From: Alan R. <ala...@gm...> - 2007-06-28 19:56:25
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It should work now to open the obi.owl file directly in Protege (by clicking on the "open other" button in the welcome to Protege dialog). Until recently one could only open the pprj file directly and had to go through the "create new project" rigamarole if you wanted to open the owl file. We've discovered the problem with the windows setup - the protege bug that was allegedly fixed wasn't fixed for windows. Daniel has the modified owl.repository file we created (like the old owl.repository.template2). When I get it from him, I will put in in the repository and amend the instructions. If you would like to have a phone call before that to set things up, as I did with Daniel, let me know. -Alan On Jun 28, 2007, at 2:50 PM, Liju Fan wrote: > Hi, Daniel. > > Alan's strategy has not worked for me on window, either. I agree > with you that we need to have separate svn spaces for each of us > (Alan, Daniel and myself) to work out independent strategies for > branch merging. This is NOT competition but will save time if one > strategy does not work. My strategy seems to work but is being on > hold because of the current svn set-up and I don't want to mess up > Alan's files. > > I personally believe one should always open obi from the owl file, > not the pprj file. This is because previous Protege versions may > have generated .pprj files that cannot be recognized by the newer > versions. A stable owl file of obi should stand Protege's version > updates. > > Cheers, > Liju > > > > On 6/28/07, J Greenbaum <jg...@gm...> wrote: 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.getInputS >>> t >>> > 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.getReposi >>> t >>> > ory(Unknown Source) >>> > at >>> > >>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.getReposi >>> t >>> > ory(Unknown Source) >>> > at >>> > >>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.runImport >>> ( >>> > Unknown Source) >>> > at >>> > >>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.processIm >>> p >>> > orts(Unknown Source) >>> > at >>> > >>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTripl >>> e >>> > 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.loadKnow >>> l >>> > 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 >>> > 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 >>> > >>> >>> -------------------------------------------------------------------- >>> ----- >>> 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 >>> >>> >>> >>> -- >>> 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 > > > > ---------------------------------------------------------------------- > --- > 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 > > > > > -- > Liju Fan, Ph.D. > Ontology Workshop, LLC > P.O. Box 182 > Columbia, MD 21045-9998 > Phone: (410) 880-8988 > Mobile: (443) 745-7412 > email: lij...@gm... > ---------------------------------------------------------------------- > --- > 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 |