Re: "Transaction has already committed or aborted" while posting data

Thu, 11 Mar 2021 05:34:51 -0800

Looks similar to JENA-2055. An exception in the operation not handled very well.
It looks like problem in the data (e.g. a syntax error at about the count length) and the recovery throws an exception recovering (c.f. JENA-2055). The data is not committed, the system should still be operational. (it's a WARN, not ERROR). 


It should be handled in a neater fashion - could you let us know what 
the data problem is and it can be handled better.


    Andy

On 11/03/2021 12:41, Mikael Pesonen wrote:



I'm posting into Fuseki (3.17) a 75Mb turtle file with command line curl 
and get this error. What might be the cause and how to fix this?



14:31:40 INFO  Fuseki          :: [1] Body: Content-Length=78221624, 
Content-Type=text/turtle, Charset=null => Turtle : Count=1099567 
Triples=1099567 Quads=0
14:31:45 WARN  HttpAction      :: Transaction still active - no commit 
or abort seen (forced abort)
14:31:45 WARN  HttpAction      :: Exception in forced abort (trying to 
continue)
org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has 
already committed or aborted
         at 
org.apache.jena.tdb.transaction.Transaction.abort(Transaction.java:305) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.tdb.transaction.DatasetGraphTxn.abort(DatasetGraphTxn.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.tdb.transaction.DatasetGraphTransaction.abort(DatasetGraphTransaction.java:208) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.sparql.core.DatasetGraphWrapper.abort(DatasetGraphWrapper.java:275) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.query.text.DatasetGraphText.lambda$new$1(DatasetGraphText.java:59) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.query.text.DatasetGraphText.abort(DatasetGraphText.java:192) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.HttpAction.end(HttpAction.java:300) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.addDataIntoTxn(GSP_RW.java:184) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.doPutPostGSP(GSP_RW.java:129) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.execPostGSP(GSP_RW.java:78) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.doPost(GSP_RW.java:75) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.doPost$(ActionREST.java:102) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.execute(ActionREST.java:51) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:58) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.execAny(ActionREST.java:165) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionProcessor.execPost(ActionProcessor.java:48) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionProcessor.process(ActionProcessor.java:34) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionBase.process(ActionBase.java:55) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionExecLib.execAction(ActionExecLib.java:106) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.dispatchAction(Dispatcher.java:118) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.process(Dispatcher.java:110) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.dispatch(Dispatcher.java:96) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:51) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:284) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:247) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1612) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501) ~[fuseki-server.jar:3.17.0] 

         at 
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1582) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:716) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) 
~[fuseki-server.jar:3.17.0]
         at org.eclipse.jetty.server.Server.handle(Server.java:516) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:556) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) 
[fuseki-server.jar:3.17.0]

         at java.lang.Thread.run(Thread.java:832) [?:?]

14:31:45 WARN  Fuseki          :: [1] RC = 500 : Transaction has already 
committed or aborted
org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has 
already committed or aborted
         at 
org.apache.jena.tdb.transaction.Transaction.abort(Transaction.java:305) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.tdb.transaction.DatasetGraphTxn.abort(DatasetGraphTxn.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.tdb.transaction.DatasetGraphTransaction.abort(DatasetGraphTransaction.java:208) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.sparql.core.DatasetGraphWrapper.abort(DatasetGraphWrapper.java:275) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.query.text.DatasetGraphText.lambda$new$1(DatasetGraphText.java:59) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.query.text.DatasetGraphText.end(DatasetGraphText.java:284) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.HttpAction.end(HttpAction.java:306) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.addDataIntoTxn(GSP_RW.java:184) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.doPutPostGSP(GSP_RW.java:129) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.execPostGSP(GSP_RW.java:78) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.GSP_RW.doPost(GSP_RW.java:75) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.doPost$(ActionREST.java:102) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.execute(ActionREST.java:51) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:58) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionREST.execAny(ActionREST.java:165) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionProcessor.execPost(ActionProcessor.java:48) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionProcessor.process(ActionProcessor.java:34) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionBase.process(ActionBase.java:55) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.ActionExecLib.execAction(ActionExecLib.java:106) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.dispatchAction(Dispatcher.java:118) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.process(Dispatcher.java:110) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.server.Dispatcher.dispatch(Dispatcher.java:96) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:51) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:284) 
~[fuseki-server.jar:3.17.0]
         at 
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:247) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1612) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501) ~[fuseki-server.jar:3.17.0] 

         at 
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1582) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:716) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) 
~[fuseki-server.jar:3.17.0]
         at org.eclipse.jetty.server.Server.handle(Server.java:516) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383) 
~[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:556) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) 
[fuseki-server.jar:3.17.0]
         at 
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) 
[fuseki-server.jar:3.17.0]

         at java.lang.Thread.run(Thread.java:832) [?:?]
14:31:45 INFO  Fuseki          :: [1] 500 Server Error (30.937 s)























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