Upgrade cql to version 4.0.0

cqf-fhir-benchmark/pom.xml

@@ -36,13 +36,6 @@
             <artifactId>jsonassert</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-jackson</artifactId>
-            <version>3.28.0-SNAPSHOT</version>
-            <type>pom</type>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-simple</artifactId>

cqf-fhir-bom/pom.xml

@@ -38,18 +38,6 @@
         <artifactId>cqf-fhir-cql</artifactId>
         <version>3.28.0-SNAPSHOT</version>
       </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-jackson</artifactId>
-        <version>3.28.0-SNAPSHOT</version>
-        <type>pom</type>
-      </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-jaxb</artifactId>
-        <version>3.28.0-SNAPSHOT</version>
-        <type>pom</type>
-      </dependency>
       <dependency>
         <groupId>org.opencds.cqf.fhir</groupId>
         <artifactId>cqf-fhir-cr</artifactId>

cqf-fhir-cql/pom.xml

@@ -32,31 +32,35 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
       <artifactId>cql-to-elm</artifactId>
     </dependency>
-      <dependency>
-          <groupId>info.cqframework</groupId>
-          <artifactId>elm-fhir</artifactId>
-      </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
+      <artifactId>ucum</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.cqframework</groupId>
+      <artifactId>elm-fhir</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.cqframework</groupId>
       <artifactId>quick</artifactId>
     </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
       <artifactId>engine</artifactId>
     </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
       <artifactId>engine-fhir</artifactId>
     </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
       <artifactId>cqf-fhir</artifactId>
     </dependency>
     <dependency>
-      <groupId>info.cqframework</groupId>
+      <groupId>org.cqframework</groupId>
       <artifactId>cqf-fhir-npm</artifactId>
     </dependency>
     <dependency>
@@ -65,13 +69,6 @@
       <version>3.28.0-SNAPSHOT</version>
       <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>org.opencds.cqf.fhir</groupId>
-      <artifactId>cqf-fhir-jackson</artifactId>
-      <version>3.28.0-SNAPSHOT</version>
-      <type>pom</type>
-      <scope>test</scope>
-    </dependency>
     <dependency>
         <groupId>com.github.valfirst</groupId>
         <artifactId>slf4j-test</artifactId>

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

@@ -195,7 +195,7 @@ private static CqlEngine createEngine(Environment environment, EvaluationSetting
                 environment, settings.getCqlOptions().getCqlEngineOptions().getOptions());
         if (settings.getCqlOptions().getCqlEngineOptions().isDebugLoggingEnabled()) {
             var map = new DebugMap();
-            map.setIsLoggingEnabled(true);
+            map.setLoggingEnabled(true);
             engine.getState().setDebugMap(map);
         }
 

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

@@ -1,9 +1,12 @@
 package org.opencds.cqf.fhir.cql.cql2elm.content;
 
 import static java.util.Objects.requireNonNull;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
 
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
+import kotlinx.io.Source;
 import org.cqframework.cql.cql2elm.LibraryContentType;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
@@ -26,7 +29,7 @@ protected BaseFhirLibrarySourceProvider(IAdapterFactory adapterFactory) {
     }
 
     @Override
-    public InputStream getLibraryContent(VersionedIdentifier libraryIdentifier, LibraryContentType libraryContentType) {
+    public Source getLibraryContent(VersionedIdentifier libraryIdentifier, LibraryContentType libraryContentType) {
         requireNonNull(libraryIdentifier, "versionedIdentifier can not be null.");
         requireNonNull(libraryContentType, "libraryContentType can not be null.");
 
@@ -35,7 +38,8 @@ public InputStream getLibraryContent(VersionedIdentifier libraryIdentifier, Libr
             return null;
         }
 
-        return this.getContentStream(library, libraryContentType.mimeType());
+        var inputStream = this.getContentStream(library, libraryContentType.mimeType());
+        return inputStream == null ? null : buffered(asSource(inputStream));
     }
 
     protected InputStream getContentStream(IBaseResource library, String contentType) {
@@ -56,7 +60,7 @@ protected InputStream getContentStream(IBaseResource library, String contentType
     }
 
     @Override
-    public InputStream getLibrarySource(VersionedIdentifier libraryIdentifier) {
+    public Source getLibrarySource(VersionedIdentifier libraryIdentifier) {
         return getLibraryContent(libraryIdentifier, LibraryContentType.CQL);
     }
 

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

@@ -1,15 +1,16 @@
 package org.opencds.cqf.fhir.cql.cql2elm.content;
 
 import static java.util.Objects.requireNonNull;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+import static org.hl7.elm_modelinfo.r1.serializing.XmlModelInfoReaderKt.parseModelInfoXml;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.repository.IRepository;
-import java.io.IOException;
 import java.util.ArrayList;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
-import org.hl7.elm_modelinfo.r1.serializing.ModelInfoReaderFactory;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.fhir.cql.cql2elm.util.LibraryVersionSelector;
@@ -52,10 +53,9 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
             return null;
         }
 
-        var xmlReader = ModelInfoReaderFactory.getReader(ModelInfoContentType.XML.mimeType());
         try {
-            return xmlReader.read(is);
-        } catch (IOException e) {
+            return parseModelInfoXml(buffered(asSource(is)));
+        } catch (Exception e) {
             logger.error(
                     "Error encountered while loading model info for {}: {}", modelIdentifier.getId(), e.getMessage());
             return null;

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

@@ -108,7 +108,8 @@ public IBaseParameters toFhirParameters(EvaluationResult evaluationResult) {
 
         IParametersAdapter pa = this.adapterFactory.createParameters(params);
 
-        for (Map.Entry<String, ExpressionResult> entry : evaluationResult.expressionResults.entrySet()) {
+        for (Map.Entry<String, ExpressionResult> entry :
+                evaluationResult.getExpressionResults().entrySet()) {
             String name = entry.getKey();
             Object value = entry.getValue().value();
 

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

@@ -98,7 +98,7 @@ void duplicateSettingsNpmProcessor() {
 
         var engine = getEngine(settings);
 
-        assertTrue(engine.getState().getDebugMap().getIsLoggingEnabled());
+        assertTrue(engine.getState().getDebugMap().isLoggingEnabled());
 
         assertDataProviders(engine);
     }
@@ -124,7 +124,7 @@ void duplicateSettingsNullNpmProcessor() {
 
         var engine = getEngine(settings);
 
-        assertTrue(engine.getState().getDebugMap().getIsLoggingEnabled());
+        assertTrue(engine.getState().getDebugMap().isLoggingEnabled());
 
         assertDataProviders(engine);
     }
@@ -154,7 +154,7 @@ void debugLoggingEnabled() {
         var settings = EvaluationSettings.getDefault();
         settings.getCqlOptions().getCqlEngineOptions().setDebugLoggingEnabled(true);
         var engine = getEngine(settings);
-        assertTrue(engine.getState().getDebugMap().getIsLoggingEnabled());
+        assertTrue(engine.getState().getDebugMap().isLoggingEnabled());
 
         assertDataProviders(engine);
     }

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

@@ -1,5 +1,7 @@
 package org.opencds.cqf.fhir.cql;
 
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
@@ -10,11 +12,11 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.repository.IRepository;
 import java.io.ByteArrayInputStream;
-import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Map;
+import kotlinx.io.Source;
 import org.cqframework.cql.cql2elm.LibraryContentType;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
@@ -140,15 +142,15 @@ void expressionWithLibraryResourceProvider() {
         var libraryResourceProvider = new ArrayList<LibrarySourceProvider>();
         libraryResourceProvider.add(new LibrarySourceProvider() {
             @Override
-            public InputStream getLibrarySource(VersionedIdentifier libraryIdentifier) {
+            public Source getLibrarySource(VersionedIdentifier libraryIdentifier) {
                 return null;
             }
 
             @Override
-            public InputStream getLibraryContent(VersionedIdentifier libraryIdentifier, LibraryContentType type) {
+            public Source getLibraryContent(VersionedIdentifier libraryIdentifier, LibraryContentType type) {
                 if ("MyLibrary".equals(libraryIdentifier.getId()))
-                    return new ByteArrayInputStream(libraryCql.getBytes(StandardCharsets.UTF_8));
-                else return LibrarySourceProvider.super.getLibraryContent(libraryIdentifier, type);
+                    return buffered(asSource(new ByteArrayInputStream(libraryCql.getBytes(StandardCharsets.UTF_8))));
+                else return LibrarySourceProvider.DefaultImpls.getLibraryContent(this, libraryIdentifier, type);
             }
         });
         var evaluationSettings = EvaluationSettings.getDefault().withLibrarySourceProviders(libraryResourceProvider);

cqf-fhir-cql/src/test/java/org/opencds/cqf/fhir/cql/cql2elm/content/RepositoryFhirModelInfoProviderTest.java

@@ -22,8 +22,7 @@ class RepositoryFhirModelInfoProviderTest {
     private IRepository repository;
     private IAdapterFactory adapterFactory;
     private RepositoryFhirModelInfoProvider fixture;
-    private ModelIdentifier usCoreModelId =
-            new ModelIdentifier().withId("USCore").withVersion("7.0.0");
+    private ModelIdentifier usCoreModelId = new ModelIdentifier("USCore", null, "7.0.0");
 
     @BeforeEach
     void beforeEach() {
@@ -53,7 +52,7 @@ void testLoadModelInfo() {
 
     @Test
     void testLoadModelInfo_Exception() {
-        var actual = fixture.load(new ModelIdentifier().withId("Invalid").withVersion("1.0.0"));
+        var actual = fixture.load(new ModelIdentifier("Invalid", null, "1.0.0"));
         assertNull(actual);
     }
 }

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

@@ -64,8 +64,8 @@ void evaluationResultToParameters() {
         expected.addParameter().setName("Numerator").setValue(new BooleanType(true));
 
         var testData = new EvaluationResult();
-        testData.expressionResults.put("Patient", new ExpressionResult(new Patient(), null));
-        testData.expressionResults.put("Numerator", new ExpressionResult(true, null));
+        testData.getExpressionResults().put("Patient", new ExpressionResult(new Patient(), null));
+        testData.getExpressionResults().put("Numerator", new ExpressionResult(true, null));
 
         var actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);
 
@@ -79,8 +79,8 @@ void evaluationResultToEmptyListParameters() {
         expected.addParameter().setName("Encounters").setValue(emptyListMarker());
 
         var testData = new EvaluationResult();
-        testData.expressionResults.put("Patient", new ExpressionResult(new Patient(), null));
-        testData.expressionResults.put("Encounters", new ExpressionResult(Collections.emptyList(), null));
+        testData.getExpressionResults().put("Patient", new ExpressionResult(new Patient(), null));
+        testData.getExpressionResults().put("Encounters", new ExpressionResult(Collections.emptyList(), null));
 
         Parameters actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);
 
@@ -98,7 +98,7 @@ void evalutionResultsWithListContainingNullValue() {
         testList.add(5);
 
         var testData = new EvaluationResult();
-        testData.expressionResults.put("NullInList", new ExpressionResult(testList, null));
+        testData.getExpressionResults().put("NullInList", new ExpressionResult(testList, null));
 
         var actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);
 
@@ -112,8 +112,8 @@ void evaluationResultNullParameters() {
         expected.addParameter().setName("Null").setValue(nullValueMarker());
 
         var testData = new EvaluationResult();
-        testData.expressionResults.put("Patient", new ExpressionResult(new Patient(), null));
-        testData.expressionResults.put("Null", new ExpressionResult(null, null));
+        testData.getExpressionResults().put("Patient", new ExpressionResult(new Patient(), null));
+        testData.getExpressionResults().put("Null", new ExpressionResult(null, null));
 
         var actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);
 

cqf-fhir-cr-cli/pom.xml

@@ -32,12 +32,6 @@
             <artifactId>cqf-fhir-cql</artifactId>
             <version>3.28.0-SNAPSHOT</version>
         </dependency>
-        <dependency>
-            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-jackson</artifactId>
-            <version>3.28.0-SNAPSHOT</version>
-            <type>pom</type>
-        </dependency>
         <dependency>
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>

cqf-fhir-cr-cli/src/main/java/org/opencds/cqf/fhir/cr/cli/command/CqlCommand.java

@@ -82,7 +82,8 @@ public static Stream<SubjectAndResult> evaluate(CqlCommandArgument arguments) {
         return arguments.parameters.context.stream().map(c -> {
             var engine = Engines.forRepository(repository, evaluationSettings);
             if (arguments.content.cqlPath != null) {
-                var provider = new DefaultLibrarySourceProvider(Path.of(arguments.content.cqlPath));
+                var provider = new DefaultLibrarySourceProvider(new kotlinx.io.files.Path(
+                        Path.of(arguments.content.cqlPath).toFile()));
                 engine.getEnvironment()
                         .getLibraryManager()
                         .getLibrarySourceLoader()

cqf-fhir-cr-cli/src/main/java/org/opencds/cqf/fhir/cr/cli/command/Utilities.java

@@ -14,7 +14,6 @@
 import java.util.stream.StreamSupport;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions.Options;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
-import org.cqframework.cql.cql2elm.CqlTranslatorOptionsMapper;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -57,7 +56,8 @@ public static EvaluationSettings createEvaluationSettings(String cqlPath, boolea
 
         var optionPath = Path.of(cqlPath).resolve("cql-options.json");
         if (Files.exists(optionPath)) {
-            CqlTranslatorOptions options = CqlTranslatorOptionsMapper.fromFile(optionPath.toString());
+            CqlTranslatorOptions options =
+                    CqlTranslatorOptions.fromFile(new kotlinx.io.files.Path(optionPath.toFile()));
             cqlOptions.setCqlCompilerOptions(options.getCqlCompilerOptions());
         }
 
@@ -160,7 +160,8 @@ public static void writeResult(EvaluationResult result, OutputStream outputStrea
         var writer = new BufferedWriter(new OutputStreamWriter(outputStream, StandardCharsets.UTF_8));
         try {
             // Write the result to the output stream
-            for (Map.Entry<String, ExpressionResult> libraryEntry : result.expressionResults.entrySet()) {
+            for (Map.Entry<String, ExpressionResult> libraryEntry :
+                    result.getExpressionResults().entrySet()) {
                 String key = libraryEntry.getKey();
                 Object value = Utilities.tempConvert(libraryEntry.getValue().value());
                 writer.write(key + "=" + value);

cqf-fhir-cr-hapi/pom.xml

@@ -48,13 +48,6 @@
     </dependencyManagement>
 
     <dependencies>
-        <dependency>
-            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-jackson</artifactId>
-            <version>${project.version}</version>
-            <type>pom</type>
-        </dependency>
-
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-validation</artifactId>
@@ -194,6 +187,7 @@
                                                     <include>org.opencds.cqf.cql:*</include>
                                                     <include>org.opencds.cqf.fhir:*</include>
                                                     <include>info.cqframework:*</include>
+                                                    <include>org.cqframework:*</include>
                                                 </includes>
                                             </requireReleaseDeps>
                                         </rules>