Stéphane,
How are you running Jena (command line, in a webapp server, ... ?) and
what is the classpath?
It looks as if it is not using the new I/O subsystem (RIOT).
Do you have all the jena jars on the classpath? not just jena-core and
its dependencies?
Another possibility is that system initialization is not happening -
that's usually an environment issue which as repacking the jars.
Andy
On 23/03/17 12:51, Stéphane Dervaux wrote:
Here the full stacktrace
8955 [Thread-3] ERROR
org.apache.jena.rdf.model.impl.RDFDefaultErrorHandler -
http://purl.obolibrary.org/obo/bfo.owl(line 1 column 50): White spaces
are required between publicId and systemId.
8956 [Thread-3] WARN org.apache.jena.ontology.OntDocumentManager - An
error occurred while attempting to read from
http://purl.obolibrary.org/obo/bfo.owl. Msg was
'org.xml.sax.SAXParseException; systemId:
http://purl.obolibrary.org/obo/bfo.owl; lineNumber: 1; columnNumber: 50;
White spaces are required between publicId and systemId.'.
org.apache.jena.shared.JenaException: org.xml.sax.SAXParseException;
systemId: http://purl.obolibrary.org/obo/bfo.owl; lineNumber: 1;
columnNumber: 50; White spaces are required between publicId and systemId.
at
org.apache.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:60)
at
org.apache.jena.rdfxml.xmlinput.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:47)
at
org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.warning(XMLHandler.java:199)
at
org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.fatalError(XMLHandler.java:229)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source)
at
org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.jena.rdfxml.xmlinput.impl.RDFXMLParser.parse(RDFXMLParser.java:150)
at org.apache.jena.rdfxml.xmlinput.JenaReader.read(JenaReader.java:166)
at org.apache.jena.rdfxml.xmlinput.JenaReader.read(JenaReader.java:153)
at org.apache.jena.rdfxml.xmlinput.JenaReader.read(JenaReader.java:224)
at org.apache.jena.rdfxml.xmlinput.JenaReader.read(JenaReader.java:92)
at org.apache.jena.rdf.model.impl.ModelCom.read(ModelCom.java:281)
at
org.apache.jena.util.FileManager.readModelWorker(FileManager.java:374)
at org.apache.jena.util.FileManager.readModel(FileManager.java:341)
at org.apache.jena.util.FileManager.readModel(FileManager.java:325)
at
org.apache.jena.ontology.OntDocumentManager.read(OntDocumentManager.java:1062)
at
org.apache.jena.ontology.OntDocumentManager$1.readModel(OntDocumentManager.java:1032)
at
org.apache.jena.rdf.model.impl.ModelMakerImpl.getModel(ModelMakerImpl.java:104)
at
org.apache.jena.ontology.OntDocumentManager.fetchLoadedImportModel(OntDocumentManager.java:1029)
at
org.apache.jena.ontology.OntDocumentManager.fetchPossiblyCachedImportModel(OntDocumentManager.java:1001)
at
org.apache.jena.ontology.OntDocumentManager.loadImport(OntDocumentManager.java:974)
at
org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:768)
at
org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:706)
at
org.apache.jena.ontology.impl.OntModelImpl.loadImports(OntModelImpl.java:1964)
at
org.apache.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:2234)
at
org.apache.jena.util.FileManager.readModelWorker(FileManager.java:401)
at org.apache.jena.util.FileManager.readModel(FileManager.java:341)
at org.apache.jena.util.FileManager.readModel(FileManager.java:325)
at fr.inra.po2vocabmanager.utils.JenaTools.loadModel(JenaTools.java:56)
at fr.inra.po2vocabmanager.MainApp.createVocab(MainApp.java:73)
at fr.inra.po2vocabmanager.MainApp.access$0(MainApp.java:70)
at fr.inra.po2vocabmanager.MainApp$1.call(MainApp.java:96)
at fr.inra.po2vocabmanager.MainApp$1.call(MainApp.java:1)
at javafx.concurrent.Task$TaskCallable.call(Task.java:1423)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.xml.sax.SAXParseException; systemId:
http://purl.obolibrary.org/obo/bfo.owl; lineNumber: 1; columnNumber: 50;
White spaces are required between publicId and systemId.
at
org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown
Source)
... 43 more
Le 23/03/2017 à 13:28, Andy Seaborne a écrit :
Stéphane,
Do you have the full stacktrace?
Andy
On 23/03/17 12:21, Stéphane Dervaux wrote:
Hi,
I try to load an ontology with two imports with jena 3.2.0 (also 3.1.0):
- http://www.w3.org/2006/time
- http://purl.obolibrary.org/obo/bfo.owl
No problem for the time ontology but there is a SaxParserException for
the second (bfo).
org.apache.jena.shared.JenaException: org.xml.sax.SAXParseException;
systemId: http://purl.obolibrary.org/obo/bfo.owl; lineNumber: 1;
columnNumber: 50; White spaces are required between publicId and
systemId.
The problem is the redirection from
"http://purl.obolibrary.org/obo/bfo.owl"; to
"https://raw.githubusercontent.com/BFO-ontology/BFO/v2.0/bfo.owl";
The parser try to parse :
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>302 Found</title>
</head><body>
<h1>Found</h1>
<p>The document has moved <a
href="https://raw.githubusercontent.com/BFO-ontology/BFO/v2.0/bfo.owl";>here</a>.</p>
<hr>
<address>Apache/2.4.7 (Ubuntu) Server at purl.obolibrary.org Port
80</address>
</body></html>
Is there any way to solve this error ?
Thanks
--
Signature electronique
INRA <http://www.inra.fr>
*Stéphane Dervaux*
*Ingénieur d'étude en informatique / Engenieer in Computer Science*
[email protected] <mailto:#>
*Unité MIA Paris*
Tèl. : +33 1 (0)1 44 08 18 89
16, rue Claude Bernard
75 231 Paris Cedex 05
France
www.inra.fr <http://www.inra.fr>
--
Signature electronique
INRA <http://www.inra.fr>
*Stéphane Dervaux*
*Ingénieur d'étude en informatique / Engenieer in Computer Science*
[email protected] <mailto:#>
*Unité MIA Paris*
Tèl. : +33 1 (0)1 44 08 18 89
16, rue Claude Bernard
75 231 Paris Cedex 05
France
www.inra.fr <http://www.inra.fr>
