[Ambra-dev] errors when publishing articles

Russell Uman ruman at plos.org
Thu Apr 23 17:12:50 PDT 2009 

howdy!

since 0.9.1, publishing articles has been an extremely slow process -
which is odd, because we're just flipping a bit and invalidating a cache
entry.

we've seen occasional errors on publish, but they usually resolve on the
second try.

today, for some reason, we can't publish more than 2 articles at a time
without getting an error, and those 2 articles take 5-10 minutes to
publish:

2009-04-23 15:04:32,011 ERROR BaseAdminActionSupport(PLoSCompBiol)>
Admin console Exception [TP-Processor1176
org.topazproject.ambra.admin.action.BaseAdminActionSupport]
org.topazproject.ambra.ApplicationException:
org.topazproject.ambra.ApplicationException:
org.topazproject.otm.query.QueryException: error performing query
'select id from Article o where id := cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
Caused by: org.topazproject.ambra.ApplicationException:
org.topazproject.otm.query.QueryException: error performing query
'select id from Article o where id:= cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
Caused by: org.topazproject.otm.query.QueryException: error performing
query 'select id from Article o where id := cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
Caused by: java.io.IOException: Error running query 'select $o from
<local:///topazproject#filter:graph=ri> where $o <rdf:type>
<http://rdf.topazproject.org/RDF/Article> in
<local:///topazproject#filter:graph=ri> and $o <mulgara:is>
<info:doi/10.1371/journal.pcbi.1000365> and $o
<http://prismstandard.org/namespaces/1.2/basic/eIssn> '1935-2735' in
<local:///topazproject#filter:graph=ri> and $o
<http://prismstandard.org/namespaces/1.2/basic/eIssn> '1935-2735' in
<local:///topazproject#filter:graph=ri>;'
Caused by: org.mulgara.query.QueryException: Query failed: No externally
mediated transaction associated with session - last transaction was
rolled back with error: transaction-timeout

i'm not sure if we're tracking this issue as a separate bug in trac - i
think we've lumped it in with "site slow during ingest", but we probably
should open a separate ticket. there's no good reason for this action to
be slow (so it's probably a bad reason)

full trace follows:

2009-04-23 15:04:32,011 ERROR BaseAdminActionSupport(PLoSCompBiol)>
Admin console Exception [TP-Processor1176
org.topazproject.ambra.admin.action.BaseAdminActionSupport]
org.topazproject.ambra.ApplicationException:
org.topazproject.ambra.ApplicationException:
org.topazproject.otm.query.QueryException: error performing query
'select id from Article o where id := cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
        at
org.topazproject.ambra.admin.service.DocumentManagementService.getPublis
hableFiles(DocumentManagementService.java:352)
        at
org.topazproject.ambra.admin.service.DocumentManagementService$$FastClas
sByCGLIB$$bf95593d.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:623)
        at
org.topazproject.ambra.admin.service.DocumentManagementService$$Enhancer
ByCGLIB$$91a173cb.getPublishableFiles(<generated>)
        at
org.topazproject.ambra.admin.action.BaseAdminActionSupport.base(BaseAdmi
nActionSupport.java:46)
        at
org.topazproject.ambra.admin.action.PublishArchivesAction.execute(Publis
hArchivesAction.java:69)
        at
org.topazproject.ambra.admin.action.PublishArchivesAction$$FastClassByCG
LIB$$cc8b2cff.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at
org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.i
nvokeJoinpoint(Cglib2AopProxy.java:695)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:144)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:107)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.admin.action.PublishArchivesAction$$EnhancerByCGL
IB$$4d7b17e5.execute(<generated>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
        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:51)
        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: org.topazproject.ambra.ApplicationException:
org.topazproject.otm.query.QueryException: error performing query
'select id from Article o where id := cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
        at
org.topazproject.ambra.article.service.FetchArticleService.getArticleIds
(FetchArticleService.java:235)
        at
org.topazproject.ambra.admin.service.DocumentManagementService.getPublis
hableFiles(DocumentManagementService.java:347)
        ... 168 more
Caused by: org.topazproject.otm.query.QueryException: error performing
query 'select id from Article o where id := cast(o, Article).id and id =
<info:doi/10.1371/journal.pcbi.1000365>;'
        at
org.topazproject.otm.stores.ItqlStore.doQuery(ItqlStore.java:851)
        at
org.topazproject.otm.impl.QueryImpl.execute(QueryImpl.java:86)
        at
org.topazproject.ambra.journal.JournalCarrierService.getObjects(JournalC
arrierService.java:169)
        at
org.topazproject.ambra.journal.JournalCarrierService.buildCarrierMap(Jou
rnalCarrierService.java:147)
        at
org.topazproject.ambra.journal.JournalCarrierService.access$200(JournalC
arrierService.java:56)
        at
org.topazproject.ambra.journal.JournalCarrierService$2.lookup(JournalCar
rierService.java:187)
        at
org.topazproject.ambra.journal.JournalCarrierService$2.lookup(JournalCar
rierService.java:186)
        at
org.topazproject.ambra.cache.EhcacheProvider$1.execute(EhcacheProvider.j
ava:123)
        at
org.topazproject.ambra.cache.Cache$SynchronizedLookup.execute(Cache.java
:220)
        at
org.topazproject.ambra.cache.EhcacheProvider.get(EhcacheProvider.java:11
3)
        at
org.topazproject.ambra.journal.JournalCarrierService.getJournalKeysForOb
ject(JournalCarrierService.java:184)
        at
org.topazproject.ambra.journal.JournalCarrierService.getJournalsForObjec
t(JournalCarrierService.java:198)
        at
org.topazproject.ambra.journal.JournalService.getJournalsForObject(Journ
alService.java:163)
        at
org.topazproject.ambra.journal.JournalService$$FastClassByCGLIB$$3e152a5
7.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at
org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.i
nvokeJoinpoint(Cglib2AopProxy.java:695)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:144)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:107)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.journal.JournalService$$EnhancerByCGLIB$$dc36c2ad
.getJournalsForObject(<generated>)
        at
org.topazproject.ambra.article.service.ArticleFeedService$Invalidator.ma
tchesJournal(ArticleFeedService.java:638)
        at
org.topazproject.ambra.article.service.ArticleFeedService$Invalidator.ma
tches(ArticleFeedService.java:532)
        at
org.topazproject.ambra.article.service.ArticleFeedService$Invalidator.in
validateFeedCacheForArticle(ArticleFeedService.java:478)
        at
org.topazproject.ambra.article.service.ArticleFeedService$Invalidator.ob
jectChanged(ArticleFeedService.java:425)
        at
org.topazproject.ambra.cache.CacheManager.objectChanged(CacheManager.jav
a:163)
        at
org.topazproject.ambra.cache.OtmInterceptor.onPostWrite(OtmInterceptor.j
ava:232)
        at
org.topazproject.otm.impl.SessionImpl.write(SessionImpl.java:584)
        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.QueryImpl.execute(QueryImpl.java:81)
        at
org.topazproject.ambra.article.service.ArticleOtmService.getArticleIds(A
rticleOtmService.java:246)
        at
org.topazproject.ambra.article.service.ArticleOtmService$$FastClassByCGL
IB$$cdd3990.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at
org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.i
nvokeJoinpoint(Cglib2AopProxy.java:695)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:144)
        at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:107)
        at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Ref
lectiveMethodInvocation.java:166)
        at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:630)
        at
org.topazproject.ambra.article.service.ArticleOtmService$$EnhancerByCGLI
B$$8eb5fd20.getArticleIds(<generated>)
        at
org.topazproject.ambra.article.service.FetchArticleService.getArticleIds
(FetchArticleService.java:233)
        ... 169 more
Caused by: java.io.IOException: Error running query 'select $o from
<local:///topazproject#filter:graph=ri> where $o <rdf:type>
<http://rdf.topazproject.org/RDF/Article> in
<local:///topazproject#filter:graph=ri> and $o <mulgara:is>
<info:doi/10.1371/journal.pcbi.1000365> and $o
<http://prismstandard.org/namespaces/1.2/basic/eIssn> '1935-2735' in
<local:///topazproject#filter:graph=ri> and $o
<http://prismstandard.org/namespaces/1.2/basic/eIssn> '1935-2735' in
<local:///topazproject#filter:graph=ri>;'
        at
org.topazproject.mulgara.itql.TIClient.doQuery(TIClient.java:101)
        at
org.topazproject.otm.stores.ItqlStore.doQuery(ItqlStore.java:849)
        ... 209 more
Caused by: org.mulgara.query.QueryException: Query failed: No externally
mediated transaction associated with session - last transaction was
rolled back with error: transaction-timeout
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:755)
        at
org.mulgara.resolver.DatabaseSession.query(DatabaseSession.java:465)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.query(SessionWrapperR
emoteSession.java:396)
        at sun.reflect.GeneratedMethodAccessor9.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.query(Unknown
Source)
        at
org.mulgara.server.rmi.RemoteSessionWrapperSession.query(RemoteSessionWr
apperSession.java:541)
        at org.mulgara.query.Query.execute(Query.java:568)
        at org.mulgara.query.Query.execute(Query.java:57)
        at
org.topazproject.mulgara.itql.TIClient.doQuery(TIClient.java:82)
        ... 210 more
Caused by: org.mulgara.query.MulgaraTransactionException: No externally
mediated transaction associated with session - last transaction was
rolled back with error: transaction-timeout
        at
org.mulgara.resolver.MulgaraExternalTransactionFactory.getTransaction(Mu
lgaraExternalTransactionFactory.java:66)
        at
org.mulgara.resolver.DatabaseSession.execute(DatabaseSession.java:751)
        at
org.mulgara.resolver.DatabaseSession.query(DatabaseSession.java:465)
        at
org.mulgara.server.rmi.SessionWrapperRemoteSession.query(SessionWrapperR
emoteSession.java:396)
        at sun.reflect.GeneratedMethodAccessor9.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
2009-04-23 15:04:32,023 ERROR UnhandledException(PLoSCompBiol)>
Transaction rolled back because it has been marked as rollback-only
[TP-Processor1176 org.topazproject.ambra.UnhandledException]
org.springframework.transaction.UnexpectedRollbackException: Transaction
rolled back because it has been marked as rollback-only
        at
org.springframework.transaction.support.AbstractPlatformTransactionManag
er.commit(AbstractPlatformTransactionManager.java:626)
        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.PublishArchivesAction$$EnhancerByCGL
IB$$4d7b17e5.execute(<generated>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
        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:51)
        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)

Russell Uman
Web Engineer
Public Library of Science

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