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[protege-owl] Very slow ontology load

Timothy Redmond tredmond at stanford.edu
Fri Feb 3 15:29:11 PST 2012


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(HttpURLConnec
> tion.java:1072)
>         - locked<0x000000010a061970>  (a
> sun.net.www.protocol.http.HttpURLConnection)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEnt
> ity(XMLEntityManager.java:677)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XML
> EntityManager.java:1315)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(
> XMLEntityManager.java:1282)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource
> (XMLDTDScannerImpl.java:283)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver
> .dispatch(XMLDocumentScannerImpl.java
> 1193)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver
> .next(XMLDocumentScannerImpl.java:109
> )
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDri
> ver.next(XMLDocumentScannerImpl.java:
> 003)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLD
> ocumentScannerImpl.java:648)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.s
> canDocument(XMLDocumentFragmentScanne
> Impl.java:510)
>         at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML1
> 1Configuration.java:807)
>         at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML1
> 1Configuration.java:737)
>         at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.jav
> a:107)
>         at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Abstr
> actSAXParser.java:1205)
>         at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.pars
> 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.getSuggesti
> ons(XmlBaseAlgorithm.java:41)
>         at
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDi
> skEntries(FolderGroupManager.java:276
>
>         at
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDi
> skEntries(FolderGroupManager.java:285
>
>         at
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDi
> skEntries(FolderGroupManager.java:285
>
>         at
> org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDi
> 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(Ontol
> ogyCatalogManager.java:159)
>         at
> org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalo
> 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(OWLModelM
> anagerImpl.java:357)
>         at
> org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysica
> lURI(OWLModelManagerImpl.java:313)
>         at
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:180
> )
>         at
> org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit
> .java:168)
>         at
> org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(Prote
> geManager.java:200)
>         at
> org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$6.action
> 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.java
> :68)
>         at java.awt.Component.processMouseEvent(Component.java:6263)
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