Merge pull request #34033 from gsmet/3.1.2-backports-1

3.1.2 backports 1

bom/application/pom.xml

@@ -57,17 +57,17 @@
         <microprofile-openapi.version>3.1</microprofile-openapi.version>
         <smallrye-common.version>2.1.0</smallrye-common.version>
         <smallrye-config.version>3.2.1</smallrye-config.version>
-        <smallrye-health.version>4.0.1</smallrye-health.version>
+        <smallrye-health.version>4.0.2</smallrye-health.version>
         <smallrye-metrics.version>4.0.0</smallrye-metrics.version>
         <smallrye-open-api.version>3.3.4</smallrye-open-api.version>
-        <smallrye-graphql.version>2.2.0</smallrye-graphql.version>
+        <smallrye-graphql.version>2.2.1</smallrye-graphql.version>
         <smallrye-opentracing.version>3.0.3</smallrye-opentracing.version>
         <smallrye-fault-tolerance.version>6.2.3</smallrye-fault-tolerance.version>
         <smallrye-jwt.version>4.2.1</smallrye-jwt.version>
         <smallrye-context-propagation.version>2.1.0</smallrye-context-propagation.version>
         <smallrye-reactive-streams-operators.version>1.0.13</smallrye-reactive-streams-operators.version>
         <smallrye-reactive-types-converter.version>3.0.0</smallrye-reactive-types-converter.version>
-        <smallrye-mutiny-vertx-binding.version>3.4.1</smallrye-mutiny-vertx-binding.version>
+        <smallrye-mutiny-vertx-binding.version>3.4.2</smallrye-mutiny-vertx-binding.version>
         <smallrye-reactive-messaging.version>4.5.0</smallrye-reactive-messaging.version>
         <smallrye-stork.version>2.2.0</smallrye-stork.version>
         <jakarta.activation.version>2.1.2</jakarta.activation.version>
@@ -119,15 +119,15 @@
         <wildfly-client-config.version>1.0.1.Final</wildfly-client-config.version>
         <wildfly-elytron.version>2.1.0.Final</wildfly-elytron.version>
         <jboss-threads.version>3.5.0.Final</jboss-threads.version>
-        <vertx.version>4.4.2</vertx.version>
+        <vertx.version>4.4.3</vertx.version>
         <httpclient.version>4.5.14</httpclient.version>
         <httpcore.version>4.4.16</httpcore.version>
         <httpasync.version>4.1.5</httpasync.version>
         <cronutils.version>9.2.1</cronutils.version>
         <quartz.version>2.3.2</quartz.version>
         <h2.version>2.1.214</h2.version> <!-- When updating, needs to be matched in io.quarkus.hibernate.orm.runtime.config.DialectVersions -->
         <postgresql-jdbc.version>42.6.0</postgresql-jdbc.version>
-        <mariadb-jdbc.version>3.1.3</mariadb-jdbc.version>
+        <mariadb-jdbc.version>3.1.4</mariadb-jdbc.version>
         <mysql-jdbc.version>8.0.30</mysql-jdbc.version>
         <mssql-jdbc.version>12.2.0.jre11</mssql-jdbc.version>
         <adal4j.version>1.6.7</adal4j.version>
@@ -141,10 +141,10 @@
         <infinispan.version>14.0.9.Final</infinispan.version>
         <infinispan.protostream.version>4.6.2.Final</infinispan.protostream.version>
         <caffeine.version>3.1.5</caffeine.version>
-        <netty.version>4.1.92.Final</netty.version>
+        <netty.version>4.1.93.Final</netty.version>
         <brotli4j.version>1.11.0</brotli4j.version>
         <reactive-streams.version>1.0.4</reactive-streams.version>
-        <jboss-logging.version>3.5.0.Final</jboss-logging.version>
+        <jboss-logging.version>3.5.1.Final</jboss-logging.version>
         <mutiny.version>2.1.0</mutiny.version>
         <kafka3.version>3.4.0</kafka3.version>
         <lz4.version>1.8.0</lz4.version> <!-- dependency of the kafka-clients that could be overridden by other imported BOMs in the platform -->
@@ -332,6 +332,12 @@
                 <scope>import</scope>
                 <type>pom</type>
             </dependency>
+            <dependency>
+                <!-- Override the dependency on the vertx-jdbc-client, because of https://github.com/vert-x3/vertx-jdbc-client/pull/306 -->
+                <groupId>io.vertx</groupId>
+                <artifactId>vertx-jdbc-client</artifactId>
+                <version>${vertx.version}.1</version>
+            </dependency>
 
             <!-- gRPC dependencies, imported as a BOM -->
             <dependency>
@@ -4749,6 +4755,11 @@
                 <artifactId>jna</artifactId>
                 <version>${jna.version}</version>
             </dependency>
+            <dependency>
+                <groupId>net.java.dev.jna</groupId>
+                <artifactId>jna-platform</artifactId>
+                <version>${jna.version}</version>
+            </dependency>
             <dependency>
                 <groupId>org.codehaus.plexus</groupId>
                 <artifactId>plexus-component-annotations</artifactId>
@@ -4853,6 +4864,11 @@
                 <artifactId>jaxb-core</artifactId>
                 <version>${jaxb-runtime.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.glassfish.jaxb</groupId>
+                <artifactId>txw2</artifactId>
+                <version>${jaxb-runtime.version}</version>
+            </dependency>
             <dependency>
                 <groupId>jakarta.xml.bind</groupId>
                 <artifactId>jakarta.xml.bind-api</artifactId>

build-parent/pom.xml

@@ -64,7 +64,7 @@
         <supported-maven-versions>[3.8.2,)</supported-maven-versions>
 
         <!-- These 2 properties are used by CreateProjectMojo to add the Maven Wrapper -->
-        <proposed-maven-version>3.9.1</proposed-maven-version>
+        <proposed-maven-version>3.9.2</proposed-maven-version>
         <maven-wrapper.version>3.2.0</maven-wrapper.version>
         <gradle-wrapper.version>8.1.1</gradle-wrapper.version>
         <quarkus-gradle-plugin.version>${project.version}</quarkus-gradle-plugin.version>

core/deployment/src/main/java/io/quarkus/deployment/dev/testing/TestTracingProcessor.java

@@ -298,7 +298,7 @@ protected String configKey() {
 
         @Override
         protected void configure(TestSupport testSupport) {
-            testSupport.setPatterns(pattern, testSupport.exclude.pattern());
+            testSupport.setPatterns(pattern, testSupport.exclude != null ? testSupport.exclude.pattern() : null);
         }
     }
 
@@ -320,7 +320,7 @@ protected String configKey() {
 
         @Override
         protected void configure(TestSupport testSupport) {
-            testSupport.setPatterns(testSupport.include.pattern(), pattern);
+            testSupport.setPatterns(testSupport.include != null ? testSupport.include.pattern() : null, pattern);
         }
     }
 

core/deployment/src/main/java/io/quarkus/deployment/pkg/steps/JarResultBuildStep.java

@@ -88,6 +88,7 @@
 import io.quarkus.maven.dependency.ResolvedDependency;
 import io.quarkus.paths.PathVisit;
 import io.quarkus.paths.PathVisitor;
+import io.quarkus.utilities.JavaBinFinder;
 
 /**
  * This build step builds both the thin jars and uber jars.
@@ -1681,7 +1682,7 @@ public boolean decompile(Path jarToDecompile) {
                     int dotIndex = jarToDecompile.getFileName().toString().indexOf('.');
                     String fileName = jarToDecompile.getFileName().toString().substring(0, dotIndex);
                     ProcessBuilder processBuilder = new ProcessBuilder(
-                            Arrays.asList("java", "-jar", decompilerJar.toAbsolutePath().toString(),
+                            Arrays.asList(JavaBinFinder.findBin(), "-jar", decompilerJar.toAbsolutePath().toString(),
                                     jarToDecompile.toAbsolutePath().toString(),
                                     context.decompiledOutputDir.resolve(fileName).toAbsolutePath().toString()));
                     if (log.isDebugEnabled()) {

devtools/gradle/gradle-application-plugin/src/main/java/io/quarkus/gradle/tasks/QuarkusBuild.java

@@ -303,6 +303,7 @@ private void assembleFastJar() {
         getLogger().info("Synchronizing Quarkus build for {} packaging from {} and {} into {}", packageType(),
                 appBuildDir, depBuildDir, appTargetDir);
         getFileSystemOperations().sync(sync -> {
+            sync.eachFile(new CopyActionDeleteNonWriteableTarget(appTargetDir.toPath()));
             sync.into(appTargetDir);
             sync.from(appBuildDir, depBuildDir);
         });

devtools/gradle/gradle-application-plugin/src/main/java/io/quarkus/gradle/tasks/QuarkusBuildDependencies.java

@@ -5,6 +5,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Set;
@@ -33,6 +34,8 @@
 public abstract class QuarkusBuildDependencies extends QuarkusBuildTask {
     static final String CLASS_LOADING_REMOVED_ARTIFACTS = "quarkus.class-loading.removed-artifacts";
     static final String CLASS_LOADING_PARENT_FIRST_ARTIFACTS = "quarkus.class-loading.parent-first-artifacts";
+    static final String FILTER_OPTIONAL_DEPENDENCIES = "quarkus.package.filter-optional-dependencies";
+    static final String INCLUDED_OPTIONAL_DEPENDENCIES = "quarkus.package.included-optional-dependencies";
 
     @Inject
     public QuarkusBuildDependencies() {
@@ -138,33 +141,36 @@ private void jarDependencies(Path libBoot, Path libMain) {
         Map<String, String> configMap = extension().buildEffectiveConfiguration(appModel.getAppArtifact()).configMap();
 
         // see https://quarkus.io/guides/class-loading-reference#configuring-class-loading
-        String removedArtifactsProp = configMap.getOrDefault(CLASS_LOADING_PARENT_FIRST_ARTIFACTS, "");
-        java.util.Optional<Set<ArtifactKey>> optionalDependencies = java.util.Optional.ofNullable(
+        Set<ArtifactKey> removedArtifacts = java.util.Optional.ofNullable(
                 configMap.getOrDefault(CLASS_LOADING_REMOVED_ARTIFACTS, null))
-                .map(s -> Arrays.stream(s.split(","))
-                        .map(String::trim)
-                        .filter(gact -> !gact.isEmpty())
-                        .map(ArtifactKey::fromString)
-                        .collect(Collectors.toSet()));
-        Set<ArtifactKey> removedArtifacts = Arrays.stream(removedArtifactsProp.split(","))
-                .map(String::trim)
-                .filter(gact -> !gact.isEmpty())
-                .map(ArtifactKey::fromString)
-                .collect(Collectors.toSet());
+                .map(QuarkusBuildDependencies::dependenciesListToArtifactKeySet)
+                .orElse(Collections.emptySet());
+        getLogger().info("Removed artifacts: {}", configMap.getOrDefault(CLASS_LOADING_REMOVED_ARTIFACTS, "(none)"));
+
+        String parentFirstArtifactsProp = configMap.getOrDefault(CLASS_LOADING_PARENT_FIRST_ARTIFACTS, "");
+        Set<ArtifactKey> parentFirstArtifacts = dependenciesListToArtifactKeySet(parentFirstArtifactsProp);
+        getLogger().info("parent first artifacts: {}", configMap.getOrDefault(CLASS_LOADING_PARENT_FIRST_ARTIFACTS, "(none)"));
+
+        String optionalDependenciesProp = configMap.getOrDefault(INCLUDED_OPTIONAL_DEPENDENCIES, "");
+        boolean filterOptionalDependencies = Boolean
+                .parseBoolean(configMap.getOrDefault(FILTER_OPTIONAL_DEPENDENCIES, "false"));
+        Set<ArtifactKey> optionalDependencies = filterOptionalDependencies
+                ? dependenciesListToArtifactKeySet(optionalDependenciesProp)
+                : Collections.emptySet();
 
         appModel.getRuntimeDependencies().stream()
                 .filter(appDep -> {
                     // copied from io.quarkus.deployment.pkg.steps.JarResultBuildStep.includeAppDep
                     if (!appDep.isJar()) {
                         return false;
                     }
-                    if (appDep.isOptional()) {
-                        return optionalDependencies.map(appArtifactKeys -> appArtifactKeys.contains(appDep.getKey()))
-                                .orElse(true);
+                    if (filterOptionalDependencies && appDep.isOptional()) {
+                        return optionalDependencies.contains(appDep.getKey());
                     }
                     return !removedArtifacts.contains(appDep.getKey());
                 })
-                .map(dep -> Map.entry(dep.isFlagSet(DependencyFlags.CLASSLOADER_RUNNER_PARENT_FIRST) ? libBoot : libMain, dep))
+                .map(dep -> Map.entry(dep.isFlagSet(DependencyFlags.CLASSLOADER_RUNNER_PARENT_FIRST)
+                        || parentFirstArtifacts.contains(dep.getKey()) ? libBoot : libMain, dep))
                 .peek(depAndTarget -> {
                     ResolvedDependency dep = depAndTarget.getValue();
                     Path targetDir = depAndTarget.getKey();
@@ -186,4 +192,12 @@ private void jarDependencies(Path libBoot, Path libMain) {
                 .collect(Collectors.toMap(Map.Entry::getKey, depAndTarget -> 1, Integer::sum))
                 .forEach((path, count) -> getLogger().info("Copied {} files into {}", count, path));
     }
+
+    private static Set<ArtifactKey> dependenciesListToArtifactKeySet(String optionalDependenciesProp) {
+        return Arrays.stream(optionalDependenciesProp.split(","))
+                .map(String::trim)
+                .filter(gact -> !gact.isEmpty())
+                .map(ArtifactKey::fromString)
+                .collect(Collectors.toSet());
+    }
 }

devtools/gradle/gradle-application-plugin/src/main/java/io/quarkus/gradle/tasks/QuarkusBuildTask.java

@@ -1,14 +1,18 @@
 package io.quarkus.gradle.tasks;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Map;
 import java.util.stream.Collectors;
 
 import javax.inject.Inject;
 
+import org.gradle.api.Action;
 import org.gradle.api.GradleException;
 import org.gradle.api.file.FileCollection;
+import org.gradle.api.file.FileCopyDetails;
 import org.gradle.api.file.FileSystemOperations;
 import org.gradle.api.logging.LogLevel;
 import org.gradle.api.tasks.Classpath;
@@ -168,6 +172,9 @@ void generateBuild() {
         PackageConfig.BuiltInType packageType = packageType();
         getLogger().info("Building Quarkus app for package type {} in {}", packageType, genDir);
 
+        // Need to delete app-cds.jsa specially, because it's usually read-only and Gradle's delete file-system
+        // operation doesn't delete "read only" files :(
+        deleteFileIfExists(genDir.resolve(outputDirectory()).resolve("app-cds.jsa"));
         getFileSystemOperations().delete(delete -> {
             // Caching and "up-to-date" checks depend on the inputs, this 'delete()' should ensure that the up-to-date
             // checks work against "clean" outputs, considering that the outputs depend on the package-type.
@@ -223,6 +230,7 @@ void generateBuild() {
         getFileSystemOperations().copy(copy -> {
             copy.from(buildDir);
             copy.into(genDir);
+            copy.eachFile(new CopyActionDeleteNonWriteableTarget(genDir));
             switch (packageType) {
                 case NATIVE:
                     copy.include(nativeRunnerFileName());
@@ -261,4 +269,32 @@ void abort(String message, Object... args) {
                 });
         throw new StopExecutionException();
     }
+
+    public static final class CopyActionDeleteNonWriteableTarget implements Action<FileCopyDetails> {
+        private final Path destDir;
+
+        public CopyActionDeleteNonWriteableTarget(Path destDir) {
+            this.destDir = destDir;
+        }
+
+        @Override
+        public void execute(FileCopyDetails details) {
+            // Delete a pre-existing non-writeable file, otherwise a copy or sync operation would fail.
+            // This situation happens for 'app-cds.jsa' files, which are created as "read only" files,
+            // prefer to keep those files read-only.
+
+            Path destFile = destDir.resolve(details.getPath());
+            if (Files.exists(destFile) && !Files.isWritable(destFile)) {
+                deleteFileIfExists(destFile);
+            }
+        }
+    }
+
+    protected static void deleteFileIfExists(Path file) {
+        try {
+            Files.deleteIfExists(file);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
 }

devtools/gradle/gradle-application-plugin/src/main/java/io/quarkus/gradle/tasks/QuarkusGenerateCode.java

@@ -15,6 +15,7 @@
 import org.gradle.api.file.FileCollection;
 import org.gradle.api.tasks.CacheableTask;
 import org.gradle.api.tasks.CompileClasspath;
+import org.gradle.api.tasks.Input;
 import org.gradle.api.tasks.InputFiles;
 import org.gradle.api.tasks.OutputDirectory;
 import org.gradle.api.tasks.PathSensitive;
@@ -62,6 +63,11 @@ public void setCompileClasspath(Configuration compileClasspath) {
         this.compileClasspath = compileClasspath;
     }
 
+    @Input
+    public Map<String, String> getCachingRelevantInput() {
+        return extension().baseConfig().quarkusProperties();
+    }
+
     @InputFiles
     @PathSensitive(PathSensitivity.RELATIVE)
     public Set<File> getInputDirectory() {

devtools/gradle/gradle-application-plugin/src/main/java/io/quarkus/gradle/tasks/QuarkusTask.java

@@ -20,6 +20,9 @@
 import io.quarkus.utilities.OS;
 
 public abstract class QuarkusTask extends DefaultTask {
+    private static final List<String> WORKER_BUILD_FORK_OPTIONS = List.of("quarkus.package.",
+            "quarkus.application.", "quarkus.gradle-worker.");
+
     private final transient QuarkusPluginExtension extension;
     protected final File projectDir;
     protected final File buildDir;
@@ -85,15 +88,17 @@ private void configureProcessWorkerSpec(ProcessWorkerSpec processWorkerSpec, Map
             forkOptions.environment("PATH", javaBin + File.pathSeparator + System.getenv("PATH"));
         }
 
-        // It's kind of a "very big hammer" here, but this way we ensure that all 'quarkus.*' properties from
-        // all configuration sources are (forcefully) used in the Quarkus build - even properties defined on the
-        // QuarkusPluginExtension.
+        // It's kind of a "very big hammer" here, but this way we ensure that all necessary properties
+        // ("quarkus.package.*","quarkus.application,*", "quarkus.gradle-worker.*") from all configuration sources
+        // are (forcefully) used in the Quarkus build - even properties defined on the QuarkusPluginExtension.
         // This prevents that settings from e.g. a application.properties takes precedence over an explicit
         // setting in Gradle project properties, the Quarkus extension or even via the environment or system
         // properties.
+        // see https://github.com/quarkusio/quarkus/issues/33321 why not all properties are passed as system properties
         // Note that we MUST NOT mess with the system properties of the JVM running the build! And that is the
         // main reason why build and code generation happen in a separate process.
-        configMap.entrySet().stream().filter(e -> e.getKey().startsWith("quarkus."))
+        configMap.entrySet().stream()
+                .filter(e -> WORKER_BUILD_FORK_OPTIONS.stream().anyMatch(e.getKey().toLowerCase()::startsWith))
                 .forEach(e -> forkOptions.systemProperty(e.getKey(), e.getValue()));
 
         // populate worker classpath with additional content?