Re: [Owlim-discussion] Strange BigOWLIM behaviour when accessing loadedstatements

Mon, 01 Feb 2010 02:46:28 -0800 

Hi Peter,
it looks to me that this exception is due to either corrupted data or a concurrency issue - for some reason the string representation of an URI was not read correctly (invalid file position, etc). How do you process your data? Are you first initialize a new repository, load the data, shutdown it, initialize it again and do the graph fetching, which cause the exception or You just load everything and process it in a single run(same JVM from start to end)? Which ruleset you are using (it could be that for some VERY strange reason we inferred a triple with a literal as subject but this is very unlikely - there are special checks to avoid that)? 


Are you simultaneously add data while fetching from repository (a possible 
concurrency issue)?


regards,
Damyan


----- Original Message ----- 
From: "Peter Kostelnik, PhD." <[email protected]>

To: <[email protected]>
Sent: Friday, January 29, 2010 6:16 PM

Subject: [Owlim-discussion] Strange BigOWLIM behaviour when accessing 
loadedstatements




hi there,

we've getting the really strange exception in BigOWLIM ..
unfortunately, we are not able to reproduce the setup (gigabytes of data),
but the scenario is as follows:

we've loaded the lots of data into repository ..

we need to load the graphs (the set of connected statements) for concrete 
URI

when calling the RepositoryConnection getStatements method, e.g.:

URIImpl base = new URIImpl("http://some.uri.to/fetch/";)
RepositoryResult<Statement> result =
 getStatements(base, null, null, false, null)

we're getting the repository exception:
Error 500 Not a valid (absolute) URI:
??????????????????????????????????????ª???????????????????????????????
full exception: see at the end of this message ..

the same situation happens when trying to call SPARQL query on problem
data ..

the repository connection is remote..

we've no idea, where the problem should be, cause:
1. rio parser is ok with N3 format
2. RDF converter/validator tells - no problem
3. for the same N3 representation, only some of cases caused error (the
totally syntactically same pieces of N3 didn't cause this problem .. we've
found this problem only accidentally)
4. when we load only set of statements causing error into empty
repository, there is no problem (tried in sesame memory store and also
BigOWLIM repository (using the same configuration and template as the
problem case))

there were no error reports or exceptions while loading the content of
repository .. and before the data were loaded, the repository was newly
created, thus not corrupted for sure ..

please, do you have any ideas where can be the problem?

thanks a lot in advance,
                                Peter K.

The full exception trace from server (BigOWLIM is running remotelly)::

HTTP ERROR 500

Problem accessing /itlis/search. Reason:

   <html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 500 Not a valid (absolute) URI:
??????????????????????????????????????ª???????????????????????????????</title>
</head>
<body><h2>HTTP ERROR 500</h2>
<p>Problem accessing /openrdf-sesame/repositories/itlisTest/statements.
Reason:
<pre>    Not a valid (absolute) URI:
??????????????????????????????????????ª???????????????????????????????</pre></p><h3>Caused
by:</h3><pre>java.lang.IllegalArgumentException: Not a valid (absolute)
URI:
??????????????????????????????????????ª???????????????????????????????
at org.openrdf.model.impl.URIImpl.setURIString(URIImpl.java:68)
at org.openrdf.model.impl.URIImpl.&lt;init&gt;(URIImpl.java:57)
at com.ontotext.trree.t.toObject(Unknown Source)
at com.ontotext.trree.e.if(Unknown Source)
at com.ontotext.trree.e.toString(Unknown Source)
at org.openrdf.rio.turtle.TurtleWriter.writeURI(TurtleWriter.java:320)

at 
org.openrdf.rio.turtle.TurtleWriter.writeResource(TurtleWriter.java:310)

at
org.openrdf.rio.turtle.TurtleWriter.handleStatement(TurtleWriter.java:217)
at org.openrdf.rio.trig.TriGWriter.handleStatement(TriGWriter.java:129)
at
org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:202)
at
org.openrdf.http.server.repository.statements.ExportStatementsView.render(ExportStatementsView.java:99)
at
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1160)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:901)
at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:809)
at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
at
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
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.security.SecurityHandler.handle(SecurityHandler.java:216)

at 
org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at 
org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)

at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at
org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:230)
at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)

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$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
</pre>
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</body>
</html>

Caused by:

org.openrdf.repository.RepositoryException: <html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 500 Not a valid (absolute) URI:
??????????????????????????????????????ª???????????????????????????????</title>
</head>
<body><h2>HTTP ERROR 500</h2>
<p>Problem accessing /openrdf-sesame/repositories/itlisTest/statements.
Reason:
<pre>    Not a valid (absolute) URI:
??????????????????????????????????????ª???????????????????????????????</pre></p><h3>Caused
by:</h3><pre>java.lang.IllegalArgumentException: Not a valid (absolute)
URI:
??????????????????????????????????????ª???????????????????????????????
at org.openrdf.model.impl.URIImpl.setURIString(URIImpl.java:68)
at org.openrdf.model.impl.URIImpl.&lt;init&gt;(URIImpl.java:57)
at com.ontotext.trree.t.toObject(Unknown Source)
at com.ontotext.trree.e.if(Unknown Source)
at com.ontotext.trree.e.toString(Unknown Source)
at org.openrdf.rio.turtle.TurtleWriter.writeURI(TurtleWriter.java:320)

at 
org.openrdf.rio.turtle.TurtleWriter.writeResource(TurtleWriter.java:310)

at
org.openrdf.rio.turtle.TurtleWriter.handleStatement(TurtleWriter.java:217)
at org.openrdf.rio.trig.TriGWriter.handleStatement(TriGWriter.java:129)
at
org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:202)
at
org.openrdf.http.server.repository.statements.ExportStatementsView.render(ExportStatementsView.java:99)
at
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1160)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:901)
at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:809)
at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
at
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
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.security.SecurityHandler.handle(SecurityHandler.java:216)

at 
org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at 
org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)

at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at
org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:230)
at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)

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$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
</pre>
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</body>
</html>
at org.openrdf.http.client.HTTPClient.getRDF(HTTPClient.java:1066)
at org.openrdf.http.client.HTTPClient.getStatements(HTTPClient.java:536)
at
org.openrdf.repository.http.HTTPRepositoryConnection.exportStatements(HTTPRepositoryConnection.java:199)
at
org.openrdf.repository.http.HTTPRepositoryConnection.getStatements(HTTPRepositoryConnection.java:185)
at
eu.itlis.repository.OwlimRepository.collectRecordStatements(OwlimRepository.scala:159)

at 
eu.itlis.repository.OwlimRepository.getRecord(OwlimRepository.scala:173)

at
eu.itlis.repository.OwlimRepository$$anonfun$personsForNames$1.apply(OwlimRepository.scala:48)
at
eu.itlis.repository.OwlimRepository$$anonfun$personsForNames$1.apply(OwlimRepository.scala:47)
at scala.List.map(List.scala:812)
at
eu.itlis.repository.OwlimRepository.personsForNames(OwlimRepository.scala:47)
at eu.itlis.webui.Search.findPersons(Search.scala:189)
at eu.itlis.webui.Search$$anonfun$5.apply(Search.scala:154)
at eu.itlis.webui.Search$$anonfun$5.apply(Search.scala:154)
at eu.itlis.webui.Page.toString(Page.scala:18)
at eu.itlis.webui.Search.doGet(Search.scala:156)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
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.security.SecurityHandler.handle(SecurityHandler.java:216)

at 
org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
at 
org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)

at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
at
org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:230)
at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)

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$RequestHandler.headerComplete(HttpConnection.java:923)
at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)

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