Move test code back to cqf-fhir-cr and delete cqf-fhir-cr-test.

cqf-fhir-benchmark/pom.xml

@@ -31,11 +31,6 @@
             <artifactId>jmh-core</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-cr-test</artifactId>
-            <version>3.19.0-SNAPSHOT</version>
-        </dependency>
         <dependency>
             <groupId>org.skyscreamer</groupId>
             <artifactId>jsonassert</artifactId>

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/ActivityDefinitionProcessorFactory.java

@@ -0,0 +1,14 @@
+package org.opencds.cqf.fhir.benchmark;
+
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.activitydefinition.ActivityDefinitionProcessor;
+import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessor;
+import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessorFactory;
+
+public class ActivityDefinitionProcessorFactory implements IActivityDefinitionProcessorFactory {
+
+    @Override
+    public IActivityDefinitionProcessor create(Repository repository) {
+        return new ActivityDefinitionProcessor(repository);
+    }
+}

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/Measures.java

@@ -5,12 +5,12 @@
 import java.time.ZoneId;
 import java.util.HashMap;
 import java.util.concurrent.TimeUnit;
+import org.opencds.cqf.fhir.benchmark.measure.r4.Measure;
+import org.opencds.cqf.fhir.benchmark.measure.r4.Measure.When;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.SEARCH_FILTER_MODE;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.TERMINOLOGY_FILTER_MODE;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_EXPANSION_MODE;
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
-import org.opencds.cqf.fhir.cr.measure.r4.Measure;
-import org.opencds.cqf.fhir.cr.measure.r4.Measure.When;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/MeasuresAdditionalData.java

@@ -7,12 +7,12 @@
 import java.util.HashMap;
 import java.util.concurrent.TimeUnit;
 import org.hl7.fhir.r4.model.Bundle;
+import org.opencds.cqf.fhir.benchmark.measure.r4.Measure;
+import org.opencds.cqf.fhir.benchmark.measure.r4.Measure.When;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.SEARCH_FILTER_MODE;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.TERMINOLOGY_FILTER_MODE;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_EXPANSION_MODE;
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
-import org.opencds.cqf.fhir.cr.measure.r4.Measure;
-import org.opencds.cqf.fhir.cr.measure.r4.Measure.When;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/PlanDefinitions.java

@@ -1,12 +1,12 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import static org.opencds.cqf.fhir.cr.plandefinition.TestPlanDefinition.given;
+import static org.opencds.cqf.fhir.benchmark.plandefinition.TestPlanDefinition.given;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
 
 import ca.uhn.fhir.context.FhirContext;
 import java.util.concurrent.TimeUnit;
-import org.opencds.cqf.fhir.cr.plandefinition.TestPlanDefinition.When;
+import org.opencds.cqf.fhir.benchmark.plandefinition.TestPlanDefinition.When;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/PlanDefinitionsWithGenerate.java

@@ -1,12 +1,12 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import static org.opencds.cqf.fhir.cr.plandefinition.TestPlanDefinition.given;
+import static org.opencds.cqf.fhir.benchmark.plandefinition.TestPlanDefinition.given;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
 
 import ca.uhn.fhir.context.FhirContext;
 import java.util.concurrent.TimeUnit;
-import org.opencds.cqf.fhir.cr.plandefinition.TestPlanDefinition.When;
+import org.opencds.cqf.fhir.benchmark.plandefinition.TestPlanDefinition.When;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/Questionnaires.java

@@ -1,13 +1,13 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import static org.opencds.cqf.fhir.cr.questionnaire.TestQuestionnaire.given;
+import static org.opencds.cqf.fhir.benchmark.questionnaire.TestQuestionnaire.given;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 
 import ca.uhn.fhir.context.FhirContext;
 import java.util.concurrent.TimeUnit;
 import org.hl7.fhir.r4.model.IdType;
-import org.opencds.cqf.fhir.cr.questionnaire.TestQuestionnaire.When;
+import org.opencds.cqf.fhir.benchmark.questionnaire.TestQuestionnaire.When;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/TerminologyProviders.java

@@ -5,8 +5,8 @@
 import java.util.concurrent.TimeUnit;
 import org.opencds.cqf.cql.engine.runtime.Code;
 import org.opencds.cqf.cql.engine.terminology.ValueSetInfo;
+import org.opencds.cqf.fhir.benchmark.measure.r4.Measure;
 import org.opencds.cqf.fhir.cql.engine.terminology.RepositoryTerminologyProvider;
-import org.opencds.cqf.fhir.cr.measure.r4.Measure;
 import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/TestOperationProvider.java

@@ -0,0 +1,10 @@
+package org.opencds.cqf.fhir.benchmark;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.opencds.cqf.fhir.utility.repository.operations.RepositoryOperationProvider;
+
+public class TestOperationProvider {
+    public static RepositoryOperationProvider newProvider(FhirContext fhirContext) {
+        return new RepositoryOperationProvider(fhirContext, new ActivityDefinitionProcessorFactory(), null, null, null);
+    }
+}

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/helpers/DataRequirementsLibrary.java

@@ -0,0 +1,26 @@
+package org.opencds.cqf.fhir.benchmark.helpers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
+
+public class DataRequirementsLibrary {
+    final IBaseResource library;
+    final ILibraryAdapter libraryAdapter;
+
+    public DataRequirementsLibrary(IBaseResource library) {
+        this.library = library;
+        libraryAdapter = (ILibraryAdapter) IAdapterFactory.createAdapterForResource(library);
+    }
+
+    public DataRequirementsLibrary hasDataRequirements(int count) {
+        assertEquals(count, libraryAdapter.getDataRequirement().size());
+        return this;
+    }
+
+    public IBaseResource getLibrary() {
+        return library;
+    }
+}

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/helpers/GeneratedPackage.java

@@ -0,0 +1,34 @@
+package org.opencds.cqf.fhir.benchmark.helpers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.opencds.cqf.fhir.utility.BundleHelper.getEntry;
+import static org.opencds.cqf.fhir.utility.BundleHelper.getEntryResourceFirstRep;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public class GeneratedPackage {
+    final IBaseBundle generatedBundle;
+    final IParser jsonParser;
+
+    public GeneratedPackage(IBaseBundle generatedBundle, FhirContext fhirContext) {
+        this.generatedBundle = generatedBundle;
+        jsonParser = fhirContext.newJsonParser().setPrettyPrint(true);
+    }
+
+    public GeneratedPackage hasEntry(int count) {
+        assertEquals(count, getEntry(generatedBundle).size());
+        return this;
+    }
+
+    public <R extends IBaseResource> GeneratedPackage firstEntryIsType(Class<R> resourceType) {
+        assertEquals(resourceType, getEntryResourceFirstRep(generatedBundle).getClass());
+        return this;
+    }
+
+    public IBaseBundle getBundle() {
+        return generatedBundle;
+    }
+}

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/helpers/RequestHelpers.java

@@ -0,0 +1,194 @@
+package org.opencds.cqf.fhir.benchmark.helpers;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.cql.engine.model.ModelResolver;
+import org.opencds.cqf.fhir.cql.LibraryEngine;
+import org.opencds.cqf.fhir.cr.inputparameters.IInputParameterResolver;
+import org.opencds.cqf.fhir.cr.library.evaluate.EvaluateRequest;
+import org.opencds.cqf.fhir.cr.questionnaire.generate.GenerateRequest;
+import org.opencds.cqf.fhir.cr.questionnaire.populate.PopulateRequest;
+import org.opencds.cqf.fhir.cr.questionnaireresponse.extract.ExtractRequest;
+import org.opencds.cqf.fhir.utility.Ids;
+import org.opencds.cqf.fhir.utility.model.FhirModelResolverCache;
+
+public class RequestHelpers {
+    public static final String PATIENT_ID = "patientId";
+    public static final String ENCOUNTER_ID = "encounterId";
+    public static final String PRACTITIONER_ID = "practitionerId";
+    public static final String ORGANIZATION_ID = "organizationId";
+    public static final String PLANDEFINITION_ID = "planDefinitionId";
+    public static final String PLANDEFINITION_URL = "http://test.fhir.org/fhir/PlanDefinition/";
+    public static final String PROFILE_ID = "profileId";
+    public static final String PROFILE_URL = "http://test.fhir.org/fhir/StructureDefinition/";
+
+    public static org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest newPDApplyRequestForVersion(
+            FhirVersionEnum fhirVersion, LibraryEngine libraryEngine) {
+        return newPDApplyRequestForVersion(fhirVersion, libraryEngine, null, null);
+    }
+
+    public static org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest newPDApplyRequestForVersion(
+            FhirVersionEnum fhirVersion, LibraryEngine libraryEngine, ModelResolver modelResolver) {
+        return newPDApplyRequestForVersion(fhirVersion, libraryEngine, modelResolver, null);
+    }
+
+    public static org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest newPDApplyRequestForVersion(
+            FhirVersionEnum fhirVersion,
+            LibraryEngine libraryEngine,
+            ModelResolver modelResolver,
+            IInputParameterResolver inputParameterResolver) {
+        var fhirContext = FhirContext.forCached(fhirVersion);
+        IBaseResource planDefinition = null;
+        try {
+            planDefinition = fhirContext
+                    .getResourceDefinition("PlanDefinition")
+                    .newInstance()
+                    .setId(PLANDEFINITION_ID);
+        } catch (Exception e) {
+            // Do nothing
+        }
+        return newPDApplyRequestForVersion(
+                fhirVersion, planDefinition, libraryEngine, modelResolver, inputParameterResolver);
+    }
+
+    public static org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest newPDApplyRequestForVersion(
+            FhirVersionEnum fhirVersion,
+            IBaseResource planDefinition,
+            LibraryEngine libraryEngine,
+            ModelResolver modelResolver,
+            IInputParameterResolver inputParameterResolver) {
+        try {
+            if (modelResolver == null) {
+                modelResolver = FhirModelResolverCache.resolverForVersion(fhirVersion);
+            }
+            var planDefinitionUrl = modelResolver.resolvePath(planDefinition, "url");
+            if (planDefinitionUrl == null) {
+                var url = PLANDEFINITION_URL + planDefinition.getIdElement().getIdPart();
+                IBaseDatatype urlType;
+                switch (fhirVersion) {
+                    case DSTU3:
+                        urlType = new org.hl7.fhir.dstu3.model.StringType(url);
+                        break;
+                    case R4:
+                        urlType = new org.hl7.fhir.r4.model.CanonicalType(url);
+                        break;
+                    case R5:
+                        urlType = new org.hl7.fhir.r5.model.CanonicalType(url);
+                        break;
+
+                    default:
+                        urlType = null;
+                        break;
+                }
+                modelResolver.setValue(planDefinition, "url", urlType);
+            }
+        } catch (Exception e) {
+            // Do nothing
+        }
+        IBaseDatatype userLanguage;
+        switch (fhirVersion) {
+            case DSTU3:
+                userLanguage = new org.hl7.fhir.dstu3.model.CodeableConcept(
+                        new org.hl7.fhir.dstu3.model.Coding("test", "test", "test"));
+                break;
+            case R4:
+                userLanguage = new org.hl7.fhir.r4.model.CodeableConcept(
+                        new org.hl7.fhir.r4.model.Coding("test", "test", "test"));
+                break;
+            case R5:
+                userLanguage = new org.hl7.fhir.r5.model.CodeableConcept(
+                        new org.hl7.fhir.r5.model.Coding("test", "test", "test"));
+                break;
+
+            default:
+                userLanguage = null;
+                break;
+        }
+        return new org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest(
+                planDefinition,
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Encounter")),
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Practitioner")),
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Organization")),
+                null,
+                userLanguage,
+                null,
+                null,
+                null,
+                null,
+                true,
+                null,
+                null,
+                libraryEngine,
+                modelResolver,
+                inputParameterResolver);
+    }
+
+    public static GenerateRequest newGenerateRequestForVersion(
+            FhirVersionEnum fhirVersion, LibraryEngine libraryEngine) {
+        IBaseResource profile = null;
+        try {
+            var fhirContext = FhirContext.forCached(fhirVersion);
+            profile = fhirContext
+                    .getResourceDefinition("StructureDefinition")
+                    .newInstance()
+                    .setId(PROFILE_ID);
+        } catch (Exception e) {
+            // Do nothing
+        }
+        return newGenerateRequestForVersion(fhirVersion, profile, libraryEngine);
+    }
+
+    public static GenerateRequest newGenerateRequestForVersion(
+            FhirVersionEnum fhirVersion, IBaseResource profile, LibraryEngine libraryEngine) {
+        return new GenerateRequest(
+                profile, false, true, libraryEngine, FhirModelResolverCache.resolverForVersion(fhirVersion));
+    }
+
+    public static PopulateRequest newPopulateRequestForVersion(
+            FhirVersionEnum fhirVersion, LibraryEngine libraryEngine, IBaseResource questionnaire) {
+        return new PopulateRequest(
+                questionnaire,
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
+                null,
+                null,
+                null,
+                null,
+                true,
+                libraryEngine,
+                FhirModelResolverCache.resolverForVersion(fhirVersion));
+    }
+
+    public static ExtractRequest newExtractRequestForVersion(
+            FhirVersionEnum fhirVersion,
+            LibraryEngine libraryEngine,
+            IBaseResource questionnaireResponse,
+            IBaseResource questionnaire) {
+        return new ExtractRequest(
+                questionnaireResponse,
+                questionnaire,
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
+                null,
+                null,
+                true,
+                libraryEngine,
+                FhirModelResolverCache.resolverForVersion(fhirVersion),
+                null);
+    }
+
+    public static EvaluateRequest newEvaluateRequestForVersion(
+            FhirVersionEnum fhirVersion, LibraryEngine libraryEngine, IBaseResource library) {
+        return new EvaluateRequest(
+                library,
+                Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
+                null,
+                null,
+                true,
+                null,
+                null,
+                libraryEngine,
+                FhirModelResolverCache.resolverForVersion(fhirVersion));
+    }
+}