SortedDataBag is closed, no operations can be performed on it. - Fuseki 2

[Paul Worrall <pa...@interition.net>]

Hi

TIA

I am trying Fuseki 2.  I encountered the issue with the query timeout default being too small for UI created datasets. I noticed that a JIRA had been raised and closed for it but nothing has yet been released since 2.0. So I cloned the Jena git repo and built it to produce apache-jena-fuseki-2.3.0-SNAPSHOT.zip. I installed and configured.

I created one dataset using the UI and loaded 3m triples into it in 14 graphs.  I wanted to get a list of the graphs. Although the following query works with a limit of 14 anything after 15 causes the error below.

Query:

SELECT distinct ?g WHERE {
  graph ?g {
    ?s ?p ?o .
  }
} limit 15


Log:

[2015-05-20 17:50:32] Fuseki     WARN  [117] RC = 500 : SortedDataBag is closed, no operations can be performed on it.
org.apache.jena.atlas.AtlasException: SortedDataBag is closed, no operations can be performed on it.
	at org.apache.jena.atlas.data.SortedDataBag.checkClosed(SortedDataBag.java:87)
	at org.apache.jena.atlas.data.SortedDataBag.add(SortedDataBag.java:105)
	at org.apache.jena.atlas.data.DistinctDataNet.netAdd(DistinctDataNet.java:58)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIterDistinct.isFreshSighting(QueryIterDistinct.java:66)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIterDistinctReduced.hasNextBinding(QueryIterDistinctReduced.java:61)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIterSlice.hasNextBinding(QueryIterSlice.java:76)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
	at com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
	at com.hp.hpl.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:75)
	at com.hp.hpl.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.java:59)
	at com.hp.hpl.jena.sparql.resultset.ResultSetApply.apply(ResultSetApply.java:41)
	at com.hp.hpl.jena.sparql.resultset.JSONOutput.format(JSONOutput.java:36)
	at com.hp.hpl.jena.query.ResultSetFormatter.outputAsJSON(ResultSetFormatter.java:560)
	at org.apache.jena.fuseki.servlets.ResponseResultSet$2.output(ResponseResultSet.java:212)
	at org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:304)
	at org.apache.jena.fuseki.servlets.ResponseResultSet.jsonOutput(ResponseResultSet.java:230)
	at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:150)
	at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:94)
	at org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:376)
	at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:257)
	at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:213)
	at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:109)
	at org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:130)
	at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.serviceDispatch(SPARQL_UberServlet.java:324)
	at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:235)
	at org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:84)
	at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:81)
	at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:71)
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1632)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
	at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
	at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
	at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
	at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1624)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:550)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:568)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1110)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:479)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:183)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1044)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
	at org.eclipse.jetty.server.Server.handle(Server.java:459)
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:281)
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:232)
	at org.eclipse.jetty.io.AbstractConnection$1.run(AbstractConnection.java:505)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:607)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:536)
	at java.lang.Thread.run(Thread.java:745)
[2015-05-20 17:50:32] Fuseki     INFO  [117] 500 SortedDataBag is closed, no operations can be performed on it. (3.002 s)





Paul Worrall
Interition: wisdom in the web

Re: [Bulk] Re: SortedDataBag is closed, no operations can be performed on it. - Fuseki 2

[Paul Worrall <pa...@interition.net>]

When I do it the way you suggest it works ok. I hope the dummy way I did it uncovered a problem that will be useful to solve :-)

thanks


On 20 May 2015, at 21:21, Andy Seaborne <an...@apache.org> wrote:

> On 20/05/15 17:03, Paul Worrall wrote:
>> SELECT distinct ?g WHERE {
>>   graph ?g {
>>     ?s ?p ?o .
>>   }
> 
> The query you are looking for is
> 
> SELECT ?g WHERE { GRAPH ?g {} }
> 
> not that the one you gave shouldn't at least work (eventually).
> 
> Recorded as JENA-949
> 
> 	Andy
> 

Re: SortedDataBag is closed, no operations can be performed on it. - Fuseki 2

[Andy Seaborne <an...@apache.org>]

On 20/05/15 17:03, Paul Worrall wrote:
> SELECT distinct ?g WHERE {
>    graph ?g {
>      ?s ?p ?o .
>    }

The query you are looking for is

SELECT ?g WHERE { GRAPH ?g {} }

not that the one you gave shouldn't at least work (eventually).

Recorded as JENA-949

	Andy

Re: SortedDataBag is closed, no operations can be performed on it. - Fuseki 2

[Andy Seaborne <an...@apache.org>]

On 20/05/15 17:03, Paul Worrall wrote:
> So I cloned the Jena git repo and built it to produce apache-jena-fuseki-2.3.0-SNAPSHOT.zip. I installed and configured.

Aside:
development builds are built daily:

https://repository.apache.org/content/repositories/snapshots/org/apache/jena/jena-fuseki/

	Andy