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[protege-owl] Very slow ontology load

Iordanov, Borislav (CIAO) boris at miamidade.gov
Fri Feb 3 13:20:48 PST 2012


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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