egonw opened a new issue, #2816:
URL: https://github.com/apache/jena/issues/2816
### Version
5.1.0
### What happened?
Code that worked well for validation with ShEx now gives a
`NoClassDefFoundError`. The code used:
```java
public ShexReport validateAllOfType(IRDFStore store, String shexFile,
String shapeURI, String type) {
if (!(store instanceof IJenaStore))
throw new RuntimeException("Can only handle IJenaStore's for
now.");
Graph dataGraph = ((IJenaStore)store).getModel().getGraph();
ShexSchema shapes = Shex.readSchema(workspaceRoot + shexFile);
Builder shapeMapBuilder = ShapeMap.newBuilder();
Triple instance = Triple.create(Shex.FOCUS, RDF.type.asNode(),
NodeFactory.createURI(type));
shapeMapBuilder.add(instance, NodeFactory.createURI(shapeURI));
ShapeMap shapeMap = shapeMapBuilder.build();
return ShexValidator.get().validate(dataGraph, shapes, shapeMap);
}
```
With the Maven `dependency:tree`:
```
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ managers-rdf ---
[INFO] io.github.egonw.bacting:managers-rdf:jar:1.0.4-SNAPSHOT
[INFO] +- io.github.egonw.bacting:bioclipse-rdf:jar:2.8.1.2:compile
[INFO] | +- org.apache.jena:jena-arq:jar:4.10.0:compile
[INFO] | | +- org.apache.jena:jena-core:jar:4.10.0:compile
[INFO] | | | +- org.apache.jena:jena-iri:jar:4.10.0:compile
[INFO] | | | +- commons-cli:commons-cli:jar:1.5.0:compile
[INFO] | | | \- org.roaringbitmap:RoaringBitmap:jar:1.0.0:compile
[INFO] | | +- com.github.jsonld-java:jsonld-java:jar:0.13.4:compile
[INFO] | | +- com.google.code.gson:gson:jar:2.10.1:compile
[INFO] | | +- org.apache.httpcomponents:httpclient-cache:jar:4.5.14:compile
[INFO] | | +- com.apicatalog:titanium-json-ld:jar:1.3.2:compile
[INFO] | | +- org.glassfish:jakarta.json:jar:2.0.1:compile
[INFO] | | +- com.google.protobuf:protobuf-java:jar:3.24.3:compile
[INFO] | | \- org.apache.thrift:libthrift:jar:0.19.0:compile
[INFO] | +- org.apache.jena:jena-tdb:jar:4.10.0:compile
[INFO] | \- io.github.egonw.bacting:bioclipse-rdfcore:jar:2.8.1.2:compile
[INFO] +- org.apache.jena:jena-shex:jar:5.1.0:compile
[INFO] +- org.apache.jena:jena-base:jar:5.1.0:compile
[INFO] | +- org.apache.commons:commons-csv:jar:1.11.0:compile
[INFO] | +- commons-io:commons-io:jar:2.16.1:compile
[INFO] | +- org.apache.commons:commons-lang3:jar:3.14.0:compile
[INFO] | +- commons-codec:commons-codec:jar:1.17.0:compile
[INFO] | +- org.apache.commons:commons-compress:jar:1.26.2:compile
[INFO] | +- org.apache.commons:commons-collections4:jar:4.4:compile
[INFO] | +- com.github.ben-manes.caffeine:caffeine:jar:3.1.8:compile
[INFO] | \- com.github.andrewoma.dexx:collection:jar:0.7:compile
[INFO] +- commons-logging:commons-logging:jar:1.3.4:runtime
[INFO] +- io.github.egonw.bacting:bioclipse-core:jar:2.8.1.2:compile
[INFO] | +- org.eclipse.platform:org.eclipse.core.runtime:jar:3.30.0:compile
[INFO] | | +- org.eclipse.platform:org.eclipse.osgi:jar:3.18.600:compile
[INFO] | | +-
org.eclipse.platform:org.eclipse.equinox.common:jar:3.18.200:compile
[INFO] | | +-
org.eclipse.platform:org.eclipse.core.jobs:jar:3.15.100:compile
[INFO] | | +-
org.eclipse.platform:org.eclipse.equinox.registry:jar:3.11.400:compile
[INFO] | | +-
org.eclipse.platform:org.eclipse.core.contenttype:jar:3.9.200:compile
[INFO] | | \-
org.eclipse.platform:org.eclipse.equinox.app:jar:1.6.400:compile
[INFO] | +-
org.eclipse.platform:org.eclipse.core.resources:jar:3.20.0:compile
[INFO] | | +-
org.eclipse.platform:org.eclipse.core.expressions:jar:3.9.200:compile
[INFO] | | \-
org.eclipse.platform:org.eclipse.core.filesystem:jar:1.10.200:compile
[INFO] | \-
org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.400:compile
[INFO] | \- org.osgi:org.osgi.service.prefs:jar:1.1.2:compile
[INFO] | \- org.osgi:osgi.annotation:jar:8.0.1:compile
[INFO] +- org.slf4j:slf4j-simple:jar:2.0.13:compile
[INFO] | \- org.slf4j:slf4j-api:jar:2.0.13:compile
[INFO] +- org.junit.jupiter:junit-jupiter:jar:5.11.0:test
[INFO] | +- org.junit.jupiter:junit-jupiter-api:jar:5.11.0:test
[INFO] | | +- org.opentest4j:opentest4j:jar:1.3.0:test
[INFO] | | \- org.junit.platform:junit-platform-commons:jar:1.11.0:test
[INFO] | \- org.junit.jupiter:junit-jupiter-params:jar:5.11.0:test
[INFO] +- org.junit.jupiter:junit-jupiter-engine:jar:5.11.0:test
[INFO] | +- org.junit.platform:junit-platform-engine:jar:1.11.0:test
[INFO] | \- org.apiguardian:apiguardian-api:jar:1.1.2:test
[INFO] \- io.github.egonw.bacting:managers-ui:jar:1.0.4-SNAPSHOT:test
[INFO] +- io.github.egonw.bacting:bacting-core:jar:1.0.4-SNAPSHOT:test
[INFO] +- io.github.egonw.bacting:bioclipse-report:jar:2.8.1.2:test
[INFO] +- org.apache.httpcomponents:httpclient:jar:4.5.14:compile
[INFO] | \- org.apache.httpcomponents:httpcore:jar:4.4.16:compile
[INFO] \- com.github.egonw:jqudt:jar:1.5.0:test
[INFO] +- org.eclipse.rdf4j:rdf4j-model:jar:3.7.7:test
[INFO] | +- org.eclipse.rdf4j:rdf4j-model-api:jar:3.7.7:test
[INFO] | +- org.eclipse.rdf4j:rdf4j-model-vocabulary:jar:3.7.7:test
[INFO] | \- org.eclipse.rdf4j:rdf4j-util:jar:3.7.7:test
[INFO] +- org.eclipse.rdf4j:rdf4j-rio-api:jar:3.7.7:test
[INFO] | \- javax.xml.bind:jaxb-api:jar:2.3.1:test
[INFO] | \- javax.activation:javax.activation-api:jar:1.2.0:test
[INFO] +- org.eclipse.rdf4j:rdf4j-rio-rdfxml:jar:3.7.7:test
[INFO] | +- org.eclipse.rdf4j:rdf4j-rio-datatypes:jar:3.7.7:test
[INFO] | \- org.eclipse.rdf4j:rdf4j-rio-languages:jar:3.7.7:test
[INFO] \- org.eclipse.rdf4j:rdf4j-rio-turtle:jar:3.7.7:test
```
### Relevant output and stacktrace
```shell
java.lang.NoClassDefFoundError: org/apache/jena/system/G
at org.apache.jena.shex.eval.ShapeEval.arcsOut(ShapeEval.java:186)
at
org.apache.jena.shex.eval.ShapeEval.matchesTripleExpr(ShapeEval.java:68)
at
org.apache.jena.shex.expressions.ShapeExprTripleExpr.satisfies(ShapeExprTripleExpr.java:81)
at org.apache.jena.shex.ShexShape.satisfies(ShexShape.java:50)
at
org.apache.jena.shex.sys.ShexValidatorImpl.validationStepWorker(ShexValidatorImpl.java:172)
at
org.apache.jena.shex.sys.ShexValidatorImpl.validationStep(ShexValidatorImpl.java:164)
at
org.apache.jena.shex.sys.ShexValidatorImpl.lambda$validate$0(ShexValidatorImpl.java:59)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1596)
at
java.base/java.util.Collections$UnmodifiableCollection.forEach(Collections.java:1116)
at
org.apache.jena.shex.sys.ShexValidatorImpl.validate(ShexValidatorImpl.java:53)
at
net.bioclipse.managers.RDFManager.validateAllOfType(RDFManager.java:674)
at
net.bioclipse.managers.RDFManagerTest.validateShEx(RDFManagerTest.java:429)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1596)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1596)
Caused by: java.lang.ClassNotFoundException: org.apache.jena.system.G
at
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
at
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:526)
... 15 more
```
### Are you interested in making a pull request?
None
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