Re: [Obi-devel] still can't open todays obi.pprj

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Yes, it is working for me on Linux, but Bjoern gets the same error messages
under windows.

-Jay

On 6/28/07, Daniel Schober <sc...@eb...> wrote:
>
>  Hi Frank,
> No, it wasn't a proxy problem. It could not work because the bug in
> Protege was not fixed for the windows versions.
> Cheers, Daniel.
>
> frank gibson wrote:
>
> Are you behind a proxy?
>
> Frank
>
> On 6/28/07, Daniel Schober <sc...@eb...> wrote:
> >
> > Yes, of course I copied the templates and renamed them accordingly. I
> > guess the current svn obi.owl.template (and the derived obi.owl)  just
> > tries to import from a wrong URL or the locations specified in the
> > obi.repository file can not be resolved.
> > Cheers, Daniel
> >
> > Allyson Lister wrote:
> >
> > Did you make sure you copied all template files to regular files?
> >
> > On 6/28/07, Trish Whetzel <wh...@pc... > wrote:
> > >
> > > I have not yet had time on my personal To Do list to try this out. I
> > > do
> > > know that Jay and I think someone else other than Alan has been able
> > > to
> > > get this methodology to work so that makes at least 3 people that have
> > > done this successfully.
> > >
> > > As for the SVN "experimental" folders to try out different
> > > methodologies,
> > > I don't think that there is a hard and fast rule that would speak
> > > against
> > > this, but I personally would be extremely hesitant to do this since
> > > the
> > > current methodology does work and my impression is that it is a matter
> > > of
> > > fine tuning the instructions so that all steps are crystal clear.
> > >
> > > Trish
> > >
> > >
> > > > I just installed the new P.3.3. beta build 411. Following the
> > > > instructions in svn by this morning, I was not able to open the
> > > obi.pprj
> > > > file without being asked for a repository.
> > > > Liju, Trish, have you been able to open the pprj according to the
> > > > instructions provided?
> > > > Alan, I put the cmd out below. Any idea what has gone wrong here? I
> > > > guess the import statements in the owl file should refer to a valid
> > > URL,
> > > > e.g. to
> > > > "https://svn.sourceforge.net/svnroot/obi/branchDevelopment/trunk/DataTransformation.owl
> > > "
> > > > instead of "http://obi.sourceforge.net/ontology/OBI/DataTransformation.owl
> > > "
> > > >
> > > > An other question:
> > > > What would speak against having  'experimental' folders under our
> > > svn
> > > > repository (e.g. BranchingProposalAlan, BranchingProposalLiju, and
> > > > BranchingProposalSchober, ... BranchingProposalWhoever), where all
> > > who
> > > > wants can work out working solutions in parallel and then if we have
> > > a
> > > > workinjg one we can choose?
> > > > Cheers,
> > > >    Daniel Schober.
> > > >
> > > >
> > > > ----
> > > > cwd: C:\Program Files\Protege_3.3_beta411\
> > > > cmd: "C:\Program Files\Protege_3.3_beta411\jre\bin\java.exe"
> > > > -Xms10000000 -Xmx10
> > > > 0000000 -classpath "C:\Program
> > > > Files\Protege_3.3_beta411\protege.jar;C:\Program
> > > > Files\Protege_3.3_beta411\looks-2.1.3.jar;C:\Program
> > > > Files\Protege_3.3_beta411\u
> > > > nicode_panel.jar;C:\Program
> > > > Files\Protege_3.3_beta411\driver.jar;C:\Program File
> > > > s\Protege_3.3_beta411\driver0.jar;C:\Program
> > > > Files\Protege_3.3_beta411\driver1.j
> > > > ar;C:\Program Files\Protege_3.3_beta411\driver2.jar;C:\Program
> > > > Files\Protege_3.3
> > > > _beta411\plugins\edu.stanford.smi.protegex.changes\change-model.jar
> > > ;C:\Program
> > > > F
> > > > iles\Protege_3.3_beta411\lax.jar;" com.zerog.lax.LAX "C:/Program
> > > > Files/Protege_3
> > > > .3_beta411/Protege.lax" "C:/Documents and Settings/schober/Local
> > > > Settings/Temp/l
> > > > ax4.tmp" "C:\\Program
> > > > Files\\Protege_3.3_beta\\obi\\branchDevelopment\\trunk\\ob
> > > > i.pprj"
> > > > CONFIG: Protege 3.3 Build 411, JVM 1.5.0_11-b03, memory=99M, Windows
> > > XP,
> > > > encodin
> > > > g=UTF-8, language=en, country=GB
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
> > > > CONFIG: Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
> > > > CONFIG: Loaded plugin dfki.protege.ontoviz
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF
> > > Backend
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes
> > > tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
> > > > CONFIG: Loaded plugin edu.stanford.smi.protege.collab -
> > > CollaborativeProtege
> > > > CONFIG: Loaded plugin edu.stanford.smi.protege.script - Script
> > > Plugin
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions-
> > > > Graph Widg
> > > > et, Table Widget
> > > > CONFIG: Loaded plugin edu.stanford.smi.protege.stringsearch - String
> > > > Search Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.datamaster -
> > > DataMaster Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.facets_tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.instance_tree
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet
> > > Tab
> > > > CONFIG: Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
> > > > CONFIG: Loaded plugin org.algernon - Algernon
> > > > CONFIG: Loaded plugin se.liu.ida.JessTab - JessTab Plugin
> > > > CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.debugger
> > > > CONFIG: Loaded plugin
> > > uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owldoc
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlunittest
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlviz
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic
> > > Wizards
> > > > CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl -
> > > OWL
> > > > Wizards
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\Biomaterial.owl)
> > > -- Lo
> > > > calFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\DataTransformation.owl
> > > > ) -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\DigitalEntityPlus.owl)
> > > > -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\InstrumentAndPart.owl)
> > > > -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\Obsolete.owl)
> > > > -- Local
> > > > FolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram Files\Protege_3.3_beta\obi\branchDevelopment\trunk\Plan.owl)
> > > --
> > > > LocalFold
> > > > erRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\ProtocolApplication.ow
> > > > l) -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\Relations.owl)
> > > > -- Loca
> > > > lFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram Files\Protege_3.3_beta\obi\branchDevelopment\trunk\Role.owl)
> > > --
> > > > LocalFold
> > > > erRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\TheRest.owl)
> > > > -- LocalF
> > > > olderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\bfo\bfo.owl)
> > > > -- LocalF
> > > > olderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\external\protege-
> > > dc.ow
> > > > l) -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\external\protege.owl)
> > > > -- LocalFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\external\ro.owl)
> > > -- Lo
> > > > calFolderRepository.update()
> > > > WARNING: [Local Folder Repository] The specified file must be a
> > > > directory. (C:\P
> > > > rogram
> > > >
> > > Files\Protege_3.3_beta\obi\branchDevelopment\trunk\external\ro_bfo_bridge
> > > > .owl) -- LocalFolderRepository.update()
> > > > INFO: Loading triples
> > > > INFO: Start processing ontology:
> > > > file:/C:/Program%20Files/Protege_3.3_beta/obi/b
> > > > ranchDevelopment/trunk/obi.owl Time: Thu Jun 28 16:10:49 BST 2007
> > > > SEVERE: Exception caught -- java.io.FileNotFoundException:
> > > > http://obi.sourceforg
> > > > e.net/ontology/OBI/Plan.owl
> > > >        at
> > > > sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown
> > > So
> > > > urce)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.getInputSt
> > > > ream(Unknown Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.repository.impl.HTTPRepository.update
> > > (U
> > > > nknown Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.repository.impl.HTTPRepository.<init>(U
> > >
> > > > nknown Source)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.repository.RepositoryManager.getReposit
> > > > ory(Unknown Source)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.getReposit
> > > > ory(Unknown Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.runImport
> > > (
> > > > Unknown Source)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.processImp
> > > > orts(Unknown Source)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriple
> > > > s(Unknown Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknow
> > > > n Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run
> > > (Unknow
> > > > n Source)
> > > >        at
> > > > edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknow
> > > > n Source)
> > > >        at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load
> > > (Unknown
> > > > Source)
> > > >        at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load
> > > (Unknown
> > > > Source)
> > > >        at
> > > >
> > > edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowl
> > > > edgeBase(Unknown Source)
> > > >        at edu.stanford.smi.protege.model.Project.loadDomainKB
> > > (Unknown
> > > > Source)
> > > >        at
> > > > edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase
> > > (Unkn
> > > > own Source)
> > > >        at edu.stanford.smi.protege.model.Project.<init>(Unknown
> > > Source)
> > > >        at edu.stanford.smi.protege.model.Project .<init>(Unknown
> > > Source)
> > > >        at
> > > > edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown
> > > Sou
> > > > rce)
> > > >        at
> > > > edu.stanford.smi.protege.ui.ProjectManager.loadProjectFromURI(Unknown
> > > > Source)
> > > >        at
> > > > edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown
> > > Source
> > > > )
> > > >        at edu.stanford.smi.protege.Application.init(Unknown Source)
> > > >        at edu.stanford.smi.protege.Application.realmain(Unknown
> > > Source)
> > > >        at edu.stanford.smi.protege.Application$3.run(Unknown Source)
> > > >
> > > >
> > > > --
> > > >
> > > __________________________________________________________________________________________
> > >
> > > >
> > > > Dr. Daniel Schober
> > > >
> > > > NET Project - Ontologist
> > > >
> > > > The European Bioinformatics Institute   email:  sc...@eb...
> > > > EMBL Outstation - Hinxton               direct:   +44 (0)1223 494410
> > > > Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
> > > > Cambridge CB10 1SD, UK                        Room: A3-141
> > > (extension building)
> > > >
> > > > Project page: www.ebi.ac.uk/net-project
> > > >
> > > > Personal page:    http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> > >
> > > > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
> > > >
> > > >
> > > >
> > > >
> > > -------------------------------------------------------------------------
> > > > This SF.net email is sponsored by DB2 Express
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> > > > control of your XML. No limits. Just data. Click to get it now.
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> > > > _______________________________________________
> > > > Obi-devel mailing list
> > > > Obi...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/obi-devel
> > > >
> > >
> > >
> > > -------------------------------------------------------------------------
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> > > _______________________________________________
> > > Obi-devel mailing list
> > > Obi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/obi-devel
> > >
> >
> >
> >
> > --
> > Thanks,
> > Allyson :)
> >
> > Allyson Lister
> > Research Associate
> > Centre for Integrated Systems Biology for Ageing and Nutrition
> > Newcastle University
> > http://www.cisban.ac.uk
> > School of Computing Science
> > Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> >
> >
> >  --
> > __________________________________________________________________________________________
> >
> > Dr. Daniel Schober
> >
> > NET Project - Ontologist
> >
> > The European Bioinformatics Institute   email:
> > sc...@eb...
> > EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
> > Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
> > Cambridge CB10 1SD, UK                 	Room: A3-141 (extension building)
> >
> > Project page: www.ebi.ac.uk/net-project
> >
> > Personal page:    http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> >
> > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
> >
> >
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > Obi-devel mailing list
> > Obi...@li...
> > https://lists.sourceforge.net/lists/listinfo/obi-devel
> >
> >
>
>
> --
> Frank Gibson
> Research Associate
> Room 2.19, Devonshire Building
> School of Computing Science,
> University of Newcastle upon Tyne,
> Newcastle upon Tyne, NE1 7RU
> United Kingdom
> Telephone: +44-191-246-4933
> Fax: +44-191-246-4905
>
>
> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute   email:  sc...@eb...
> EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK                 	Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:    http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> Obi-devel mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>