Ontology in WebProtege not accessible

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Ontology in WebProtege not accessible

Timo Homburg
A few days ago, I posted this bug report
https://github.com/protegeproject/protege/issues/26#issuecomment-38367410
about an ontology which was previously inaccessible using Protege.
Thanks to your support loading the ontology and saving it works fine now.
However, before sending this bug report I also imported the corresponding ontology in my Web Protege account "Timo Homburg" and was able to work with it.
Yet only a Turtle export of the ontology was possible.
RDF/XML and OWL exports of the (modified) ontology failed because of the same exception as stated in the bug report.
While a turtle export was enough for my purposes, I continued working and finished my ontology modifications using WebProtege on Friday.
After having finished those modifications I experienced that I could not access the ontology
named WikiTaaable http://wikitaaable.loria.fr in WebProtege anymore using my account.
What I get is the following exception:

*type* Exception report

*message*

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

*exception*

java.lang.RuntimeException: Failed to load project: null
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:228)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
    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)

*root cause*

org.semanticweb.owlapi.io.OWLOntologyCreationIOException
    uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:214)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:829)
    uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:782)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
    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)

*root cause*

java.io.EOFException
    java.io.DataInputStream.readFully(DataInputStream.java:180)
    java.io.DataInputStream.readUTF(DataInputStream.java:592)
    java.io.DataInputStream.readUTF(DataInputStream.java:547)
    org.semanticweb.binaryowl.lookup.IRILookupTable.readNonIndexedIRI(IRILookupTable.java:206)
    org.semanticweb.binaryowl.lookup.IRILookupTable.readIRI(IRILookupTable.java:192)
    org.semanticweb.binaryowl.lookup.IRILookupTable.readClassIRI(IRILookupTable.java:265)
    org.semanticweb.binaryowl.lookup.LookupTable.readClassIRI(LookupTable.java:119)
    org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readClassIRI(BinaryOWLInputStream.java:107)
    org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.java:75)
    org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.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.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:67)
    org.semanticweb.binaryowl.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:58)
    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:782)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
    edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
    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)
This exception seems to point to the OWL API which was also mentioned as a cause for the problems I posted in the bug report.
Loading the ontology and exporting the ontology both does not work.
As I put much effort in extending this ontology, I would appreciate it if you could provide me a dump of the ontology in RDF/XML or OWL so that I using the workaround mentioned in the bug report can use it in Protege again.
Reply | Threaded
Open this post in threaded view
|

Re: Ontology in WebProtege not accessible

Matthew Horridge-2
Administrator
Hi Timo,

I’m sorry about this issue that you’re having.  I’ll do my best to resolve it as soon as I can.  

Cheers,

Matthew

p.s. I don’t think this issue is related to the previous issue that you filed.




On 26 Mar 2014, at 06:43, Timo Homburg <[hidden email]> wrote:

> A few days ago, I posted this bug report
> https://github.com/protegeproject/protege/issues/26#issuecomment-38367410
> about an ontology which was previously inaccessible using Protege.
> Thanks to your support loading the ontology and saving it works fine now.
> However, before sending this bug report I also imported the corresponding
> ontology in my Web Protege account "Timo Homburg" and was able to work with
> it.
> Yet only a Turtle export of the ontology was possible.
> RDF/XML and OWL exports of the (modified) ontology failed because of the
> same exception as stated in the bug report.
> While a turtle export was enough for my purposes, I continued working and
> finished my ontology modifications using WebProtege on Friday.
> After having finished those modifications I experienced that I could not
> access the ontology
> named WikiTaaable http://wikitaaable.loria.fr in WebProtege anymore using my
> account.
> What I get is the following exception:
>
> *type* Exception report
>
> *message*
>
> *description* _The server encountered an internal error () that prevented it
> from fulfilling this request._
>
> *exception*
>
> java.lang.RuntimeException: Failed to load project: null
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:228)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>
> 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)
>
> *root cause*
>
> org.semanticweb.owlapi.io.OWLOntologyCreationIOException
>
> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:214)
>
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:829)
>
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:782)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>
> 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)
>
> *root cause*
>
> java.io.EOFException
>    java.io.DataInputStream.readFully(DataInputStream.java:180)
>    java.io.DataInputStream.readUTF(DataInputStream.java:592)
>    java.io.DataInputStream.readUTF(DataInputStream.java:547)
>
> org.semanticweb.binaryowl.lookup.IRILookupTable.readNonIndexedIRI(IRILookupTable.java:206)
>
> org.semanticweb.binaryowl.lookup.IRILookupTable.readIRI(IRILookupTable.java:192)
>
> org.semanticweb.binaryowl.lookup.IRILookupTable.readClassIRI(IRILookupTable.java:265)
>
> org.semanticweb.binaryowl.lookup.LookupTable.readClassIRI(LookupTable.java:119)
>
> org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readClassIRI(BinaryOWLInputStream.java:107)
>
> org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.java:75)
>
> org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.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.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:67)
>
> org.semanticweb.binaryowl.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:58)
>
> 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:782)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
>
> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>
> 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)
> This exception seems to point to the OWL API which was also mentioned as a
> cause for the problems I posted in the bug report.
> Loading the ontology and exporting the ontology both does not work.
> As I put much effort in extending this ontology, I would appreciate it if
> you could provide me a dump of the ontology in RDF/XML or OWL so that I
> using the workaround mentioned in the bug report can use it in Protege
> again.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Ontology-in-WebProtege-not-accessible-tp4660111.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> 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
Reply | Threaded
Open this post in threaded view
|

Re: Ontology in WebProtege not accessible

Matthew Horridge-2
Administrator
Hi Timo,

You should be able to access your project now.  You should be o.k., but please let me know if you have any other problems related to accessing it.

With regards to downloading the ontology, there is still the issue that you can only download it in turtle for the time being - this is indeed related to the bug report that you filed before and we need an update to the OWL API to fix this.

Cheers,

Matthew



On 26 Mar 2014, at 07:53, Matthew Horridge <[hidden email]> wrote:

> Hi Timo,
>
> I’m sorry about this issue that you’re having.  I’ll do my best to resolve it as soon as I can.  
>
> Cheers,
>
> Matthew
>
> p.s. I don’t think this issue is related to the previous issue that you filed.
>
>
>
>
> On 26 Mar 2014, at 06:43, Timo Homburg <[hidden email]> wrote:
>
>> A few days ago, I posted this bug report
>> https://github.com/protegeproject/protege/issues/26#issuecomment-38367410
>> about an ontology which was previously inaccessible using Protege.
>> Thanks to your support loading the ontology and saving it works fine now.
>> However, before sending this bug report I also imported the corresponding
>> ontology in my Web Protege account "Timo Homburg" and was able to work with
>> it.
>> Yet only a Turtle export of the ontology was possible.
>> RDF/XML and OWL exports of the (modified) ontology failed because of the
>> same exception as stated in the bug report.
>> While a turtle export was enough for my purposes, I continued working and
>> finished my ontology modifications using WebProtege on Friday.
>> After having finished those modifications I experienced that I could not
>> access the ontology
>> named WikiTaaable http://wikitaaable.loria.fr in WebProtege anymore using my
>> account.
>> What I get is the following exception:
>>
>> *type* Exception report
>>
>> *message*
>>
>> *description* _The server encountered an internal error () that prevented it
>> from fulfilling this request._
>>
>> *exception*
>>
>> java.lang.RuntimeException: Failed to load project: null
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:228)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>>
>> 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)
>>
>> *root cause*
>>
>> org.semanticweb.owlapi.io.OWLOntologyCreationIOException
>>
>> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:214)
>>
>> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:829)
>>
>> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:782)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>>
>> 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)
>>
>> *root cause*
>>
>> java.io.EOFException
>>   java.io.DataInputStream.readFully(DataInputStream.java:180)
>>   java.io.DataInputStream.readUTF(DataInputStream.java:592)
>>   java.io.DataInputStream.readUTF(DataInputStream.java:547)
>>
>> org.semanticweb.binaryowl.lookup.IRILookupTable.readNonIndexedIRI(IRILookupTable.java:206)
>>
>> org.semanticweb.binaryowl.lookup.IRILookupTable.readIRI(IRILookupTable.java:192)
>>
>> org.semanticweb.binaryowl.lookup.IRILookupTable.readClassIRI(IRILookupTable.java:265)
>>
>> org.semanticweb.binaryowl.lookup.LookupTable.readClassIRI(LookupTable.java:119)
>>
>> org.semanticweb.binaryowl.stream.BinaryOWLInputStream.readClassIRI(BinaryOWLInputStream.java:107)
>>
>> org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.java:75)
>>
>> org.semanticweb.binaryowl.owlobject.serializer.OWLEntitySerializer.readObject(OWLEntitySerializer.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.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:67)
>>
>> org.semanticweb.binaryowl.owlobject.serializer.OWLDeclarationSerializer.readAxiom(OWLDeclarationSerializer.java:58)
>>
>> 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:782)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProjectDocumentStore.loadRootOntologyIntoManager(OWLAPIProjectDocumentStore.java:311)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.loadProject(OWLAPIProject.java:202)
>>
>> edu.stanford.bmir.protege.web.server.owlapi.OWLAPIProject.<init>(OWLAPIProject.java:188)
>>
>> 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)
>> This exception seems to point to the OWL API which was also mentioned as a
>> cause for the problems I posted in the bug report.
>> Loading the ontology and exporting the ontology both does not work.
>> As I put much effort in extending this ontology, I would appreciate it if
>> you could provide me a dump of the ontology in RDF/XML or OWL so that I
>> using the workaround mentioned in the bug report can use it in Protege
>> again.
>>
>>
>>
>> --
>> View this message in context: http://protege-project.136.n4.nabble.com/Ontology-in-WebProtege-not-accessible-tp4660111.html
>> Sent from the Protege User mailing list archive at Nabble.com.
>> _______________________________________________
>> 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

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Ontology in WebProtege not accessible

Timo Homburg
In reply to this post by Matthew Horridge-2
Thank you for fixing this issue.
I am able to access the ontology again!