Migrates Workflow to CQL Evaluator 3.0.0-PRE9-SNAPSHOT (google#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
santosh-pingle · Oct 18, 2023 · de585d2 · de585d2
1 parent 7a87ccc
commit de585d2
Show file tree

Hide file tree

Showing 287 changed files with 286,878 additions and 153,644 deletions.
diff --git a/buildSrc/src/main/kotlin/Dependencies.kt b/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() {

diff --git a/buildSrc/src/main/kotlin/LicenseeConfig.kt b/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") {

diff --git a/knowledge/build.gradle.kts b/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)

diff --git a/workflow-testing/build.gradle.kts b/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.

diff --git a/workflow-testing/src/main/java/com/google/android/fhir/workflow/testing/CqlBuilder.kt b/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
     }
 

diff --git a/workflow-testing/src/main/java/com/google/android/fhir/workflow/testing/FakeFhirDal.kt b/workflow-testing/src/main/java/com/google/android/fhir/workflow/testing/FakeFhirDal.kt
diff --git a/...ting/src/main/java/com/google/android/fhir/workflow/testing/FhirEngineProviderTestRule.kt b/...ting/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()
         }
       }
     }