Server Connection Error - Ontology Unopenable

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Server Connection Error - Ontology Unopenable

Lizbeth Moore

Hi,

We have been collaboratively working on a largish ontology in WebProtege (in excess of 100 classes, 250 properties, 1300 changes) which has been imported from Protege 4.3 and includes an imported ontology from an external web source for determining equivalency mappings.  On two occasions while working on the ontology in WebProtege a message is generated saying that connection to the Protege server has been lost.  When attempting to reopen the ontology the opening sequence hangs with the following error message (note: it is not possible to determine the text in the box behind ‘Loading project’:

 

 

The ontology is now no longer accessible from WebProtege and the following error report is generated when we try to download the ontology:

 

type Exception report

message

description The server encountered an internal error () that prevented it from fulfilling this request.

exception

java.lang.NegativeArraySizeException

        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readBytes(OWLLiteralSerializer.java:205)

        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readRawLiteral(OWLLiteralSerializer.java:124)

        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readLiteral(OWLLiteralSerializer.java:102)

        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readLiteral(BinaryOWLInputStream.java:132)

        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readObject(OWLLiteralSerializer.java:97)

        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readObject(OWLLiteralSerializer.java:59)

        org.semanticweb.binaryowl.owlobject.serializer.OWLObjectSerializer.read(OWLObjectSerializer.java:69)

        org.semanticweb.binaryowl.owlobject.OWLObjectBinaryType.read(OWLObjectBinaryType.java:397)

        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readOWLObject(BinaryOWLInputStream.java:68)

        org.semanticweb.binaryowl.owlobject.serializer.OWLDataPropertyAssertionAxiomSerializer.readAxiom(OWLDataPropertyAssertionAxiomSerializer.java:69)

        org.semanticweb.binaryowl.owlobject.serializer.OWLDataPropertyAssertionAxiomSerializer.readAxiom(OWLDataPropertyAssertionAxiomSerializer.java:56)

        org.semanticweb.binaryowl.owlobject.serializer.AbstractAxiomSerializer.readObject(AbstractAxiomSerializer.java:70)

        org.semanticweb.binaryowl.owlobject.serializer.AbstractAxiomSerializer.readObject(AbstractAxiomSerializer.java:57)

        org.semanticweb.binaryowl.owlobject.serializer.OWLObjectSerializer.read(OWLObjectSerializer.java:69)

        org.semanticweb.binaryowl.owlobject.OWLObjectBinaryType.read(OWLObjectBinaryType.java:397)

        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readOWLObject(BinaryOWLInputStream.java:68)

        org.semanticweb.binaryowl.change.serializer.AddAxiomDataSerializer.read(AddAxiomDataSerializer.java:66)

        org.semanticweb.binaryowl.change.serializer.AddAxiomDataSerializer.read(AddAxiomDataSerializer.java:56)

        org.semanticweb.binaryowl.change.OntologyChangeDataType.read(OntologyChangeDataType.java:117)

        org.semanticweb.binaryowl.change.OntologyChangeDataList.readChangeRecordData(OntologyChangeDataList.java:177)

        org.semanticweb.binaryowl.change.OntologyChangeDataList.read(OntologyChangeDataList.java:169)

        org.semanticweb.binaryowl.change.OntologyChangeDataList.<init>(OntologyChangeDataList.java:101)

        org.semanticweb.binaryowl.serializer.v1.BinaryOWLV1DocumentBodySerializer.readOntologyChanges(BinaryOWLV1DocumentBodySerializer.java:94)

        org.semanticweb.binaryowl.serializer.v1.BinaryOWLV1DocumentBodySerializer.read(BinaryOWLV1DocumentBodySerializer.java:86)

        org.semanticweb.binaryowl.BinaryOWLOntologyDocumentSerializer.read(BinaryOWLOntologyDocumentSerializer.java:91)

        org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser.parse(BinaryOWLOntologyDocumentParser.java:94)

        org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser.parse(BinaryOWLOntologyDocumentParser.java:76)

        uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:206)

        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:829)

        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:775)

        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:788)

        edu.stanford.bmir.protege.web.server.notes.OWLAPINotesManagerNotesAPIImpl.loadExistingNotesOntology(OWLAPINotesManagerNotesAPIImpl.java:128)

        edu.stanford.bmir.protege.web.server.notes.OWLAPINotesManagerNotesAPIImpl.<init>(OWLAPINotesManagerNotesAPIImpl.java:77)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.initialiseProjectMachinery(OWLAPIProject.java:259)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:189)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.getProject(OWLAPIProject.java:139)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectCache.getProjectInternal(OWLAPIProjectCache.java:140)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectCache.getProject(OWLAPIProjectCache.java:108)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectManager.getProject(OWLAPIProjectManager.java:30)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.createDownloadCacheIfNecessary(OWLAPIProjectDocumentStore.java:433)

        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProject(OWLAPIProjectDocumentStore.java:159)

        edu.stanford.bmir.protege.web.server.filedownload.OWLAPIProjectDownloader.writeProject(OWLAPIProjectDownloader.java:49)

        edu.stanford.bmir.protege.web.server.filedownload.FileDownloadServlet.doGet(FileDownloadServlet.java:34)

        javax.servlet.http.HttpServlet.service(HttpServlet.java:617)

        javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

        edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:65)

note The full stack trace of the root cause is available in the Apache Tomcat/6.0.29 logs.

This has now happened twice and before recreating the ontology and mappings again, I was wondering if there was any way of repairing/reaccessing the ontology?

 

Thank you.

 

Lizbeth Moore

 


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Re: Server Connection Error - Ontology Unopenable

Matthew Horridge-2
Administrator
Hi Lizbeth,

Sorry about the problems that you’re having.  I’ll take a look at this and get back to you as soon as I can.  In the mean time, would it be possible to send me the name of the project and the original source files from Protege 4.3?   (off list if you prefer).

Many thanks,

Matthew


On 2 Mar 2014, at 17:32, Lizbeth Moore <[hidden email]> wrote:

Hi,
We have been collaboratively working on a largish ontology in WebProtege (in excess of 100 classes, 250 properties, 1300 changes) which has been imported from Protege 4.3 and includes an imported ontology from an external web source for determining equivalency mappings.  On two occasions while working on the ontology in WebProtege a message is generated saying that connection to the Protege server has been lost.  When attempting to reopen the ontology the opening sequence hangs with the following error message (note: it is not possible to determine the text in the box behind ‘Loading project’:
 
<image001.png>
 
The ontology is now no longer accessible from WebProtege and the following error report is generated when we try to download the ontology:
 
type Exception report
message
description The server encountered an internal error () that prevented it from fulfilling this request.
exception
java.lang.NegativeArraySizeException
        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readBytes(OWLLiteralSerializer.java:205)
        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readRawLiteral(OWLLiteralSerializer.java:124)
        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readLiteral(OWLLiteralSerializer.java:102)
        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readLiteral(BinaryOWLInputStream.java:132)
        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readObject(OWLLiteralSerializer.java:97)
        org.semanticweb.binaryowl.owlobject.serializer.OWLLiteralSerializer.readObject(OWLLiteralSerializer.java:59)
        org.semanticweb.binaryowl.owlobject.serializer.OWLObjectSerializer.read(OWLObjectSerializer.java:69)
        org.semanticweb.binaryowl.owlobject.OWLObjectBinaryType.read(OWLObjectBinaryType.java:397)
        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readOWLObject(BinaryOWLInputStream.java:68)
        org.semanticweb.binaryowl.owlobject.serializer.OWLDataPropertyAssertionAxiomSerializer.readAxiom(OWLDataPropertyAssertionAxiomSerializer.java:69)
        org.semanticweb.binaryowl.owlobject.serializer.OWLDataPropertyAssertionAxiomSerializer.readAxiom(OWLDataPropertyAssertionAxiomSerializer.java:56)
        org.semanticweb.binaryowl.owlobject.serializer.AbstractAxiomSerializer.readObject(AbstractAxiomSerializer.java:70)
        org.semanticweb.binaryowl.owlobject.serializer.AbstractAxiomSerializer.readObject(AbstractAxiomSerializer.java:57)
        org.semanticweb.binaryowl.owlobject.serializer.OWLObjectSerializer.read(OWLObjectSerializer.java:69)
        org.semanticweb.binaryowl.owlobject.OWLObjectBinaryType.read(OWLObjectBinaryType.java:397)
        org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readOWLObject(BinaryOWLInputStream.java:68)
        org.semanticweb.binaryowl.change.serializer.AddAxiomDataSerializer.read(AddAxiomDataSerializer.java:66)
        org.semanticweb.binaryowl.change.serializer.AddAxiomDataSerializer.read(AddAxiomDataSerializer.java:56)
        org.semanticweb.binaryowl.change.OntologyChangeDataType.read(OntologyChangeDataType.java:117)
        org.semanticweb.binaryowl.change.OntologyChangeDataList.readChangeRecordData(OntologyChangeDataList.java:177)
        org.semanticweb.binaryowl.change.OntologyChangeDataList.read(OntologyChangeDataList.java:169)
        org.semanticweb.binaryowl.change.OntologyChangeDataList.<init>(OntologyChangeDataList.java:101)
        org.semanticweb.binaryowl.serializer.v1.BinaryOWLV1DocumentBodySerializer.readOntologyChanges(BinaryOWLV1DocumentBodySerializer.java:94)
        org.semanticweb.binaryowl.serializer.v1.BinaryOWLV1DocumentBodySerializer.read(BinaryOWLV1DocumentBodySerializer.java:86)
        org.semanticweb.binaryowl.BinaryOWLOntologyDocumentSerializer.read(BinaryOWLOntologyDocumentSerializer.java:91)
        org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser.parse(BinaryOWLOntologyDocumentParser.java:94)
        org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser.parse(BinaryOWLOntologyDocumentParser.java:76)
        uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:206)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:829)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:775)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:788)
        edu.stanford.bmir.protege.web.server.notes.OWLAPINotesManagerNotesAPIImpl.loadExistingNotesOntology(OWLAPINotesManagerNotesAPIImpl.java:128)
        edu.stanford.bmir.protege.web.server.notes.OWLAPINotesManagerNotesAPIImpl.<init>(OWLAPINotesManagerNotesAPIImpl.java:77)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.initialiseProjectMachinery(OWLAPIProject.java:259)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:189)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.getProject(OWLAPIProject.java:139)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectCache.getProjectInternal(OWLAPIProjectCache.java:140)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectCache.getProject(OWLAPIProjectCache.java:108)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectManager.getProject(OWLAPIProjectManager.java:30)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.createDownloadCacheIfNecessary(OWLAPIProjectDocumentStore.java:433)
        edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.exportProject(OWLAPIProjectDocumentStore.java:159)
        edu.stanford.bmir.protege.web.server.filedownload.OWLAPIProjectDownloader.writeProject(OWLAPIProjectDownloader.java:49)
        edu.stanford.bmir.protege.web.server.filedownload.FileDownloadServlet.doGet(FileDownloadServlet.java:34)
        javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
        javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
        edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:65)
note The full stack trace of the root cause is available in the Apache Tomcat/6.0.29 logs.
This has now happened twice and before recreating the ontology and mappings again, I was wondering if there was any way of repairing/reaccessing the ontology?
 
Thank you.
 
Lizbeth Moore
 

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Please consider the environment before printing this e-mail.

The information contained in this email and any attachment is confidential and may contain legally privileged or copyright material. It is intended only for the use of the addressee(s). If you are not the intended recipient of this email, you are not permitted to disseminate, distribute or copy this email or any attachments. If you have received this message in error, please notify the sender immediately and delete this email from your system. The ABC does not represent or warrant that this transmission is secure or virus free. Before opening any attachment you should check for viruses. The ABC's liability is limited to resupplying any email and attachments.
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user