[
https://issues.apache.org/jira/browse/JENA-1025?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14742559#comment-14742559
]
mw james commented on JENA-1025:
--------------------------------
> How is the server being run?
fuseki-server.bat --update --port=3030 --memTDB --set
tdb:unionDefaultGraph=true /db (as indicated by the environment tab)
> How was the dataset created in the first place?
Using cURL via [0] which uses an immediate sync from a wiki page and POST's and
update (delete/insert) to the Fuseki TDB for all involved/changed entities
(Sesame 2.7.14 works fine same dataset on the same server).
> If it was created pre-2.3, then it is possible a timeout was set in the
> configuration; this bug is fixed. Delete the system database and reinstall
> it.
It uses --memTDB which is restarted for each test run.
> What is the data, and how much? It's only a partial sort on a non-returned
> variable so there is a non-determinism in the query; just looking at the
> query is not enough to know what's going on.
I'm not sure how to determine this, we build the turtle set via [0] from the
wiki page content.
> Did you try Fuseki 1.3.0?
The same wiki page (which means the same selected entities) have been
successfully tested with 1.3.0.
The following turtle set [1] (as var dump) caused under some situations (not
always, indeterministic) the above issue but I'm sure it can't be used for
replication without other related data to be present (redirects for property
paths etc.).
A simple query like below caused the same
"org.apache.jena.atlas.AtlasException: SortedDataBag is closed" issue to be
reported.
```
ResponseMapper.php: A SPARQL query error has occurred
Query:
PREFIX wiki: <http://example.org/id/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX swivt: <http://semantic-mediawiki.org/swivt/1.0#>
PREFIX property: <http://example.org/id/Property-3A>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT DISTINCT ?result WHERE {
?result swivt:wikiPageSortKey ?resultsk .
{
?result property:Has_subobject-23aux ?v1 .
?result property:Has_area ?v2 .
} UNION {
?result property:Has_wattage ?v3 .
}
}
ORDER BY ASC(?resultsk)
OFFSET 0
LIMIT 51
Error: Query refused
Endpoint: http://192.168.1.103:3030/db/query
HTTP response code: 500
```
By trying to replicate the issue on a more deterministic way (a full
replication was purposely cancelled in between) another error occurred (not
sure the following error belongs into the same category, well it is brought out
by 2.3) as well:
```
[2015-09-14 01:38:28] Fuseki INFO [1049] Query = PREFIX wiki:
<http://example.org/id/> PRE
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:
<http://www.w3.org/2000/01/rdf-
ma#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX swivt:
<http://semantic-mediawiki.org/
t/1.0#> PREFIX property: <http://example.org/id/Property-3A> PREFIX xsd:
<http://www.w3.org/200
LSchema#> PREFIX category: <http://example.org/id/Category-3A> SELECT * WHERE {
category:Sample
es swivt:wikiPageSortKey ?s OPTIONAL { category:Sample_pages swivt:redirectsTo
?r } } LIMIT 1
[2015-09-14 01:38:28] Fuseki INFO [1049] exec/select
[2015-09-14 01:38:28] Fuseki WARN [1049] Runtime IO Exception (client
left?) RC = 500 : or
lipse.jetty.io.EofException
org.apache.jena.atlas.RuntimeIOException: org.eclipse.jetty.io.EofException
at org.apache.jena.atlas.io.IO.exception(IO.java:216)
at org.apache.jena.atlas.io.IO.flush(IO.java:233)
at
org.apache.jena.atlas.io.BufferingWriter.flush(BufferingWriter.java:153)
at
org.apache.jena.atlas.io.IndentedWriter.flush(IndentedWriter.java:201)
at
org.apache.jena.sparql.resultset.XMLOutputResultSet.finish(XMLOutputResultSet.java:1
at
org.apache.jena.sparql.resultset.ResultSetApply.apply(ResultSetApply.java:53)
at org.apache.jena.sparql.resultset.XMLOutput.format(XMLOutput.java:52)
at
org.apache.jena.query.ResultSetFormatter.outputAsXML(ResultSetFormatter.java:365)
at
org.apache.jena.fuseki.servlets.ResponseResultSet$1.output(ResponseResultSet.java:19
at
org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:303)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.sparqlXMLOutput(ResponseResultSet.
:201)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResul
.java:147)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResult
java:93)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:380)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:256)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:
at
org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:108)
at
org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132)
at
org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet
a:330)
at
org.apache.jena.fuseki.servlets.SPARQL_UberServlet.serviceDispatch(SPARQL_UberServle
va:294)
at
org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.
:255)
at
org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83)
at
org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:79)
at
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:71)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:16
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
)
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.ja
49)
at
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365
at
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:38
at
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilte
va:362)
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java
)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:16
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$3.run(QueuedThreadPool.java:536)
at java.lang.Thread.run(Unknown Source)
Caused by: org.eclipse.jetty.io.EofException
at org.eclipse.jetty.io.ChannelEndPoint.flush(ChannelEndPoint.java:188)
at org.eclipse.jetty.io.WriteFlusher.write(WriteFlusher.java:335)
at
org.eclipse.jetty.io.AbstractEndPoint.write(AbstractEndPoint.java:125)
at
org.eclipse.jetty.server.HttpConnection$CommitCallback.process(HttpConnection.java:5
at
org.eclipse.jetty.util.IteratingCallback.processIterations(IteratingCallback.java:16
at
org.eclipse.jetty.util.IteratingCallback.iterate(IteratingCallback.java:126)
at org.eclipse.jetty.server.HttpConnection.send(HttpConnection.java:296)
at
org.eclipse.jetty.server.HttpChannel.sendResponse(HttpChannel.java:715)
at org.eclipse.jetty.server.HttpChannel.write(HttpChannel.java:751)
at org.eclipse.jetty.server.HttpOutput.write(HttpOutput.java:128)
at org.eclipse.jetty.server.HttpOutput.write(HttpOutput.java:122)
at org.eclipse.jetty.server.HttpOutput.flush(HttpOutput.java:201)
at sun.nio.cs.StreamEncoder.implFlush(Unknown Source)
at sun.nio.cs.StreamEncoder.flush(Unknown Source)
at java.io.OutputStreamWriter.flush(Unknown Source)
... 54 more
Caused by: java.io.IOException: 既存の接続はリモート ホストに強制的に切断されました。
at sun.nio.ch.SocketDispatcher.writev0(Native Method)
at sun.nio.ch.SocketDispatcher.writev(Unknown Source)
at sun.nio.ch.IOUtil.write(Unknown Source)
at sun.nio.ch.SocketChannelImpl.write(Unknown Source)
at org.eclipse.jetty.io.ChannelEndPoint.flush(ChannelEndPoint.java:169)
... 68 more
[2015-09-14 01:38:29] Response WARN Committed before 500
org.eclipse.jetty.io.EofException
[2015-09-14 01:38:29] Fuseki INFO [1049] 500
org.eclipse.jetty.io.EofException (765 ms)
```
[0]
https://github.com/SemanticMediaWiki/SemanticMediaWiki/blob/master/src/SPARQLStore/RepositoryConnector/FusekiHttpRepositoryConnector.php
[1] https://gist.github.com/mwjames/1327834743afd2d416b2
> org.apache.jena.atlas.AtlasException: SortedDataBag is closed, no operations
> can be performed on it
> ---------------------------------------------------------------------------------------------------
>
> Key: JENA-1025
> URL: https://issues.apache.org/jira/browse/JENA-1025
> Project: Apache Jena
> Issue Type: Bug
> Components: Fuseki
> Affects Versions: Fuseki 2.3.0
> Environment: java version "1.8.0_60"
> Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
> Java HotSpot(TM) Client VM (build 25.60-b23, mixed mode)
> fuseki-server.bat --update --port=3030 --memTDB --set tdb:unionDefaultG
> raph=true /db
> [2015-09-13 01:15:08] Server INFO Fuseki 2.3.0 2015-07-25T17:11:28+0000
> [2015-09-13 01:15:12] Config INFO
> FUSEKI_HOME=C:\apache-jena-fuseki-2.3.0\.
> [2015-09-13 01:15:12] Config INFO
> FUSEKI_BASE=C:\apache-jena-fuseki-2.3.0\run
> [2015-09-13 01:15:12] Servlet INFO Initializing Shiro environment
> [2015-09-13 01:15:12] Config INFO Shiro file:
> file://C:\apache-jena-fuseki-2.3.0\run\shiro.ini
> [2015-09-13 01:15:14] Config INFO Template file: templates/config-tdb-mem
> [2015-09-13 01:15:14] Config INFO TDB dataset: in-memory
> [2015-09-13 01:15:24] Config INFO Register: /db
> [2015-09-13 01:15:25] Server INFO Started 2015/09/13 01:15:25 JST on
> port 3030
> Reporter: mw james
>
> This issue occurred with 2.3 (1.1 worked with the same dataset just fine).
> {noformat}
> [2015-09-13 01:09:50] Fuseki INFO [2181] Query = PREFIX wiki:
> <http://example.org/id/> PREFIX
> rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:
> <http://www.w3.org/2000/01/rdf-sche
> ma#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX swivt:
> <http://semantic-mediawiki.org/swiv
> t/1.0#> PREFIX property: <http://example.org/id/Property-3A> PREFIX xsd:
> <http://www.w3.org/2001/XM
> LSchema#> SELECT * WHERE { <http://example.org/id/Berlin/2>
> swivt:wikiPageSortKey ?s OPTIONAL { <h
> ttp://example.org/id/Berlin/2> swivt:redirectsTo ?r } } LIMIT 1
> [2015-09-13 01:09:50] Fuseki INFO [2181] exec/select
> [2015-09-13 01:09:50] Fuseki INFO [2181] 200 OK (95 ms)
> [2015-09-13 01:09:50] Fuseki INFO [2182] POST
> http://192.168.1.103:3030/db/update
> [2015-09-13 01:09:50] Fuseki INFO [2182] POST /db :: 'update' ::
> [application/x-www-form-urlen
> coded charset=UTF-8] ?
> [2015-09-13 01:09:51] Fuseki INFO [2182] 200 OK (324 ms)
> [2015-09-13 01:09:51] Fuseki INFO [2183] POST
> http://192.168.1.103:3030/db/query
> [2015-09-13 01:09:51] Fuseki INFO [2183] POST /db :: 'query' ::
> [application/x-www-form-urlenc
> oded charset=UTF-8] ?
> [2015-09-13 01:09:51] Fuseki INFO [2183] Query = PREFIX wiki:
> <http://example.org/id/> PREFIX
> rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:
> <http://www.w3.org/2000/01/rdf-sche
> ma#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX swivt:
> <http://semantic-mediawiki.org/swiv
> t/1.0#> PREFIX property: <http://example.org/id/Property-3A> PREFIX xsd:
> <http://www.w3.org/2001/XM
> LSchema#> SELECT DISTINCT ?result WHERE { ?result swivt:wikiPageSortKey
> ?resultsk . { ?result prope
> rty:Has_subobject-23aux ?v1 . ?result property:Has_area ?v2 . } UNION {
> ?result property:Has_wattage ?v3 . } } ORDER BY ASC(?resultsk) OFFSET 0
> LIMIT 51
> [2015-09-13 01:09:53] Fuseki WARN [2183] 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.iterator(SortedDataBag.java:195)
> at
> org.apache.jena.atlas.data.SortedDataBag.iterator(SortedDataBag.java:189)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterator.initializeIte
> rator(QueryIterSort.java:98)
> at
> org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init(IteratorDelayedInitial
> ization.java:40)
> at
> org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext(IteratorDelayedInit
> ialization.java:50)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding(QueryIterPla
> inWrapper.java:53)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterConvert.hasNextBinding(QueryIterConvert.
> java:58)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDis
> tinct.java:104)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinc
> t.java:70)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.iterator.QueryIterSlice.hasNextBinding(QueryIterSlice.java
> :76)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIterator
> Wrapper.java:39)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIterator
> Wrapper.java:39)
> at
> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:
> 111)
> at
> org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74)
> at
> org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.ja
> va:59)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:305)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:254)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:212)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:108)
> at
> org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132)
> at
> org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.jav
> a:330)
> at
> org.apache.jena.fuseki.servlets.SPARQL_UberServlet.serviceDispatch(SPARQL_UberServlet.ja
> va:294)
> at
> org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java
> :255)
> at
> org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83)
> at
> org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:79)
> 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:4
> 49)
> at
> org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
> at
> org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
> at
> org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
> at
> org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
> at
> org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.ja
> va:362)
> at
> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125
> )
> at
> org.eclipse.jetty.servlet.ServletHandler$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(Unknown Source)
> [2015-09-13 01:09:54] Fuseki INFO [2183] 500 SortedDataBag is closed, no
> operations can be per
> formed on it. (2.973 s)
> {noformat}
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