Use jakarta (#25)

- Uses an xjc gradle plugin that has been updated recently (previous is
basically dead)
- Does as much as possible in groovy, rather than via the plugin, which
hopefully means we can drop-in replacement since no special
functionality is required
- jakarta is now used

---------

Co-authored-by: Lars-Olav Vågene <42863501+LarsV123@users.noreply.github.com>

.github/workflows/build.yml

@@ -0,0 +1,16 @@
+name: Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  build:
+    uses: BIBSYSDEV/nva-github-workflows/.github/workflows/java.yml@v1
+    with:
+      lint_openapi: false
+      lint_cloudformation: false
+    secrets:
+      codacy_token: ${{ secrets.CODACY_PROJECT_TOKEN }}

build.gradle

@@ -1,5 +1,12 @@
 plugins {
-    id 'nebula.lint' version '18.1.0'
+    id 'nebula.lint' version '20.3.0'
+    id 'jacoco-report-aggregation'
+}
+
+dependencies {
+    subprojects.forEach {
+        jacocoAggregation it
+    }
 }
 
 allprojects {
@@ -14,23 +21,27 @@ allprojects {
     apply plugin: 'checkstyle'
     apply plugin: 'pmd'
     apply plugin: 'nebula.lint'
+    apply plugin: 'jacoco-report-aggregation'
 
     group 'no.unit.nva'
-    version '0.5.8'
+    version '0.5.9'
 
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
+    java {
+        sourceCompatibility = JavaVersion.VERSION_21
+        targetCompatibility = JavaVersion.VERSION_21
+    }
 
 
     gradleLint.rules = ['unused-dependency']
 
-    def junit5Version = '5.9.3'
+    def junit5Version = '5.11.3'
 
     dependencies {
-        testImplementation group: 'org.hamcrest', name: 'hamcrest', version: '2.2'
+        implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.2'
+        testImplementation group: 'org.hamcrest', name: 'hamcrest', version: '3.0'
         testImplementation group: 'org.junit.jupiter', name: 'junit-jupiter-api', version: junit5Version
         testImplementation group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: junit5Version
-        testRuntimeOnly group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: junit5Version
+        testRuntimeOnly group: 'org.junit.platform', name: 'junit-platform-launcher', version: '1.11.3'
     }
 
     test {
@@ -52,9 +63,10 @@ allprojects {
         ruleSetConfig = rootProject.resources.text.fromFile('config/pmd/ruleset.xml')
         ruleSets = []
         ignoreFailures = false
+        toolVersion = "7.8.0"
     }
 
-    tasks.withType(Pmd) {
+    tasks.withType(Pmd).configureEach {
         exclude '**/org/datacite/schema/**'
     }
 
@@ -63,11 +75,11 @@ allprojects {
         showViolations = true
     }
 
-    tasks.withType(Checkstyle) {
+    tasks.withType(Checkstyle).configureEach {
         exclude '**/org/datacite/schema/**'
     }
 
-    tasks.withType(Checkstyle) {
+    tasks.withType(Checkstyle).configureEach {
         reports {
             xml.required = false
             html.required = true
@@ -100,6 +112,18 @@ allprojects {
         }
     }
 
+    tasks.named('check') {
+        dependsOn tasks.named('testCodeCoverageReport', JacocoReport)
+    }
+
+    reporting {
+        reports {
+            testCodeCoverageReport(JacocoCoverageReport) {
+                testType = TestSuiteType.UNIT_TEST
+            }
+        }
+    }
+
     java {
         withSourcesJar()
     }

config/pmd/ruleset.xml

@@ -11,9 +11,7 @@
   <exclude-pattern>.*/datacite-data/.*</exclude-pattern>
 
   <rule ref="category/java/errorprone.xml">
-    <exclude name="DataflowAnomalyAnalysis"/>
     <exclude name="MissingSerialVersionUID"/>
-    <exclude name="BeanMembersShouldSerialize"/>
   </rule>
 
   <rule ref="category/java/multithreading.xml"/>
@@ -38,9 +36,7 @@
     <exclude name="TooManyStaticImports"/>
     <exclude name="ClassNamingConventions"/>
     <exclude name="UnnecessaryConstructor"/>
-
-    <!--<exclude name="BeanMembersShouldSerialize"/>-->
-
+    <exclude name="UseExplicitTypes"/>
     <exclude name="ConfusingTernary"/>
 
     <!-- printStackTrace is used in the Default Amazon handler in a static clause

datacite-transform/build.gradle

@@ -1,41 +1,80 @@
-import java.nio.file.Files
-import java.nio.file.Paths
-
 plugins {
     id 'java'
-    id "org.unbroken-dome.xjc" version "2.0.0"
+    id("com.github.bjornvester.xjc") version "1.8.1"
+    id "de.undercouch.download" version "5.6.0"
 }
 
 group 'no.unit.nva'
 
 dependencies {
-    implementation group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
-    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
-    runtimeOnly group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.1'
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.2'
+    runtimeOnly group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '4.0.5'
 }
 
-def schemaDir = "${buildDir}/tmp/schema/"
+ext.SCHEMA_VERSION = '4.5'
+ext.SCHEMA_DIR = file(layout.buildDirectory.asFile.get().toURI().toString() + '/tmp/schema')
+ext.METADATA_XSD = 'metadata.xsd'
+ext.DID_DOWNLOAD = new HashMap<String, Boolean>()
+
+tasks.register('fetchSchema') {
+    doLast {
+        getUris().forEach {
+            downloadFile(it.toString())
+        }
+        if (DID_DOWNLOAD.any { it.value == false }) {
+            System.out.println("WARN: Some XSD files were cached from a previous run, to avoid this, run ./gradlew clean")
+        }
+    }
+}
 
-task fetchSchema() {
-    def schemaVersion = '4.4'
+private List<String> getUris() {
 
-    mkdir(schemaDir)
+    def source = downloadFile(METADATA_XSD)
 
-    def urlFile = "datacite.url"
+    def xml = new groovy.xml.XmlSlurper().parseText(source.getText())
 
-    if (!file(schemaDir + urlFile).exists()) {
-        Files.createFile(Paths.get(schemaDir + urlFile))
-                .text = "https://schema.datacite.org/meta/kernel-${schemaVersion}/metadata.xsd"
+    return xml.'**'.findAll {
+        it.name() == 'include' || it.name() == 'import'
+    }.collect {
+        it.@'schemaLocation'
     }
 }
 
+private File downloadFile(String path) {
+    def uri = "https://schema.datacite.org/meta/kernel-${SCHEMA_VERSION}/${path}"
+    def file = file(SCHEMA_DIR.toURI().toString() + '/' + path)
+
+    if (!file.exists()) {
+        def destination = path.contains("/") ? file.parentFile : SCHEMA_DIR
+        destination.mkdirs()
+        download.run {
+            src uri
+            dest destination
+        }
+        DID_DOWNLOAD.put(path, true)
+    } else {
+        DID_DOWNLOAD.put(path, false)
+    }
+    return file;
+}
+
 jar {
-    from "$buildDir/classes/java/main"
+    from "${layout.buildDirectory}/classes/java/main"
+}
+
+tasks.named('sourcesJar') {
+    dependsOn('xjc')
 }
 
-System.setProperty('javax.xml.accessExternalSchema', 'all')
+
 xjc {
-    srcDirName = schemaDir
+    xsdDir.set(layout.projectDirectory.dir(SCHEMA_DIR.toURI().toString()))
+}
+
+tasks.named('xjc') {
+    dependsOn('fetchSchema')
 }
 
-build.dependsOn("fetchSchema")
+tasks.named('compileJava') {
+    dependsOn('xjc')
+}

datacite-transform/src/main/java/no/unit/nva/transformer/Transformer.java

@@ -1,11 +1,11 @@
 package no.unit.nva.transformer;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
 import java.io.StringWriter;
 import java.util.List;
 import java.util.stream.Collectors;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
 import no.unit.nva.transformer.dto.AlternateIdentifierDto;
 import no.unit.nva.transformer.dto.CreatorDto;
 import no.unit.nva.transformer.dto.DataCiteMetadataDto;

datacite-transform/src/main/java/no/unit/nva/transformer/dto/DataCiteMetadataDto.java

@@ -1,8 +1,8 @@
 package no.unit.nva.transformer.dto;
 
 import static java.util.Objects.isNull;
+import jakarta.xml.bind.JAXBException;
 import java.util.List;
-import javax.xml.bind.JAXBException;
 import no.unit.nva.transformer.Transformer;
 
 public final class DataCiteMetadataDto {

datacite-transform/src/main/java/no/unit/nva/transformer/dto/IdentifierType.java

@@ -11,7 +11,7 @@ public enum IdentifierType {
     }
 
     public static IdentifierType fromValue(String v) {
-        for (IdentifierType c : IdentifierType.values()) {
+        for (IdentifierType c : values()) {
             if (c.getValue().equalsIgnoreCase(v)) {
                 return c;
             }

datacite-transform/src/test/java/no/unit/nva/transformer/TransformationTest.java

@@ -1,5 +1,6 @@
 package no.unit.nva.transformer;
 
+import jakarta.xml.bind.JAXBException;
 import no.unit.nva.transformer.dto.AlternateIdentifierDto;
 import no.unit.nva.transformer.dto.CreatorDto;
 import no.unit.nva.transformer.dto.DataCiteMetadataDto;
@@ -10,7 +11,6 @@
 import no.unit.nva.transformer.dto.TitleDto;
 import org.junit.jupiter.api.Test;
 
-import javax.xml.bind.JAXBException;
 import java.util.List;
 
 import static java.util.Objects.nonNull;
@@ -132,8 +132,8 @@ private DataCiteMetadataDto generateRecord(String doi,
     }
 
     private List<AlternateIdentifierDto> getAlternateIdentifiers(String resourceIdentifier) {
-        return nonNull(resourceIdentifier) ?
-                   List.of(new AlternateIdentifierDto.Builder().withValue(resourceIdentifier).build())
+        return nonNull(resourceIdentifier)
+                   ? List.of(new AlternateIdentifierDto.Builder().withValue(resourceIdentifier).build())
                    : List.of();
     }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

jitpack.yml

@@ -1,5 +1,5 @@
 jdk:
-  - openjdk11
+  - openjdk21
 install:
   - ./gradlew build
-  - ./gradlew -Pgroup=com.github.BIBSYSDEV -Pversion=v0.5.8 -xtest assemble publishToMavenLocal
+  - ./gradlew -Pgroup=com.github.BIBSYSDEV -Pversion=v0.5.9 -xtest assemble publishToMavenLocal