Fix warnings in adapter classes and interfaces (#562)

* Fix warnings in adapter classes and interfaces

* cleanup

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

@@ -34,7 +34,7 @@
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
 import org.opencds.cqf.fhir.cql.engine.terminology.RepositoryTerminologyProvider;
 import org.opencds.cqf.fhir.utility.Constants;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.opencds.cqf.fhir.utility.model.FhirModelResolverCache;
 import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
 import org.slf4j.Logger;
@@ -92,7 +92,7 @@ public static CqlEngine forRepositoryAndSettings(
     }
 
     private static LibrarySourceProvider buildLibrarySource(Repository repository) {
-        var adapterFactory = AdapterFactory.forFhirContext(repository.fhirContext());
+        var adapterFactory = IAdapterFactory.forFhirContext(repository.fhirContext());
         return new RepositoryFhirLibrarySourceProvider(
                 repository, adapterFactory, new LibraryVersionSelector(adapterFactory));
     }
@@ -185,6 +185,6 @@ public static CqlFhirParametersConverter getCqlFhirParametersConverter(FhirConte
         var fhirTypeConverter =
                 new FhirTypeConverterFactory().create(fhirContext.getVersion().getVersion());
         return new CqlFhirParametersConverter(
-                fhirContext, AdapterFactory.forFhirContext(fhirContext), fhirTypeConverter);
+                fhirContext, IAdapterFactory.forFhirContext(fhirContext), fhirTypeConverter);
     }
 }

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

@@ -9,19 +9,19 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
-import org.opencds.cqf.fhir.utility.adapter.AttachmentAdapter;
-import org.opencds.cqf.fhir.utility.adapter.LibraryAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAttachmentAdapter;
+import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
 
 /**
  * This class implements logic for extracting content from a FHIR Library resource and provides an
  * extension point for implementing the fetch of a FHIR library matching a specific identifier.
  */
 public abstract class BaseFhirLibrarySourceProvider implements LibrarySourceProvider {
 
-    protected AdapterFactory adapterFactory;
+    protected IAdapterFactory adapterFactory;
 
-    protected BaseFhirLibrarySourceProvider(AdapterFactory adapterFactory) {
+    protected BaseFhirLibrarySourceProvider(IAdapterFactory adapterFactory) {
         this.adapterFactory = requireNonNull(adapterFactory, "adapterFactory can not be null");
     }
 
@@ -40,11 +40,11 @@ public InputStream getLibraryContent(VersionedIdentifier libraryIdentifier, Libr
 
     protected InputStream getContentStream(IBaseResource library, String contentType) {
 
-        LibraryAdapter libraryAdapter = this.adapterFactory.createLibrary(library);
+        ILibraryAdapter libraryAdapter = this.adapterFactory.createLibrary(library);
 
         if (libraryAdapter.hasContent()) {
             for (ICompositeType attachment : libraryAdapter.getContent()) {
-                AttachmentAdapter attachmentAdapter = this.adapterFactory.createAttachment(attachment);
+                IAttachmentAdapter attachmentAdapter = this.adapterFactory.createAttachment(attachment);
                 if (attachmentAdapter.getContentType().equals(contentType)) {
                     // get externalized extension if present and add custom load data
                     return new ByteArrayInputStream(attachmentAdapter.getData());

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

@@ -9,7 +9,7 @@
 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.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.opencds.cqf.fhir.utility.iterable.BundleIterable;
 import org.opencds.cqf.fhir.utility.search.Searches;
 
@@ -20,7 +20,7 @@ public class RepositoryFhirLibrarySourceProvider extends BaseFhirLibrarySourcePr
     private final LibraryVersionSelector libraryVersionSelector;
 
     public RepositoryFhirLibrarySourceProvider(
-            Repository repository, AdapterFactory adapterFactory, LibraryVersionSelector libraryVersionSelector) {
+            Repository repository, IAdapterFactory adapterFactory, LibraryVersionSelector libraryVersionSelector) {
         super(adapterFactory);
         this.repository = requireNonNull(repository, "repository can not be null");
         this.fhirContext = repository.fhirContext();

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/cql2elm/util/LibraryVersionSelector.java

@@ -7,14 +7,14 @@
 import java.util.stream.Collectors;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
-import org.opencds.cqf.fhir.utility.adapter.LibraryAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.ILibraryAdapter;
 
 public class LibraryVersionSelector {
 
-    private final AdapterFactory adapterFactory;
+    private final IAdapterFactory adapterFactory;
 
-    public LibraryVersionSelector(AdapterFactory adapterFactory) {
+    public LibraryVersionSelector(IAdapterFactory adapterFactory) {
         this.adapterFactory = adapterFactory;
     }
 
@@ -24,14 +24,14 @@ public IBaseResource select(VersionedIdentifier libraryIdentifier, Collection<IB
 
         String targetVersion = libraryIdentifier.getVersion();
 
-        List<LibraryAdapter> adapters = libraries.stream()
+        List<ILibraryAdapter> adapters = libraries.stream()
                 .map(x -> this.adapterFactory.createLibrary(x))
                 .collect(Collectors.toList());
 
-        LibraryAdapter library = null;
-        LibraryAdapter maxLibrary = null;
+        ILibraryAdapter library = null;
+        ILibraryAdapter maxLibrary = null;
 
-        for (LibraryAdapter l : adapters) {
+        for (ILibraryAdapter l : adapters) {
 
             if (!l.getName().equals(libraryIdentifier.getId())) {
                 continue;

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/parameters/CqlFhirParametersConverter.java

@@ -20,24 +20,24 @@
 import org.opencds.cqf.cql.engine.execution.ExpressionResult;
 import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverter;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
-import org.opencds.cqf.fhir.utility.adapter.ParametersAdapter;
-import org.opencds.cqf.fhir.utility.adapter.ParametersParameterComponentAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IParametersAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IParametersParameterComponentAdapter;
 import org.opencds.cqf.fhir.utility.model.FhirModelResolverCache;
 import org.slf4j.LoggerFactory;
 
 public class CqlFhirParametersConverter {
 
     org.slf4j.Logger logger = LoggerFactory.getLogger(CqlFhirParametersConverter.class);
 
-    protected AdapterFactory adapterFactory;
+    protected IAdapterFactory adapterFactory;
     protected FhirTypeConverter fhirTypeConverter;
     protected FhirContext fhirContext;
     // private IFhirPath fhirPath;
     private ModelResolver modelResolver;
 
     public CqlFhirParametersConverter(
-            FhirContext fhirContext, AdapterFactory adapterFactory, FhirTypeConverter fhirTypeConverter) {
+            FhirContext fhirContext, IAdapterFactory adapterFactory, FhirTypeConverter fhirTypeConverter) {
         this.fhirContext = requireNonNull(fhirContext);
         this.adapterFactory = requireNonNull(adapterFactory);
         this.fhirTypeConverter = requireNonNull(fhirTypeConverter);
@@ -60,7 +60,7 @@ public IBaseParameters toFhirParameters(EvaluationResult evaluationResult) {
             throw new RuntimeException(e);
         }
 
-        ParametersAdapter pa = this.adapterFactory.createParameters(params);
+        IParametersAdapter pa = this.adapterFactory.createParameters(params);
 
         for (Map.Entry<String, ExpressionResult> entry : evaluationResult.expressionResults.entrySet()) {
             String name = entry.getKey();
@@ -84,17 +84,17 @@ public IBaseParameters toFhirParameters(EvaluationResult evaluationResult) {
         return params;
     }
 
-    protected ParametersParameterComponentAdapter addPart(ParametersAdapter pa, String name) {
+    protected IParametersParameterComponentAdapter addPart(IParametersAdapter pa, String name) {
         IBaseBackboneElement ppc = pa.addParameter();
-        ParametersParameterComponentAdapter ppca = this.adapterFactory.createParametersParameters(ppc);
+        IParametersParameterComponentAdapter ppca = this.adapterFactory.createParametersParameters(ppc);
         ppca.setName(name);
 
         return ppca;
     }
 
     @SuppressWarnings("unchecked")
-    protected void addPart(ParametersAdapter pa, String name, Object value) {
-        ParametersParameterComponentAdapter ppca = this.addPart(pa, name);
+    protected void addPart(IParametersAdapter pa, String name, Object value) {
+        IParametersParameterComponentAdapter ppca = this.addPart(pa, name);
 
         if (value == null) {
             return;
@@ -124,18 +124,18 @@ protected void addPart(ParametersAdapter pa, String name, Object value) {
         }
     }
 
-    protected ParametersParameterComponentAdapter addSubPart(
-            ParametersParameterComponentAdapter ppcAdapter, String name) {
+    protected IParametersParameterComponentAdapter addSubPart(
+            IParametersParameterComponentAdapter ppcAdapter, String name) {
         IBaseBackboneElement ppc = ppcAdapter.addPart();
-        ParametersParameterComponentAdapter ppca = this.adapterFactory.createParametersParameters(ppc);
+        IParametersParameterComponentAdapter ppca = this.adapterFactory.createParametersParameters(ppc);
         ppca.setName(name);
 
         return ppca;
     }
 
     @SuppressWarnings("unchecked")
-    protected void addSubPart(ParametersParameterComponentAdapter ppcAdapter, String name, Object value) {
-        ParametersParameterComponentAdapter ppca = this.addSubPart(ppcAdapter, name);
+    protected void addSubPart(IParametersParameterComponentAdapter ppcAdapter, String name, Object value) {
+        IParametersParameterComponentAdapter ppca = this.addSubPart(ppcAdapter, name);
 
         if (value == null) {
             return;
@@ -170,15 +170,15 @@ public List<CqlParameterDefinition> toCqlParameterDefinitions(IBaseParameters pa
             return Collections.emptyList();
         }
 
-        ParametersAdapter parametersAdapter = this.adapterFactory.createParameters(parameters);
+        IParametersAdapter parametersAdapter = this.adapterFactory.createParameters(parameters);
 
-        Map<String, List<ParametersParameterComponentAdapter>> children = parametersAdapter.getParameter().stream()
+        Map<String, List<IParametersParameterComponentAdapter>> children = parametersAdapter.getParameter().stream()
                 .map(x -> this.adapterFactory.createParametersParameters(x))
                 .filter(x -> x.getName() != null)
-                .collect(Collectors.groupingBy(ParametersParameterComponentAdapter::getName));
+                .collect(Collectors.groupingBy(IParametersParameterComponentAdapter::getName));
 
         List<CqlParameterDefinition> cqlParameterDefinitions = new ArrayList<>();
-        for (Map.Entry<String, List<ParametersParameterComponentAdapter>> entry : children.entrySet()) {
+        for (Map.Entry<String, List<IParametersParameterComponentAdapter>> entry : children.entrySet()) {
             // Meta data extension, if present
             Optional<IBaseExtension<?, ?>> ext = entry.getValue().stream()
                     .filter(x -> x.hasExtension())
@@ -299,7 +299,7 @@ private Boolean isListType(IBaseExtension<?, ?> parameterDefinitionExtension) {
         return false;
     }
 
-    private Object convertToCql(ParametersParameterComponentAdapter ppca) {
+    private Object convertToCql(IParametersParameterComponentAdapter ppca) {
         if (ppca.hasValue()) {
             return this.fhirTypeConverter.toCqlType(ppca.getValue());
         } else if (ppca.hasResource()) {

cqf-fhir-cql/src/test/java/org/opencds/cqf/fhir/cql/engine/parameters/CqlFhirParametersConverterTests.java

@@ -27,7 +27,7 @@
 import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverterFactory;
 import org.opencds.cqf.cql.engine.runtime.Date;
 import org.opencds.cqf.cql.engine.runtime.Interval;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 
 class CqlFhirParametersConverterTests {
 
@@ -37,7 +37,7 @@ class CqlFhirParametersConverterTests {
     static void setup() {
         FhirContext fhirContext = FhirContext.forCached(FhirVersionEnum.R4);
 
-        AdapterFactory adapterFactory = new org.opencds.cqf.fhir.utility.adapter.r4.AdapterFactory();
+        IAdapterFactory adapterFactory = new org.opencds.cqf.fhir.utility.adapter.r4.AdapterFactory();
         FhirTypeConverter fhirTypeConverter =
                 new FhirTypeConverterFactory().create(fhirContext.getVersion().getVersion());
 

cqf-fhir-cr-spring/src/main/java/org/opencds/cqf/fhir/cr/spring/fhir/adapter/AdapterConfiguration.java

@@ -1,15 +1,15 @@
 package org.opencds.cqf.fhir.cr.spring.fhir.adapter;
 
 import ca.uhn.fhir.context.FhirContext;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
 @Configuration
 public class AdapterConfiguration {
 
     @Bean
-    AdapterFactory adapterFactory(FhirContext fhirContext) {
+    IAdapterFactory adapterFactory(FhirContext fhirContext) {
         switch (fhirContext.getVersion().getVersion()) {
             case DSTU3:
                 return new org.opencds.cqf.fhir.utility.adapter.dstu3.AdapterFactory();

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/activitydefinition/apply/ApplyRequest.java

@@ -13,7 +13,7 @@
 import org.opencds.cqf.fhir.cql.LibraryEngine;
 import org.opencds.cqf.fhir.cr.common.ICpgRequest;
 import org.opencds.cqf.fhir.cr.inputparameters.IInputParameterResolver;
-import org.opencds.cqf.fhir.utility.adapter.QuestionnaireAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IQuestionnaireAdapter;
 
 public class ApplyRequest implements ICpgRequest {
     private final IBaseResource activityDefinition;
@@ -215,7 +215,7 @@ public IBaseResource getQuestionnaire() {
     }
 
     @Override
-    public QuestionnaireAdapter getQuestionnaireAdapter() {
+    public IQuestionnaireAdapter getQuestionnaireAdapter() {
         return null;
     }
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/DataRequirementsProcessor.java

@@ -9,7 +9,7 @@
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.EvaluationSettings;
 import org.opencds.cqf.fhir.cr.visitor.DataRequirementsVisitor;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 
 public class DataRequirementsProcessor implements IDataRequirementsProcessor {
     protected final Repository repository;
@@ -29,7 +29,7 @@ public DataRequirementsProcessor(Repository repository, EvaluationSettings evalu
     @Override
     public IBaseResource getDataRequirements(IBaseResource resource, IBaseParameters parameters) {
         return (IBaseResource) dataRequirementsVisitor.visit(
-                AdapterFactory.forFhirVersion(fhirVersion).createKnowledgeArtifactAdapter((IDomainResource) resource),
+                IAdapterFactory.forFhirVersion(fhirVersion).createKnowledgeArtifactAdapter((IDomainResource) resource),
                 repository,
                 parameters == null ? newParameters(repository.fhirContext()) : parameters);
     }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/IOperationRequest.java

@@ -18,7 +18,7 @@
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.opencds.cqf.fhir.api.Repository;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 
 public interface IOperationRequest {
     String getOperationName();
@@ -39,8 +39,8 @@ default FhirContext getFhirContext() {
 
     void setOperationOutcome(IBaseOperationOutcome operationOutcome);
 
-    default AdapterFactory getAdapterFactory() {
-        return AdapterFactory.forFhirVersion(getFhirVersion());
+    default IAdapterFactory getAdapterFactory() {
+        return IAdapterFactory.forFhirVersion(getFhirVersion());
     }
 
     default void logException(String exceptionMessage) {

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/IQuestionnaireRequest.java

@@ -12,12 +12,12 @@
 import org.hl7.fhir.instance.model.api.IDomainResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.opencds.cqf.fhir.utility.Constants;
-import org.opencds.cqf.fhir.utility.adapter.QuestionnaireAdapter;
+import org.opencds.cqf.fhir.utility.adapter.IQuestionnaireAdapter;
 
 public interface IQuestionnaireRequest extends ICqlOperationRequest {
     IBaseResource getQuestionnaire();
 
-    QuestionnaireAdapter getQuestionnaireAdapter();
+    IQuestionnaireAdapter getQuestionnaireAdapter();
 
     default void addQuestionnaireItem(IBaseBackboneElement item) {
         getModelResolver().setValue(getQuestionnaire(), "item", Collections.singletonList(item));

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/PackageProcessor.java

@@ -9,7 +9,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IDomainResource;
 import org.opencds.cqf.fhir.api.Repository;
-import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.opencds.cqf.fhir.utility.visitor.PackageVisitor;
 
 public class PackageProcessor implements IPackageProcessor {
@@ -41,7 +41,7 @@ public IBaseBundle packageResource(IBaseResource resource, String method) {
     @Override
     public IBaseBundle packageResource(IBaseResource resource, IBaseParameters parameters) {
         return (IBaseBundle) packageVisitor.visit(
-                AdapterFactory.forFhirVersion(fhirVersion).createKnowledgeArtifactAdapter((IDomainResource) resource),
+                IAdapterFactory.forFhirVersion(fhirVersion).createKnowledgeArtifactAdapter((IDomainResource) resource),
                 repository,
                 parameters);
     }