Usage of Jena 5.2.0 in a native-image build failing #2934

jerdebsp · 2025-01-09T09:43:12Z

jerdebsp
Jan 9, 2025

Hi all,

I am using Jena as part of a Spring boot application that I am trying to build as a native image using graalvm. Whilst the whole process works, Jena seems to be failing, mainly the Jena system and subsystems are not being loaded - see exception below:

Exception in thread "main" java.lang.IllegalStateException: java.lang.ExceptionInInitializerError
        at org.springframework.boot.SpringApplication.handleRunFailure(SpringApplication.java:825)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1363)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1352)
        at com.sp.Application.main(Application.java:15)
        at [email protected]/java.lang.invoke.LambdaForm$DMH/sa346b79c.invokeStaticInit(LambdaForm$DMH)
Caused by: java.lang.ExceptionInInitializerError
        at org.apache.jena.ext.xerces.impl.dv.SchemaDVFactory.<clinit>(SchemaDVFactory.java:45)
        at org.apache.jena.datatypes.xsd.XSDDatatype.<init>(XSDDatatype.java:234)
        at org.apache.jena.datatypes.xsd.XSDDatatype.<init>(XSDDatatype.java:246)
        at org.apache.jena.datatypes.xsd.impl.XSDFloat.<init>(XSDFloat.java:49)
        at org.apache.jena.datatypes.xsd.XSDDatatype.<clinit>(XSDDatatype.java:54)
        at org.apache.jena.sparql.function.StandardFunctions.loadStdDefs(StandardFunctions.java:69)
        at org.apache.jena.sparql.function.FunctionRegistry.init(FunctionRegistry.java:50)
        at org.apache.jena.query.ARQ.init(ARQ.java:665)
        at org.apache.jena.sparql.system.InitARQ.start(InitARQ.java:29)
        at org.apache.jena.base.module.Subsystem.lambda$initialize$1(Subsystem.java:117)
        at [email protected]/java.util.ArrayList.forEach(ArrayList.java:1597)
        at org.apache.jena.base.module.Subsystem.forEach(Subsystem.java:193)
        at org.apache.jena.base.module.Subsystem.forEach(Subsystem.java:169)
        at org.apache.jena.base.module.Subsystem.initialize(Subsystem.java:115)
        at org.apache.jena.sys.JenaSystem.init(JenaSystem.java:90)
        at org.apache.jena.sparql.core.DatasetGraphFactory.<clinit>(DatasetGraphFactory.java:34)
        at org.apache.jena.query.DatasetFactory.createTxnMem(DatasetFactory.java:69)
        at com.sp.Processor.<init>(Processor.java:49)
        at com.sp.Processor.getInstance(Processor.java:54)
        at com.sp.shell.commands.EngineCommand.init(EngineCommand.java:72)
        at [email protected]/java.lang.reflect.Method.invoke(Method.java:580)
        at org.springframework.shell.command.invocation.InvocableShellMethod.doInvoke(InvocableShellMethod.java:306)
        at org.springframework.shell.command.invocation.InvocableShellMethod.invoke(InvocableShellMethod.java:232)
        at org.springframework.shell.command.CommandExecution$DefaultCommandExecution.evaluate(CommandExecution.java:230)
        at org.springframework.shell.Shell.evaluate(Shell.java:248)
        at org.springframework.shell.Shell.run(Shell.java:159)
        at org.springframework.shell.jline.InteractiveShellRunner.run(InteractiveShellRunner.java:72)
        at org.springframework.shell.DefaultShellApplicationRunner.run(DefaultShellApplicationRunner.java:66)
        at org.springframework.boot.SpringApplication.lambda$callRunner$4(SpringApplication.java:786)
        at org.springframework.util.function.ThrowingConsumer$1.acceptWithException(ThrowingConsumer.java:83)
        at org.springframework.util.function.ThrowingConsumer.accept(ThrowingConsumer.java:60)
        at org.springframework.util.function.ThrowingConsumer$1.accept(ThrowingConsumer.java:88)
        at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:798)
        at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:786)
        at org.springframework.boot.SpringApplication.lambda$callRunners$3(SpringApplication.java:774)
        at [email protected]/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
        at [email protected]/java.util.stream.SortedOps$SizedRefSortingSink.end(SortedOps.java:357)
        at [email protected]/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:557)
        at [email protected]/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:546)
        at [email protected]/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
        at [email protected]/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
        at [email protected]/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:265)
        at [email protected]/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:611)
        at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:774)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:342)
        ... 4 more
Caused by: java.lang.RuntimeException: internal error
        at org.apache.jena.ext.xerces.impl.dv.xs.XSSimpleTypeDecl.applyFacets1(XSSimpleTypeDecl.java:768)
        at org.apache.jena.ext.xerces.impl.dv.xs.BaseSchemaDVFactory.createBuiltInTypes(BaseSchemaDVFactory.java:205)
        at org.apache.jena.ext.xerces.impl.dv.xs.SchemaDVFactoryImpl.createBuiltInTypes(SchemaDVFactoryImpl.java:44)
        at org.apache.jena.ext.xerces.impl.dv.xs.SchemaDVFactoryImpl.<clinit>(SchemaDVFactoryImpl.java:39)
        ... 49 more

Just to give some more context, the application is loading, however hitting this error first time I am creating an instance and calling DatasetFactory.createTxnMem(); in the constructor.

I am using the Jena POM dependency and also create and use the shaded JAR in the packaging:

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <executions>
                    <execution>
                        <id>shade-jar-with-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <shadedArtifactAttached>true</shadedArtifactAttached>
                            <transformers>
                                <transformer
                                        implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>META-INF/spring.handlers</resource>
                                </transformer>
                                <transformer
                                        implementation="org.springframework.boot.maven.PropertiesMergingResourceTransformer">
                                    <resource>META-INF/spring.factories</resource>
                                </transformer>
                                <transformer
                                        implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>META-INF/spring.schemas</resource>
                                </transformer>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>com.sp.Application</mainClass>
                                    <manifestEntries>
                                        <Multi-Release>true</Multi-Release>
                                    </manifestEntries>
                                </transformer>
                            </transformers>

                            <filters>
                                <filter>
                                    <artifact>*:*</artifact>
                                    <excludes>
                                        <!-- Some jars are signed but shading breaks that. Don't
                                          include signing files. -->
                                        <exclude>META-INF/*.SF</exclude>
                                        <exclude>META-INF/*.DSA</exclude>
                                        <exclude>META-INF/*.RSA</exclude>
                                        <exclude>META-INF/DEPENDENCIES</exclude>
                                        <exclude>META-INF/MANIFEST.MF</exclude>
                                        <exclude>**/module-info.class</exclude>
                                    </excludes>
                                </filter>
                            </filters>

                        </configuration>
                    </execution>
                </executions>
            </plugin>
....
            <plugin>
                <groupId>org.graalvm.buildtools</groupId>
                <artifactId>native-maven-plugin</artifactId>
                <extensions>true</extensions>
                <executions>
                    <execution>
                        <id>build-native</id>
                        <goals>
                            <goal>build</goal>
                        </goals>
                        <phase>package</phase>
                    </execution>
                </executions>
                <configuration>
                    <skip>false</skip>
                    <useArgFile>true</useArgFile>
                    <fallback>false</fallback>
                    <classpath>
                        <param>${project.build.directory}/${project.artifactId}-${project.version}-shaded.jar</param>
                    </classpath>
                </configuration>
            </plugin>

I've tried various things, including using the direct dependencies instead of the Jena POM, but nothing seemed to work. Any potential ideas what i might be missing?

Thanks
Jer

afs · 2025-01-09T10:51:38Z

afs
Jan 9, 2025
Collaborator

It looks like the service loader setup has been broken.

Does the shared jar work before making into a native image?
In the shared jar, do the service/ files appear and look right? (There are several transforms and there may be an interaction between them).

I found mention of -H:+TraceServiceLoaderFeature to debug in Graalvm.

0 replies

jerdebsp · 2025-01-09T13:15:28Z

jerdebsp
Jan 9, 2025
Author

Hi Andy,

Does the shared jar work before making into a native image?

Yes it does.

In the shared jar, do the service/ files appear and look right? (There are several transforms and there may be an interaction between them).

I've got the services/ folder in META-INF, with a number of files including the JenaSubsystemLifecycle

-H:+TraceServiceLoaderFeature didn't help

2 replies

afs Jan 9, 2025
Collaborator

What's in JenaSubsystemLifcycle? It should be

Another possibility is that problem is specific to ext.xerces. It has some classpath resources under org.apache.jena.ext.xerces. Given GraalVM does class-pruning, maybe these don't get to the native image.

jerdebsp Jan 9, 2025
Author

In JenaSubsystemLifecycle I have the following:

org.apache.jena.riot.system.InitRIOT
org.apache.jena.sparql.system.InitARQ
org.apache.jena.rdfs.sys.InitRDFS
org.apache.jena.sys.InitJenaCore
org.apache.jena.rdfpatch.system.InitPatch
org.apache.jena.ontapi.sys.InitOntAPI
org.apache.jena.shacl.sys.InitShacl
org.apache.jena.shex.sys.InitShex
org.apache.jena.tdb1.sys.InitTDB
org.apache.jena.tdb2.sys.InitTDB2

Seems correct.

Another possibility is that problem is specific to ext.xerces

Good point. I'll check if this is a problem

afs · 2025-01-11T18:37:23Z

afs
Jan 11, 2025
Collaborator

Caused by: java.lang.RuntimeException: internal error
        at org.apache.jena.ext.xerces.impl.dv.xs.XSSimpleTypeDecl.applyFacets1(XSSimpleTypeDecl.java:768)
        at org.apache.jena.ext.xerces.impl.dv.xs.BaseSchemaDVFactory.createBuiltInTypes(BaseSchemaDVFactory.java:205)
        at org.apache.jena.ext.xerces.impl.dv.xs.SchemaDVFactoryImpl.createBuiltInTypes(SchemaDVFactoryImpl.java:44)
        at org.apache.jena.ext.xerces.impl.dv.xs.SchemaDVFactoryImpl.<clinit>(SchemaDVFactoryImpl.java:39)

(unfortunately, it hides the exception stacktrace for the exception that turned into "internal error")

Chasing this and it does seem to happen because of a subclass of DatatypeException and DatatypeException loads Java resource bundles as data files from the classpath. Specifically, XMLSchemaMessages.properties in from jena-core/src/main/resources/org/apache/jena/ext/xerces/impl/msg/ (there are other properties files as well).

This doesn't prove that's the cause but it is somewhere near. A web search suggests -H:IncludeResourceBundles is needed.

For 5.3.0, we have been cleaning up the Xerces code incorporated in Jena, reducing it to just what Jena uses. I have just converted all ResourceBundles (#2938) that still get used to data in java source code so in the next release there will be no use of ResourceBundle anywhere.

1 reply

jerdebsp Jan 13, 2025
Author

I tried with -H:IncludeResourceBundles and adding the bundle directly in resource-config.json. I will wait for 5.3.0 release and test again

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Usage of Jena 5.2.0 in a native-image build failing #2934

jerdebsp Jan 9, 2025

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