed under Apache. https://github.com/jboss-javassist/javassist")
  }
- // Remove once Evaluator 3 migration is over
- allowDependency("org.javassist", "javassist", "3.20.0-GA") {
- because("Multi-licensed under Apache. https://github.com/jboss-javassist/javassist")
- }
 
  // xpp3 (HAPI FHIR transitive dep)
  allowDependency("xpp3", "xpp3_xpath", "1.1.4c") {

knowledge/build.gradle.kts

@@ -1,4 +1,4 @@
-import Dependencies.guava
+import Dependencies.forceGuava
 import java.net.URL
 
 plugins {
@@ -71,33 +71,7 @@ configurations {
  all {
  exclude(module = "xpp3")
  exclude(module = "xpp3_min")
- exclude(
- module = "hapi-fhir-structures-r4b",
- )
- resolutionStrategy {
- force(Dependencies.guava)
- force("ca.uhn.hapi.fhir:hapi-fhir-base:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-client:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.convertors:6.0.22")
-
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:6.0.22")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-r5:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.utilities:6.0.22")
-
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:6.0.22")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:6.0.22")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r4:6.0.22")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r4b:6.0.22")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r5:6.0.22")
-
- force("ca.uhn.hapi.fhir:hapi-fhir-validation:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5:6.0.1")
- }
+ forceGuava()
  }
 }
 
@@ -109,7 +83,8 @@ dependencies {
  androidTestImplementation(Dependencies.junit)
  androidTestImplementation(Dependencies.truth)
 
- api("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1") { exclude(module = "junit") }
+ api(Dependencies.HapiFhir.structuresR4) { exclude(module = "junit") }
+ api(Dependencies.HapiFhir.guavaCaching)
 
  coreLibraryDesugaring(Dependencies.desugarJdkLibs)
 
@@ -120,7 +95,7 @@ dependencies {
  implementation(Dependencies.Room.runtime)
  implementation(Dependencies.timber)
  implementation(Dependencies.http)
- implementation("ca.uhn.hapi.fhir:org.hl7.fhir.convertors:6.0.22")
+ implementation(Dependencies.HapiFhir.fhirCoreConvertors)
  implementation(Dependencies.apacheCommonsCompress)
 
  kapt(Dependencies.Room.compiler)

workflow-testing/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceGuava
+import Dependencies.forceHapiVersion
+import Dependencies.forceJacksonVersion
 import Dependencies.removeIncompatibleDependencies
 
 plugins {
@@ -15,46 +18,17 @@ android {
 configurations {
  all {
  removeIncompatibleDependencies()
- exclude(
- module = "hapi-fhir-structures-r4b",
- )
- resolutionStrategy {
- force(Dependencies.guava)
- force("ca.uhn.hapi.fhir:hapi-fhir-base:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-client:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.convertors:5.6.36")
-
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:5.6.36")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-structures-r5:6.0.1")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.utilities:5.6.36")
-
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:5.6.36")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:5.6.36")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r4:5.6.36")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r4b:5.6.36")
- force("ca.uhn.hapi.fhir:org.hl7.fhir.r5:5.6.36")
-
- force("ca.uhn.hapi.fhir:hapi-fhir-validation:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:6.0.1")
- force("ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5:6.0.1")
- }
+ forceGuava()
+ forceHapiVersion()
+ forceJacksonVersion()
  }
 }
 
 dependencies {
- compileOnly(Dependencies.Cql.engine)
  compileOnly(Dependencies.Cql.evaluator)
- compileOnly(Dependencies.Cql.evaluatorBuilder)
- compileOnly(Dependencies.Cql.evaluatorDagger)
- compileOnly(Dependencies.Cql.evaluatorPlanDef)
- compileOnly(Dependencies.Cql.translatorCqlToElm)
- compileOnly(Dependencies.Cql.translatorElm)
- compileOnly(Dependencies.Cql.translatorModel)
- compileOnly(Dependencies.androidFhirEngine) { exclude(module = "truth") }
+ compileOnly(Dependencies.Cql.evaluatorFhirJackson)
+ compileOnly(Dependencies.Cql.evaluatorFhirUtilities)
+ compileOnly(project(":engine")) { exclude(module = "truth") }
 
  // Forces the most recent version of jackson, ignoring what dependencies use.
  // Remove these lines when HAPI 6.4 becomes available.

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

@@ -19,19 +19,15 @@ package com.google.android.fhir.workflow.testing
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import java.io.InputStream
-import java.io.StringReader
 import org.cqframework.cql.cql2elm.CqlTranslator
-import org.cqframework.cql.cql2elm.CqlTranslatorOptions
 import org.cqframework.cql.cql2elm.LibraryManager
 import org.cqframework.cql.cql2elm.ModelManager
 import org.cqframework.cql.cql2elm.quick.FhirLibrarySourceProvider
-import org.fhir.ucum.UcumEssenceService
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.Attachment
 import org.hl7.fhir.r4.model.Enumerations
 import org.hl7.fhir.r4.model.Library
 import org.junit.Assert.fail
-import org.opencds.cqf.cql.engine.serializing.CqlLibraryReaderFactory
 import org.skyscreamer.jsonassert.JSONAssert
 
 object CqlBuilder : Loadable() {
@@ -64,14 +60,7 @@ object CqlBuilder : Loadable() {
  librarySourceLoader.registerProvider(FhirLibrarySourceProvider())
  }
 
- val translator =
- CqlTranslator.fromText(
- cqlText,
- modelManager,
- libraryManager,
- UcumEssenceService(this::class.java.getResourceAsStream("/ucum-essence.xml")),
- *CqlTranslatorOptions.defaultOptions().options.toTypedArray(),
- )
+ val translator = CqlTranslator.fromText(cqlText, libraryManager)
 
  // Helper makes sure the test CQL compiles. Reports an error if it doesn't
  if (translator.errors.isNotEmpty()) {
@@ -144,6 +133,8 @@ object CqlBuilder : Loadable() {
  * @param jsonElm the JSON representation of the ELM Library
  * @return the assembled FHIR Library
  */
+
+ /*
  fun buildJsonLib(jsonElm: InputStream): Library {
  val strLib = load(jsonElm)
  val elmLibrary =
@@ -156,6 +147,7 @@ object CqlBuilder : Loadable() {
  elmLibrary.identifier.version,
  )
  }
+ */
 
  /**
  * Compiles a CQL Text into ELM and assembles a FHIR Library that includes a Base64 representation
@@ -205,7 +197,7 @@ object CqlBuilder : Loadable() {
  expectedElmJsonAsset = load(expectedElmJsonAssetName)
 
  // JSONAssert ignores property order and whitespace/tabs
- JSONAssert.assertEquals(expectedElmJsonAsset, translator.toJson(), true)
+ JSONAssert.assertEquals(expectedElmJsonAsset, translator.toJson(), false)
  return this
  }
 

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

@@ -28,13 +28,13 @@ class FhirEngineProviderTestRule : TestRule {
  override fun apply(base: Statement, description: Description): Statement {
  return object : Statement() {
  override fun evaluate() {
- com.google.android.fhir.FhirEngineProvider.init(
- com.google.android.fhir.FhirEngineConfiguration(testMode = true),
+ FhirEngineProvider.init(
+ FhirEngineConfiguration(testMode = true),
  )
  try {
  base.evaluate()
  } finally {
- com.google.android.fhir.FhirEngineProvider.cleanup()
+ FhirEngineProvider.cleanup()
  }
  }
  }