[
https://issues.apache.org/jira/browse/JENA-1415?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Christian Bay updated JENA-1415:
--------------------------------
Description:
Hey there,
I'm getting a _ConversionException_ when converting a resource to an individual
by using _as_.
[EDIT] Edited this report because I could reproduce this error in a little
example.
Jena throws a _ConversionErrorException_ when trying to cast a Resource with
_as_ to an individual. The resource is received by a query as suggested here
[https://github.com/Galigator/openllet/blob/integration/examples/src/main/java/openllet/examples/SPARQLDLExample.java]
This is the test code:
{code:java}
package bug;
import openllet.jena.PelletReasonerFactory;
import openllet.query.sparqldl.jena.SparqlDLExecutionFactory;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.ResultSetFormatter;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.ontology.Individual;
import org.apache.jena.ontology.OntClass;
import org.apache.jena.util.iterator.ExtendedIterator;
import java.util.ArrayList;
public class SPARQLDLBug
{
// The ontology loaded as dataset
private static final String ontology = "ontologies/simple.owl";
private static final String query = "query.sparql";
public void run()
{
// First create a Jena ontology model backed by the
Pellet reasoner
// (note, the Pellet reasoner is required)
final OntModel m =
ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
// Then read the _data from the file into the ontology
model
m.read(ontology);
// Now read the query file into a query object
final Query q = QueryFactory.read(query);
// Create a SPARQL-DL query execution for the given
query and
// ontology model
final QueryExecution qe =
SparqlDLExecutionFactory.create(q, m);
// We want to execute a SELECT query, do it, and return
the result set
final ResultSet rs = qe.execSelect();
ArrayList<String> result = new ArrayList<String>();
while(rs.hasNext()){
QuerySolution qs = rs.next();
// The Bug occurs in the next line
Individual in =
qs.getResource("x").as(Individual.class);
ExtendedIterator<OntClass> it =
in.listOntClasses(true);
String className = "";
while(it.hasNext()){
className = it.next().toString();
}
result.add(className);
}
qe.close();
}
public static void main(final String[] args)
{
final SPARQLDLBug app = new SPARQLDLBug();
app.run();
}
}
{code}
The error message is:
{code}
Exception in thread "main" org.apache.jena.ontology.ConversionException: Cannot
convert node
http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia to
Individual
at
org.apache.jena.ontology.impl.IndividualImpl$1.wrap(IndividualImpl.java:61)
at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:152)
at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:31)
at org.apache.jena.enhanced.Polymorphic.asInternal(Polymorphic.java:62)
at org.apache.jena.enhanced.EnhNode.as(EnhNode.java:107)
at bug.SPARQLDLBug.run(SPARQLDLBug.java:58)
at bug.SPARQLDLBug.main(SPARQLDLBug.java:75)
{code}
This Query is:
{code:xml}
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bio: <http://www8.cs.fau.de/research:cgm/schizophrenia#>
SELECT ?x
WHERE { ?x rdf:type bio:AcuteSchizophrenia }
{code}
And the Ontology consist only of a class and one individual.
{code:xml}
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www8.cs.fau.de/research:cgm/schizophrenia#";
xml:base="http://www8.cs.fau.de/research:cgm/schizophrenia";
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
xmlns:owl="http://www.w3.org/2002/07/owl#";
xmlns:xml="http://www.w3.org/XML/1998/namespace";
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#";
xmlns:swrl="http://www.w3.org/2003/11/swrl#";
xmlns:xsd="http://www.w3.org/2001/XMLSchema#";
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#";
xmlns:dc="http://purl.org/dc/elements/1.1/";>
<owl:Ontology rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia";>
</owl:Ontology>
<!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
<rdfs:Datatype
rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
<owl:Class
rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia#AcuteSchizophrenia";>
<rdfs:label xml:lang="en">Acute schizophrenia</rdfs:label>
</owl:Class>
<owl:NamedIndividual
rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia";>
<rdf:type
rdf:resource="http://www8.cs.fau.de/research:cgm/schizophrenia#AcuteSchizophrenia"/>
</owl:NamedIndividual>
</rdf:RDF>
{code}
was:
Hey there,
I'm getting a _ConversionException_ when converting a resource to an individual
by using _as_. In another bugreport
[https://issues.apache.org/jira/browse/JENA-1380] this exception occured
because of lacking OWL2 support. Is it something similiar here? Below is the
relevant part of the OWL File:
{code:xml}
<!-- http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia
-->
<owl:NamedIndividual
rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia";>
<rdf:type
rdf:resource="http://www8.cs.fau.de/research:cgm/schizophrenia#AcuteSchizophrenia"/>
</owl:NamedIndividual>
{code}
The code snippet sets up a query on a OntModel which uses the Openllet
reasoner.
{code:java}
private ArrayList<String> queryForRecommended(Query query){;
OntDocumentManager mgr = new OntDocumentManager();
//imports
mgr.addAltEntry(Misc.STR_TIME,Misc.PATH_TIME);
mgr.addAltEntry(Misc.STR_SCHIZO,Misc.PATH_SCHIZO);
// Create OntModel
OntModelSpec s = new
OntModelSpec(PelletReasonerFactory.THE_SPEC);
s.setDocumentManager(mgr);
OntModel ontModel = ModelFactory.createOntologyModel(s);
try{
ontModel.read(patient.getFile().toURI().toString());
}catch(Exception e){
e.printStackTrace();
return null;
}
QueryExecution qe = QueryExecutionFactory.create(query,
ontModel);
ResultSet rs = qe.execSelect();
ArrayList<String> result = new ArrayList<String>();
while(rs.hasNext()){
QuerySolution qs = rs.next();
// ------- ERROR ---------
Individual in =
qs.getResource("diag").as(Individual.class);
ExtendedIterator it = in.listOntClasses(true);
String className = "";
while(it.hasNext()){
className = it.next().toString();
}
result.add(className);
}
qe.close();
return result;
}
{code}
This is the error message I'm getting. The Jena Api mention the following: 'In
order to be recognised as an individual, rather than a generic resource, at
least one rdf:type statement' .
But a rdf:type statement does exist. I'm a bit clueless.
{code}
Exception in thread "main" org.apache.jena.ontology.ConversionException: Cannot
convert node
http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia to
Individual
at
org.apache.jena.ontology.impl.IndividualImpl$1.wrap(IndividualImpl.java:61)
at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:152)
at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:31)
at org.apache.jena.enhanced.Polymorphic.asInternal(Polymorphic.java:62)
at org.apache.jena.enhanced.EnhNode.as(EnhNode.java:107)
at gui.OWLHandler.queryForRecommended(OWLHandler.java:655)
[...]
{code}
It is worth mentioning that I'm refactoring this code and it worked quite well
with the Jena version 2.1.0 and the Pellet Reasoner for Owlapiv3.
> ConversionException for individuals
> -----------------------------------
>
> Key: JENA-1415
> URL: https://issues.apache.org/jira/browse/JENA-1415
> Project: Apache Jena
> Issue Type: Bug
> Components: ARQ, Jena
> Affects Versions: Jena 3.4.0
> Environment: Linux, Maven, Openllet Reasoner
> Reporter: Christian Bay
> Priority: Minor
>
> Hey there,
> I'm getting a _ConversionException_ when converting a resource to an
> individual by using _as_.
> [EDIT] Edited this report because I could reproduce this error in a little
> example.
> Jena throws a _ConversionErrorException_ when trying to cast a Resource with
> _as_ to an individual. The resource is received by a query as suggested here
> [https://github.com/Galigator/openllet/blob/integration/examples/src/main/java/openllet/examples/SPARQLDLExample.java]
> This is the test code:
> {code:java}
> package bug;
> import openllet.jena.PelletReasonerFactory;
> import openllet.query.sparqldl.jena.SparqlDLExecutionFactory;
> import org.apache.jena.ontology.OntModel;
> import org.apache.jena.query.Query;
> import org.apache.jena.query.QueryExecution;
> import org.apache.jena.query.QueryFactory;
> import org.apache.jena.query.QuerySolution;
> import org.apache.jena.query.ResultSet;
> import org.apache.jena.query.ResultSetFormatter;
> import org.apache.jena.rdf.model.ModelFactory;
> import org.apache.jena.ontology.Individual;
> import org.apache.jena.ontology.OntClass;
> import org.apache.jena.util.iterator.ExtendedIterator;
> import java.util.ArrayList;
> public class SPARQLDLBug
> {
> // The ontology loaded as dataset
> private static final String ontology = "ontologies/simple.owl";
> private static final String query = "query.sparql";
> public void run()
> {
> // First create a Jena ontology model backed by the
> Pellet reasoner
> // (note, the Pellet reasoner is required)
> final OntModel m =
> ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
> // Then read the _data from the file into the ontology
> model
> m.read(ontology);
> // Now read the query file into a query object
> final Query q = QueryFactory.read(query);
> // Create a SPARQL-DL query execution for the given
> query and
> // ontology model
> final QueryExecution qe =
> SparqlDLExecutionFactory.create(q, m);
> // We want to execute a SELECT query, do it, and return
> the result set
> final ResultSet rs = qe.execSelect();
> ArrayList<String> result = new ArrayList<String>();
> while(rs.hasNext()){
> QuerySolution qs = rs.next();
> // The Bug occurs in the next line
> Individual in =
> qs.getResource("x").as(Individual.class);
> ExtendedIterator<OntClass> it =
> in.listOntClasses(true);
> String className = "";
> while(it.hasNext()){
> className = it.next().toString();
> }
> result.add(className);
> }
> qe.close();
> }
> public static void main(final String[] args)
> {
> final SPARQLDLBug app = new SPARQLDLBug();
> app.run();
> }
> }
> {code}
> The error message is:
> {code}
> Exception in thread "main" org.apache.jena.ontology.ConversionException:
> Cannot convert node
> http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia to
> Individual
> at
> org.apache.jena.ontology.impl.IndividualImpl$1.wrap(IndividualImpl.java:61)
> at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:152)
> at org.apache.jena.enhanced.EnhNode.convertTo(EnhNode.java:31)
> at
> org.apache.jena.enhanced.Polymorphic.asInternal(Polymorphic.java:62)
> at org.apache.jena.enhanced.EnhNode.as(EnhNode.java:107)
> at bug.SPARQLDLBug.run(SPARQLDLBug.java:58)
> at bug.SPARQLDLBug.main(SPARQLDLBug.java:75)
> {code}
> This Query is:
> {code:xml}
> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> PREFIX owl: <http://www.w3.org/2002/07/owl#>
> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX bio: <http://www8.cs.fau.de/research:cgm/schizophrenia#>
> SELECT ?x
> WHERE { ?x rdf:type bio:AcuteSchizophrenia }
> {code}
> And the Ontology consist only of a class and one individual.
> {code:xml}
> <?xml version="1.0"?>
> <rdf:RDF xmlns="http://www8.cs.fau.de/research:cgm/schizophrenia#";
> xml:base="http://www8.cs.fau.de/research:cgm/schizophrenia";
> xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
> xmlns:owl="http://www.w3.org/2002/07/owl#";
> xmlns:xml="http://www.w3.org/XML/1998/namespace";
> xmlns:swrlb="http://www.w3.org/2003/11/swrlb#";
> xmlns:swrl="http://www.w3.org/2003/11/swrl#";
> xmlns:xsd="http://www.w3.org/2001/XMLSchema#";
> xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#";
> xmlns:dc="http://purl.org/dc/elements/1.1/";>
> <owl:Ontology
> rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia";>
> </owl:Ontology>
> <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
> <rdfs:Datatype
> rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
> <owl:Class
> rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia#AcuteSchizophrenia";>
> <rdfs:label xml:lang="en">Acute schizophrenia</rdfs:label>
> </owl:Class>
> <owl:NamedIndividual
> rdf:about="http://www8.cs.fau.de/research:cgm/schizophrenia#R_AcuteSchizophrenia";>
> <rdf:type
> rdf:resource="http://www8.cs.fau.de/research:cgm/schizophrenia#AcuteSchizophrenia"/>
> </owl:NamedIndividual>
> </rdf:RDF>
> {code}
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