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[protege-owl] Very slow ontology load

Iordanov, Borislav (CIAO) boris at miamidade.gov
Fri Feb 3 13:27:00 PST 2012


This is the beginning of the file:

<?xml version="1.0"?>


<!DOCTYPE rdf:RDF [
    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
    <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
    <!ENTITY ontology "http://www.miamidade.gov/ontology#" >
    <!ENTITY skos "http://www.w3.org/2004/02/skos/core#" >
    <!ENTITY xml "http://www.w3.org/XML/1998/namespace" >
    <!ENTITY ontology2 "http://www.miamidade.gov/ontology#311" >
    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
    <!ENTITY amp "http://www.miamidade.gov/ontology#Film_&amp;" >
    <!ENTITY amp2 "http://www.miamidade.gov/ontology#Planning_&amp;"
>
]>


<rdf:RDF xmlns="http://www.miamidade.gov/ontology#"
     xml:base="http://www.miamidade.gov/ontology"
     xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:ontology="http://www.miamidade.gov/ontology#"
     xmlns:amp2="&ontology;Planning_&amp;"
     xmlns:skos="http://www.w3.org/2004/02/skos/core#"
     xmlns:amp="&ontology;Film_&amp;"
     xmlns:ontology2="&ontology;311">
    <owl:Ontology rdf:about="http://www.miamidade.gov/ontology"/>

The rest is just a list of axioms in RDF/XML.

> -----Original Message-----
> From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-
> bounces at lists.stanford.edu] On Behalf Of Iordanov, Borislav (CIAO)
> Sent: Friday, February 03, 2012 4:21 PM
> To: User support for the Protege-OWL editor
> Subject: [protege-owl] Very slow ontology load
> 
> 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(HttpURLConne
> c
> tion.java:1072)
>        - locked <0x000000010a061970> (a
> sun.net.www.protocol.http.HttpURLConnection)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEn
> t
> ity(XMLEntityManager.java:677)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XM
> L
> 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.setInputSourc
> e
> (XMLDTDScannerImpl.java:283)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDrive
> r
> .dispatch(XMLDocumentScannerImpl.java
> 1193)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDrive
> r
> .next(XMLDocumentScannerImpl.java:109
> )
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDr
> i
> ver.next(XMLDocumentScannerImpl.java:
> 003)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XML
> D
> ocumentScannerImpl.java:648)
>        at
>
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.
> s
> canDocument(XMLDocumentFragmentScanne
> Impl.java:510)
>        at
>
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML
> 1
> 1Configuration.java:807)
>        at
>
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML
> 1
> 1Configuration.java:737)
>        at
>
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.ja
> v
> a:107)
>        at
>
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Abst
> r
> actSAXParser.java:1205)
>        at
>
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.par
> s
> 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.getSuggest
> i
> ons(XmlBaseAlgorithm.java:41)
>        at
>
org.protege.editor.owl.model.library.folder.FolderGroupManager.examineD
> i
> skEntries(FolderGroupManager.java:276
> 
>        at
>
org.protege.editor.owl.model.library.folder.FolderGroupManager.examineD
> i
> skEntries(FolderGroupManager.java:285
> 
>        at
>
org.protege.editor.owl.model.library.folder.FolderGroupManager.examineD
> i
> skEntries(FolderGroupManager.java:285
> 
>        at
>
org.protege.editor.owl.model.library.folder.FolderGroupManager.examineD
> i
> skEntries(FolderGroupManager.java:285
> 
>        at
>
org.protege.editor.owl.model.library.folder.FolderGroupManager.update(F
> o
> lderGroupManager.java:128)
>        at
>
org.protege.editor.owl.model.library.OntologyCatalogManager.update(Onto
> l
> ogyCatalogManager.java:159)
>        at
>
org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatal
> o
> gExists(OntologyCatalogManager.java:1
> 6)
>        at
>
org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(O
> n
> tologyCatalogManager.java:189)
>        at
>
org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModel
> M
> anagerImpl.java:357)
>        at
>
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysic
> a
> lURI(OWLModelManagerImpl.java:313)
>        at
>
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:18
> 0
> )
>        at
>
org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKi
> t
> .java:168)
>        at
>
org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(Prot
> e
> geManager.java:200)
>        at
>
org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$6.actio
> n
> Performed(ProtegeWelcomeFrame.java:30
> )
>        at
>
org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:1
> 0
> 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.jav
> a
> :68)
>        at java.awt.Component.processMouseEvent(Component.java:6263)
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