Replace xjc with custom XSD Kotlin code gen

Src/java/buildSrc/build.gradle.kts

@@ -15,6 +15,8 @@ dependencies {
     implementation("ru.vyarus:gradle-animalsniffer-plugin:1.7.2")
     implementation("com.github.spotbugs.snom:spotbugs-gradle-plugin:5.0.14")
     implementation("com.diffplug.spotless:spotless-plugin-gradle:6.25.0")
+    implementation("com.github.node-gradle:gradle-node-plugin:7.1.0")
+    implementation("org.jetbrains.kotlin:kotlin-serialization:2.0.20")
 }
 
 kotlin {

Src/java/buildSrc/src/main/kotlin/cql.java-conventions.gradle.kts

@@ -36,6 +36,7 @@ spotless {
         palantirJavaFormat()
     }
     kotlin {
+        targetExclude("**/generated/**")
         ktfmt().kotlinlangStyle()
     }
 }

Src/java/buildSrc/src/main/kotlin/cql.xjc-temp-conventions.gradle.kts

@@ -0,0 +1,42 @@
+import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
+
+plugins {
+    kotlin("jvm")
+}
+
+val xjc: Configuration by configurations.creating
+
+dependencies {
+    xjc("codes.rafael.jaxb2_commons:jaxb2-basics-ant:3.0.0")
+    xjc("codes.rafael.jaxb2_commons:jaxb2-basics:3.0.0")
+    xjc("codes.rafael.jaxb2_commons:jaxb2-fluent-api:3.0.0")
+    // Eclipse has taken over all Java EE reference components
+    // https://www.infoworld.com/article/3310042/eclipse-takes-over-all-java-ee-reference-components.html
+    // https://wiki.eclipse.org/Jakarta_EE_Maven_Coordinates
+    xjc("jakarta.xml.bind:jakarta.xml.bind-api:4.0.1")
+    xjc("org.glassfish.jaxb:jaxb-xjc:3.0.2")
+    xjc("org.glassfish.jaxb:jaxb-runtime:4.0.3")
+    xjc("org.eclipse.persistence:org.eclipse.persistence.moxy:4.0.2")
+    xjc("org.slf4j:slf4j-simple:1.7.36")
+    xjc("org.apache.ant:ant:1.10.14")
+}
+
+var buildDir = project.layout.buildDirectory.get().toString()
+val destDir = "${buildDir}/generated/sources/$name-xjc-temp/main/java"
+
+tasks.withType<KotlinCompile>().configureEach {
+    dependsOn(tasks.withType<XjcTask>())
+}
+
+tasks.withType<JavaCompile>().configureEach {
+    dependsOn(tasks.withType<XjcTask>())
+}
+
+tasks.withType<XjcTask>().configureEach {
+    outputDir = destDir
+    outputs.dir(outputDir)
+}
+
+tasks.withType<Delete>().configureEach {
+    delete(destDir)
+}

Src/java/buildSrc/src/main/kotlin/cql.xsd-kotlin-gen-conventions.gradle.kts

@@ -0,0 +1,50 @@
+import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
+import com.github.gradle.node.task.NodeTask
+import org.gradle.kotlin.dsl.kotlin
+
+plugins {
+    kotlin("jvm")
+    kotlin("plugin.serialization")
+    id("com.github.node-gradle.node")
+}
+
+dependencies {
+    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")
+
+    implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:1.7.0")
+}
+
+node {
+    download = true
+    nodeProjectDir.set(file("../../js/xsd-kotlin-gen"))
+}
+
+val buildDir = project.layout.buildDirectory.get().toString()
+val destDir = "${buildDir}/generated/sources/$name/main/java"
+
+val runXsdKotlinGenTask = tasks.register<NodeTask>("runXsdKotlinGen") {
+    dependsOn(tasks.npmInstall)
+    script.set(file("../../js/xsd-kotlin-gen/generate.js"))
+}
+
+tasks.withType<KotlinCompile>().configureEach {
+    dependsOn(runXsdKotlinGenTask)
+}
+
+tasks.withType<JavaCompile>().configureEach {
+    dependsOn(runXsdKotlinGenTask)
+}
+
+tasks.withType<Delete>().configureEach {
+    delete(destDir)
+}
+
+sourceSets {
+    main {
+        java {
+            srcDir(destDir)
+        }
+    }
+}

Src/java/cqf-fhir-npm/build.gradle.kts

@@ -5,6 +5,7 @@ plugins {
 dependencies {
     implementation(project(":cql-to-elm"))
     implementation(project(":cqf-fhir"))
+    implementation(project(":model-xmlutil"))
     implementation("com.google.code.gson:gson:2.9.1")
     implementation("org.apache.commons:commons-compress:1.24.0")
 }

Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java

@@ -1,13 +1,13 @@
 package org.cqframework.fhir.npm;
 
-import jakarta.xml.bind.JAXB;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
+import org.hl7.elm_modelinfo.r1.serializing.xmlutil.XmlModelInfoReader;
 import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.Library;
 import org.hl7.fhir.utilities.npm.NpmPackage;
@@ -51,7 +51,8 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
                                 modelIdentifier.setSystem(identifier.getSystem());
                             }
                             InputStream is = new ByteArrayInputStream(a.getData());
-                            return JAXB.unmarshal(is, ModelInfo.class);
+                            var reader = new XmlModelInfoReader();
+                            return reader.read(is);
                         }
                     }
                 }

Src/java/cql-to-elm-cli/build.gradle.kts

@@ -9,16 +9,17 @@ application {
 
 dependencies {
     implementation(project(":cql-to-elm"))
-    implementation(project(":cql-to-elm-jackson"))
+    // Is this needed once JAXB and Jackson are replaced with XmlUtil?
+    // implementation(project(":cql-to-elm-jackson"))
     implementation(project(":quick"))
     implementation(project(":qdm"))
-    implementation(project(":model-jaxb"))
-    implementation(project(":elm-jaxb"))
+    implementation(project(":model-xmlutil"))
+    implementation(project(":elm-xmlutil"))
     implementation(project(":ucum"))
     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-jaxb"))
-    testImplementation(project(":elm-jaxb"))
+    testImplementation(project(":model-xmlutil"))
+    testImplementation(project(":elm-xmlutil"))
 }

Src/java/cql-to-elm-jackson/src/test/java/org/cqframework/cql/cql2elm/CqlTranslatorOptionsToJsonSchema.java

@@ -8,6 +8,7 @@
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
+
 import org.junit.jupiter.api.Test;
 
 class CqlTranslatorOptionsToJsonSchema {

Src/java/cql-to-elm/build.gradle.kts

@@ -6,8 +6,13 @@ dependencies {
     api(project(":cql"))
     api(project(":model"))
     api(project(":elm"))
-    testImplementation(project(":elm-jaxb"))
-    testImplementation(project(":model-jaxb"))
+
+    // 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")
+
+    testImplementation(project(":elm-xmlutil"))
+    testImplementation(project(":model-xmlutil"))
     testImplementation(project(":quick"))
     testImplementation(project(":qdm"))
     testImplementation(project(":ucum"))

Src/java/cql-to-elm/src/main/kotlin/org/cqframework/cql/cql2elm/CompilerOptions.kt

@@ -18,7 +18,7 @@ object CompilerOptions {
      */
     @JvmStatic
     fun getCompilerOptions(library: Library): Set<CqlCompilerOptions.Options>? {
-        if (library.annotation.isNullOrEmpty()) {
+        if (library.annotation.isEmpty()) {
             return null
         }
         val compilerOptions = getCompilerOptions(library.annotation)
@@ -38,7 +38,7 @@ object CompilerOptions {
 
     /**
      * Parses a string representing CQL compiler Options into an EnumSet. The string is expected to
-     * be a comma delimited list of values from the CqlCompiler.Options enumeration. For example
+     * be a comma-delimited list of values from the CqlCompiler.Options enumeration. For example
      * "EnableListPromotion, EnableListDemotion".
      *
      * @param compilerOptions the string to parse
@@ -52,11 +52,7 @@ object CompilerOptions {
         val optionSet: EnumSet<CqlCompilerOptions.Options> =
             EnumSet.noneOf(CqlCompilerOptions.Options::class.java)
         val options =
-            compilerOptions
-                .trim { it <= ' ' }
-                .split(",".toRegex())
-                .dropLastWhile { it.isEmpty() }
-                .toTypedArray()
+            compilerOptions.trim { it <= ' ' }.split(",".toRegex()).dropLastWhile { it.isEmpty() }
         for (option in options) {
             optionSet.add(CqlCompilerOptions.Options.valueOf(option))
         }
@@ -74,7 +70,7 @@ object CompilerOptions {
      */
     @JvmStatic
     fun getCompilerVersion(library: Library): String? {
-        if (library.annotation.isNullOrEmpty()) {
+        if (library.annotation.isEmpty()) {
             return null
         }
         return getCompilerVersion(library.annotation)