Dataverse: Datasets: Internal Server Error - An unexpected error was encountered, no more information is available.

Created on 15 Sep 2020  ·  18Comments  ·  Source: IQSS/dataverse

Hello!

Today our datasets are throwing the following error:

image

in adition the console and the source section of chrome is showing this:

image

image

and the server log is throwing this warning everytime we try to access a dataset:

[2020-09-15T14:50:11.155-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=28 _ThreadName=http-listener-1(3)] [timeMillis: 1600199411155] [levelValue: 900] [[ StandardWrapperValve[Faces Servlet]: Servlet.service() for servlet Faces Servlet threw exception java.lang.NoClassDefFoundError: Could not initialize class edu.harvard.iq.dataverse.provenance.ProvInvestigator at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean.<init>(ProvPopupFragmentBean.java:90) at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean$Proxy$_$$_WeldClientProxy.<init>(Unknown Source) at sun.reflect.GeneratedConstructorAccessor317.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at java.lang.Class.newInstance(Class.java:442) at org.jboss.weld.bean.proxy.DefaultProxyInstantiator.newInstance(DefaultProxyInstantiator.java:43) at org.jboss.weld.bean.proxy.ProxyFactory.run(ProxyFactory.java:307) at org.jboss.weld.bean.proxy.ProxyFactory.create(ProxyFactory.java:299) at org.jboss.weld.bean.proxy.ClientProxyFactory.create(ClientProxyFactory.java:83) at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:198) at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:188) at org.jboss.weld.bean.proxy.ClientProxyProvider.access$100(ClientProxyProvider.java:46) at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:57) at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:53) at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3589) at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2374) at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2337) at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2252) at com.google.common.cache.LocalCache.get(LocalCache.java:3990) at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3994) at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4878) at org.jboss.weld.util.cache.LoadingCacheUtils.getCacheValue(LoadingCacheUtils.java:49) at org.jboss.weld.util.cache.LoadingCacheUtils.getCastCacheValue(LoadingCacheUtils.java:74) at org.jboss.weld.bean.proxy.ClientProxyProvider.getClientProxy(ClientProxyProvider.java:222) at org.jboss.weld.manager.BeanManagerImpl.getReference(BeanManagerImpl.java:755) at org.jboss.weld.manager.BeanManagerImpl.getInjectableReference(BeanManagerImpl.java:861) at org.jboss.weld.injection.FieldInjectionPoint.inject(FieldInjectionPoint.java:92) at org.jboss.weld.util.Beans.injectBoundFields(Beans.java:375) at org.jboss.weld.util.Beans.injectFieldsAndInitializers(Beans.java:386) at org.jboss.weld.injection.producer.ResourceInjector$1.proceed(ResourceInjector.java:70) at org.glassfish.weld.services.InjectionServicesImpl.aroundInject(InjectionServicesImpl.java:172) at org.jboss.weld.injection.InjectionContextImpl.run(InjectionContextImpl.java:46) at org.jboss.weld.injection.producer.ResourceInjector.inject(ResourceInjector.java:72) at org.jboss.weld.injection.producer.BasicInjectionTarget.inject(BasicInjectionTarget.java:121) at org.glassfish.weld.services.JCDIServiceImpl.injectManagedObject(JCDIServiceImpl.java:285) at org.glassfish.faces.integration.GlassFishInjectionProvider.inject(GlassFishInjectionProvider.java:189) at com.sun.faces.application.ApplicationImpl.newThing(ApplicationImpl.java:1759) at com.sun.faces.application.ApplicationImpl.createConverter(ApplicationImpl.java:1334) at org.omnifaces.cdi.converter.ConverterManager.createConverter(ConverterManager.java:68) at org.omnifaces.cdi.converter.ConverterManager$Proxy$_$$_WeldClientProxy.createConverter(Unknown Source) at org.omnifaces.application.OmniApplication.createConverter(OmniApplication.java:70) at javax.faces.application.ApplicationWrapper.createConverter(ApplicationWrapper.java:393) at com.sun.faces.facelets.tag.jsf.ValueHolderRule$LiteralConverterMetadata.applyMetadata(ValueHolderRule.java:85) at com.sun.faces.facelets.tag.MetadataImpl.applyMetadata(MetadataImpl.java:81) at javax.faces.view.facelets.MetaTagHandler.setAttributes(MetaTagHandler.java:129) at javax.faces.view.facelets.DelegatingMetaTagHandler.setAttributes(DelegatingMetaTagHandler.java:102) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.doNewComponentActions(ComponentTagHandlerDelegateImpl.java:473) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:179) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:203) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:203) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:203) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at com.sun.faces.facelets.tag.ui.CompositionHandler.apply(CompositionHandler.java:194) at com.sun.faces.facelets.compiler.NamespaceHandler.apply(NamespaceHandler.java:93) at com.sun.faces.facelets.compiler.EncodingHandler.apply(EncodingHandler.java:87) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:312) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:371) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:350) at com.sun.faces.facelets.impl.DefaultFaceletContext.includeFacelet(DefaultFaceletContext.java:199) at com.sun.faces.facelets.tag.ui.IncludeHandler.apply(IncludeHandler.java:124) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:203) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at com.sun.faces.facelets.tag.ui.DefineHandler.applyDefinition(DefineHandler.java:106) at com.sun.faces.facelets.tag.ui.CompositionHandler.apply(CompositionHandler.java:206) at com.sun.faces.facelets.impl.DefaultFaceletContext$TemplateManager.apply(DefaultFaceletContext.java:395) at com.sun.faces.facelets.impl.DefaultFaceletContext.includeDefinition(DefaultFaceletContext.java:366) at com.sun.faces.facelets.tag.ui.InsertHandler.apply(InsertHandler.java:111) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at javax.faces.view.facelets.DelegatingMetaTagHandler.applyNextHandler(DelegatingMetaTagHandler.java:137) at com.sun.faces.facelets.tag.jsf.ComponentTagHandlerDelegateImpl.apply(ComponentTagHandlerDelegateImpl.java:203) at javax.faces.view.facelets.DelegatingMetaTagHandler.apply(DelegatingMetaTagHandler.java:120) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at com.sun.faces.facelets.tag.jsf.core.ViewHandler.apply(ViewHandler.java:225) at javax.faces.view.facelets.CompositeFaceletHandler.apply(CompositeFaceletHandler.java:95) at com.sun.faces.facelets.compiler.NamespaceHandler.apply(NamespaceHandler.java:93) at com.sun.faces.facelets.compiler.EncodingHandler.apply(EncodingHandler.java:87) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:312) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:371) at com.sun.faces.facelets.impl.DefaultFacelet.include(DefaultFacelet.java:350) at com.sun.faces.facelets.impl.DefaultFaceletContext.includeFacelet(DefaultFaceletContext.java:199) at com.sun.faces.facelets.tag.ui.CompositionHandler.apply(CompositionHandler.java:174) at com.sun.faces.facelets.compiler.NamespaceHandler.apply(NamespaceHandler.java:93) at com.sun.faces.facelets.compiler.EncodingHandler.apply(EncodingHandler.java:87) at com.sun.faces.facelets.impl.DefaultFacelet.apply(DefaultFacelet.java:161) at com.sun.faces.application.view.FaceletViewHandlingStrategy.buildView(FaceletViewHandlingStrategy.java:990) at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:99) at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101) at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219) at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647) at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174) at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545) at java.lang.Thread.run(Thread.java:748) ]]

can you guys help us with a solution for this error? (we're running dataverse 4.9.4)

best regards,

Juan

picture ipcraiurosario

Most helpful comment

@landreev It worked!!! thank you very much for all the help guys, we can't than you enough!

picture ipcraiurosario on 1 Oct 2020
🎉4

All 18 comments

@ipcraiurosario sent server.log (below) via https://help.hmdc.harvard.edu/Ticket/Display.html?id=294425 but I'm not sure what the problem is.

server.log.txt

It's easy to reproduce the problem by clicking on any of their datasets (the homepage is fine). Here's a screenshot:

Screen Shot 2020-09-15 at 4 54 32 PM

pdurbin picture pdurbin on 15 Sep 2020

Odd - looks like ProvInvestigator blew up on the first invocation with an error parsing the prov schema and, after that, isn't found as a class. The only guess I have is that the initial connection error could have just been some problem with the validator trying to reference the schema URL, but how/why that results in not being able to find the ProvInvestigator class, I don't know.

Has a restart been tried? With a delete of the generated and osgi-cache dirs?

qqmyers picture qqmyers on 15 Sep 2020

I restarted the server and deleted the generated dir ... but not the osgi-cache, so I'll try right now!

ipcraiurosario picture ipcraiurosario on 16 Sep 2020

unfortunately the issue persist, at first it shows this:
image

and then this:
image

ipcraiurosario picture ipcraiurosario on 16 Sep 2020

This "NoClassDefFoundError" in the stack trace is usually a sign of the application and/or Glassfish stuck in a bad state after a failed redeployment. I would just keep trying to restart and redeploy everything.
Maybe in the following order:

undeploy the application (.../glassfish4/bin/asadmin undeploy dataverse-4.9.4)
stop Glassfish (.../glassfish4/bin/asadmin stop-domain domain1)
remove the "generated" and "osgi-cache" again;
restart postgres ("service postgresql restart" - or an equivalent, depending on how it's set up on your system)
start Glassfish: (.../glassfish4/bin/asadmin start-domain domain1)
redeploy the war file: (.../glassfish4/bin/asadmin deploy dataverse-4.9.4.war)

(you may need to further adjust the commands above to match your environment and/or version...)

landreev picture landreev on 16 Sep 2020

Ok I'll try that, in the meantime here is the server.log after the reboot:

server-log-after-reboot.txt

ipcraiurosario picture ipcraiurosario on 16 Sep 2020

We're trying to make a clean installation on a virtual machine to make sure that this process can be done on the production server without any problem... however, the ./install script is showing this at the end:

`Finished configuring Glassfish and deploying the dataverse application.

populating the database with reference data:

EXECUTING PSQL COMMAND: PGPASSWORD=secret; export PGPASSWORD; /usr/bin/psql -h 127.0.0.1 -p 5432 -U dvnapp -d dvndb -f ../database/reference_data.sql
psql:../database/reference_data.sql:2: ERROR: no existe la relación «foreignmetadataformatmapping»
LÍNEA 1: INSERT INTO foreignmetadataformatmapping(id, name, startelem...
^
psql:../database/reference_data.sql:3: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:4: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:5: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:6: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:7: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:8: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:9: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:10: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:11: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:12: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:13: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:14: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:15: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:16: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:17: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:18: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:19: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:20: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:21: ERROR: no existe la relación «foreignmetadatafieldmapping»
LÍNEA 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa...
^
psql:../database/reference_data.sql:27: ERROR: no existe la relación «guestbook»
LÍNEA 1: INSERT INTO guestbook(
^
psql:../database/reference_data.sql:31: ERROR: no existe la relación «dataverse»
psql:../database/reference_data.sql:32: ERROR: no existe la relación «authenticateduser»
psql:../database/reference_data.sql:38: ERROR: no existe la relación «datasetversion»
psql:../database/reference_data.sql:51: ERROR: no existe la relación «worldmapauth_tokentype»
LÍNEA 1: INSERT INTO worldmapauth_tokentype
^

OK, done!

OK, the Dataverse application appears to be running...

ERROR: Can't find the metadata and user/dataverse setup scripts!
Are you running the installer in the right directory?
`

and the database shows "no relations found" when I execute dt

ipcraiurosario picture ipcraiurosario on 18 Sep 2020

Hi... We've been trying to do what @landreev suggested but it did not work ... we used the same database (because we need to use it) and the error continues ... here is what the log says when whe clic on a dataset or try to add a new dataset:

[2020-09-29T07:54:06.859-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=28 _ThreadName=http-listener-1(3)] [timeMillis: 1601384046859] [levelValue: 900] [[
StandardWrapperValve[Faces Servlet]: Servlet.service() for servlet Faces Servlet threw exception
java.lang.NoClassDefFoundError: Could not initialize class edu.harvard.iq.dataverse.provenance.ProvInvestigator
at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean.(ProvPopupFragmentBean.java:90)
at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean$Proxy$_$$_WeldClientProxy.(Unknown Source)
at sun.reflect.GeneratedConstructorAccessor328.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at org.jboss.weld.bean.proxy.DefaultProxyInstantiator.newInstance(DefaultProxyInstantiator.java:43)
at org.jboss.weld.bean.proxy.ProxyFactory.run(ProxyFactory.java:307)
at org.jboss.weld.bean.proxy.ProxyFactory.create(ProxyFactory.java:299)
at org.jboss.weld.bean.proxy.ClientProxyFactory.create(ClientProxyFactory.java:83)
at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:198)
at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:188)
at org.jboss.weld.bean.proxy.ClientProxyProvider.access$100(ClientProxyProvider.java:46)
at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:57)
at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:53)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3589)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2374)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2337)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2252)
at com.google.common.cache.LocalCache.get(LocalCache.java:3990)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3994)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4878)
at org.jboss.weld.util.cache.LoadingCacheUtils.getCacheValue(LoadingCacheUtils.java:49)
at org.jboss.weld.util.cache.LoadingCacheUtils.getCastCacheValue(LoadingCacheUtils.java:74)
at org.jboss.weld.bean.proxy.ClientProxyProvider.getClientProxy(ClientProxyProvider.java:222)
at org.jboss.weld.manager.BeanManagerImpl.getReference(BeanManagerImpl.java:755)
at org.jboss.weld.manager.BeanManagerImpl.getInjectableReference(BeanManagerImpl.java:861)
at org.jboss.weld.injection.FieldInjectionPoint.inject(FieldInjectionPoint.java:92)
at org.jboss.weld.util.Beans.injectBoundFields(Beans.java:375)
at org.jboss.weld.util.Beans.injectFieldsAndInitializers(Beans.java:386)
at org.jboss.weld.injection.producer.ResourceInjector$1.proceed(ResourceInjector.java:70)
at org.glassfish.weld.services.InjectionServicesImpl.aroundInject(InjectionServicesImpl.java:172)
at org.jboss.weld.injection.InjectionContextImpl.run(InjectionContextImpl.java:46)
at org.jboss.weld.injection.producer.ResourceInjector.inject(ResourceInjector.java:72)
at org.jboss.weld.injection.producer.BasicInjectionTarget.inject(BasicInjectionTarget.java:121)
at org.jboss.weld.bean.ManagedBean.create(ManagedBean.java:159)
at org.jboss.weld.util.bean.IsolatedForwardingBean.create(IsolatedForwardingBean.java:45)
at com.sun.faces.application.view.ViewScopeContextManager.createBean(ViewScopeContextManager.java:144)
at com.sun.faces.application.view.ViewScopeContext.get(ViewScopeContext.java:137)
at org.jboss.weld.context.PassivatingContextWrapper$AbstractPassivatingContextWrapper.get(PassivatingContextWrapper.java:76)
at org.jboss.weld.bean.ContextualInstanceStrategy$DefaultContextualInstanceStrategy.get(ContextualInstanceStrategy.java:101)
at org.jboss.weld.bean.ContextualInstance.get(ContextualInstance.java:50)
at org.jboss.weld.manager.BeanManagerImpl.getReference(BeanManagerImpl.java:761)
at org.jboss.weld.el.AbstractWeldELResolver.lookup(AbstractWeldELResolver.java:107)
at org.jboss.weld.el.AbstractWeldELResolver.getValue(AbstractWeldELResolver.java:90)
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:188)
at com.sun.faces.el.DemuxCompositeELResolver._getValue(DemuxCompositeELResolver.java:176)
at com.sun.faces.el.DemuxCompositeELResolver.getValue(DemuxCompositeELResolver.java:203)
at com.sun.el.parser.AstIdentifier.getValue(AstIdentifier.java:116)
at com.sun.el.parser.AstValue.getBase(AstValue.java:151)
at com.sun.el.parser.AstValue.getTarget(AstValue.java:170)
at com.sun.el.parser.AstValue.getType(AstValue.java:86)
at com.sun.el.ValueExpressionImpl.getType(ValueExpressionImpl.java:201)
at org.jboss.weld.el.WeldValueExpression.getType(WeldValueExpression.java:93)
at com.sun.faces.facelets.el.TagValueExpression.getType(TagValueExpression.java:98)
at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getConvertedValue(HtmlBasicInputRenderer.java:95)
at javax.faces.component.UIViewParameter.getConvertedValue(UIViewParameter.java:437)
at javax.faces.component.UIInput.validate(UIInput.java:975)
at javax.faces.component.UIInput.executeValidate(UIInput.java:1248)
at javax.faces.component.UIInput.processValidators(UIInput.java:712)
at javax.faces.component.UIViewParameter.processValidators(UIViewParameter.java:278)
at javax.faces.component.UIComponentBase.processValidators(UIComponentBase.java:1258)
at javax.faces.component.UIComponentBase.processValidators(UIComponentBase.java:1258)
at javax.faces.component.UIViewRoot.processValidators(UIViewRoot.java:1195)
at com.sun.faces.lifecycle.ProcessValidationsPhase.execute(ProcessValidationsPhase.java:76)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:646)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
at java.lang.Thread.run(Thread.java:748)
]]

ipcraiurosario picture ipcraiurosario on 29 Sep 2020

Hi!

We've been trying to find a solution to this issue, here is what we've done:

  1. We ran a "vacuum" over our database to see if this could fix any problem with any troublesome data. It did not solve the problem.

  2. We made a back up from our public server and restore it on a new deploy in the development server but the problem persist on the development server.

  3. The first time we try to access a dataset after restarting glassfish, we get this messages on the log:

[2020-09-30T16:03:04.614-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=28 _ThreadName=http-
listener-1(2)] [timeMillis: 1601499784614] [levelValue: 900] [[
org.apache.catalina.core.StandardHostValve@2994ec2c: Exception processing ErrorPage[errorCode=500, location=/500.xhtml]
java.io.IOException: Broken pipe
at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
at sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:47)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:93)
at sun.nio.ch.IOUtil.write(IOUtil.java:51)
at sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:468)
at org.glassfish.grizzly.nio.transport.TCPNIOUtils.flushByteBuffer(TCPNIOUtils.java:149)
at org.glassfish.grizzly.nio.transport.TCPNIOUtils.writeCompositeBuffer(TCPNIOUtils.java:87)
at org.glassfish.grizzly.nio.transport.TCPNIOAsyncQueueWriter.write0(TCPNIOAsyncQueueWriter.java:112)
at org.glassfish.grizzly.nio.transport.TCPNIOAsyncQueueWriter.write0(TCPNIOAsyncQueueWriter.java:91)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:261)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:170)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:70)
at org.glassfish.grizzly.nio.transport.TCPNIOTransportFilter.handleWrite(TCPNIOTransportFilter.java:126)
at org.glassfish.grizzly.filterchain.TransportFilter.handleWrite(TransportFilter.java:191)
at org.glassfish.grizzly.filterchain.ExecutorResolver$8.execute(ExecutorResolver.java:111)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:848)
at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:817)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBuffer(OutputBuffer.java:1024)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBinaryBuffers(OutputBuffer.java:1011)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBinaryBuffersIfNeeded(OutputBuffer.java:1173)
at org.glassfish.grizzly.http.io.OutputBuffer.flushCharsToBuf(OutputBuffer.java:1166)
at org.glassfish.grizzly.http.io.OutputBuffer.flushCharsToBuf(OutputBuffer.java:1115)
at org.glassfish.grizzly.http.io.OutputBuffer.write(OutputBuffer.java:448)
at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:405)
at org.apache.catalina.connector.CoyoteWriter.write(CoyoteWriter.java:217)
at org.apache.catalina.connector.CoyoteWriter.write(CoyoteWriter.java:225)
at com.sun.faces.application.view.WriteBehindStateWriter.flushToWriter(WriteBehindStateWriter.java:240)
at com.sun.faces.application.view.FaceletViewHandlingStrategy.renderView(FaceletViewHandlingStrategy.java:473)
at com.sun.faces.application.view.MultiViewHandler.renderView(MultiViewHandler.java:133)
at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
at org.ocpsoft.rewrite.faces.RewriteViewHandler.renderView(RewriteViewHandler.java:196)
at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:120)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:577)
at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546)
at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:505)
at org.apache.catalina.core.StandardHostValve.dispatchToErrorPage(StandardHostValve.java:699)
at org.apache.catalina.core.StandardHostValve.status(StandardHostValve.java:380)
at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:334)
at org.apache.catalina.core.StandardHostValve.postInvoke(StandardHostValve.java:232)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:417)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
at java.lang.Thread.run(Thread.java:748)
]]

[2020-09-30T16:03:04.625-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=27 _ThreadName=http-listener-1(1)] [timeMillis: 1601499784625] [levelValue: 900] [[
org.apache.catalina.core.StandardHostValve@2994ec2c: Exception processing ErrorPage[errorCode=500, location=/500.xhtml]
java.io.IOException: Broken pipe
at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
at sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:47)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:93)
at sun.nio.ch.IOUtil.write(IOUtil.java:51)
at sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:468)
at org.glassfish.grizzly.nio.transport.TCPNIOUtils.flushByteBuffer(TCPNIOUtils.java:149)
at org.glassfish.grizzly.nio.transport.TCPNIOUtils.writeCompositeBuffer(TCPNIOUtils.java:87)
at org.glassfish.grizzly.nio.transport.TCPNIOAsyncQueueWriter.write0(TCPNIOAsyncQueueWriter.java:112)
at org.glassfish.grizzly.nio.transport.TCPNIOAsyncQueueWriter.write0(TCPNIOAsyncQueueWriter.java:91)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:261)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:170)
at org.glassfish.grizzly.nio.AbstractNIOAsyncQueueWriter.write(AbstractNIOAsyncQueueWriter.java:70)
at org.glassfish.grizzly.nio.transport.TCPNIOTransportFilter.handleWrite(TCPNIOTransportFilter.java:126)
at org.glassfish.grizzly.filterchain.TransportFilter.handleWrite(TransportFilter.java:191)
at org.glassfish.grizzly.filterchain.ExecutorResolver$8.execute(ExecutorResolver.java:111)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:848)
at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:817)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBuffer(OutputBuffer.java:1024)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBinaryBuffers(OutputBuffer.java:1011)
at org.glassfish.grizzly.http.io.OutputBuffer.flushBinaryBuffersIfNeeded(OutputBuffer.java:1173)
at org.glassfish.grizzly.http.io.OutputBuffer.flushCharsToBuf(OutputBuffer.java:1166)
at org.glassfish.grizzly.http.io.OutputBuffer.flushCharsToBuf(OutputBuffer.java:1115)
at org.glassfish.grizzly.http.io.OutputBuffer.write(OutputBuffer.java:448)
at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:405)
at org.apache.catalina.connector.CoyoteWriter.write(CoyoteWriter.java:217)
at org.apache.catalina.connector.CoyoteWriter.write(CoyoteWriter.java:225)
at com.sun.faces.application.view.WriteBehindStateWriter.flushToWriter(WriteBehindStateWriter.java:240)
at com.sun.faces.application.view.FaceletViewHandlingStrategy.renderView(FaceletViewHandlingStrategy.java:473)
at com.sun.faces.application.view.MultiViewHandler.renderView(MultiViewHandler.java:133)
at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
at org.ocpsoft.rewrite.faces.RewriteViewHandler.renderView(RewriteViewHandler.java:196)
at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:120)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:577)
at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546)
at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:505)
at org.apache.catalina.core.StandardHostValve.dispatchToErrorPage(StandardHostValve.java:699)
at org.apache.catalina.core.StandardHostValve.status(StandardHostValve.java:380)
at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:334)
at org.apache.catalina.core.StandardHostValve.postInvoke(StandardHostValve.java:232)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:417)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
at java.lang.Thread.run(Thread.java:748)
]]

[2020-09-30T16:05:07.187-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=28 _ThreadName=http-listener-1(2)] [timeMillis: 1601499907187] [levelValue: 900] [[
StandardWrapperValve[Faces Servlet]: Servlet.service() for servlet Faces Servlet threw exception
java.lang.NoClassDefFoundError: Could not initialize class edu.harvard.iq.dataverse.provenance.ProvInvestigator
at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean.(ProvPopupFragmentBean.java:90)
at edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean$Proxy$_$$_WeldClientProxy.(Unknown Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at org.jboss.weld.bean.proxy.DefaultProxyInstantiator.newInstance(DefaultProxyInstantiator.java:43)
at org.jboss.weld.bean.proxy.ProxyFactory.run(ProxyFactory.java:307)
at org.jboss.weld.bean.proxy.ProxyFactory.create(ProxyFactory.java:299)
at org.jboss.weld.bean.proxy.ClientProxyFactory.create(ClientProxyFactory.java:83)
at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:198)
at org.jboss.weld.bean.proxy.ClientProxyProvider.createClientProxy(ClientProxyProvider.java:188)
at org.jboss.weld.bean.proxy.ClientProxyProvider.access$100(ClientProxyProvider.java:46)
at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:57)
at org.jboss.weld.bean.proxy.ClientProxyProvider$CreateClientProxy.load(ClientProxyProvider.java:53)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3589)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2374)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2337)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2252)
at com.google.common.cache.LocalCache.get(LocalCache.java:3990)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3994)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4878)
at org.jboss.weld.util.cache.LoadingCacheUtils.getCacheValue(LoadingCacheUtils.java:49)
at org.jboss.weld.util.cache.LoadingCacheUtils.getCastCacheValue(LoadingCacheUtils.java:74)
at org.jboss.weld.bean.proxy.ClientProxyProvider.getClientProxy(ClientProxyProvider.java:222)
at org.jboss.weld.manager.BeanManagerImpl.getReference(BeanManagerImpl.java:755)
at org.jboss.weld.manager.BeanManagerImpl.getInjectableReference(BeanManagerImpl.java:861)
at org.jboss.weld.injection.FieldInjectionPoint.inject(FieldInjectionPoint.java:92)
at org.jboss.weld.util.Beans.injectBoundFields(Beans.java:375)
at org.jboss.weld.util.Beans.injectFieldsAndInitializers(Beans.java:386)
at org.jboss.weld.injection.producer.ResourceInjector$1.proceed(ResourceInjector.java:70)
at org.glassfish.weld.services.InjectionServicesImpl.aroundInject(InjectionServicesImpl.java:172)
at org.jboss.weld.injection.InjectionContextImpl.run(InjectionContextImpl.java:46)
at org.jboss.weld.injection.producer.ResourceInjector.inject(ResourceInjector.java:72)
at org.jboss.weld.injection.producer.BasicInjectionTarget.inject(BasicInjectionTarget.java:121)
at org.jboss.weld.bean.ManagedBean.create(ManagedBean.java:159)
at org.jboss.weld.util.bean.IsolatedForwardingBean.create(IsolatedForwardingBean.java:45)
at com.sun.faces.application.view.ViewScopeContextManager.createBean(ViewScopeContextManager.java:144)
at com.sun.faces.application.view.ViewScopeContext.get(ViewScopeContext.java:137)
at org.jboss.weld.context.PassivatingContextWrapper$AbstractPassivatingContextWrapper.get(PassivatingContextWrapper.java:76)
at org.jboss.weld.bean.ContextualInstanceStrategy$DefaultContextualInstanceStrategy.get(ContextualInstanceStrategy.java:101)
at org.jboss.weld.bean.ContextualInstance.get(ContextualInstance.java:50)
at org.jboss.weld.manager.BeanManagerImpl.getReference(BeanManagerImpl.java:761)
at org.jboss.weld.el.AbstractWeldELResolver.lookup(AbstractWeldELResolver.java:107)
at org.jboss.weld.el.AbstractWeldELResolver.getValue(AbstractWeldELResolver.java:90)
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:188)
at com.sun.faces.el.DemuxCompositeELResolver._getValue(DemuxCompositeELResolver.java:176)
at com.sun.faces.el.DemuxCompositeELResolver.getValue(DemuxCompositeELResolver.java:203)
at com.sun.el.parser.AstIdentifier.getValue(AstIdentifier.java:116)
at com.sun.el.parser.AstValue.getBase(AstValue.java:151)
at com.sun.el.parser.AstValue.getTarget(AstValue.java:170)
at com.sun.el.parser.AstValue.getType(AstValue.java:86)
at com.sun.el.ValueExpressionImpl.getType(ValueExpressionImpl.java:201)
at org.jboss.weld.el.WeldValueExpression.getType(WeldValueExpression.java:93)
at com.sun.faces.facelets.el.TagValueExpression.getType(TagValueExpression.java:98)
at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getConvertedValue(HtmlBasicInputRenderer.java:95)
at javax.faces.component.UIViewParameter.getConvertedValue(UIViewParameter.java:437)
at javax.faces.component.UIInput.validate(UIInput.java:975)
at javax.faces.component.UIInput.executeValidate(UIInput.java:1248)
at javax.faces.component.UIInput.processValidators(UIInput.java:712)
at javax.faces.component.UIViewParameter.processValidators(UIViewParameter.java:278)
at javax.faces.component.UIComponentBase.processValidators(UIComponentBase.java:1258)
at javax.faces.component.UIComponentBase.processValidators(UIComponentBase.java:1258)
at javax.faces.component.UIViewRoot.processValidators(UIViewRoot.java:1195)
at com.sun.faces.lifecycle.ProcessValidationsPhase.execute(ProcessValidationsPhase.java:76)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:646)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
at java.lang.Thread.run(Thread.java:748)
]]

  1. A wget to a datasets shows the same errors in the log: wget http://localhost:8080/dataset.xhtml?persistentId=doi:10.34848/FK2/RD5NIK

  2. A fresh install with a new database works fine... but then again, we can't lose the data of the current database.

ipcraiurosario picture ipcraiurosario on 30 Sep 2020

@ipcraiurosario I still don't have any ideas on what's going on with your installation. It saddens me that it's been down for 16 days!

You said a fresh installation worked. I'm wondering what would happen if you swap in your old database into the new installation (on a test server, of course). That is to say, I'm hoping that your database is just fine and that something horribly wrong has happened to Glassfish. Since you have a fresh, working installation of Glassfish, maybe it can be used with your old database?

pdurbin picture pdurbin on 1 Oct 2020

It looks like v4.9.4 references http://provenance.ecs.soton.ac.uk/prov-json/schema in trying to load the schema and I'm unable to access that URL. v4.10 and later no longer use that URL - see https://github.com/IQSS/dataverse/commit/92bd5b559b519c393381b0b4a2f1b93c4a458400#diff-fe7e3d53ba5953c12930c0463fd844a5 .

(From the stack trace linked above, it looks like that http call fails first and then the class can't be loaded after that)

I'm not sure what can be done to address that unless that web address is restored except to update at least to 4.10.

qqmyers picture qqmyers on 1 Oct 2020
🎉2

If you have reasons to stay on 4.9.4, I can build a patched 4.9.4 war file for you, with the change referenced in the previous comment applied.
But if you are running your own, modified version of 4.9.4, you will need to rebuild it, with the commit above added.
Apologies for the delay with this. Thank you @qqmyers for identifying the problem.

landreev picture landreev on 1 Oct 2020
👍2

Just to build on what @qqmyers is saying (yes, thank you for identifying the problem!), #5154 is the issue where we talked about the network dependency the provenance feature had in 4.9.4. In pull request #5157 you can also see the diff mentioned above (92bd5b5), which is probably the fix you need if you want to stay on 4.9.4 (we had discussed previously that you're running at least a slight fork: http://irclog.iq.harvard.edu/dataverse/2020-09-16#i_129163 ).

pdurbin picture pdurbin on 1 Oct 2020

Great to read this! @qqmyers Thank you very much for your help!!!

@landreev we need to stay on 4.9.4 for the moment and we have running a 4.9.4 with some developments, so I made the changes that @qqmyers suggested... how can we make a war file from our source code?

ipcraiurosario picture ipcraiurosario on 1 Oct 2020

Do you really need to build a war file from source code though?
At the moment you appear to be running our normal, released war file (based on the output of the version API).
So when you say that you have some local "developments" added, what do you mean by that - just some edits of xhtml files and such, added to our application?
I can give you another 4.9.4 war file, with this fix added (I have already built it).

But, all you need to patch is really just one class file:

glassfish4/glassfish/domains/domain1/applications/dataverse-4.9.4/WEB-INF/classes/edu/harvard/iq/dataverse/provenance/ProvInvestigator.class

You can try stopping glassfish; then replacing the file above with this, patched version I just put up:

https://github.com/IQSS/dataverse/releases/download/v4.9.4/ProvInvestigator.class

Then start glassfish again.
Let us know if that worked?

landreev picture landreev on 1 Oct 2020
🚀1

@landreev It worked!!! thank you very much for all the help guys, we can't than you enough!

ipcraiurosario picture ipcraiurosario on 1 Oct 2020
🎉4

Thanks all for the work and successful resolution here! I'm going to close this issue.

djbrooke picture djbrooke on 2 Oct 2020

@landreev, It worked!!! it happens at our end too, @ipcraiurosario, it solved now;

umuchlish picture umuchlish on 14 Nov 2020
👍1
Was this page helpful?
0 / 5 - 0 ratings

Related issues

BPeuch picture BPeuch  ·  3Comments
shlake picture shlake  ·  4Comments
Fernand0S picture Fernand0S  ·  4Comments
atrisovic picture atrisovic  ·  3Comments
amberleahey picture amberleahey  ·  3Comments