Problem with pellet and data properties

[Stefan]

Hi,

I get some massive pellet related java errors when I try to sync the reasoner on an ontology that contains data properties. This works even on very simple ontologies containing only a single individual with a data property. This is independent of the infer_data_property_values parameter.

I'm going to use hermit for now, but it would be great if this could be fixed.

[Jiba]

Hi,

Could you send me a small example of ontology that causes this problem, please?

Jiba

[Marie]

Hi Jiba,

thanks for your response. Stefan and I are working together, so I will send you a small example:

ONTOLOGY

<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.example.org/onto#"
     xml:base="http://www.example.org/onto"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
    <owl:Ontology rdf:about="http://www.example.org/onto"/>
   


   

   


   

    <owl:DatatypeProperty rdf:about="http://www.example.org/onto#testDP">
        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
    </owl:DatatypeProperty>
   


   

   


   

    <owl:Class rdf:about="http://www.example.org/onto#A"/>
   


   

   


   

    <owl:NamedIndividual rdf:about="http://www.example.org/onto#I1">
        <rdf:type rdf:resource="http://www.example.org/onto#A"/>
        <testDP rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1.0</testDP>
    </owl:NamedIndividual>
</rdf:RDF>







PYTHON CODE

with onto:
    or2.sync_reasoner_pellet()


Although running a reasoner in Protégé does not indicate any inconsistencies, we get Java related exceptions running the above code.

Best,
Marie

[Jiba]

Hi,

I've tried your ontology, but I get no error (using Owlready 0.18). Can you give me the error traceback please?

I notice you use float in your ontology; by default Owlready uses decimal for representing float numbers. Maybe this can be a source of troubles. You can force Owlready to use float with:

set_datatype_iri(float, "http://www.w3.org/2001/XMLSchema#float")

Best regards,
Jiba

[Marie]

Hello Jiba,

I tried the set_datatype function, but I get the same error message. Moreover, I tried to use decimal in the ontology instead of float - still the same error. The following message is produced running Pellet on the ontology with decimal values:

Traceback (most recent call last):
  File ".../venv/lib/python3.6/site-packages/owlready2/reasoning.py", line 239, in sync_reasoner_pellet
    output = subprocess.run(command, stdout = subprocess.PIPE, stderr = subprocess.PIPE, check = True).stdout
  File "/usr/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['java', '-Xmx2000M', '-cp', '.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-ntriples-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/xml-apis-1.4.01.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/jena-core-2.13.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-owlapi-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/slf4j-api-1.7.5.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-model-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/guice-4.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/jena-arq-2.13.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/javax.inject-1.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/jena-iri-1.1.2.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-datatypes-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/xz-1.5.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/commons-lang3-3.3.2.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/commons-csv-1.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-turtle-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-languages-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/owlapi-distribution-4.1.4.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/aopalliance-1.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-explanation-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/xercesImpl-2.11.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/aterm-java-1.8.2-p1.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/commons-io-2.4.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/jjtraveler-0.6.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/jgrapht-jdk1.5-0.7.3.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-pellint-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/guice-assistedinject-4.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/antlr-runtime-3.4.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-jena-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/guava-18.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/trove4j-3.0.3.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-cli-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/shared-objects-1.4.9-p1.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/stringtemplate-3.2.1.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/slf4j-simple-1.7.5.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-util-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-query-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-api-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/sesame-rio-nquads-2.7.16.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/guice-multibindings-4.0.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/pellet-core-2.4.0-SNAPSHOT.jar:.../venv/lib/python3.6/site-packages/owlready2/pellet/commons-codec-1.6.jar', 'pellet.Pellet', 'realize', '--ignore-imports', '/tmp/tmp8q7gh6dz']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ".../pellet_test.py", line 6, in <module>
    or2.sync_reasoner_pellet()
  File ".../venv/lib/python3.6/site-packages/owlready2/reasoning.py", line 244, in sync_reasoner_pellet
    raise OwlReadyJavaError("Java error message is:\n%s" % (e.stderr or b"").decode("utf8"))
owlready2.base.OwlReadyJavaError: Java error message is:
[main] WARN org.apache.jena.riot.RDFLanguages - java-jsonld classes not on the classpath - JSON-LD input-output not available.
[main] WARN org.apache.jena.riot.RDFLanguages - Minimum jarfiles are jsonld-java, jackson-core, jackson-annotations
[main] WARN org.apache.jena.riot.RDFLanguages - If using a Jena distribution, put all jars in the lib/ directory on the classpath
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$2 (file:.../venv/lib/python3.6/site-packages/owlready2/pellet/guice-4.0.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$2
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[main] WARN org.semanticweb.owlapi.util.SAXParsers - http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
[main] WARN org.semanticweb.owlapi.util.SAXParsers - entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
[main] WARN org.semanticweb.owlapi.util.SAXParsers - http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
[main] WARN org.semanticweb.owlapi.util.SAXParsers - entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
[main] INFO org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - dumping remaining triples
[main] INFO org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - done dumping remaining triples
Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/bind/DatatypeConverter
        at com.clarkparsia.pellet.datatypes.types.real.XSDDecimal.getCanonicalRepresentation(XSDDecimal.java:71)
        at com.clarkparsia.pellet.datatypes.DatatypeReasonerImpl.getCanonicalRepresentation(DatatypeReasonerImpl.java:365)
        at org.mindswap.pellet.ABox.createLiteral(ABox.java:1746)
        at org.mindswap.pellet.ABox.addLiteral(ABox.java:1725)
        at org.mindswap.pellet.KnowledgeBase.addPropertyValue(KnowledgeBase.java:1002)
        at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:1275)
        at uk.ac.manchester.cs.owl.owlapi.OWLDataPropertyAssertionAxiomImpl.accept(OWLDataPropertyAssertionAxiomImpl.java:124)
        at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:839)
        at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.accept(OWLImmutableOntologyImpl.java:850)
        at com.clarkparsia.pellet.owlapiv3.PelletReasoner.refresh(PelletReasoner.java:967)
        at com.clarkparsia.pellet.owlapiv3.PelletReasoner.<init>(PelletReasoner.java:345)
        at com.clarkparsia.pellet.owlapiv3.PelletReasoner.<init>(PelletReasoner.java:304)
        at com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory.createReasoner(PelletReasonerFactory.java:61)
        at com.clarkparsia.pellet.owlapiv3.OWLAPILoader.load(OWLAPILoader.java:119)
        at org.mindswap.pellet.KBLoader.createKB(KBLoader.java:66)
        at pellet.PelletCmdApp.getKB(PelletCmdApp.java:232)
        at pellet.PelletCmdApp.getKB(PelletCmdApp.java:220)
        at pellet.PelletRealize.run(PelletRealize.java:67)
        at pellet.Pellet.run(Pellet.java:105)
        at pellet.Pellet.main(Pellet.java:59)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.DatatypeConverter
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
        ... 20 more

Best,
Marie

[Jiba]

Hi,

Maybe you are not using the right version of Java: the java.lang.ClassNotFoundException: javax.xml.bind.DatatypeConverter suggest that a class is missing in javax.xml, but javax.xml is normally part of Java itself.

Which version of Java are you using? I think you need JDK 1.8; here is my version:

jiba dans src :  java -version
openjdk version "1.8.0_212"
OpenJDK Runtime Environment (build 1.8.0_212-b03)
OpenJDK 64-Bit Server VM (build 25.212-b03, mixed mode)

Jiba