Use HAPI Repository interface and classes (#659)

* use hapi repository

* use hapi repository

* remove unused cdsConfigService

* handle contained id change

* fix measure test

* fix tests

* fix merge stompage

* bump hapi to release version

* spotless

* fix warnings

* fix tests

* fix merge stompage

* spotless

* fix tests

* fix tests

* fix some warnings

* fix tests and bump cql version to release

* Fix CPG IT test

* Fix Cql Evaluation Service Test

* Fix tests for errors

* fix tests

* Fix tests for real

* For realz fixed for realz

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: JP <jonathan.percival@smilecdr.com>

Author: barhodes

cqf-fhir-api/src/main/java/org/opencds/cqf/fhir/api/Repository.java

@@ -7,7 +7,6 @@
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
-import com.google.common.annotations.Beta;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -66,8 +65,10 @@
  * </p>
  *
  * @see <a href="https://www.hl7.org/fhir/http.html">FHIR REST API</a>
+ *
+ * @deprecated Use class from HAPI
  */
-@Beta
+@Deprecated(since = "3.25.0", forRemoval = true)
 public interface Repository {
 
     // CRUD starts here

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

@@ -1,14 +1,14 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import org.opencds.cqf.fhir.api.Repository;
+import ca.uhn.fhir.repository.IRepository;
 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) {
+    public IActivityDefinitionProcessor create(IRepository repository) {
         return new ActivityDefinitionProcessor(repository);
     }
 }

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/measure/r4/Measure.java

@@ -3,13 +3,13 @@
 import static org.opencds.cqf.fhir.test.Resources.getResourcePath;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.repository.IRepository;
 import java.nio.file.Path;
 import java.time.ZonedDateTime;
 import java.util.function.Supplier;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.MeasureReport;
-import org.opencds.cqf.fhir.api.Repository;
 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;
@@ -45,7 +45,7 @@ public static Given given() {
     }
 
     public static class Given {
-        private Repository repository;
+        private IRepository repository;
         private MeasureEvaluationOptions evaluationOptions;
         private final MeasurePeriodValidator measurePeriodValidator;
         private final R4MeasureServiceUtils measureServiceUtils;

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/plandefinition/TestPlanDefinition.java

@@ -17,6 +17,7 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.repository.IRepository;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
@@ -36,7 +37,6 @@
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.json.JSONException;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.benchmark.TestOperationProvider;
 import org.opencds.cqf.fhir.benchmark.helpers.DataRequirementsLibrary;
 import org.opencds.cqf.fhir.benchmark.helpers.GeneratedPackage;
@@ -99,10 +99,10 @@ public static Given given() {
     }
 
     public static class Given {
-        private Repository repository;
+        private IRepository repository;
         private EvaluationSettings evaluationSettings;
 
-        public Given repository(Repository repository) {
+        public Given repository(IRepository repository) {
             this.repository = repository;
             return this;
         }
@@ -119,7 +119,7 @@ public Given evaluationSettings(EvaluationSettings evaluationSettings) {
             return this;
         }
 
-        public PlanDefinitionProcessor buildProcessor(Repository repository) {
+        public PlanDefinitionProcessor buildProcessor(IRepository repository) {
             if (repository instanceof IgRepository igRepository) {
                 igRepository.setOperationProvider(TestOperationProvider.newProvider(repository.fhirContext()));
             }
@@ -143,7 +143,7 @@ public When when() {
     }
 
     public static class When {
-        private final Repository repository;
+        private final IRepository repository;
         private final PlanDefinitionProcessor processor;
         private final IParser jsonParser;
 
@@ -154,16 +154,16 @@ public static class When {
         private String practitionerId;
         private String organizationId;
         private boolean useServerData;
-        private Repository dataRepository;
-        private Repository contentRepository;
-        private Repository terminologyRepository;
+        private IRepository dataRepository;
+        private IRepository contentRepository;
+        private IRepository terminologyRepository;
         private IBaseBundle additionalData;
         private IIdType additionalDataId;
         private List<? extends IBaseBackboneElement> prefetchData;
         private IBaseParameters parameters;
         private boolean isPackagePut;
 
-        public When(Repository repository, PlanDefinitionProcessor processor) {
+        public When(IRepository repository, PlanDefinitionProcessor processor) {
             this.repository = repository;
             this.processor = processor;
             jsonParser = repository.fhirContext().newJsonParser();
@@ -335,15 +335,15 @@ public DataRequirementsLibrary thenDataRequirements() {
     }
 
     public static class GeneratedBundle {
-        final Repository repository;
+        final IRepository repository;
         final IBaseBundle generatedBundleInner;
         final IParser jsonParser;
         final ModelResolver modelResolver;
         IBaseResource questionnaire;
         IBaseResource questionnaireResponse;
         Map<String, IBaseBackboneElement> items;
 
-        public GeneratedBundle(Repository repository, IBaseBundle generatedBundleInner) {
+        public GeneratedBundle(IRepository repository, IBaseBundle generatedBundleInner) {
             this.repository = repository;
             this.generatedBundleInner = generatedBundleInner;
             jsonParser = this.repository.fhirContext().newJsonParser().setPrettyPrint(true);
@@ -466,12 +466,12 @@ public GeneratedBundle entryHasOperationOutcome(int entry) {
     }
 
     public static class GeneratedCarePlan {
-        final Repository repository;
+        final IRepository repository;
         final IBaseResource generatedCarePlanInner;
         final IParser jsonParser;
         final ModelResolver modelResolver;
 
-        public GeneratedCarePlan(Repository repository, IBaseResource generatedCarePlanInner) {
+        public GeneratedCarePlan(IRepository repository, IBaseResource generatedCarePlanInner) {
             this.repository = repository;
             this.generatedCarePlanInner = generatedCarePlanInner;
             jsonParser = this.repository.fhirContext().newJsonParser().setPrettyPrint(true);

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/questionnaire/TestQuestionnaire.java

@@ -3,6 +3,7 @@
 import static org.opencds.cqf.fhir.test.Resources.getResourcePath;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.repository.IRepository;
 import java.nio.file.Path;
 import java.util.List;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@@ -12,7 +13,6 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.EvaluationSettings;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.SEARCH_FILTER_MODE;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.TERMINOLOGY_FILTER_MODE;
@@ -29,7 +29,7 @@ public static Given given() {
     }
 
     public static class Given {
-        private Repository repository;
+        private IRepository repository;
         private EvaluationSettings evaluationSettings;
 
         public Given repositoryFor(FhirContext fhirContext, String repositoryPath) {
@@ -38,7 +38,7 @@ public Given repositoryFor(FhirContext fhirContext, String repositoryPath) {
             return this;
         }
 
-        public QuestionnaireProcessor buildProcessor(Repository repository) {
+        public QuestionnaireProcessor buildProcessor(IRepository repository) {
             if (evaluationSettings == null) {
                 evaluationSettings = EvaluationSettings.getDefault();
                 evaluationSettings

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/Engines.java

@@ -3,6 +3,7 @@
 import static com.google.common.base.Preconditions.checkNotNull;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.repository.IRepository;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -24,7 +25,6 @@
 import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverterFactory;
 import org.opencds.cqf.cql.engine.retrieve.RetrieveProvider;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.cql2elm.content.RepositoryFhirLibrarySourceProvider;
 import org.opencds.cqf.fhir.cql.cql2elm.util.LibraryVersionSelector;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
@@ -45,16 +45,16 @@ public class Engines {
 
     private Engines() {}
 
-    public static CqlEngine forRepository(Repository repository) {
+    public static CqlEngine forRepository(IRepository repository) {
         return forRepository(repository, EvaluationSettings.getDefault());
     }
 
-    public static CqlEngine forRepository(Repository repository, EvaluationSettings settings) {
+    public static CqlEngine forRepository(IRepository repository, EvaluationSettings settings) {
         return forRepository(repository, settings, null);
     }
 
     public static CqlEngine forRepository(
-            Repository repository, EvaluationSettings settings, IBaseBundle additionalData) {
+            IRepository repository, EvaluationSettings settings, IBaseBundle additionalData) {
         checkNotNull(settings);
         checkNotNull(repository);
 
@@ -67,7 +67,7 @@ public static CqlEngine forRepository(
     }
 
     private static Environment buildEnvironment(
-            Repository repository,
+            IRepository repository,
             EvaluationSettings settings,
             TerminologyProvider terminologyProvider,
             Map<String, DataProvider> dataProviders) {
@@ -85,7 +85,7 @@ private static Environment buildEnvironment(
     }
 
     private static void registerLibrarySourceProviders(
-            EvaluationSettings settings, LibraryManager manager, Repository repository) {
+            EvaluationSettings settings, LibraryManager manager, IRepository repository) {
         var loader = manager.getLibrarySourceLoader();
         loader.clearProviders();
 
@@ -134,14 +134,14 @@ private static void registerNpmSupport(
         }
     }
 
-    private static LibrarySourceProvider buildLibrarySource(Repository repository) {
+    private static LibrarySourceProvider buildLibrarySource(IRepository repository) {
         var adapterFactory = IAdapterFactory.forFhirContext(repository.fhirContext());
         return new RepositoryFhirLibrarySourceProvider(
                 repository, adapterFactory, new LibraryVersionSelector(adapterFactory));
     }
 
     private static Map<String, DataProvider> buildDataProviders(
-            Repository repository,
+            IRepository repository,
             IBaseBundle additionalData,
             TerminologyProvider terminologyProvider,
             RetrieveSettings retrieveSettings) {

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryEngine.java

@@ -3,6 +3,7 @@
 import static java.util.Objects.requireNonNull;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.repository.IRepository;
 import ca.uhn.fhir.util.ParametersUtil;
 import com.google.common.collect.Lists;
 import jakarta.annotation.Nullable;
@@ -24,7 +25,6 @@
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.opencds.cqf.cql.engine.execution.CqlEngine;
 import org.opencds.cqf.cql.engine.execution.EvaluationResult;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
 import org.opencds.cqf.fhir.utility.CqfExpression;
@@ -35,17 +35,17 @@ public class LibraryEngine {
 
     private static final Logger logger = LoggerFactory.getLogger(LibraryEngine.class);
 
-    protected final Repository repository;
+    protected final IRepository repository;
     protected final FhirContext fhirContext;
     protected final EvaluationSettings settings;
 
-    public LibraryEngine(Repository repository, EvaluationSettings evaluationSettings) {
+    public LibraryEngine(IRepository repository, EvaluationSettings evaluationSettings) {
         this.repository = requireNonNull(repository, "repository can not be null");
         this.settings = requireNonNull(evaluationSettings, "evaluationSettings can not be null");
         fhirContext = repository.fhirContext();
     }
 
-    public Repository getRepository() {
+    public IRepository getRepository() {
         return repository;
     }
 

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/cql2elm/content/RepositoryFhirLibrarySourceProvider.java

@@ -3,31 +3,31 @@
 import static java.util.Objects.requireNonNull;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.repository.IRepository;
 import java.util.ArrayList;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.cql2elm.util.LibraryVersionSelector;
 import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.opencds.cqf.fhir.utility.iterable.BundleIterable;
 import org.opencds.cqf.fhir.utility.search.Searches;
 
 public class RepositoryFhirLibrarySourceProvider extends BaseFhirLibrarySourceProvider {
 
-    private final Repository repository;
+    private final IRepository repository;
     private final FhirContext fhirContext;
     private final LibraryVersionSelector libraryVersionSelector;
 
     public RepositoryFhirLibrarySourceProvider(
-            Repository repository, IAdapterFactory adapterFactory, LibraryVersionSelector libraryVersionSelector) {
+            IRepository repository, IAdapterFactory adapterFactory, LibraryVersionSelector libraryVersionSelector) {
         super(adapterFactory);
         this.repository = requireNonNull(repository, "repository can not be null");
         this.fhirContext = repository.fhirContext();
         this.libraryVersionSelector = requireNonNull(libraryVersionSelector, "libraryVersionSelector can not be null");
     }
 
-    protected Repository getRepository() {
+    protected IRepository getRepository() {
         return this.repository;
     }
 

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/RepositoryRetrieveProvider.java

@@ -4,6 +4,7 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.repository.IRepository;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -14,15 +15,14 @@
 import org.opencds.cqf.cql.engine.runtime.Code;
 import org.opencds.cqf.cql.engine.runtime.Interval;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.utility.iterable.BundleMappingIterable;
 
 public class RepositoryRetrieveProvider extends BaseRetrieveProvider {
-    private final Repository repository;
+    private final IRepository repository;
     private final FhirContext fhirContext;
 
     public RepositoryRetrieveProvider(
-            final Repository repository, final TerminologyProvider terminologyProvider, RetrieveSettings settings) {
+            final IRepository repository, final TerminologyProvider terminologyProvider, RetrieveSettings settings) {
         super(repository.fhirContext(), terminologyProvider, settings);
         this.repository = requireNonNull(repository, "repository can not be null.");
         this.fhirContext = repository.fhirContext();