Task #1614 (new)
Opened 14 years ago
Last modified 14 years ago
Raw File Store: concurrency problem
Reported by: | jburel | Owned by: | jburel |
---|---|---|---|
Priority: | blocker | Milestone: | Unscheduled |
Component: | Services | Version: | 4.1 |
Keywords: | n.a. | Cc: | cxallan, dzmacdonald, jason, josh |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by jmoore)
As part of the publication workflow, we create figures (jpeg or png) that we link to an image (in that case) as a file annotation.
When the user click on the image, we load the file annotation, since it is a jpeg, we download the file to display the jpeg. Problem can be reproduced simply by attaching multiple jpg files to an image (see logs.zip attached.) It works if we have 1 or 2, after that, we keep on having the following error when doing
rawFileStore.setId(id)
Cannot set the file's id. at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:453) at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2748) ... see comments ... at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.api._RawFileStoreDelM.setFileId(_RawFileStoreDelM.java:138) at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:184) at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:156) at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2746) ... 9 more
Attachments (2)
Change History (10)
comment:1 Changed 14 years ago by jburel
comment:2 Changed 14 years ago by jburel
- Type changed from User Story to defect
Changed 14 years ago by jburel
Changed 14 years ago by wmoore
comment:3 Changed 14 years ago by wmoore
- Description modified (diff)
comment:4 Changed 14 years ago by jmoore
- Type changed from Bug to Task
comment:5 Changed 14 years ago by jmoore
- Owner jmoore deleted
comment:6 Changed 14 years ago by jmoore
- Description modified (diff)
Cannot set the file's id. at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:453) at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2748) at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1279) at org.openmicroscopy.shoola.env.data.views.calls.FilesLoader$1.doCall(FilesLoader.java:78) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:613) Caused by: omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (org.postgresql.util.PSQLException): Cannot change transaction read-only property in the middle of a transaction. at org.postgresql.jdbc2.AbstractJdbc2Connection.setReadOnly(AbstractJdbc2Connection.java:586) at bitronix.tm.resource.jdbc.lrc.LrcConnectionHandle.setReadOnly(LrcConnectionHandle.java:149) at bitronix.tm.resource.jdbc.JdbcConnectionHandle.setReadOnly(JdbcConnectionHandle.java:346) at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.getTargetConnection(LazyConnectionDataSourceProxy.java:398) at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:364) at $Proxy46.createStatement(Unknown Source) at sun.reflect.GeneratedMethodAccessor95.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:225) at $Proxy46.createStatement(Unknown Source) at sun.reflect.GeneratedMethodAccessor194.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:50) at $Proxy56.createStatement(Unknown Source) at ome.security.basic.EventHandler.invoke(EventHandler.java:110) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:100) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy65.setFileId(Unknown Source) at sun.reflect.GeneratedMethodAccessor841.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:310) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:78) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:35) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy65.setFileId(Unknown Source) at sun.reflect.GeneratedMethodAccessor993.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at ome.services.blitz.util.IceMethodInvoker.callOrClose(IceMethodInvoker.java:257) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) at ome.services.throttling.Callback.run(Callback.java:55) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:37) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:115) at ome.services.blitz.impl.RawFileStoreI.setFileId_async(RawFileStoreI.java:55) at omero.api._RawFileStoreTie.setFileId_async(_RawFileStoreTie.java:78) at omero.api._RawFileStoreDisp.___setFileId(_RawFileStoreDisp.java:141) at omero.api._RawFileStoreDisp.__dispatch(_RawFileStoreDisp.java:284) at IceInternal.Incoming.invoke(Incoming.java:159) at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) at Ice.ConnectionI.message(ConnectionI.java:972) at IceInternal.ThreadPool.run(ThreadPool.java:577) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (org.postgresql.util.PSQLException): Cannot change transaction read-only property in the middle of a transaction." at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:501) at java.lang.Class.newInstance0(Class.java:350) at java.lang.Class.newInstance(Class.java:303) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.api._RawFileStoreDelM.setFileId(_RawFileStoreDelM.java:138) at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:184) at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:156) at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2746) ... 9 more
comment:7 Changed 14 years ago by jburel
- Owner set to jburel
Put jburel as owner. I will write a test to try to reproduce the logic that generated the bug
comment:8 Changed 14 years ago by jburel
- Milestone changed from OMERO-Beta4.2 to Unscheduled
A way to prevent the crash is to create each time a new raw file store service and close it.