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[protege-owl] Very slow ontology load

Iordanov, Borislav (CIAO) boris at miamidade.gov
Fri Feb 3 20:49:09 PST 2012


Timothy,

Thanks so much, that fixed it! I was short of debugging Protege's source
code, after a several frustrating hours of trial and error, re-install
and re-start and re-configure and what not. 

Best,
Boris

> -----Original Message-----
> From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-
> bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
> Sent: Friday, February 03, 2012 6:29 PM
> To: protege-owl at lists.stanford.edu
> Subject: Re: [protege-owl] Very slow ontology load
> 
> 
> The problem is occurring when Protege is scanning the directory for
> possible imports.  This problem occurs when some file in the directory
> containing the OWL file or one of its sub-directories contains DTD
> information.  When Protege scans the disk for files on the disk that
> can be imported, it runs into trouble with these files.  The problem
> occurs even when loading a file that has no import statements.  This
is
> a known bug and needs to be fixed.
> 
> There are two workarounds - you can move the OWL file to a different
> directory so that Protege does not find the XML files with the DTD.
Or
> you can disable/control the way that Protege scans the disk by
> replacing the catalog-v001.xml file with an empty one (attached).
> 
> I added a GForge for this item (http://goo.gl/EIMuJ).
> 
> -Timothy
> 
> 
> On 2/3/12 1:20 PM, Iordanov, Borislav (CIAO) wrote:
> > Hi,
> >
> > I have downloaded and installed a fresh copy of Protege 4.1 release.
> I
> > load a relatively small ontology (under 1MB in RDF/XML) and takes
> > 10-15 minutes to load. I tried "Save As" in OWL Functional Syntax,
> > after it eventually opens, but then it's not even able to read it,
> > throwing a parser exception on the file that it had saved itself!
> >
> > Doing Ctrl-Break on the MS-DOS console reveals that it's stuck on
> > reading from some HTTP connection (see below). Why would it want to
> > open an HTTP connection? There are no imports, no DTD, nothing
> > special. I have configured the proxy server in Protege.lax, but that
> didn't help.
> >
> > Any ideas?
> > Thanks!
> > Boris
> >
> > AWT-EventQueue-0" prio=6 tid=0x0000000008762800 nid=0x558 runnable
> > [0x000000000850d000]
> >
> >    java.lang.Thread.State: RUNNABLE
> >         at java.net.SocketInputStream.socketRead0(Native Method)
> >         at
> java.net.SocketInputStream.read(SocketInputStream.java:129)
> >         at
> java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
> >         at
> > java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
> >         at
> java.io.BufferedInputStream.read(BufferedInputStream.java:317)
> >         - locked<0x000000010a06c538>  (a
java.io.BufferedInputStream)
> >         at
> > sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:687)
> >         at
sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:632)
> >         at
> >
> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConn
> > ec
> > tion.java:1072)
> >         - locked<0x000000010a061970>  (a
> > sun.net.www.protocol.http.HttpURLConnection)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentE
> > nt
> > ity(XMLEntityManager.java:677)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(X
> > ML
> > EntityManager.java:1315)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntit
> > y(
> > XMLEntityManager.java:1282)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSour
> > ce
> > (XMLDTDScannerImpl.java:283)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriv
> > er
> > .dispatch(XMLDocumentScannerImpl.java
> > 1193)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriv
> > er
> > .next(XMLDocumentScannerImpl.java:109
> > )
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologD
> > ri
> > ver.next(XMLDocumentScannerImpl.java:
> > 003)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XM
> > LD
> > ocumentScannerImpl.java:648)
> >         at
> >
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
> > .s
> > canDocument(XMLDocumentFragmentScanne
> > Impl.java:510)
> >         at
> >
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XM
> > L1
> > 1Configuration.java:807)
> >         at
> >
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XM
> > L1
> > 1Configuration.java:737)
> >         at
> >
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.j
> > av
> > a:107)
> >         at
> >
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Abs
> > tr
> > actSAXParser.java:1205)
> >         at
> >
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.pa
> > rs
> > e(SAXParserImpl.java:522)
> >         at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
> >         at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
> >         at
> >
> org.protege.editor.owl.model.library.folder.XmlBaseAlgorithm.getSugges
> > ti
> > ons(XmlBaseAlgorithm.java:41)
> >         at
> >
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examine
> > Di
> > skEntries(FolderGroupManager.java:276
> >
> >         at
> >
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examine
> > Di
> > skEntries(FolderGroupManager.java:285
> >
> >         at
> >
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examine
> > Di
> > skEntries(FolderGroupManager.java:285
> >
> >         at
> >
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examine
> > Di
> > skEntries(FolderGroupManager.java:285
> >
> >         at
> >
> org.protege.editor.owl.model.library.folder.FolderGroupManager.update(
> > Fo
> > lderGroupManager.java:128)
> >         at
> >
> org.protege.editor.owl.model.library.OntologyCatalogManager.update(Ont
> > ol
> > ogyCatalogManager.java:159)
> >         at
> >
> org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCata
> > lo
> > gExists(OntologyCatalogManager.java:1
> > 6)
> >         at
> >
> org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(
> > On
> > tologyCatalogManager.java:189)
> >         at
> >
> org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLMode
> > lM
> > anagerImpl.java:357)
> >         at
> >
> org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysi
> > ca
> > lURI(OWLModelManagerImpl.java:313)
> >         at
> >
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:1
> > 80
> > )
> >         at
> >
> org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorK
> > it
> > .java:168)
> >         at
> >
> org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(Pro
> > te
> > geManager.java:200)
> >         at
> >
> org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$6.acti
> > on
> > Performed(ProtegeWelcomeFrame.java:30
> > )
> >         at
> >
> org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:
> > 10
> > 2)
> >         at
> >
>
org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
> >         at
> >
> org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.ja
> > va
> > :68)
> >         at java.awt.Component.processMouseEvent(Component.java:6263)
> > _______________________________________________
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> > protege-owl at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
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