web protege error

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web protege error

alexandergarciacastrobalu
Hi all. I opened an OBO file in protege 5, save it as OWL and then tried to open it in web based protege and it did not work. below  the error msg I am getting. I can open it in protege desktop but the web based protege gives me the parsing error msg.



org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/srv/protege/webprotege-data/uploads/upload-7222306014464361505
Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
The following parsers were tried:
1) org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser@1f667a8e
2) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@202f8eaf
3) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@1bc10033
4) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@1ec850a9
5) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
6) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4a963aa5
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@58fefd7b
16) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
17) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@4e870b46
18) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2fb842d3
19) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d


Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser@1f667a8e
    Stack trace:
Corrupt file or not a binary OWL format (Magic Number Not Present)        org.semanticweb.binaryowl.BinaryOWLOntologyDocumentPreamble.read(BinaryOWLOntologyDocumentPreamble.java:79)
        org.semanticweb.binaryowl.BinaryOWLOntologyDocumentPreamble.

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Re: web protege error

MihalyF
Hi,

I've just had a same issue, but figured out that my error was as banal as a
missing access right to the file for tomcat user.
Hope it helps

Mihaly



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Re: web protege error

Matthew Horridge-2
Administrator
In reply to this post by alexandergarciacastrobalu
Hi Alex,

Did you manage to sort this out?

Cheers,

Matthew


> On 12 Dec 2018, at 04:55, alexander garcia <[hidden email]> wrote:
>
> Hi all. I opened an OBO file in protege 5, save it as OWL and then tried to open it in web based protege and it did not work. below  the error msg I am getting. I can open it in protege desktop but the web based protege gives me the parsing error msg.
>
>
>
> org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/srv/protege/webprotege-data/uploads/upload-7222306014464361505
> Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
> The following parsers were tried:
> 1) org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser@1f667a8e
> 2) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@202f8eaf
> 3) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@1bc10033
> 4) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@1ec850a9
> 5) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
> 6) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4a963aa5
> 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
> 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
> 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
> 10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
> 11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
> 12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
> 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
> 14) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
> 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@58fefd7b
> 16) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
> 17) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@4e870b46
> 18) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2fb842d3
> 19) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
>
>
> Detailed logs:
> --------------------------------------------------------------------------------
> Parser: org.semanticweb.binaryowl.owlapi.BinaryOWLOntologyDocumentParser@1f667a8e
>     Stack trace:
> Corrupt file or not a binary OWL format (Magic Number Not Present)        org.semanticweb.binaryowl.BinaryOWLOntologyDocumentPreamble.read(BinaryOWLOntologyDocumentPreamble.java:79)
>         org.semanticweb.binaryowl.BinaryOWLOntologyDocumentPreamble.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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