Re: Ontonet scope manager Upload of Ontologies

Tue, 07 Aug 2012 04:40:17 -0700

I finally could reproduce the issue, appended logfile 'prgProblem.log' to https://issues.apache.org/jira/browse/STANBOL-422 . 

Am 07.08.2012 13:18, schrieb Melanie Reiplinger:

Hi Alessandro.
About the 'OutOfMemoryError: GC overhead limit exceeded' it might helpt to specify a larger heap size when launching stanbol? 
What do you usually pass as parameters when launching?
Anyway it is a bit weird that this problem never showed up during the last few days when I was uploading ontologies and libraries (and I always used the same 1-2 ontologies and libs in my samples because I know that they are stored permanently.
I wanted to kill and restart stanbol, but the process didn't die. There was one of my testing curl PUT commands hanging in the list of my processes for about the last hour. I killed it, but still I could not kill stanbol. A kill -9 succeeded, but no shutdown messages were written to the log any more.
This is very much like the behaviour when we had the 'too many open files' error for ontologies.
After the restart I can create scopes again, so I will now try to reproduce the redirect/get problem and upload the log file to JIRA. 


Am 07.08.2012 12:02, schrieb Melanie Reiplinger:

Am 06.08.2012 17:47, schrieb Alessandro Adamou:
Then I think I'm going to need a detailed log. That also says something about the time taken for loading ontologies and stuff. Would you mind setting up a "Debug" logger for the ontology manager classes before you try loading an ontology again? 

To do so,

1. go to [stanbol]/system/console/configMgr with your browser
2. create a new "Apache Sling Logging Logger Configuration" (click on the "+" button) 3. Set log level to "Debug", give the log file the name you want and for "Logger" type "org.apache.stanbol.ontologymanager" 
4. Click "Save"
5. do your stuff (e.g. upload an ontology onto a scope, do a GET afterwards) 6. Post the new logfile as an attachment of ticket https://issues.apache.org/jira/browse/STANBOL-422
We might need to increase the log verbosity incrementally and produce further logs, so I'll keep you posted after that.
JIRA is unavailable, so I append the logs below (sorry for this format). This is really strange now, because since a few minutes, it won't even create new scopes. It fails with a time out error. Until an hour or so it would create scopes and then fail when trying the redirected GET after loading an ontology or a library, but now nothing seems to work anymore. I did not change the code, though; and I kept deleting scopes as soon as they weren't needed any more in order to not overcharge the service.
The whole stanbol REST interface has gotten really slow again, waiting minutes for loading of pages. So this might then be the reason for the new timeouts in places where they had't been before, but there has to be something wrong then. Also the curl commands (e.g. to delete a scope) take several minuts. At least, the disc space consumption is stable this time.
These logs are from an attempted PUT done via jQuery ajax call, where I try to create a scope named paramScope and upload a library and an ontology at creation. Below, separated by -----------, there are usual logs from stanbol I get, some of them talk about out of space exceptions
07.08.2012 12:36:13.854 *INFO* [11482418@qtp-746842-244] org.apache.stanbol.ontologymanager.web.resources.ScopeResource <init> with scope paramScope 07.08.2012 12:36:23.616 *INFO* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.web.resources.ScopeResource <init> with scope paramScope 07.08.2012 12:36:23.621 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.web.resources.ScopeResource Request URI http://lnv-89012.dfki.uni-sb.de:9001/ontonet/ontology/paramScope?corereg=http://stanbol.apache.org/ontologies/registries/stanbol_network/SocialNetworks&coreont=http://www.ontologydesignpatterns.org/cp/owl/sequence.owl&; 07.08.2012 12:36:23.622 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.registry.io.LibrarySource Got library SocialNetworks, expected http://stanbol.apache.org/ontologies/registries/stanbol_network/SocialNetworks 07.08.2012 12:36:23.622 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.registry.impl.RegistryManagerImpl In class org.apache.stanbol.ontologymanager.registry.impl.RegistryManagerImpl registry content was requested on SocialNetworks. 07.08.2012 12:36:33.448 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://purl.org/stuff/rev> is <ontonet::http://purl.org/stuff/rev> 07.08.2012 12:36:33.449 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider Filling reverse imports for <http://purl.org/stuff/rev> 07.08.2012 12:36:33.449 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://purl.org/stuff/rev> is <ontonet::http://purl.org/stuff/rev> 07.08.2012 12:37:36.016 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://purl.org/net/provenance/ns> is <ontonet::http://purl.org/net/provenance/ns> 07.08.2012 12:37:36.016 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider Filling reverse imports for <http://purl.org/net/provenance/ns> 07.08.2012 12:37:36.017 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://purl.org/net/provenance/ns> is <ontonet::http://purl.org/net/provenance/ns> 07.08.2012 12:37:36.111 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://www.holygoat.co.uk/owl/redwood/0.1/tags/> is <ontonet::http://www.holygoat.co.uk/owl/redwood/0.1/tags/> 07.08.2012 12:37:36.112 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider Filling reverse imports for <http://www.holygoat.co.uk/owl/redwood/0.1/tags/> 07.08.2012 12:37:36.112 *DEBUG* [23544983@qtp-746842-247] org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider key for <http://www.holygoat.co.uk/owl/redwood/0.1/tags/> is <ontonet::http://www.holygoat.co.uk/owl/redwood/0.1/tags/>
----------------------------------------------------------------------------
Aug 7, 2012 11:15:59 AM com.sun.jersey.spi.container.servlet.WebComponent filterFormParameters WARNING: A servlet POST request, to the URI http://lnv-89012.dfki.uni-sb.de:9001/contenthub/ldpath/program, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected. Aug 7, 2012 11:16:30 AM com.sun.jersey.spi.container.servlet.WebComponent filterFormParameters WARNING: A servlet POST request, to the URI http://lnv-89012.dfki.uni-sb.de:9001/contenthub/ldpath/program, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected. Aug 7, 2012 11:16:42 AM com.sun.jersey.spi.container.ContainerResponse logException 
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException: com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:751) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:96) at org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:79) at org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:42) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:49) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:78) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:75) at org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:88) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:76) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:48) at org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:39) at org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) 
    at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:926) 
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) Caused by: com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:45) at com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:35) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:225) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.fatalError(XMLHandler.java:255) at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) 
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:142) 
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:158)
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:145)
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:215)
    at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:226)
at org.apache.clerezza.rdf.jena.parser.JenaParserProvider.parse(JenaParserProvider.java:68) at org.apache.stanbol.commons.owl.transformation.OWLAPIToClerezzaConverter.owlOntologyToClerezzaMGraph(OWLAPIToClerezzaConverter.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.loadInStore(ClerezzaOntologyProvider.java:953) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.AbstractOntologyCollectorImpl.addOntology(AbstractOntologyCollectorImpl.java:147) at org.apache.stanbol.ontologymanager.ontonet.impl.ontology.OntologyScopeImpl.<init>(OntologyScopeImpl.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl.createOntologyScope(ONManagerImpl.java:390) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:743) 
    ... 48 more
Caused by: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) 
    ... 75 more
Aug 7, 2012 11:16:46 AM com.sun.jersey.spi.container.servlet.WebComponent filterFormParameters WARNING: A servlet POST request, to the URI http://lnv-89012.dfki.uni-sb.de:9001/contenthub/ldpath/program, contains form parameters in the request body but the request body has been consumed by the servlet or a servlet filter accessing the request parameters. Only resource methods using @FormParam will work as expected. Resource methods consuming the request body by other means will not work as expected. Aug 7, 2012 11:33:35 AM com.sun.jersey.spi.container.ContainerResponse logException 
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException: java.util.ConcurrentModificationException at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:751) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:96) at org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:79) at org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:42) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:49) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:78) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:75) at org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:88) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:76) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:48) at org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:39) at org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) 
    at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:926) 
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) 
Caused by: java.util.ConcurrentModificationException
at com.hp.hpl.jena.tdb.store.GraphTDBBase$MapperIteratorTriples.checkCourrentModification(GraphTDBBase.java:208) at com.hp.hpl.jena.tdb.store.GraphTDBBase$MapperIteratorTriples.hasNext(GraphTDBBase.java:216) at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.hasNext(JenaGraphAdaptor.java:106) at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.hasNext(AbstractTripleCollection.java:78) at org.apache.clerezza.rdf.core.access.LockingIterator.hasNext(LockingIterator.java:47) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider$OntologyToTcMapper.mapLocator(ClerezzaOntologyProvider.java:299) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.setLocatorMapping(ClerezzaOntologyProvider.java:1285) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.AbstractOntologyCollectorImpl.addOntology(AbstractOntologyCollectorImpl.java:154) at org.apache.stanbol.ontologymanager.ontonet.impl.ontology.OntologyScopeImpl.<init>(OntologyScopeImpl.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl.createOntologyScope(ONManagerImpl.java:390) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:743) 
    ... 48 more
Aug 7, 2012 12:10:37 PM com.sun.jersey.spi.container.ContainerResponse logException 
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException: java.lang.NullPointerException
at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:751) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:96) at org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:79) at org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:42) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:49) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:78) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:75) at org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:88) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:76) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:48) at org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:39) at org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) 
    at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:926) 
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) 
Caused by: java.lang.NullPointerException
at org.apache.stanbol.commons.owl.util.OWLUtils.guessOntologyIdentifier(OWLUtils.java:76) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.loadInStore(ClerezzaOntologyProvider.java:967) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.AbstractOntologyCollectorImpl.addOntology(AbstractOntologyCollectorImpl.java:147) at org.apache.stanbol.ontologymanager.ontonet.impl.ontology.OntologyScopeImpl.<init>(OntologyScopeImpl.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl.createOntologyScope(ONManagerImpl.java:390) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:743) 
    ... 48 more
Aug 7, 2012 12:10:37 PM com.sun.jersey.spi.container.ContainerResponse logException 
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException: com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:751) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:96) at org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:79) at org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:42) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:49) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:78) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:75) at org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:88) at org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:76) at org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:47) at org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:33) at org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:48) at org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:39) at org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67) 
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) 
    at org.mortbay.jetty.Server.handle(Server.java:326)
at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:926) 
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) Caused by: com.hp.hpl.jena.shared.JenaException: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:45) at com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:35) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:225) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.fatalError(XMLHandler.java:255) at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) 
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:142) 
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:158)
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:145)
    at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:215)
    at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:226)
at org.apache.clerezza.rdf.jena.parser.JenaParserProvider.parse(JenaParserProvider.java:68) at org.apache.stanbol.commons.owl.transformation.OWLAPIToClerezzaConverter.owlOntologyToClerezzaMGraph(OWLAPIToClerezzaConverter.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.loadInStore(ClerezzaOntologyProvider.java:953) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.AbstractOntologyCollectorImpl.addOntology(AbstractOntologyCollectorImpl.java:147) at org.apache.stanbol.ontologymanager.ontonet.impl.ontology.OntologyScopeImpl.<init>(OntologyScopeImpl.java:106) at org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl.createOntologyScope(ONManagerImpl.java:390) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:743) 
    ... 48 more
Caused by: org.xml.sax.SAXParseException: The prefix "xmlns" cannot be bound to any namespace explicitly; neither can the namespace for "xmlns" be bound to any prefix explicitly. at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) 
    ... 75 more
Aug 7, 2012 12:33:43 PM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The exception contained within MappableContainerException could not be mapped to a response, re-throwing to the HTTP container 
java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOf(Arrays.java:2894)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:117) at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:407) 
    at java.lang.StringBuffer.append(StringBuffer.java:241)
    at java.io.StringWriter.write(StringWriter.java:112)
    at java.io.PrintWriter.write(PrintWriter.java:429)
    at java.io.PrintWriter.write(PrintWriter.java:446)
    at java.io.PrintWriter.append(PrintWriter.java:977)
at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.printTriple(OWLRDFConsumer.java:1251) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.dumpRemainingTriples(OWLRDFConsumer.java:1288) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1409) at org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:174) at org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120) at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:688) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:700) at org.apache.stanbol.commons.owl.transformation.OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(OWLAPIToClerezzaConverter.java:152) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.toOWLOntology(ClerezzaOntologyProvider.java:1320) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:821) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:782) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:773) at org.apache.stanbol.ontologymanager.registry.impl.model.LibraryImpl.getOntologies(LibraryImpl.java:114) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:163) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:123) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:81) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:712) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) Aug 7, 2012 12:37:31 PM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The exception contained within MappableContainerException could not be mapped to a response, re-throwing to the HTTP container 
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.addAxiom(OWLRDFConsumer.java:824) at org.coode.owlapi.rdfxml.parser.AbstractTripleHandler.addAxiom(AbstractTripleHandler.java:121) at org.coode.owlapi.rdfxml.parser.GTPAnnotationResourceTripleHandler.handleTriple(GTPAnnotationResourceTripleHandler.java:105) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.handle(OWLRDFConsumer.java:1230) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer$1.handleResourceTriple(OWLRDFConsumer.java:1361) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.iterateResourceTriples(OWLRDFConsumer.java:2334) at org.coode.owlapi.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1359) at org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:174) at org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120) at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:688) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:700) at org.apache.stanbol.commons.owl.transformation.OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(OWLAPIToClerezzaConverter.java:152) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.toOWLOntology(ClerezzaOntologyProvider.java:1320) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:821) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:782) at org.apache.stanbol.ontologymanager.ontonet.impl.clerezza.ClerezzaOntologyProvider.getStoredOntology(ClerezzaOntologyProvider.java:773) at org.apache.stanbol.ontologymanager.registry.impl.model.LibraryImpl.getOntologies(LibraryImpl.java:114) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:163) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:123) at org.apache.stanbol.ontologymanager.registry.io.LibrarySource.<init>(LibrarySource.java:81) at org.apache.stanbol.ontologymanager.web.resources.ScopeResource.registerScope(ScopeResource.java:712) 
    at sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
    at java.lang.reflect.Method.invoke(Method.java:616)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)

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