Update clinical reasoning dependencies (#2637)

* Update clinical reasoning dependencies

* Fix smart immunizations tests

* Fix build for PlanDefinition.kt

* Add licencee exceptions

* Update tests

* Fix cql builder and add package exclusion

* Fix build for workflow benchmark

* Update tests and build

* Run spotless

* Fix logback dependency in workflow:benchmark

* Add exclusion of logback-classic for the whole project

Author: jingtang10

buildSrc/src/main/kotlin/Dependencies.kt

@@ -19,14 +19,6 @@ import org.gradle.api.artifacts.DependencyConstraint
 import org.gradle.kotlin.dsl.exclude
 
 object Dependencies {
-  object Cql {
-    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:${Versions.Cql.clinicalReasoning}"
-  }
-
   object HapiFhir {
     const val fhirBaseModule = "ca.uhn.hapi.fhir:hapi-fhir-base"
     const val fhirClientModule = "ca.uhn.hapi.fhir:hapi-fhir-client"
@@ -139,11 +131,6 @@ object Dependencies {
   const val xmlUnit = "org.xmlunit:xmlunit-core:${Versions.xmlUnit}"
 
   object Versions {
-
-    object Cql {
-      const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
-    }
-
     const val androidFhirCommon = "0.1.0-alpha05"
     const val androidFhirEngine = "0.1.0-beta05"
     const val androidFhirKnowledge = "0.1.0-alpha03"
@@ -195,16 +182,17 @@ object Dependencies {
   }
 
   fun Configuration.removeIncompatibleDependencies() {
-    exclude(module = "xpp3")
-    exclude(module = "xpp3_min")
-    exclude(module = "xmlpull")
+    exclude(module = "hapi-fhir-caching-caffeine")
     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")
-    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(module = "xmlpull")
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(group = "ch.qos.logback", module = "logback-classic")
     exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
+    exclude(group = "org.antlr", module = "antlr4")
+    exclude(group = "org.apache.httpcomponents")
   }
 
   fun hapiFhirConstraints(): Map<String, DependencyConstraint.() -> Unit> {

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -72,17 +72,24 @@ fun Project.configureLicensee() {
     }
 
     // Jakarta XML Binding API
-    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "2.3.3") {
+    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "4.0.1") {
       because("BSD 3-clause.")
     }
 
     // Jakarta Activation API 2.1 Specification
-    allowDependency("jakarta.activation", "jakarta.activation-api", "1.2.2") {
+    allowDependency("jakarta.activation", "jakarta.activation-api", "2.1.2") {
       because(
         "Licensed under Eclipse Distribution License 1.0. http://www.eclipse.org/org/documents/edl-v10.php",
       )
     }
 
+    // Jakarta Annotation API 2.1 Specification
+    allowDependency("jakarta.annotation", "jakarta.annotation-api", "2.1.1") {
+      because(
+        "Licensed under EPL 2.0",
+      )
+    }
+
     // 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.")
@@ -108,7 +115,7 @@ fun Project.configureLicensee() {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
     // ANTLR 4
-    allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
+    allowDependency("org.antlr", "antlr4-runtime", "4.13.1") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
 
@@ -195,6 +202,12 @@ fun Project.configureLicensee() {
     allowDependency("com.ibm.icu", "icu4j", "72.1") {
       because("BSD, part MIT and Apache 2.0. https://github.com/unicode-org/icu/blob/main/LICENSE")
     }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-classic", "1.4.14") { because("LGPL") }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-core", "1.4.14") { because("LGPL") }
   }
 }
 

gradle/libs.versions.toml

@@ -25,6 +25,8 @@ junit = "4.13.2"
 kotlin-stdlib = "1.9.22"
 kotlin-test = "1.9.22"
 kotlinx-coroutines = "1.8.1"
+logback-android = "3.0.0"
+opencds-cqf-fhir = "3.8.0"
 truth = "1.1.5"
 
 [libraries]
@@ -58,13 +60,17 @@ androidx-test-runner = { module = "androidx.test:runner", version.ref = "android
 androidx-work-runtime = { module = "androidx.work:work-runtime-ktx", version.ref = "androidx-work" }
 androidx-work-testing = { module = "androidx.work:work-testing", version.ref = "androidx-work" }
 glide = { module = "com.github.bumptech.glide:glide", version.ref = "glide" }
+junit = { module = "junit:junit", version.ref = "junit" }
 kotlin-stdlib = { module = "org.jetbrains.kotlin:kotlin-stdlib", version.ref = "kotlin-stdlib" }
 kotlin-test-junit = { module = "org.jetbrains.kotlin:kotlin-test-junit", version.ref = "kotlin-test" }
 kotlinx-coroutines-android = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-android", version.ref = "kotlinx-coroutines" }
 kotlinx-coroutines-core = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-core", version.ref = "kotlinx-coroutines" }
 kotlinx-coroutines-playservices = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-play-services", version.ref = "kotlinx-coroutines" }
 kotlinx-coroutines-test = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-test", version.ref = "kotlinx-coroutines" }
-junit = { module = "junit:junit", version.ref = "junit" }
+logback-android = { module = "com.github.tony19:logback-android", version.ref = "logback-android" }
+opencds-cqf-fhir-cr = { module = "org.opencds.cqf.fhir:cqf-fhir-cr", version.ref = "opencds-cqf-fhir" }
+opencds-cqf-fhir-jackson = { module = "org.opencds.cqf.fhir:cqf-fhir-jackson", version.ref = "opencds-cqf-fhir" }
+opencds-cqf-fhir-utility = { module = "org.opencds.cqf.fhir:cqf-fhir-utility", version.ref = "opencds-cqf-fhir" }
 truth = { module = "com.google.truth:truth", version.ref = "truth" }
 
 [bundles]

workflow-testing/build.gradle.kts

@@ -15,9 +15,9 @@ android {
 configurations { all { removeIncompatibleDependencies() } }
 
 dependencies {
-  compileOnly(Dependencies.Cql.evaluator)
-  compileOnly(Dependencies.Cql.evaluatorFhirJackson)
-  compileOnly(Dependencies.Cql.evaluatorFhirUtilities)
+  compileOnly(libs.opencds.cqf.fhir.cr)
+  compileOnly(libs.opencds.cqf.fhir.jackson)
+  compileOnly(libs.opencds.cqf.fhir.utility)
   compileOnly(project(":engine")) { exclude(module = "truth") }
 
   compileOnly(Dependencies.jsonAssert)

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

@@ -120,7 +120,7 @@ object CqlBuilder : Loadable() {
       version = libVersion
       status = Enumerations.PublicationStatus.ACTIVE
       experimental = true
-      url = "http://localhost/Library/$libName|$libVersion"
+      url = "http://localhost/Library/$libName"
       attachmentCql?.let { addContent(it) }
       attachmentJson?.let { addContent(it) }
       attachmentXml?.let { addContent(it) }

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

@@ -1,5 +1,5 @@
 /*
- * Copyright 2023 Google LLC
+ * Copyright 2023-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -28,7 +28,6 @@ import ca.uhn.fhir.util.BundleBuilder
 import com.google.common.collect.ImmutableMap
 import java.io.File
 import java.io.FileNotFoundException
-import java.util.Locale
 import java.util.Objects
 import java.util.function.Consumer
 import org.hl7.fhir.instance.model.api.IBaseBundle
@@ -40,9 +39,7 @@ import org.opencds.cqf.fhir.api.Repository
 import org.opencds.cqf.fhir.utility.Ids
 import org.opencds.cqf.fhir.utility.dstu3.AttachmentUtil
 import org.opencds.cqf.fhir.utility.matcher.ResourceMatcher
-import org.opencds.cqf.fhir.utility.repository.IGLayoutMode
 import org.opencds.cqf.fhir.utility.repository.Repositories
-import org.opencds.cqf.fhir.utility.repository.ResourceCategory
 
 /**
  * This class implements the Repository interface on onto a directory structure that matches the
@@ -51,7 +48,6 @@ import org.opencds.cqf.fhir.utility.repository.ResourceCategory
 class IGInputStreamStructureRepository(
   private val fhirContext: FhirContext,
   private val root: String? = null,
-  private val layoutMode: IGLayoutMode = IGLayoutMode.DIRECTORY,
   private val encodingEnum: EncodingEnum = EncodingEnum.JSON,
 ) : Loadable(), Repository {
   private val resourceCache: MutableMap<String, IBaseResource> = HashMap()
@@ -62,42 +58,32 @@ class IGInputStreamStructureRepository(
     resourceCache.clear()
   }
 
-  protected fun <T : IBaseResource?, I : IIdType?> locationForResource(
+  private fun <T : IBaseResource?, I : IIdType?> locationForResource(
     resourceType: Class<T>,
     id: I,
   ): String {
     val directory = directoryForType(resourceType)
     return directory + "/" + fileNameForLayoutAndEncoding(resourceType.simpleName, id!!.idPart)
   }
 
-  protected fun fileNameForLayoutAndEncoding(resourceType: String, resourceId: String): String {
+  private fun fileNameForLayoutAndEncoding(resourceType: String, resourceId: String): String {
     val name = resourceId + fileExtensions[encodingEnum]
-    return if (layoutMode === IGLayoutMode.DIRECTORY) {
-      // TODO: case sensitivity!!
-      resourceType.lowercase(Locale.getDefault()) + "/" + name
-    } else {
-      "$resourceType-$name"
-    }
+    return "$resourceType-$name"
   }
 
-  protected fun <T : IBaseResource?> directoryForType(resourceType: Class<T>): String {
+  private fun <T : IBaseResource?> directoryForType(resourceType: Class<T>): String {
     val category = ResourceCategory.forType(resourceType.simpleName)
     val directory = categoryDirectories[category]
 
     // TODO: what the heck is the path separator?
     return (if (root!!.endsWith("/")) root else "$root/") + directory
   }
 
-  protected fun <T : IBaseResource?> directoryForResource(resourceType: Class<T>): String {
-    val directory = directoryForType(resourceType)
-    return if (layoutMode === IGLayoutMode.DIRECTORY) {
-      directory + "/" + resourceType.simpleName.lowercase(Locale.getDefault())
-    } else {
-      directory
-    }
+  private fun <T : IBaseResource?> directoryForResource(resourceType: Class<T>): String {
+    return directoryForType(resourceType)
   }
 
-  protected fun <T : IBaseResource, I : IIdType> readLocation(
+  private fun <T : IBaseResource, I : IIdType> readLocation(
     resourceClass: Class<T>?,
     location: String,
   ): T {
@@ -112,7 +98,7 @@ class IGInputStreamStructureRepository(
     } as T
   }
 
-  protected fun <T : IBaseResource> handleLibrary(resource: T, location: String?): T {
+  private fun <T : IBaseResource> handleLibrary(resource: T, location: String?): T {
     var resourceOutput = resource
     if (resourceOutput.fhirType() == "Library") {
       val cqlLocation: String?
@@ -161,7 +147,7 @@ class IGInputStreamStructureRepository(
     return resourceOutput
   }
 
-  protected fun getCqlContent(rootPath: String?, relativePath: String?): String {
+  private fun getCqlContent(rootPath: String?, relativePath: String?): String {
     val p = File(File(rootPath).parent, relativePath).normalize().toString()
     return try {
       load(p)
@@ -171,18 +157,14 @@ class IGInputStreamStructureRepository(
     }
   }
 
-  protected fun <T : IBaseResource> readLocation(resourceClass: Class<T>): Map<IIdType, T> {
+  private fun <T : IBaseResource> readLocation(resourceClass: Class<T>): Map<IIdType, T> {
     val location = directoryForResource(resourceClass)
     val resources = HashMap<IIdType, T>()
 
     val inputFiles = listFiles(location)
 
     for (file in inputFiles) {
-      if (
-        layoutMode.equals(IGLayoutMode.DIRECTORY) ||
-          (layoutMode.equals(IGLayoutMode.TYPE_PREFIX) &&
-            file.startsWith(resourceClass.simpleName + "-"))
-      ) {
+      if (file.startsWith(resourceClass.simpleName + "-")) {
         try {
           val r = this.readLocation<T, IIdType>(resourceClass, "$location/$file")
           if (r.fhirType() == resourceClass.simpleName) {
@@ -282,7 +264,7 @@ class IGInputStreamStructureRepository(
   ): B {
     val builder = BundleBuilder(fhirContext)
     val resourceIdMap = readLocation(resourceType)
-    if (searchParameters == null || searchParameters.isEmpty()) {
+    if (searchParameters.isEmpty()) {
       resourceIdMap.values.forEach(
         Consumer { theResource: T ->
           builder.addCollectionEntry(
@@ -442,6 +424,34 @@ class IGInputStreamStructureRepository(
   }
 
   companion object {
+    enum class ResourceCategory {
+      DATA,
+      TERMINOLOGY,
+      CONTENT,
+      ;
+
+      companion object {
+        private val TERMINOLOGY_RESOURCES: Set<String> = hashSetOf("ValueSet", "CodeSystem")
+        private val CONTENT_RESOURCES: Set<String> =
+          hashSetOf(
+            "Library",
+            "Questionnaire",
+            "Measure",
+            "PlanDefinition",
+            "StructureDefinition",
+            "ActivityDefinition",
+          )
+
+        fun forType(resourceType: String): ResourceCategory {
+          return if (TERMINOLOGY_RESOURCES.contains(resourceType)) {
+            TERMINOLOGY
+          } else {
+            if (CONTENT_RESOURCES.contains(resourceType)) CONTENT else DATA
+          }
+        }
+      }
+    }
+
     private val categoryDirectories: Map<ResourceCategory, String> =
       ImmutableMap.Builder<ResourceCategory, String>()
         .put(ResourceCategory.CONTENT, "resources")

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

@@ -1,5 +1,5 @@
 /*
- * Copyright 2022-2023 Google LLC
+ * Copyright 2022-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,7 +21,6 @@ import ca.uhn.fhir.context.FhirVersionEnum
 import ca.uhn.fhir.rest.api.EncodingEnum
 import java.io.IOException
 import org.hl7.fhir.instance.model.api.IBaseResource
-import org.hl7.fhir.instance.model.api.IPrimitiveType
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.CarePlan
 import org.hl7.fhir.r4.model.CommunicationRequest
@@ -38,8 +37,8 @@ import org.junit.Assert.fail
 import org.opencds.cqf.fhir.api.Repository
 import org.opencds.cqf.fhir.cql.EvaluationSettings
 import org.opencds.cqf.fhir.cql.LibraryEngine
-import org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor
-import org.opencds.cqf.fhir.utility.repository.IGLayoutMode
+import org.opencds.cqf.fhir.cr.plandefinition.PlanDefinitionProcessor
+import org.opencds.cqf.fhir.utility.monad.Eithers
 import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository
 import org.opencds.cqf.fhir.utility.repository.Repositories
 import org.skyscreamer.jsonassert.JSONAssert
@@ -152,7 +151,6 @@ object PlanDefinition : Loadable() {
         IGInputStreamStructureRepository(
           fhirContext,
           repositoryPath ?: ".",
-          IGLayoutMode.TYPE_PREFIX,
           EncodingEnum.JSON,
         )
       if (dataRepository == null && contentRepository == null && terminologyRepository == null) {
@@ -200,14 +198,12 @@ object PlanDefinition : Loadable() {
 
       return GeneratedBundle(
         buildProcessor(repository)
-          .applyR5<IPrimitiveType<String>>(
-            /* id = */ IdType("PlanDefinition", planDefinitionID),
-            /* canonical = */ null,
-            /* planDefinition = */ null,
-            /* patientId = */ patientID,
-            /* encounterId = */ encounterID,
-            /* practitionerId = */ practitionerID,
-            /* organizationId = */ null,
+          .applyR5(
+            /* planDefinition = */ Eithers.forMiddle3(IdType("PlanDefinition", planDefinitionID)),
+            /* subject = */ patientID,
+            /* encounter = */ encounterID,
+            /* practitioner = */ practitionerID,
+            /* organization = */ null,
             /* userType = */ null,
             /* userLanguage = */ null,
             /* userTaskContext = */ null,
@@ -253,10 +249,8 @@ object PlanDefinition : Loadable() {
 
       return GeneratedCarePlan(
         (buildProcessor(repository)
-          .apply<IPrimitiveType<String>>(
-            IdType("PlanDefinition", planDefinitionID),
-            null,
-            null,
+          .apply(
+            /* planDefinition = */ Eithers.forMiddle3(IdType("PlanDefinition", planDefinitionID)),
             patientID,
             encounterID,
             practitionerID,
@@ -280,10 +274,8 @@ object PlanDefinition : Loadable() {
       val repository = overrideRepository ?: buildRepository()
       return GeneratedPackage(
         (buildProcessor(repository)
-          .packagePlanDefinition<IPrimitiveType<String>>(
-            IdType("PlanDefinition", planDefinitionID),
-            null,
-            null,
+          .packagePlanDefinition(
+            Eithers.forMiddle3(IdType("PlanDefinition", planDefinitionID)),
             true,
           ) as Bundle),
         null,