Updating cqf library version

buildSrc/src/main/kotlin/Dependencies.kt

@@ -228,7 +228,7 @@ object Dependencies {
  }
 
  object Cql {
- const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
+ const val clinicalReasoning = "3.4.0"
  }
 
  object Kotlin {

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -25,10 +25,12 @@ fun Project.configureLicensee() {
  allow("BSD-2-Clause")
  allow("BSD-3-Clause")
  allow("MIT")
+ allow("EPL-1.0")
+ allow("LGPL-2.1-only")
 
  ignoreDependencies("com.ibm.icu", "icu4j") {
  because(
- "ICU uses an ICU license that was mispaced and cannot be loaded by this tool right now",
+ "ICU uses an ICU license that was misplaced and cannot be loaded by this tool right now",
  )
  }
 
@@ -72,17 +74,23 @@ 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:https://www.eclipse.org/org/documents/edl-v10.php",
  )
  }
 
+ allowDependency("jakarta.annotation", "jakarta.annotation-api", "2.1.1") {
+ because(
+ "Licensed under Eclipse EPL-2.0 license http:https://www.eclipse.org/legal/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 +116,7 @@ fun Project.configureLicensee() {
  because("BSD 3-clause. http:https://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:https://www.antlr.org/license.html")
  }
 

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.
@@ -20,15 +20,14 @@ import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import ca.uhn.fhir.model.api.IQueryParameterType
 import ca.uhn.fhir.parser.IParser
-import ca.uhn.fhir.rest.api.EncodingEnum
 import ca.uhn.fhir.rest.api.MethodOutcome
 import ca.uhn.fhir.rest.param.TokenParam
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException
 import ca.uhn.fhir.util.BundleBuilder
 import com.google.common.collect.ImmutableMap
+import com.google.common.collect.Sets
 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
@@ -51,11 +48,9 @@ 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()
- private val parser: IParser = parserForEncoding(fhirContext, encodingEnum)
+ private val parser: IParser = fhirContext.newJsonParser()
  private val resourceMatcher: ResourceMatcher = Repositories.getResourceMatcher(fhirContext)
 
  fun clearCache() {
@@ -71,13 +66,8 @@ class IGInputStreamStructureRepository(
  }
 
  protected 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"
- }
+ val name = "$resourceId.json"
+ return "$resourceType-$name"
  }
 
  protected fun <T : IBaseResource?> directoryForType(resourceType: Class<T>): String {
@@ -89,12 +79,7 @@ class IGInputStreamStructureRepository(
  }
 
  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
- }
+ return directoryForType(resourceType)
  }
 
  protected fun <T : IBaseResource, I : IIdType> readLocation(
@@ -178,19 +163,13 @@ class IGInputStreamStructureRepository(
  val inputFiles = listFiles(location)
 
  for (file in inputFiles) {
- if (
- layoutMode.equals(IGLayoutMode.DIRECTORY) ||
- (layoutMode.equals(IGLayoutMode.TYPE_PREFIX) &&
- file.startsWith(resourceClass.simpleName + "-"))
- ) {
- try {
- val r = this.readLocation<T, IIdType>(resourceClass, "$location/$file")
- if (r.fhirType() == resourceClass.simpleName) {
- resources[r.idElement.toUnqualifiedVersionless()] = r
- }
- } catch (e: RuntimeException) {
- e.printStackTrace()
+ try {
+ val r = this.readLocation<T, IIdType>(resourceClass, "$location/$file")
+ if (r.fhirType() == resourceClass.simpleName) {
+ resources[r.idElement.toUnqualifiedVersionless()] = r
  }
+ } catch (e: RuntimeException) {
+ e.printStackTrace()
  }
  }
  return resources
@@ -282,7 +261,7 @@ 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(
@@ -442,30 +421,43 @@ class IGInputStreamStructureRepository(
  }
 
  companion object {
+
+ enum class ResourceCategory {
+ DATA,
+ TERMINOLOGY,
+ CONTENT,
+ ;
+
+ companion object {
+ private val TERMINOLOGY_RESOURCES: Set<String> =
+ Sets.newHashSet(*arrayOf("ValueSet", "CodeSystem"))
+ private val CONTENT_RESOURCES: Set<String> =
+ Sets.newHashSet(
+ *arrayOf(
+ "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")
  .put(ResourceCategory.DATA, "tests")
  .put(ResourceCategory.TERMINOLOGY, "vocabulary")
  .build()
- private val fileExtensions: Map<EncodingEnum?, String> =
- ImmutableMap.Builder<EncodingEnum?, String>()
- .put(EncodingEnum.JSON, ".json")
- .put(EncodingEnum.XML, ".xml")
- .put(EncodingEnum.RDF, ".rdf")
- .build()
-
- private fun parserForEncoding(
- fhirContext: FhirContext,
- encodingEnum: EncodingEnum?,
- ): IParser {
- return when (encodingEnum) {
- EncodingEnum.JSON -> fhirContext.newJsonParser()
- EncodingEnum.XML -> fhirContext.newXmlParser()
- EncodingEnum.RDF -> fhirContext.newRDFParser()
- EncodingEnum.NDJSON -> throw IllegalArgumentException("NDJSON is not supported")
- else -> throw IllegalArgumentException("NDJSON is not supported")
- }
- }
  }
 }

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.
@@ -18,10 +18,8 @@ package com.google.android.fhir.workflow.testing
 
 import ca.uhn.fhir.context.FhirContext
 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 +36,8 @@ 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
@@ -152,8 +150,6 @@ object PlanDefinition : Loadable() {
  IGInputStreamStructureRepository(
  fhirContext,
  repositoryPath ?: ".",
- IGLayoutMode.TYPE_PREFIX,
- EncodingEnum.JSON,
  )
  if (dataRepository == null && contentRepository == null && terminologyRepository == null) {
  return local
@@ -200,14 +196,12 @@ 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 +247,8 @@ object PlanDefinition : Loadable() {
 
  return GeneratedCarePlan(
  (buildProcessor(repository)
- .apply<IPrimitiveType<String>>(
- IdType("PlanDefinition", planDefinitionID),
- null,
- null,
+ .apply(
+ Eithers.forMiddle3(IdType("PlanDefinition", planDefinitionID)),
  patientID,
  encounterID,
  practitionerID,
@@ -280,10 +272,8 @@ 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,
@@ -388,10 +378,10 @@ object PlanDefinition : Loadable() {
  assertEquals(count, generatedCarePlan.contained.size)
  }
 
- fun hasOperationOutcome() {
+ fun hasRequestGroup() {
  assertTrue(
  generatedCarePlan.getContained().stream().anyMatch { r ->
- r.resourceType.equals(ResourceType.OperationOutcome)
+ r.resourceType.equals(ResourceType.RequestGroup)
  },
  )
  }

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

@@ -1,28 +1,18 @@
 package com.google.android.fhir.workflow.testing;
 
 import org.opencds.cqf.fhir.api.Repository;
-import org.opencds.cqf.fhir.utility.repository.IGFileStructureRepository;
-import org.opencds.cqf.fhir.utility.repository.IGLayoutMode;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.rest.api.EncodingEnum;
 
 public class TestRepositoryFactory {
  private TestRepositoryFactory() {
  // intentionally empty
  }
 
  public static Repository createRepository(FhirContext fhirContext, String path) {
- return createRepository(fhirContext, path, IGLayoutMode.TYPE_PREFIX);
- }
-
- public static Repository createRepository(
- FhirContext fhirContext, String path, IGLayoutMode layoutMode) {
  return new IGInputStreamStructureRepository(
  fhirContext,
- path,
- layoutMode,
- EncodingEnum.JSON
+ path
  );
  }
 }

workflow-testing/src/main/resources/plan-definition/base-repo/tests/CarePlan-hello-world-patient-view.json

@@ -11,10 +11,10 @@
  "status": "draft",
  "intent": "proposal",
  "subject": {
- "reference": "helloworld-patient-1"
+ "reference": "Patient/helloworld-patient-1"
  },
  "encounter": {
- "reference": "helloworld-patient-1-encounter-1"
+ "reference": "Encounter/helloworld-patient-1-encounter-1"
  },
  "action": [
  {
@@ -40,10 +40,10 @@
  "status": "draft",
  "intent": "proposal",
  "subject": {
- "reference": "helloworld-patient-1"
+ "reference": "Patient/helloworld-patient-1"
  },
  "encounter": {
- "reference": "helloworld-patient-1-encounter-1"
+ "reference": "Encounter/helloworld-patient-1-encounter-1"
  },
  "activity": [
  {

workflow/build.gradle.kts

@@ -63,6 +63,7 @@ android {
  "META-INF/sun-jaxb.episode",
  "META-INF/*.kotlin_module",
  "readme.html",
+ "META-INF/INDEX.LIST",
  ),
  )
  }