Package operation updates

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

@@ -27,14 +27,14 @@
 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.model.FhirModelResolverCache;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
 import org.opencds.cqf.fhir.cql.engine.retrieve.FederatedDataProvider;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RepositoryRetrieveProvider;
 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.model.FhirModelResolverCache;
 import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -106,7 +106,7 @@ public static CqlEngine forRepositoryAndSettings(
     }
 
     private static LibrarySourceProvider buildLibrarySource(Repository repository) {
-        AdapterFactory adapterFactory = getAdapterFactory(repository.fhirContext());
+        var adapterFactory = AdapterFactory.forFhirContext(repository.fhirContext());
         return new RepositoryFhirLibrarySourceProvider(
                 repository, adapterFactory, new LibraryVersionSelector(adapterFactory));
     }
@@ -186,22 +186,10 @@ private static Map<String, DataProvider> buildDataProviders(
         return dataProviders;
     }
 
-    public static AdapterFactory getAdapterFactory(FhirContext fhirContext) {
-        switch (fhirContext.getVersion().getVersion()) {
-            case DSTU3:
-                return new org.opencds.cqf.fhir.utility.adapter.dstu3.AdapterFactory();
-            case R4:
-                return new org.opencds.cqf.fhir.utility.adapter.r4.AdapterFactory();
-            case R5:
-                return new org.opencds.cqf.fhir.utility.adapter.r5.AdapterFactory();
-            default:
-                throw new IllegalArgumentException(String.format("unsupported FHIR version: %s", fhirContext));
-        }
-    }
-
     public static CqlFhirParametersConverter getCqlFhirParametersConverter(FhirContext fhirContext) {
         var fhirTypeConverter =
                 new FhirTypeConverterFactory().create(fhirContext.getVersion().getVersion());
-        return new CqlFhirParametersConverter(fhirContext, getAdapterFactory(fhirContext), fhirTypeConverter);
+        return new CqlFhirParametersConverter(
+                fhirContext, AdapterFactory.forFhirContext(fhirContext), fhirTypeConverter);
     }
 }

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

@@ -10,6 +10,7 @@
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.opencds.cqf.fhir.utility.Constants;
+import org.opencds.cqf.fhir.utility.CqfExpression;
 
 /**
  * This class is used to resolve any CQFExpression extensions that exist on an extension.

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

@@ -3,6 +3,7 @@
 import static java.util.Objects.requireNonNull;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.fhirpath.IFhirPath;
 import java.util.List;
 import org.apache.commons.lang3.tuple.Pair;
@@ -46,10 +47,15 @@ private void constructExpression(StringBuilder sb, String expression) {
         sb.append(String.format("%ndefine \"return\":%n       %s", expression));
     }
 
+    private String getFhirVersionString(FhirVersionEnum fhirVersion) {
+        // The version of the DSTU3 enum is 3.0.2 which the CQL Engine does not support.
+        return fhirVersion == FhirVersionEnum.DSTU3 ? "3.0.1" : fhirVersion.getFhirVersionString();
+    }
+
     private void constructIncludes(StringBuilder sb, List<Pair<String, String>> libraries) {
         sb.append(String.format(
                 "include FHIRHelpers version '%s' called FHIRHelpers%n",
-                fhirContext.getVersion().getVersion().getFhirVersionString()));
+                getFhirVersionString(fhirContext.getVersion().getVersion())));
 
         if (libraries != null) {
             for (Pair<String, String> library : libraries) {
@@ -93,7 +99,7 @@ private String getTypeDeclaration(String type, Boolean isList) {
     private void constructUsings(StringBuilder sb) {
         sb.append(String.format(
                 "using FHIR version '%s'%n",
-                fhirContext.getVersion().getVersion().getFhirVersionString()));
+                getFhirVersionString(fhirContext.getVersion().getVersion())));
     }
 
     private void constructHeader(StringBuilder sb) {

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

@@ -10,6 +10,8 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.cqframework.cql.cql2elm.StringLibrarySourceProvider;
@@ -20,6 +22,8 @@
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
+import org.opencds.cqf.fhir.utility.Canonicals;
+import org.opencds.cqf.fhir.utility.CqfExpression;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -161,8 +165,13 @@ public List<IBase> getExpressionResult(
             case "text/cql.expression":
             case "text/cql-expression":
             case "text/fhirpath":
+                var libraries = new ArrayList<Pair<String, String>>();
+                if (!StringUtils.isBlank(libraryToBeEvaluated)) {
+                    libraries.add(new ImmutablePair<String, String>(
+                            libraryToBeEvaluated, Canonicals.getIdPart(libraryToBeEvaluated)));
+                }
                 parametersResult = this.evaluateExpression(
-                        expression, parameters, subjectId, null, bundle, contextParameter, resourceParameter);
+                        expression, parameters, subjectId, libraries, bundle, contextParameter, resourceParameter);
                 // The expression is assumed to be the parameter component name
                 // The expression evaluator creates a library with a single expression defined as "return"
                 results = resolveParameterValues(

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

@@ -46,6 +46,7 @@ protected InputStream getContentStream(IBaseResource library, String contentType
             for (ICompositeType attachment : libraryAdapter.getContent()) {
                 AttachmentAdapter 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/engine/parameters/CqlFhirParametersConverter.java

@@ -20,10 +20,10 @@
 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.cql.engine.model.FhirModelResolverCache;
 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.model.FhirModelResolverCache;
 import org.slf4j.LoggerFactory;
 
 public class CqlFhirParametersConverter {

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/terminology/RepositoryTerminologyProvider.java

@@ -22,8 +22,8 @@
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_EXPANSION_MODE;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_PRE_EXPANSION_MODE;
-import org.opencds.cqf.fhir.cql.engine.utility.ValueSets;
 import org.opencds.cqf.fhir.utility.FhirPathCache;
+import org.opencds.cqf.fhir.utility.ValueSets;
 import org.opencds.cqf.fhir.utility.search.Searches;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

cqf-fhir-cql/src/test/java/org/opencds/cqf/fhir/cql/LibraryEngineTests.java

@@ -15,17 +15,18 @@
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.Test;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.utility.CqfExpression;
 import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;
 
 class LibraryEngineTests {
+    Repository repository =
+            new IgRepository(FhirContext.forR4Cached(), Paths.get(getResourcePath(LibraryEngineTests.class)));
+    LibraryEngine libraryEngine = new LibraryEngine(repository, EvaluationSettings.getDefault());
 
     @Test
     void fhirPath() {
         var patientId = "Patient/Patient1";
-        var repository =
-                new IgRepository(FhirContext.forR4Cached(), Paths.get(getResourcePath(LibraryEngineTests.class)));
-        var libraryEngine = new LibraryEngine(repository, EvaluationSettings.getDefault());
-
         var params = parameters();
         params.addParameter(part("%subject", new Patient().addName(new HumanName().addGiven("Alice"))));
         params.addParameter(part("%practitioner", new Practitioner().addName(new HumanName().addGiven("Michael"))));
@@ -48,10 +49,6 @@ void fhirPath() {
     @Test
     void fhirPathWithResource() {
         var patientId = "Patient/Patient1";
-        var repository =
-                new IgRepository(FhirContext.forR4Cached(), Paths.get(getResourcePath(LibraryEngineTests.class)));
-        var libraryEngine = new LibraryEngine(repository, EvaluationSettings.getDefault());
-
         var params = parameters();
         params.addParameter(part("%subject", new Patient().addName(new HumanName().addGiven("Alice"))));
         params.addParameter(part("%practitioner", new Practitioner().addName(new HumanName().addGiven("Michael"))));
@@ -67,4 +64,13 @@ void fhirPathWithResource() {
                 "test-code",
                 ((CodeableConcept) result.get(0)).getCodingFirstRep().getCode());
     }
+
+    @Test
+    void expressionWithLibraryReference() {
+        var patientId = "Patient/Patient1";
+        var expression =
+                new CqfExpression("text/cql", "TestLibrary.testExpression", "http://fhir.test/Library/TestLibrary");
+        var result = libraryEngine.resolveExpression(patientId, expression, null, null, null, null);
+        assertEquals(((StringType) result.get(0)).getValue(), "I am a test");
+    }
 }

cqf-fhir-cql/src/test/resources/org/opencds/cqf/fhir/cql/cql/TestLibrary.cql

@@ -0,0 +1,8 @@
+library TestLibrary version '1.0.0'
+
+using FHIR version '4.0.1'
+
+context Patient
+
+define "testExpression":
+  'I am a test'

cqf-fhir-cql/src/test/resources/org/opencds/cqf/fhir/cql/resources/Library-TestLibrary.json

@@ -0,0 +1,13 @@
+{
+  "resourceType": "Library",
+  "id": "TestLibrary",
+  "url": "http://fhir.test/Library/TestLibrary",
+  "version": "1.0.0",
+  "name": "TestLibrary",
+  "content": [
+    {
+      "contentType": "text/cql",
+      "url": "../cql/TestLibrary.cql"
+    }
+  ] 
+}

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

@@ -18,13 +18,13 @@
 import org.opencds.cqf.fhir.cql.EvaluationSettings;
 import org.opencds.cqf.fhir.cql.ExtensionResolver;
 import org.opencds.cqf.fhir.cql.LibraryEngine;
-import org.opencds.cqf.fhir.cql.engine.model.FhirModelResolverCache;
 import org.opencds.cqf.fhir.cr.activitydefinition.apply.ApplyProcessor;
 import org.opencds.cqf.fhir.cr.activitydefinition.apply.ApplyRequest;
 import org.opencds.cqf.fhir.cr.activitydefinition.apply.IApplyProcessor;
 import org.opencds.cqf.fhir.cr.activitydefinition.apply.IRequestResolverFactory;
 import org.opencds.cqf.fhir.cr.common.ResourceResolver;
 import org.opencds.cqf.fhir.utility.Ids;
+import org.opencds.cqf.fhir.utility.model.FhirModelResolverCache;
 import org.opencds.cqf.fhir.utility.monad.Either3;
 import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessor;
 

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

@@ -6,7 +6,7 @@
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.opencds.cqf.fhir.cql.CqfExpression;
+import org.opencds.cqf.fhir.utility.CqfExpression;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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

@@ -1,5 +1,6 @@
 package org.opencds.cqf.fhir.cr.common;
 
+import ca.uhn.fhir.context.FhirVersionEnum;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
@@ -8,8 +9,8 @@
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.opencds.cqf.fhir.cql.CqfExpression;
 import org.opencds.cqf.fhir.utility.Constants;
+import org.opencds.cqf.fhir.utility.CqfExpression;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -90,37 +91,42 @@ public List<IBase> getExpressionResult(
                 .filter(e -> e.getUrl().equals(extensionUrl))
                 .findFirst()
                 .orElse(null);
-        if (extension == null) {
-            return null;
-        }
-        switch (request.getFhirVersion()) {
-            case DSTU3:
-                var languageExtension = extensions.stream()
-                        .filter(e -> e.getUrl().equals(Constants.CQF_EXPRESSION_LANGUAGE))
-                        .findFirst()
-                        .orElse(null);
-                var libraryExtension = extensions.stream()
-                        .filter(e -> e.getUrl().equals(Constants.CQF_LIBRARY))
-                        .findFirst()
-                        .orElse(null);
-                return new CqfExpression(
-                        languageExtension == null
-                                ? null
-                                : languageExtension.getValue().toString(),
-                        extension.getValue().toString(),
-                        libraryExtension == null
-                                ? request.getDefaultLibraryUrl()
-                                : libraryExtension.getValue().toString());
-            case R4:
-                return CqfExpression.of(
-                        (org.hl7.fhir.r4.model.Expression) extension.getValue(), request.getDefaultLibraryUrl());
-            case R5:
-                return CqfExpression.of(
-                        (org.hl7.fhir.r5.model.Expression) extension.getValue(), request.getDefaultLibraryUrl());
+        return extension == null ? null : CqfExpression.of(extension, request.getDefaultLibraryUrl());
+        // if (extension == null) {
+        //     return null;
+        // }
+        // switch (request.getFhirVersion()) {
+        //     case DSTU3:
+        //         // var languageExtension = extensions.stream()
+        //         var languageExtension = extension.getExtension().stream()
+        //                 .map(e -> (IBaseExtension<?, ?>) e)
+        //                 .filter(e -> e.getUrl().equals(Constants.CQF_EXPRESSION_LANGUAGE))
+        //                 .findFirst()
+        //                 .orElse(null);
+        //         // var libraryExtension = extensions.stream()
+        //         var libraryExtension = extension.getExtension().stream()
+        //                 .map(e -> (IBaseExtension<?, ?>) e)
+        //                 .filter(e -> e.getUrl().equals(Constants.CQF_LIBRARY))
+        //                 .findFirst()
+        //                 .orElse(null);
+        //         return new CqfExpression(
+        //                 languageExtension == null
+        //                         ? null
+        //                         : languageExtension.getValue().toString(),
+        //                 extension.getValue().toString(),
+        //                 libraryExtension == null
+        //                         ? request.getDefaultLibraryUrl()
+        //                         : libraryExtension.getValue().toString());
+        //     case R4:
+        //         return CqfExpression.of(
+        //                 (org.hl7.fhir.r4.model.Expression) extension.getValue(), request.getDefaultLibraryUrl());
+        //     case R5:
+        //         return CqfExpression.of(
+        //                 (org.hl7.fhir.r5.model.Expression) extension.getValue(), request.getDefaultLibraryUrl());
 
-            default:
-                return null;
-        }
+        //     default:
+        //         return null;
+        // }
     }
 
     /**
@@ -166,7 +172,10 @@ public CqfExpression getItemInitialExpression(IOperationRequest request, IBaseBa
         if (!item.hasExtension()) {
             return null;
         }
-        var cqfExpression = getCqfExpression(request, item.getExtension(), Constants.CQF_EXPRESSION);
+        var expressionExtensionUrl = request.getFhirVersion() == FhirVersionEnum.DSTU3
+                ? Constants.CQIF_CQL_EXPRESSION
+                : Constants.CQF_EXPRESSION;
+        var cqfExpression = getCqfExpression(request, item.getExtension(), expressionExtensionUrl);
         return cqfExpression != null
                 ? cqfExpression
                 : getCqfExpression(request, item.getExtension(), Constants.SDC_QUESTIONNAIRE_INITIAL_EXPRESSION);

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

@@ -1,10 +1,15 @@
 package org.opencds.cqf.fhir.cr.common;
 
 import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 public interface IPackageProcessor {
+    @Deprecated
     IBaseBundle packageResource(IBaseResource resource);
 
+    @Deprecated
     IBaseBundle packageResource(IBaseResource resource, String method);
+
+    IBaseBundle packageResource(IBaseResource resource, IBaseParameters parameters);
 }