Fix model multiplatform

cqframework · Dec 31, 2024 · 9637574 · 9637574
1 parent dd5099d
commit 9637574
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Showing 52 changed files with 399 additions and 455 deletions.
diff --git a/Src/java/buildSrc/src/main/kotlin/cql.kotlin-multiplatform-conventions.gradle.kts b/Src/java/buildSrc/src/main/kotlin/cql.kotlin-multiplatform-conventions.gradle.kts
@@ -83,7 +83,7 @@ kotlin {
 
         jvmTest {
             dependencies {
-                implementation(kotlin("test-junit"))
+                implementation(kotlin("test-junit5"))
             }
         }
 
@@ -95,6 +95,10 @@ kotlin {
     }
 }
 
+tasks.withType<Test> {
+    useJUnitPlatform()
+}
+
 tasks.register<Jar>("dokkaHtmlJar") {
     dependsOn(tasks.dokkaHtml)
     from(tasks.dokkaHtml.flatMap { it.outputDirectory })

diff --git a/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java b/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java
@@ -1,5 +1,8 @@
 package org.cqframework.fhir.npm;
 
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -52,16 +55,17 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
                             }
                             InputStream is = new ByteArrayInputStream(a.getData());
                             var reader = new XmlModelInfoReader();
-                            return reader.read(is);
+
+                            var source = buffered(asSource(is));
+                            return reader.read(source);
                         }
                     }
                 }
             } catch (IOException e) {
                 logger.logDebugMessage(
                         ILoggingService.LogCategory.PROGRESS,
                         String.format(
-                                "Exceptions occurred attempting to load npm library for model %s",
-                                modelIdentifier.toString()));
+                                "Exceptions occurred attempting to load npm library for model %s", modelIdentifier));
             }
         }
 

diff --git a/Src/java/cql-to-elm-cli/build.gradle.kts b/Src/java/cql-to-elm-cli/build.gradle.kts
@@ -16,10 +16,9 @@ dependencies {
     implementation(project(":model-xmlutil"))
     implementation(project(":elm-xmlutil"))
     implementation(project(":ucum"))
+    implementation("org.jetbrains.kotlinx:kotlinx-io-core-jvm:0.6.0")
     implementation("net.sf.jopt-simple:jopt-simple:4.7")
     implementation("org.slf4j:slf4j-simple:2.0.13")
     implementation("org.glassfish.jaxb:jaxb-runtime:4.0.5")
     implementation("org.eclipse.persistence:org.eclipse.persistence.moxy:4.0.2")
-    testImplementation(project(":model-xmlutil"))
-    testImplementation(project(":elm-xmlutil"))
 }
diff --git a/Src/java/cql-to-elm-cli/src/main/java/org/cqframework/cql/cql2elm/cli/Main.java b/Src/java/cql-to-elm-cli/src/main/java/org/cqframework/cql/cql2elm/cli/Main.java
@@ -1,9 +1,12 @@
 package org.cqframework.cql.cql2elm.cli;
 
 import static java.nio.file.FileVisitResult.CONTINUE;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
 import static org.cqframework.cql.cql2elm.CqlTranslator.fromFile;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.nio.file.FileVisitResult;
@@ -27,8 +30,9 @@
 public class Main {
     public static ModelInfoProvider getModelInfoProvider(File modelInfoXML) {
         try {
+            var source = buffered(asSource(new FileInputStream(modelInfoXML)));
             final ModelInfo modelInfo =
-                    ModelInfoReaderFactory.getReader("application/xml").read(modelInfoXML);
+                    ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(source);
             return (ModelIdentifier modelIdentifier) -> modelInfo;
         } catch (IOException e) {
             System.err.printf("Could not load model-info XML: %s%n", modelInfoXML);

diff --git a/Src/java/cql-to-elm/build.gradle.kts b/Src/java/cql-to-elm/build.gradle.kts
@@ -7,6 +7,8 @@ dependencies {
     api(project(":model"))
     api(project(":elm"))
 
+    implementation("org.jetbrains.kotlinx:kotlinx-io-core-jvm:0.6.0")
+
     // Temporary until we can get rid of the dependency on wrapping
     // the CQL annotations in a JAXBElement for narrative generation
     implementation("jakarta.xml.bind:jakarta.xml.bind-api:4.0.1")

diff --git a/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/DefaultModelInfoProvider.kt b/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/DefaultModelInfoProvider.kt
@@ -4,6 +4,8 @@ package org.cqframework.cql.cql2elm
 
 import java.io.*
 import java.nio.file.Path
+import kotlinx.io.asSource
+import kotlinx.io.buffered
 import org.cqframework.cql.cql2elm.model.Version
 import org.hl7.cql.model.ModelIdentifier
 import org.hl7.cql.model.ModelInfoProvider
@@ -100,7 +102,8 @@ class DefaultModelInfoProvider() : ModelInfoProvider, PathAware {
             }
             try {
                 val inputStream: InputStream = FileInputStream(modelFile)
-                return ModelInfoReaderFactory.getReader("application/xml")?.read(inputStream)
+                return ModelInfoReaderFactory.getReader("application/xml")
+                    ?.read(inputStream.asSource().buffered())
             } catch (e: IOException) {
                 throw IllegalArgumentException(
                     "Could not load definition for model info ${modelIdentifier.id}.",

diff --git a/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/model/ConversionMap.kt b/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/model/ConversionMap.kt
@@ -87,7 +87,7 @@ class ConversionMap {
     private fun getAllConversions(fromType: DataType?): List<Conversion> {
         val conversions: MutableList<Conversion> = ArrayList()
         var currentType = fromType
-        while (currentType != null) {
+        while (currentType != null && currentType != DataType.ANY) {
             conversions.addAll(getConversions(currentType))
             currentType = currentType.baseType
         }
@@ -339,7 +339,7 @@ class ConversionMap {
 
         if (result == null) {
             // NOTE: FHIRPath Implicit conversion from list to singleton
-            // If the from type is a list and the target type is a singleton (potentially with a
+            // If the fromType is a list and the target type is a singleton (potentially with a
             // compatible conversion),
             // Convert by invoking a singleton
             result =
@@ -361,7 +361,7 @@ class ConversionMap {
                         (allowPromotionAndDemotion || isIntervalPromotionEnabled) ->
                         findIntervalPromotion(fromType, toType, operatorMap)
 
-                    // If the from type is a choice, attempt to find a conversion from one of the
+                    // If the fromType is a choice, attempt to find a conversion from one of the
                     // choice
                     // types
                     fromType is ChoiceType ->

diff --git a/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/model/ModelImporter.kt b/Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/model/ModelImporter.kt
@@ -600,7 +600,7 @@ class ModelImporter(val modelInfo: ModelInfo, val modelManager: ModelManager?) {
                 if (t is ProfileInfo) {
                     ProfileType(
                         qualifiedName,
-                        resolveTypeNameOrSpecifier(t.baseType, t.baseTypeSpecifier)
+                        resolveTypeNameOrSpecifier(t.baseType, t.baseTypeSpecifier) ?: DataType.ANY
                     )
                 } else {
                     // Added to support generic notation in ModelInfo file for class type names
@@ -615,6 +615,7 @@ class ModelImporter(val modelInfo: ModelInfo, val modelManager: ModelManager?) {
                             ClassType(
                                 qualifiedName,
                                 resolveTypeNameOrSpecifier(t.baseType, t.baseTypeSpecifier)
+                                    ?: DataType.ANY
                             )
                         }
                     }

diff --git a/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/NamespaceTests.java b/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/NamespaceTests.java
@@ -71,17 +71,20 @@ static void setup() {
     @Test
     void namespacePath() {
         assertThat(
-                NamespaceManager.getPath(defaultNamespaceInfo.getUri(), "Main"), is("http://cql.hl7.org/public/Main"));
+                NamespaceManager.Companion.getPath(defaultNamespaceInfo.getUri(), "Main"),
+                is("http://cql.hl7.org/public/Main"));
     }
 
     @Test
     void namespaceNamePart() {
-        assertThat(NamespaceManager.getNamePart("http://cql.hl7.org/public/Main"), is("Main"));
+        assertThat(NamespaceManager.Companion.getNamePart("http://cql.hl7.org/public/Main"), is("Main"));
     }
 
     @Test
     void namespaceUriPart() {
-        assertThat(NamespaceManager.getUriPart("http://cql.hl7.org/public/Main"), is("http://cql.hl7.org/public"));
+        assertThat(
+                NamespaceManager.Companion.getUriPart("http://cql.hl7.org/public/Main"),
+                is("http://cql.hl7.org/public"));
     }
 
     /* Ensure base functionality with a defaulted namespace uri */

diff --git a/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/TestFhirModelInfoProvider.java b/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/TestFhirModelInfoProvider.java
@@ -1,6 +1,8 @@
 package org.cqframework.cql.cql2elm;
 
-import java.io.IOException;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
@@ -18,15 +20,8 @@ public TestFhirModelInfoProvider(Class clazz) {
 
     public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (modelIdentifier.getId().equals("FHIR")) {
-            try {
-                return ModelInfoReaderFactory.getReader("application/xml")
-                        .read(clazz.getResourceAsStream("fhir-modelinfo-1.8.xml"));
-            } catch (IOException e) {
-                e.printStackTrace();
-                // Do not throw, allow other providers to resolve
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the QDM model.",
-                // localVersion));
-            }
+            var source = buffered(asSource(clazz.getResourceAsStream("fhir-modelinfo-1.8.xml")));
+            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(source);
         }
 
         return null;

diff --git a/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/TestModelInfoProvider.java b/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/TestModelInfoProvider.java
@@ -1,6 +1,8 @@
 package org.cqframework.cql.cql2elm;
 
-import java.io.IOException;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
@@ -9,15 +11,8 @@
 public class TestModelInfoProvider implements ModelInfoProvider {
     public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (modelIdentifier.getId().equals("Test")) {
-            try {
-                return ModelInfoReaderFactory.getReader("application/xml")
-                        .read(TestModelInfoProvider.class.getResourceAsStream("ModelTests/test-modelinfo.xml"));
-            } catch (IOException e) {
-                e.printStackTrace();
-                // Do not throw, allow other providers to resolve
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the QDM model.",
-                // localVersion));
-            }
+            var stream = TestModelInfoProvider.class.getResourceAsStream("ModelTests/test-modelinfo.xml");
+            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
         }
 
         return null;

diff --git a/.../cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/model/GentestModelInfoProvider.java b/.../cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/model/GentestModelInfoProvider.java
@@ -1,6 +1,8 @@
 package org.cqframework.cql.cql2elm.model;
 
-import java.io.IOException;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+
 import java.io.InputStream;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
@@ -11,16 +13,9 @@ public class GentestModelInfoProvider implements ModelInfoProvider {
     @Override
     public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (modelIdentifier.getId().equals("GENTEST")) {
-            try {
-                InputStream is = GentestModelInfoProvider.class.getResourceAsStream(
-                        "/org/cqframework/cql/cql2elm/ModelTests/test-modelinfowithgenerics-happy.xml");
-                return ModelInfoReaderFactory.getReader("application/xml").read(is);
-            } catch (IOException e) {
-                e.printStackTrace();
-                // Do not throw, allow other providers to resolve
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the GENTEST model.",
-                // localVersion));
-            }
+            InputStream is = GentestModelInfoProvider.class.getResourceAsStream(
+                    "/org/cqframework/cql/cql2elm/ModelTests/test-modelinfowithgenerics-happy.xml");
+            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(is)));
         }
 
         return null;

diff --git a/...-to-elm/src/test/java/org/cqframework/cql/cql2elm/model/GentestModelInfoProviderSad1.java b/...-to-elm/src/test/java/org/cqframework/cql/cql2elm/model/GentestModelInfoProviderSad1.java
@@ -1,6 +1,8 @@
 package org.cqframework.cql.cql2elm.model;
 
-import java.io.IOException;
+import static kotlinx.io.CoreKt.buffered;
+import static kotlinx.io.JvmCoreKt.asSource;
+
 import java.io.InputStream;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
@@ -11,16 +13,9 @@ public class GentestModelInfoProviderSad1 implements ModelInfoProvider {
     @Override
     public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (modelIdentifier.equals("GENTEST")) {
-            try {
-                InputStream is = GentestModelInfoProviderSad1.class.getResourceAsStream(
-                        "/org/cqframework/cql/cql2elm/ModelTests/test-modelinfowithgenerics-sad1.xml");
-                return ModelInfoReaderFactory.getReader("application/xml").read(is);
-            } catch (IOException e) {
-                e.printStackTrace();
-                // Do not throw, allow other providers to resolve
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the GENTEST model.",
-                // localVersion));
-            }
+            InputStream is = GentestModelInfoProviderSad1.class.getResourceAsStream(
+                    "/org/cqframework/cql/cql2elm/ModelTests/test-modelinfowithgenerics-sad1.xml");
+            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(is)));
         }
 
         return null;

diff --git a/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/operators/QueryTest.java b/Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/operators/QueryTest.java
@@ -76,7 +76,7 @@ void mixedMultipleSourceQuery() {
                 def,
                 hasTypeAndResult(
                         Query.class,
-                        "list<tuple{P:tuple{id:System.Integer,name:System.String},S:tuple{id:System.Integer,name:System.String}}>"));
+                        "list<tuple{S:tuple{id:System.Integer,name:System.String},P:tuple{id:System.Integer,name:System.String}}>"));
     }
 
     @Test

diff --git a/...a/elm-fhir/src/main/java/org/cqframework/cql/elm/requirements/ElmRequirementsContext.java b/...a/elm-fhir/src/main/java/org/cqframework/cql/elm/requirements/ElmRequirementsContext.java
@@ -714,8 +714,8 @@ public CompiledLibrary resolveLibrary(VersionedIdentifier libraryIdentifier, Str
 
     public CompiledLibrary resolveLibraryFromIncludeDef(IncludeDef includeDef) {
         VersionedIdentifier targetLibraryIdentifier = new VersionedIdentifier()
-                .withSystem(NamespaceManager.getUriPart(includeDef.getPath()))
-                .withId(NamespaceManager.getNamePart(includeDef.getPath()))
+                .withSystem(NamespaceManager.Companion.getUriPart(includeDef.getPath()))
+                .withId(NamespaceManager.Companion.getNamePart(includeDef.getPath()))
                 .withVersion(includeDef.getVersion());
 
         return resolveLibrary(targetLibraryIdentifier);

diff --git a/...ir/src/main/java/org/cqframework/cql/elm/requirements/fhir/DataRequirementsProcessor.java b/...ir/src/main/java/org/cqframework/cql/elm/requirements/fhir/DataRequirementsProcessor.java
@@ -589,8 +589,8 @@ private org.hl7.fhir.r5.model.RelatedArtifact toRelatedArtifact(
     }
 
     private String getReferenceUrl(String path, String version) {
-        String uri = NamespaceManager.getUriPart(path);
-        String name = NamespaceManager.getNamePart(path);
+        String uri = NamespaceManager.Companion.getUriPart(path);
+        String name = NamespaceManager.Companion.getNamePart(path);
 
         if (uri != null) {
             // The translator has no way to correctly infer the namespace of the FHIRHelpers library, since it will

diff --git a/Src/java/elm-xmlutil/build.gradle.kts b/Src/java/elm-xmlutil/build.gradle.kts
@@ -7,6 +7,7 @@ dependencies {
     api(project(":model"))
     api(project(":elm"))
 
+    implementation("org.jetbrains.kotlinx:kotlinx-io-core:0.6.0")
     implementation("io.github.pdvrieze.xmlutil:core:0.90.3")
     implementation("io.github.pdvrieze.xmlutil:serialization:0.90.3")
     implementation("io.github.pdvrieze.xmlutil:serialization-jvm:0.90.3")

diff --git a/Src/java/engine/src/main/java/org/opencds/cqf/cql/engine/execution/CqlEngine.java b/Src/java/engine/src/main/java/org/opencds/cqf/cql/engine/execution/CqlEngine.java
@@ -303,8 +303,8 @@ private Library loadAndValidate(VersionedIdentifier libraryIdentifier) {
         if (library.getIncludes() != null && library.getIncludes().getDef() != null) {
             for (IncludeDef include : library.getIncludes().getDef()) {
                 this.loadAndValidate(new VersionedIdentifier()
-                        .withSystem(NamespaceManager.getUriPart(include.getPath()))
-                        .withId(NamespaceManager.getNamePart(include.getPath()))
+                        .withSystem(NamespaceManager.Companion.getUriPart(include.getPath()))
+                        .withId(NamespaceManager.Companion.getNamePart(include.getPath()))
                         .withVersion(include.getVersion()));
             }
         }

diff --git a/Src/java/engine/src/main/java/org/opencds/cqf/cql/engine/execution/Libraries.java b/Src/java/engine/src/main/java/org/opencds/cqf/cql/engine/execution/Libraries.java
@@ -142,8 +142,8 @@ public static List<FunctionDef> getFunctionDefs(final String name, final Library
 
     public static VersionedIdentifier toVersionedIdentifier(IncludeDef includeDef) {
         return new VersionedIdentifier()
-                .withSystem(NamespaceManager.getUriPart(includeDef.getPath()))
-                .withId(NamespaceManager.getNamePart(includeDef.getPath()))
+                .withSystem(NamespaceManager.Companion.getUriPart(includeDef.getPath()))
+                .withId(NamespaceManager.Companion.getNamePart(includeDef.getPath()))
                 .withVersion(includeDef.getVersion());
     }
 }
diff --git a/Src/java/model-xmlutil/build.gradle.kts b/Src/java/model-xmlutil/build.gradle.kts
@@ -5,6 +5,7 @@ plugins {
 dependencies {
     api(project(":model"))
 
+    implementation("org.jetbrains.kotlinx:kotlinx-io-core:0.6.0")
     implementation("io.github.pdvrieze.xmlutil:core:0.90.3")
     implementation("io.github.pdvrieze.xmlutil:serialization:0.90.3")
     implementation("io.github.pdvrieze.xmlutil:serialization-jvm:0.90.3")

diff --git a/...til/src/main/java/org/hl7/elm_modelinfo/r1/serializing/xmlutil/ModelInfoReaderProvider.kt b/...til/src/main/java/org/hl7/elm_modelinfo/r1/serializing/xmlutil/ModelInfoReaderProvider.kt
@@ -6,11 +6,7 @@ import org.hl7.elm_modelinfo.r1.serializing.ModelInfoReader
 import org.hl7.elm_modelinfo.r1.serializing.ModelInfoReaderProvider
 
 class ModelInfoReaderProvider : ModelInfoReaderProvider {
-    override fun create(contentType: String): ModelInfoReader? {
-        var contentType: String? = contentType
-        if (contentType == null) {
-            contentType = "application/xml"
-        }
+    override fun create(contentType: String): ModelInfoReader {
         return when (contentType) {
             "application/xml" -> XmlModelInfoReader()
             else ->