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opencaesar / owl-adapter

The OML adapter for OWL
Apache License 2.0
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Workaround to OWLAPI bug #48

Closed NicolasRouquette closed 3 years ago

NicolasRouquette commented 3 years ago

See https://github.com/owlcs/owlapi/issues/1002 See https://github.com/owlcs/owlapi/pull/1003

melaasar commented 3 years ago

in your PR, why you overrode the storer for rdf extension, but not xml and owl extensions, if they use the same format which is RDF/XML?

            extensions.put("owl", new RDFXMLDocumentFormat());
            extensions.put("rdf", new RioRDFXMLDocumentFormat());
            extensions.put("xml", new RDFXMLDocumentFormat());
melaasar commented 3 years ago

When I test OwlLoad with the resulting trig files, I get the following exception:

        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.lambda$run$0(DefaultPlanExecutor.java:127)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:191)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:182)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:124)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
Caused by: java.util.concurrent.ExecutionException: org.apache.jena.sparql.ARQException: Can't load quads into a graph
        at io.opencaesar.owl.load.OwlLoadApp.run(OwlLoadApp.java:178)
        at io.opencaesar.owl.load.OwlLoadApp.main(OwlLoadApp.java:121)
        at io.opencaesar.owl.load.OwlLoadTask.run(OwlLoadTask.java:49)
        ... 95 more
Caused by: org.apache.jena.sparql.ARQException: Can't load quads into a graph
        at org.apache.jena.rdfconnection.RDFConnectionRemote.upload(RDFConnectionRemote.java:403)
        at org.apache.jena.rdfconnection.RDFConnectionRemote.load(RDFConnectionRemote.java:350)
        at io.opencaesar.owl.load.OwlLoadApp.lambda$loadOntology$3(OwlLoadApp.java:224)
NicolasRouquette commented 3 years ago

I noticed this behavior as well.

Basically, with Apache Jena, we can load serializations that do not have a named graph. This seems to be a subtle conflict due to the Jena API we use to load the file where the name graph is already specified; see: https://github.com/opencaesar/owl-tools/blob/master/owl-load/src/main/java/io/opencaesar/owl/load/OwlLoadApp.java#L224

With GraphDB (see https://graphdb.ontotext.com/documentation/9.6/enterprise/devhub/workbench-rest-api/curl-commands.html#workbench-rest-api-curl-commands-repository-management), we can load Trig files with the named graphs to preserve them in the GraphDB repository.