[Ambra-dev] horrifying errors when attempting to add a volume and issue to new journal

Thu Mar 26 13:05:31 PDT 2009

howdy.

we're having trouble adding volumes and issues to plosmedicine, on
version 0.9.1, which has no volumes and issues configured yet.

one user was able to create a volume, while others got errors.

another user was able to create an issue in that volume.

however, when we tried to add articles to the issue, an error was
returned and the issue disappeared.

now, the volume has the following as it's issue string:
"rmi://ploskow01.localdomain:8111/topazproject". looks like someone
forgot to escape a tql query somewhere.

any additional attempts to set the issue string for the existing volume
empty, or delete the corrupt volume, fail.

the errors for these actions have similar "caused by" lines:

Caused by: java.io.IOException: Error running update 'delete select
Caused by: org.mulgara.query.QueryException: Unable to modify
local:///topazproject#filter:graph=ri: Attempt to remove a triple with
node number out of range: 6444093 2649 -3 55
Caused by: org.mulgara.query.QueryException:
org.mulgara.query.MulgaraTransactionException: Operation failed
Caused by: org.mulgara.query.QueryException:
org.mulgara.resolver.spi.ResolverException: Couldn't make statement
false in 55
Caused by: org.mulgara.query.QueryException:
org.mulgara.store.statement.StatementStoreException: Attempt to remove a
triple with node number out of range: 6444093 2649 -3 55

etc.

please advise what we need to do to fix this. we need to set up volumes
and issues before we migrate medicine to ambra on tuesday. i'm hesistant
to upgrade from 0.9.1 to 0.9.2 on production tonight knowing that
mulgara has bad data in it.

i can delete statements from mulgara manually if necessary, but don't
know which objects to manually remove from the caches. due to mulgara's
performance limitations we can't flush the caches and start over from
scratch.

here are some full thread dumps:

1. trying to delete the corrupt volume:

2009-03-26 13:01:16,306 WARN  BitronixTransaction(PLoSMedicine)>
Synchronization.beforeCompletion() call failed for
org.topazproject.otm.impl.AbstractSession$2 at 9059dc0, marking transaction
as rollback only [TP-Processor3573 bitronix.tm.BitronixTransaction]
org.topazproject.otm.OtmException: error performing update: delete
select $s $p $o from <local:///topazproject#filter:graph=ri> where ($s
$p $o and $s <mulgara:is> <info:doi/10.1371/volume.pmed.v01> and ($p
<mulgara:is> <rdf:type> or $p <mulgara:is>
<http://purl.org/dc/terms/isReplacedBy> or $p <mulgara:is>
<http://rdf.plos.org/RDF/editorialBoard> or $p <mulgara:is>
<http://purl.org/dc/terms/hasPart> or $p <mulgara:is>
<http://rdf.plos.org/RDF/smartCollectionRules> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/source> or $p <mulgara:is>
<http://purl.org/dc/terms/modified> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/identifier> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/title> or $p <mulgara:is>
<http://purl.org/dc/terms/dateCopyrighted> or $p <mulgara:is>
<http://purl.org/dc/terms/dateAccepted> or $p <mulgara:is>
<http://purl.org/dc/terms/created> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/language> or $p <mulgara:is>
<http://purl.org/dc/terms/references> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/publisher> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/subject> or $p <mulgara:is>
<http://purl.org/dc/terms/license> or $p <mulgara:is>
<http://purl.org/dc/terms/bibliographicCitation> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/description> or $p <mulgara:is>
<http://purl.org/dc/terms/abstract> or $p <mulgara:is>
<http://purl.org/dc/terms/issued> or $p <mulgara:is>
<http://purl.org/dc/terms/conformsTo> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/type> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/creator> or $p <mulgara:is>
<http://purl.org/dc/terms/available> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/contributor> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/date> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/rights> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/format> or $p <mulgara:is>
<http://purl.org/dc/terms/dateSubmitted> or $p <mulgara:is>
<http://purl.org/dc/terms/replaces> or $p <mulgara:is>
<http://purl.org/dc/terms/issueList> or $p <mulgara:is>
<http://rdf.plos.org/RDF/image> or $p <mulgara:is>
<http://rdf.plos.org/RDF/displayName>) ) or ($s $p $o and
<info:doi/10.1371/volume.pmed.v01> $x $s  and ($s <rdf:type> <rdf:Bag>
or $s <rdf:type> <rdf:Seq> or $s <rdf:type> <rdf:Alt>) and ($x
<mulgara:is> <http://purl.org/dc/terms/issueList>) ) from
<local:///topazproject#filter:graph=ri>;
        at
org.topazproject.otm.stores.ItqlStore.doDelete(ItqlStore.java:481)
        at
org.topazproject.otm.stores.ItqlStore.delete(ItqlStore.java:418)
        at
org.topazproject.otm.impl.SessionImpl.write(SessionImpl.java:514)
        at
org.topazproject.otm.impl.SessionImpl.doFlush(SessionImpl.java:160)
        at
org.topazproject.otm.impl.SessionImpl.flush(SessionImpl.java:131)
        at
org.topazproject.otm.impl.AbstractSession$2.beforeCompletion(AbstractSes
sion.java:448)
        at
bitronix.tm.BitronixTransaction.fireBeforeCompletionEvent(BitronixTransa
ction.java:366)
        at
bitronix.tm.BitronixTransaction.commit(BitronixTransaction.java:142)
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:87
)
        at
org.topazproject.otm.spring.OtmTransactionManager.doCommit(OtmTransactio
nManager.java:98)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.processCommit(AbstractPlatformTransactionManager.java:662)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.commit(AbstractPlatformTransactionManager.java:632)
        at
org.springframework.transaction.interceptor.TransactionAspectSupport.com
mitTransactionAfterReturning(TransactionAspectSupport.java:314)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:117)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.admin.action.ManageVolumesIssuesAction$$EnhancerB
yCGLIB$$4791ba50.execute(<generated>)
        at sun.reflect.GeneratedMethodAccessor13167.invoke(Unknown
Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActi
onInvocation.java:404)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(Default
ActionInvocation.java:267)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:229)
        at
org.topazproject.ambra.user.EnsureRoleInterceptor.intercept(EnsureRoleIn
terceptor.java:43)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.struts2.TransactionInterceptor.intercept(Transact
ionInterceptor.java:61)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.getReturnCodeDe
pendingOnDisplayName(EnsureUserAccountInterceptor.java:101)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.intercept(Ensur
eUserAccountInterceptor.java:73)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.UserAccountsInterceptor.intercept(UserAccoun
tsInterceptor.java:102)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.journal.SessionFiltersInterceptor.intercept(Sessi
onFiltersInterceptor.java:53)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doInterce
pt(DefaultWorkflowInterceptor.java:221)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(Vali
dationInterceptor.java:150)
        at
org.apache.struts2.interceptor.validation.AnnotationValidationIntercepto
r.doIntercept(AnnotationValidationInterceptor.java:48)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept
(ConversionErrorInterceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(Pa
rametersInterceptor.java:184)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercep
t(StaticParametersInterceptor.java:105)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploa
dInterceptor.java:207)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(Mod
elDrivenInterceptor.java:74)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(
DebuggingInterceptor.java:206)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterc
eptor.java:143)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(Prepa
reInterceptor.java:121)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(Servle
tConfigInterceptor.java:170)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInte
rceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.LoggingInterceptor.intercept(Logging
Interceptor.java:52)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.invokeUnderTiming(T
imerInterceptor.java:125)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.intercept(TimerInte
rceptor.java:112)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercep
t(ExceptionMappingInterceptor.java:176)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java
:50)
        at
org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:5
04)
        at
org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher
.java:419)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.cas.client.filter.CASFilter.doFilter(CASFilter.ja
va:319)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.DummySSOFilter.doFilter(DummySSOFilter.java:1
05)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.VirtualJournalContextFilter.doFilter(VirtualJ
ournalContextFilter.java:150)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java
:164)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter
.java:90)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFi
lter.java:406)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.MultipleRequestFilter.doFilter(MultipleReques
tFilter.java:95)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:213)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:172)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:127)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
74)
        at
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
        at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
        at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
        at
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
703)
        at
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
java:895)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:689)
        at java.lang.Thread.run(Thread.java:595)
Caused by: java.io.IOException: Error running update 'delete select $s
$p $o from <local:///topazproject#filter:graph=ri> where ($s $p $o and
$s <mulgara:is> <info:doi/10.1371/volume.pmed.v01> and ($p <mulgara:is>
<rdf:type> or $p <mulgara:is> <http://purl.org/dc/terms/isReplacedBy> or
$p <mulgara:is> <http://rdf.plos.org/RDF/editorialBoard> or $p
<mulgara:is> <http://purl.org/dc/terms/hasPart> or $p <mulgara:is>
<http://rdf.plos.org/RDF/smartCollectionRules> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/source> or $p <mulgara:is>
<http://purl.org/dc/terms/modified> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/identifier> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/title> or $p <mulgara:is>
<http://purl.org/dc/terms/dateCopyrighted> or $p <mulgara:is>
<http://purl.org/dc/terms/dateAccepted> or $p <mulgara:is>
<http://purl.org/dc/terms/created> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/language> or $p <mulgara:is>
<http://purl.org/dc/terms/references> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/publisher> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/subject> or $p <mulgara:is>
<http://purl.org/dc/terms/license> or $p <mulgara:is>
<http://purl.org/dc/terms/bibliographicCitation> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/description> or $p <mulgara:is>
<http://purl.org/dc/terms/abstract> or $p <mulgara:is>
<http://purl.org/dc/terms/issued> or $p <mulgara:is>
<http://purl.org/dc/terms/conformsTo> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/type> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/creator> or $p <mulgara:is>
<http://purl.org/dc/terms/available> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/contributor> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/date> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/rights> or $p <mulgara:is>
<http://purl.org/dc/elements/1.1/format> or $p <mulgara:is>
<http://purl.org/dc/terms/dateSubmitted> or $p <mulgara:is>
<http://purl.org/dc/terms/replaces> or $p <mulgara:is>
<http://purl.org/dc/terms/issueList> or $p <mulgara:is>
<http://rdf.plos.org/RDF/image> or $p <mulgara:is>
<http://rdf.plos.org/RDF/displayName>) ) or ($s $p $o and
<info:doi/10.1371/volume.pmed.v01> $x $s  and ($s <rdf:type> <rdf:Bag>
or $s <rdf:type> <rdf:Seq> or $s <rdf:type> <rdf:Alt>) and ($x
<mulgara:is> <http://purl.org/dc/terms/issueList>) ) from
<local:///topazproject#filter:graph=ri>;'
        at
org.topazproject.mulgara.itql.TIClient.doUpdate(TIClient.java:117)
        at
org.topazproject.otm.stores.ItqlStore.doDelete(ItqlStore.java:479)
        ... 169 more
Caused by: org.mulgara.query.QueryException: Unable to modify
local:///topazproject#filter:graph=ri: Attempt to remove a triple with
node number out of range: 6444093 2649 -9 55
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:755)
        at
org.mulgara.resolver.DatabaseSession.modify(DatabaseSession.java:738)
        at
org.mulgara.resolver.DatabaseSession.delete(DatabaseSession.java:354)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.delete(SessionWrapper
RemoteSession.java:176)
        at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
        at sun.rmi.transport.Transport$1.run(Transport.java:153)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:466)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.ja
va:707)
        at java.lang.Thread.run(Thread.java:595)
        at
sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRem
oteCall.java:247)
        at
sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:223
)
        at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:126)
        at org.mulgara.server.rmi.RemoteSessionImpl_Stub.delete(Unknown
Source)
        at
org.mulgara.server.rmi.RemoteSessionWrapperSession.delete(RemoteSessionW
rapperSession.java:266)
        at
org.mulgara.query.operation.Deletion.execute(Deletion.java:55)
        at
org.topazproject.mulgara.itql.TIClient.doUpdate(TIClient.java:111)
        ... 170 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.query.MulgaraTransactionException: Operation failed
        at
org.mulgara.resolver.MulgaraExternalTransaction.execute(MulgaraExternalT
ransaction.java:215)
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:752)
        at
org.mulgara.resolver.DatabaseSession.modify(DatabaseSession.java:738)
        at
org.mulgara.resolver.DatabaseSession.delete(DatabaseSession.java:354)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.delete(SessionWrapper
RemoteSession.java:176)
        at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
        at sun.rmi.transport.Transport$1.run(Transport.java:153)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:466)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.ja
va:707)
        ... 1 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.resolver.spi.ResolverException: Couldn't make statement
false in 55
        at
org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementS
toreResolver.java:377)
        at
org.mulgara.resolver.InternalResolver.modifyModel(InternalResolver.java:
164)
        at
org.topazproject.mulgara.resolver.FilterResolver.modifyModel(FilterResol
ver.java:163)
        at
org.mulgara.resolver.InternalResolver.modifyModel(InternalResolver.java:
164)
        at
org.mulgara.resolver.ModifyGraphOperation.doModify(ModifyGraphOperation.
java:247)
        at
org.mulgara.resolver.ModifyGraphOperation.execute(ModifyGraphOperation.j
ava:208)
        at
org.mulgara.resolver.MulgaraExternalTransaction.execute(MulgaraExternalT
ransaction.java:201)
        ... 14 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.store.statement.StatementStoreException: Attempt to remove a
triple with node number out of range: 6444093 2649 -9 55
        at
org.mulgara.store.statement.xa.XAStatementStoreImpl$Phase.removeTriple(X
AStatementStoreImpl.java:1633)
        at
org.mulgara.store.statement.xa.XAStatementStoreImpl.removeTriples(XAStat
ementStoreImpl.java:471)
        at
org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementS
toreResolver.java:365)
        ... 20 more
2009-03-26 13:01:16,317 ERROR UnhandledException(PLoSMedicine)> error
committing transaction; nested exception is
org.topazproject.otm.OtmException: Error committing transaction
[TP-Processor3573 org.topazproject.ambra.UnhandledException]
org.springframework.transaction.TransactionSystemException: error
committing transaction; nested exception is
org.topazproject.otm.OtmException: Error committing transaction
Caused by:
org.topazproject.otm.OtmException: Error committing transaction
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:89
)
        at
org.topazproject.otm.spring.OtmTransactionManager.doCommit(OtmTransactio
nManager.java:98)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.processCommit(AbstractPlatformTransactionManager.java:662)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.commit(AbstractPlatformTransactionManager.java:632)
        at
org.springframework.transaction.interceptor.TransactionAspectSupport.com
mitTransactionAfterReturning(TransactionAspectSupport.java:314)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:117)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.admin.action.ManageVolumesIssuesAction$$EnhancerB
yCGLIB$$4791ba50.execute(<generated>)
        at sun.reflect.GeneratedMethodAccessor13167.invoke(Unknown
Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActi
onInvocation.java:404)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(Default
ActionInvocation.java:267)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:229)
        at
org.topazproject.ambra.user.EnsureRoleInterceptor.intercept(EnsureRoleIn
terceptor.java:43)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.struts2.TransactionInterceptor.intercept(Transact
ionInterceptor.java:61)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.getReturnCodeDe
pendingOnDisplayName(EnsureUserAccountInterceptor.java:101)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.intercept(Ensur
eUserAccountInterceptor.java:73)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.UserAccountsInterceptor.intercept(UserAccoun
tsInterceptor.java:102)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.journal.SessionFiltersInterceptor.intercept(Sessi
onFiltersInterceptor.java:53)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doInterce
pt(DefaultWorkflowInterceptor.java:221)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(Vali
dationInterceptor.java:150)
        at
org.apache.struts2.interceptor.validation.AnnotationValidationIntercepto
r.doIntercept(AnnotationValidationInterceptor.java:48)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept
(ConversionErrorInterceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(Pa
rametersInterceptor.java:184)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercep
t(StaticParametersInterceptor.java:105)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploa
dInterceptor.java:207)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(Mod
elDrivenInterceptor.java:74)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(
DebuggingInterceptor.java:206)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterc
eptor.java:143)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(Prepa
reInterceptor.java:121)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(Servle
tConfigInterceptor.java:170)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInte
rceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.LoggingInterceptor.intercept(Logging
Interceptor.java:52)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.invokeUnderTiming(T
imerInterceptor.java:125)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.intercept(TimerInte
rceptor.java:112)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercep
t(ExceptionMappingInterceptor.java:176)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java
:50)
        at
org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:5
04)
        at
org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher
.java:419)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.cas.client.filter.CASFilter.doFilter(CASFilter.ja
va:319)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.DummySSOFilter.doFilter(DummySSOFilter.java:1
05)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.VirtualJournalContextFilter.doFilter(VirtualJ
ournalContextFilter.java:150)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java
:164)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter
.java:90)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFi
lter.java:406)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.MultipleRequestFilter.doFilter(MultipleReques
tFilter.java:95)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:213)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:172)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:127)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
74)
        at
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
        at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
        at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
        at
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
703)
        at
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
java:895)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:689)
        at java.lang.Thread.run(Thread.java:595)
Caused by: bitronix.tm.internal.BitronixRollbackException: transaction
was marked as rollback only and has been rolled back
        at
bitronix.tm.BitronixTransaction.commit(BitronixTransaction.java:154)
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:87
)
        ... 161 more

2. trying to clear the issue list:

2009-03-26 13:02:09,629 WARN  BitronixTransaction(PLoSMedicine)>
Synchronization.beforeCompletion() call failed for
org.topazproject.otm.impl.AbstractSession$2 at 7cb30c64, marking
transaction as rollback only [TP-Processor3587
bitronix.tm.BitronixTransaction]
org.topazproject.otm.OtmException: error performing update: delete
select $s $p $o from <local:///topazproject#filter:graph=ri> where ($s
$p $o and $s <mulgara:is> <info:doi/10.1371/volume.pmed.v01> and ($p
<mulgara:is> <http://purl.org/dc/terms/issueList>) ) or ($s $p $o and
<info:doi/10.1371/volume.pmed.v01> $x $s  and ($s <rdf:type> <rdf:Bag>
or $s <rdf:type> <rdf:Seq> or $s <rdf:type> <rdf:Alt>) and ($x
<mulgara:is> <http://purl.org/dc/terms/issueList>) ) from
<local:///topazproject#filter:graph=ri>;
        at
org.topazproject.otm.stores.ItqlStore.doDelete(ItqlStore.java:481)
        at
org.topazproject.otm.stores.ItqlStore.delete(ItqlStore.java:418)
        at
org.topazproject.otm.impl.SessionImpl.write(SessionImpl.java:554)
        at
org.topazproject.otm.impl.SessionImpl.doFlush(SessionImpl.java:167)
        at
org.topazproject.otm.impl.SessionImpl.flush(SessionImpl.java:131)
        at
org.topazproject.otm.impl.AbstractSession$2.beforeCompletion(AbstractSes
sion.java:448)
        at
bitronix.tm.BitronixTransaction.fireBeforeCompletionEvent(BitronixTransa
ction.java:366)
        at
bitronix.tm.BitronixTransaction.commit(BitronixTransaction.java:142)
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:87
)
        at
org.topazproject.otm.spring.OtmTransactionManager.doCommit(OtmTransactio
nManager.java:98)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.processCommit(AbstractPlatformTransactionManager.java:662)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.commit(AbstractPlatformTransactionManager.java:632)
        at
org.springframework.transaction.interceptor.TransactionAspectSupport.com
mitTransactionAfterReturning(TransactionAspectSupport.java:314)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:117)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.admin.action.ManageVolumesIssuesAction$$EnhancerB
yCGLIB$$4791ba50.execute(<generated>)
        at sun.reflect.GeneratedMethodAccessor13167.invoke(Unknown
Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActi
onInvocation.java:404)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(Default
ActionInvocation.java:267)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:229)
        at
org.topazproject.ambra.user.EnsureRoleInterceptor.intercept(EnsureRoleIn
terceptor.java:43)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.struts2.TransactionInterceptor.intercept(Transact
ionInterceptor.java:61)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.getReturnCodeDe
pendingOnDisplayName(EnsureUserAccountInterceptor.java:101)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.intercept(Ensur
eUserAccountInterceptor.java:73)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.UserAccountsInterceptor.intercept(UserAccoun
tsInterceptor.java:102)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.journal.SessionFiltersInterceptor.intercept(Sessi
onFiltersInterceptor.java:53)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doInterce
pt(DefaultWorkflowInterceptor.java:221)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(Vali
dationInterceptor.java:150)
        at
org.apache.struts2.interceptor.validation.AnnotationValidationIntercepto
r.doIntercept(AnnotationValidationInterceptor.java:48)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept
(ConversionErrorInterceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(Pa
rametersInterceptor.java:184)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercep
t(StaticParametersInterceptor.java:105)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploa
dInterceptor.java:207)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(Mod
elDrivenInterceptor.java:74)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(
DebuggingInterceptor.java:206)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterc
eptor.java:143)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(Prepa
reInterceptor.java:121)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(Servle
tConfigInterceptor.java:170)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInte
rceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.LoggingInterceptor.intercept(Logging
Interceptor.java:52)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.invokeUnderTiming(T
imerInterceptor.java:125)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.intercept(TimerInte
rceptor.java:112)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercep
t(ExceptionMappingInterceptor.java:176)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java
:50)
        at
org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:5
04)
        at
org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher
.java:419)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.cas.client.filter.CASFilter.doFilter(CASFilter.ja
va:319)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.DummySSOFilter.doFilter(DummySSOFilter.java:1
05)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.VirtualJournalContextFilter.doFilter(VirtualJ
ournalContextFilter.java:150)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java
:164)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter
.java:90)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFi
lter.java:406)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.MultipleRequestFilter.doFilter(MultipleReques
tFilter.java:95)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:213)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:172)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:127)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
74)
        at
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
        at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
        at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
        at
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
703)
        at
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
java:895)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:689)
        at java.lang.Thread.run(Thread.java:595)
Caused by: java.io.IOException: Error running update 'delete select $s
$p $o from <local:///topazproject#filter:graph=ri> where ($s $p $o and
$s <mulgara:is> <info:doi/10.1371/volume.pmed.v01> and ($p <mulgara:is>
<http://purl.org/dc/terms/issueList>) ) or ($s $p $o and
<info:doi/10.1371/volume.pmed.v01> $x $s  and ($s <rdf:type> <rdf:Bag>
or $s <rdf:type> <rdf:Seq> or $s <rdf:type> <rdf:Alt>) and ($x
<mulgara:is> <http://purl.org/dc/terms/issueList>) ) from
<local:///topazproject#filter:graph=ri>;'
        at
org.topazproject.mulgara.itql.TIClient.doUpdate(TIClient.java:117)
        at
org.topazproject.otm.stores.ItqlStore.doDelete(ItqlStore.java:479)
        ... 169 more
Caused by: org.mulgara.query.QueryException: Unable to modify
local:///topazproject#filter:graph=ri: Attempt to remove a triple with
node number out of range: 6444093 2649 -3 55
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:755)
        at
org.mulgara.resolver.DatabaseSession.modify(DatabaseSession.java:738)
        at
org.mulgara.resolver.DatabaseSession.delete(DatabaseSession.java:354)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.delete(SessionWrapper
RemoteSession.java:176)
        at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
        at sun.rmi.transport.Transport$1.run(Transport.java:153)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:466)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.ja
va:707)
        at java.lang.Thread.run(Thread.java:595)
        at
sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRem
oteCall.java:247)
        at
sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:223
)
        at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:126)
        at org.mulgara.server.rmi.RemoteSessionImpl_Stub.delete(Unknown
Source)
        at
org.mulgara.server.rmi.RemoteSessionWrapperSession.delete(RemoteSessionW
rapperSession.java:266)
        at
org.mulgara.query.operation.Deletion.execute(Deletion.java:55)
        at
org.topazproject.mulgara.itql.TIClient.doUpdate(TIClient.java:111)
        ... 170 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.query.MulgaraTransactionException: Operation failed
        at
org.mulgara.resolver.MulgaraExternalTransaction.execute(MulgaraExternalT
ransaction.java:215)
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:752)
        at
org.mulgara.resolver.DatabaseSession.modify(DatabaseSession.java:738)
        at
org.mulgara.resolver.DatabaseSession.delete(DatabaseSession.java:354)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.delete(SessionWrapper
RemoteSession.java:176)
        at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
        at sun.rmi.transport.Transport$1.run(Transport.java:153)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:466)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.ja
va:707)
        ... 1 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.resolver.spi.ResolverException: Couldn't make statement
false in 55
        at
org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementS
toreResolver.java:377)
        at
org.mulgara.resolver.InternalResolver.modifyModel(InternalResolver.java:
164)
        at
org.topazproject.mulgara.resolver.FilterResolver.modifyModel(FilterResol
ver.java:163)
        at
org.mulgara.resolver.InternalResolver.modifyModel(InternalResolver.java:
164)
        at
org.mulgara.resolver.ModifyGraphOperation.doModify(ModifyGraphOperation.
java:247)
        at
org.mulgara.resolver.ModifyGraphOperation.execute(ModifyGraphOperation.j
ava:208)
        at
org.mulgara.resolver.MulgaraExternalTransaction.execute(MulgaraExternalT
ransaction.java:201)
        ... 14 more
Caused by: org.mulgara.query.QueryException:
org.mulgara.store.statement.StatementStoreException: Attempt to remove a
triple with node number out of range: 6444093 2649 -3 55
        at
org.mulgara.store.statement.xa.XAStatementStoreImpl$Phase.removeTriple(X
AStatementStoreImpl.java:1633)
        at
org.mulgara.store.statement.xa.XAStatementStoreImpl.removeTriples(XAStat
ementStoreImpl.java:471)
        at
org.mulgara.resolver.store.StatementStoreResolver.modifyModel(StatementS
toreResolver.java:365)
        ... 20 more
2009-03-26 13:02:09,637 ERROR UnhandledException(PLoSMedicine)> error
committing transaction; nested exception is
org.topazproject.otm.OtmException: Error committing transaction
[TP-Processor3587 org.topazproject.ambra.UnhandledException]
org.springframework.transaction.TransactionSystemException: error
committing transaction; nested exception is
org.topazproject.otm.OtmException: Error committing transaction
Caused by:
org.topazproject.otm.OtmException: Error committing transaction
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:89
)
        at
org.topazproject.otm.spring.OtmTransactionManager.doCommit(OtmTransactio
nManager.java:98)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.processCommit(AbstractPlatformTransactionManager.java:662)
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.commit(AbstractPlatformTransactionManager.java:632)
        at
org.springframework.transaction.interceptor.TransactionAspectSupport.com
mitTransactionAfterReturning(TransactionAspectSupport.java:314)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:117)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.admin.action.ManageVolumesIssuesAction$$EnhancerB
yCGLIB$$4791ba50.execute(<generated>)
        at sun.reflect.GeneratedMethodAccessor13167.invoke(Unknown
Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActi
onInvocation.java:404)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(Default
ActionInvocation.java:267)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:229)
        at
org.topazproject.ambra.user.EnsureRoleInterceptor.intercept(EnsureRoleIn
terceptor.java:43)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.struts2.TransactionInterceptor.intercept(Transact
ionInterceptor.java:61)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.getReturnCodeDe
pendingOnDisplayName(EnsureUserAccountInterceptor.java:101)
        at
org.topazproject.ambra.user.EnsureUserAccountInterceptor.intercept(Ensur
eUserAccountInterceptor.java:73)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.user.UserAccountsInterceptor.intercept(UserAccoun
tsInterceptor.java:102)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.topazproject.ambra.journal.SessionFiltersInterceptor.intercept(Sessi
onFiltersInterceptor.java:53)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doInterce
pt(DefaultWorkflowInterceptor.java:221)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(Vali
dationInterceptor.java:150)
        at
org.apache.struts2.interceptor.validation.AnnotationValidationIntercepto
r.doIntercept(AnnotationValidationInterceptor.java:48)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept
(ConversionErrorInterceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(Pa
rametersInterceptor.java:184)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercep
t(StaticParametersInterceptor.java:105)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploa
dInterceptor.java:207)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(Mod
elDrivenInterceptor.java:74)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(
DebuggingInterceptor.java:206)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterc
eptor.java:143)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(Prepa
reInterceptor.java:121)
        at
com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(Me
thodFilterInterceptor.java:86)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(Servle
tConfigInterceptor.java:170)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInte
rceptor.java:123)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.LoggingInterceptor.intercept(Logging
Interceptor.java:52)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.invokeUnderTiming(T
imerInterceptor.java:125)
        at
com.opensymphony.xwork2.interceptor.TimerInterceptor.intercept(TimerInte
rceptor.java:112)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercep
t(ExceptionMappingInterceptor.java:176)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:224)
        at
com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultAct
ionInvocation.java:223)
        at
com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerS
tack.java:455)
        at
com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvo
cation.java:221)
        at
org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java
:50)
        at
org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:5
04)
        at
org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher
.java:419)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.cas.client.filter.CASFilter.doFilter(CASFilter.ja
va:319)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.DummySSOFilter.doFilter(DummySSOFilter.java:1
05)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.VirtualJournalContextFilter.doFilter(VirtualJ
ournalContextFilter.java:150)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java
:164)
        at
org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter
.java:90)
        at
org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFi
lter.java:406)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.topazproject.ambra.web.MultipleRequestFilter.doFilter(MultipleReques
tFilter.java:95)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:213)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:172)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:127)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
74)
        at
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
        at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
        at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
        at
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
703)
        at
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
java:895)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:689)
        at java.lang.Thread.run(Thread.java:595)
Caused by: bitronix.tm.internal.BitronixRollbackException: transaction
was marked as rollback only and has been rolled back
        at
bitronix.tm.BitronixTransaction.commit(BitronixTransaction.java:154)
        at
org.topazproject.otm.impl.TransactionImpl.commit(TransactionImpl.java:87
)
        ... 161 more

Russell Uman
Web Engineer
Public Library of Science

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