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Task #12250 (closed)

Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

Bug: Plate imported twice

Reported by: cblackburn Owned by: dlindner
Priority: blocker Milestone: 5.0.2
Component: Insight Version: 5.0.1
Keywords: n.a. Cc: ux@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

In trying to set up a scenario with one plate in a screen and another not in a screen I did this, all from Insight:

  • create a screen
  • import a MIAS plate into the screen
  • as soon as clicking Import on the first import import the same plate with no screen.

This produces three separate imports. One in the screen and two outside. The screenshots show the count (2 or 1) and the size reflect the double import. The managed repository shows three uploads:

lifesci-9511:ome cblackburn$ ls -l ~/var/omero50/ManagedRepository/user-1_52/2014-05/01/
total 105808
drwxr-xr-x  3 cblackburn  staff       102  1 May 16:45 16-45-52.061
-rw-r--r--  1 cblackburn  staff  18034883  1 May 17:20 16-45-52.061.log
drwxr-xr-x  3 cblackburn  staff       102  1 May 16:47 16-47-28.190
-rw-r--r--  1 cblackburn  staff  18014363  1 May 17:21 16-47-28.190.log
drwxr-xr-x  3 cblackburn  staff       102  1 May 16:48 16-48-54.697
-rw-r--r--  1 cblackburn  staff  18014552  1 May 17:23 16-48-54.697.log

In reproducing this bug I had an additional bug of the imports not seeming to finish. The import bars seemed both stuck on about 50% as generating thumbnails for well over 40 minutes. However, I closed the import window and the imports had in fact completed. Noting interesting in the Insight logs.

Attachments (3)

singleimport.png​ (38.7 KB) - added by cblackburn 5 years ago.
Single correct import into screen
doubleimport.png​ (38.8 KB) - added by cblackburn 5 years ago.
Incorrect duplicate import
threeplates.png​ (37.2 KB) - added by cblackburn 5 years ago.
Three plates show in tree view

Download all attachments as: .zip

Change History (20)

Changed 5 years ago by cblackburn

Single correct import into screen

Changed 5 years ago by cblackburn

Incorrect duplicate import

Changed 5 years ago by cblackburn

Three plates show in tree view

comment:1 Changed 5 years ago by cblackburn

The log files are too big to upload easily but two end like this:

...
2014-05-01 17:22:53,449 INFO  [       ome.security.basic.CurrentDetails] (l.Server-1) Adding log:INSERT,class ome.model.display.RenderingDef,98
2014-05-01 17:22:53,450 INFO  [       ome.security.basic.CurrentDetails] (l.Server-1) Adding log:INSERT,class ome.model.display.ChannelBinding,195
2014-05-01 17:22:53,450 INFO  [       ome.security.basic.CurrentDetails] (l.Server-1) Adding log:INSERT,class ome.model.display.ChannelBinding,196
2014-05-01 17:22:56,748 INFO  [ o.s.b.r.ManagedImportRequestI.@65a506b5] (2-thread-1) Cancelled
2014-05-01 17:22:56,748 INFO  [ o.s.b.r.ManagedImportRequestI.@65a506b5] (2-thread-1) Cancelled
2014-05-01 17:22:56,750 DEBUG [ o.s.b.r.ManagedImportRequestI.@65a506b5] (2-thread-1) Request cancelled by Ice.ObjectNotExistException
    id.name = "13a33f33-268b-48eb-9834-b6d7180bd6a5omero.api.IQuery"
    id.category = "8a03952d-ca17-4628-8875-ec6b537830cb"
    facet = ""
    operation = "get"
2014-05-01 17:22:56,754 INFO  [    o.s.blitz.repo.ManagedImportRequestI] (2-thread-1) Finalizing log file.

and one (with the earliest timestamp) ends like this:

2014-05-01 17:20:02,441 INFO  [       ome.security.basic.CurrentDetails] (l.Server-6) Adding log:INSERT,class ome.model.display.ChannelBinding,132
2014-05-01 17:20:03,221 DEBUG [                    omero.util.IceMapper] (l.Server-9) Handling:
ome.conditions.SessionTimeoutException: Session (started=2014-05-01 16:45:11.375, hits=15324, last access=2014-05-01 17:03:07.129) exceeded timeToIdle (600000) by 416091 ms
	at ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:424) ~[server.jar:na]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:353) ~[server.jar:na]
	at ome.services.sessions.SessionManagerImpl.getUserRoles(SessionManagerImpl.java:573) ~[server.jar:na]
	at ome.security.basic.BasicMethodSecurity.checkMethod(BasicMethodSecurity.java:117) ~[server.jar:na]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:81) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy96.createThumbnailsByLongestSideSet(Unknown Source) ~[na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) ~[blitz.jar:na]
	at ome.services.throttling.Callback.run(Callback.java:56) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) ~[blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149) ~[blitz.jar:na]
	at ome.services.blitz.impl.ThumbnailStoreI.createThumbnailsByLongestSideSet_async(ThumbnailStoreI.java:73) ~[blitz.jar:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at omero.cmd.CallContext.invoke(CallContext.java:78) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy97.createThumbnailsByLongestSideSet_async(Unknown Source) ~[na:na]
	at omero.api._ThumbnailStoreTie.createThumbnailsByLongestSideSet_async(_ThumbnailStoreTie.java:106) ~[blitz.jar:na]
	at omero.api._ThumbnailStoreDisp.___createThumbnailsByLongestSideSet(_ThumbnailStoreDisp.java:548) ~[blitz.jar:na]
	at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:656) ~[blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:159) ~[ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) ~[ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:972) ~[ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:577) ~[ice.jar:na]
	at IceInternal.ThreadPool.access$100(ThreadPool.java:12) ~[ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) ~[ice.jar:na]
2014-05-01 17:20:03,223 DEBUG [                    omero.util.IceMapper] (l.Server-9) Handling:
omero.SessionTimeoutException: null
	at omero.util.IceMapper.handleException(IceMapper.java:1289) ~[blitz.jar:na]
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:181) ~[blitz.jar:na]
	at ome.services.throttling.Callback.run(Callback.java:56) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) ~[blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149) ~[blitz.jar:na]
	at ome.services.blitz.impl.ThumbnailStoreI.createThumbnailsByLongestSideSet_async(ThumbnailStoreI.java:73) ~[blitz.jar:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at omero.cmd.CallContext.invoke(CallContext.java:78) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy97.createThumbnailsByLongestSideSet_async(Unknown Source) ~[na:na]
	at omero.api._ThumbnailStoreTie.createThumbnailsByLongestSideSet_async(_ThumbnailStoreTie.java:106) ~[blitz.jar:na]
	at omero.api._ThumbnailStoreDisp.___createThumbnailsByLongestSideSet(_ThumbnailStoreDisp.java:548) ~[blitz.jar:na]
	at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:656) ~[blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:159) ~[ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) ~[ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:972) ~[ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:577) ~[ice.jar:na]
	at IceInternal.ThreadPool.access$100(ThreadPool.java:12) ~[ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) ~[ice.jar:na]
2014-05-01 17:20:03,276 INFO  [ o.s.b.r.ManagedImportRequestI.@41c7f034] (2-thread-2) Cancelled
2014-05-01 17:20:03,293 DEBUG [                    omero.util.IceMapper] (l.Server-0) Handling:
ome.conditions.SessionTimeoutException: Session (started=2014-05-01 16:45:11.375, hits=15324, last access=2014-05-01 17:03:07.129) exceeded timeToIdle (600000) by 416163 ms
	at ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:424) ~[server.jar:na]
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:353) ~[server.jar:na]
	at ome.services.sessions.SessionManagerImpl.getUserRoles(SessionManagerImpl.java:573) ~[server.jar:na]
	at ome.security.basic.BasicMethodSecurity.checkMethod(BasicMethodSecurity.java:117) ~[server.jar:na]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:81) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy78.get(Unknown Source) ~[na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) ~[blitz.jar:na]
	at ome.services.throttling.Callback.run(Callback.java:56) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) ~[blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149) ~[blitz.jar:na]
	at ome.services.blitz.impl.QueryI.get_async(QueryI.java:110) ~[blitz.jar:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at omero.cmd.CallContext.invoke(CallContext.java:78) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy79.get_async(Unknown Source) ~[na:na]
	at omero.api._IQueryTie.get_async(_IQueryTie.java:127) ~[blitz.jar:na]
	at omero.api._IQueryDisp.___get(_IQueryDisp.java:170) ~[blitz.jar:na]
	at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:516) ~[blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:159) ~[ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) ~[ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:972) ~[ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:577) ~[ice.jar:na]
	at IceInternal.ThreadPool.access$100(ThreadPool.java:12) ~[ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) ~[ice.jar:na]
2014-05-01 17:20:03,299 DEBUG [                    omero.util.IceMapper] (l.Server-0) Handling:
omero.SessionTimeoutException: null
	at omero.util.IceMapper.handleException(IceMapper.java:1289) ~[blitz.jar:na]
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:181) ~[blitz.jar:na]
	at ome.services.throttling.Callback.run(Callback.java:56) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) ~[blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149) ~[blitz.jar:na]
	at ome.services.blitz.impl.QueryI.get_async(QueryI.java:110) ~[blitz.jar:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_25]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_25]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_25]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_25]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at omero.cmd.CallContext.invoke(CallContext.java:78) ~[blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy79.get_async(Unknown Source) ~[na:na]
	at omero.api._IQueryTie.get_async(_IQueryTie.java:127) ~[blitz.jar:na]
	at omero.api._IQueryDisp.___get(_IQueryDisp.java:170) ~[blitz.jar:na]
	at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:516) ~[blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:159) ~[ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) ~[ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:972) ~[ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:577) ~[ice.jar:na]
	at IceInternal.ThreadPool.access$100(ThreadPool.java:12) ~[ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) ~[ice.jar:na]
2014-05-01 17:20:03,594 INFO  [ o.s.b.r.ManagedImportRequestI.@41c7f034] (2-thread-2) Cancelled
2014-05-01 17:20:03,596 DEBUG [ o.s.b.r.ManagedImportRequestI.@41c7f034] (2-thread-2) Request cancelled by omero.SessionTimeoutException
    serverStackTrace = "ome.conditions.SessionTimeoutException: Session (started=2014-05-01 16:45:11.375, hits=15324, last access=2014-05-01 17:03:07.129) exceeded timeToIdle (600000) by 416163 ms
                        	at ome.services.sessions.state.SessionCache.getDataNullOrThrowOnTimeout(SessionCache.java:424)
                        	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:353)
                        	at ome.services.sessions.SessionManagerImpl.getUserRoles(SessionManagerImpl.java:573)
                        	at ome.security.basic.BasicMethodSecurity.checkMethod(BasicMethodSecurity.java:117)
                        	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:81)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy78.get(Unknown Source)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:606)
                        	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
                        	at ome.services.blitz.impl.QueryI.get_async(QueryI.java:110)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:606)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at omero.cmd.CallContext.invoke(CallContext.java:78)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy79.get_async(Unknown Source)
                        	at omero.api._IQueryTie.get_async(_IQueryTie.java:127)
                        	at omero.api._IQueryDisp.___get(_IQueryDisp.java:170)
                        	at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:516)
                        	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.SessionTimeoutException"
    message = "Session (started=2014-05-01 16:45:11.375, hits=15324, last access=2014-05-01 17:03:07.129) exceeded timeToIdle (600000) by 416163 ms"
2014-05-01 17:20:03,608 WARN  [  ome.security.basic.BasicSecurityWiring] (l.Server-2) SessionTimeoutException on close:8a03952d-ca17-4628-8875-ec6b537830cb
2014-05-01 17:20:03,665 DEBUG [                omero.util.ServantHolder] (l.Server-2) Removed omero.api._RawFileStoreTie@ec4f291f from omero.util.ServantHolder@17095b7 as cb95b446-4e15-4c05-b9f2-07a12d825a2eomero.api.RawFileStore
2014-05-01 17:20:03,665 INFO  [                      omero.cmd.SessionI] (l.Server-2) Unregistered servant:8a03952d-ca17-4628-8875-ec6b537830cb/cb95b446-4e15-4c05-b9f2-07a12d825a2eomero.api.RawFileStore(omero.api._RawFileStoreTie@ec4f291f)
2014-05-01 17:20:03,668 WARN  [  ome.security.basic.BasicSecurityWiring] (l.Server-3) SessionTimeoutException on close:8a03952d-ca17-4628-8875-ec6b537830cb
2014-05-01 17:20:03,670 DEBUG [                omero.util.ServantHolder] (l.Server-3) Removed omero.api._RawPixelsStoreTie@ec1e5716 from omero.util.ServantHolder@17095b7 as b12836b9-c779-4b87-8622-a6f1934c6f52omero.api.RawPixelsStore
2014-05-01 17:20:03,670 INFO  [                      omero.cmd.SessionI] (l.Server-3) Unregistered servant:8a03952d-ca17-4628-8875-ec6b537830cb/b12836b9-c779-4b87-8622-a6f1934c6f52omero.api.RawPixelsStore(omero.api._RawPixelsStoreTie@ec1e5716)
2014-05-01 17:20:03,671 WARN  [  ome.security.basic.BasicSecurityWiring] (l.Server-8) SessionTimeoutException on close:8a03952d-ca17-4628-8875-ec6b537830cb
2014-05-01 17:20:03,711 DEBUG [                omero.util.ServantHolder] (l.Server-8) Removed omero.api._ThumbnailStoreTie@e4de6a8a from omero.util.ServantHolder@17095b7 as d8903094-1953-4d9b-8450-7bf7ad7e9571omero.api.ThumbnailStore
2014-05-01 17:20:03,711 INFO  [                      omero.cmd.SessionI] (l.Server-8) Unregistered servant:8a03952d-ca17-4628-8875-ec6b537830cb/d8903094-1953-4d9b-8450-7bf7ad7e9571omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@e4de6a8a)
2014-05-01 17:20:03,711 DEBUG [                omero.util.ServantHolder] (l.Server-7) Removed omero.api._MetadataStoreTie@fa2edcf8 from omero.util.ServantHolder@17095b7 as 869f8ca0-e4bd-4b38-889b-b4a0b1da1eb2omero.api.MetadataStore
2014-05-01 17:20:03,711 INFO  [                      omero.cmd.SessionI] (l.Server-7) Unregistered servant:8a03952d-ca17-4628-8875-ec6b537830cb/869f8ca0-e4bd-4b38-889b-b4a0b1da1eb2omero.api.MetadataStore(omero.api._MetadataStoreTie@fa2edcf8)
2014-05-01 17:20:14,550 INFO  [    o.s.blitz.repo.ManagedImportRequestI] (2-thread-2) Finalizing log file.

comment:2 Changed 5 years ago by cblackburn

Note also that I killed the import window at about 17:50 to give an idea of the display hang following the import.

comment:3 Changed 5 years ago by jburel

The first problem looks like an issue reported by simon a while back that we never managed to reproduce. Simon could not remember how it happens.
The second one looks more like an issue in the importer itself (not insight code)

comment:4 Changed 5 years ago by jburel

  • Cc ux@… added; jamoore pwalczysko removed

comment:5 Changed 5 years ago by jburel

I followed exactly the steps described above and I have not been able to reproduce the issue.
You imported locally. Correct?

comment:6 Changed 5 years ago by cblackburn

Yes it was local. Reproducible too.

comment:7 Changed 5 years ago by jburel

  • Owner changed from jburel to dlindner

Passing to Dominik for further investigations.

comment:8 Changed 5 years ago by mtbcarroll

I failed to reproduce this locally under Linux with 5.1-latest.

comment:9 Changed 5 years ago by dlindner

I only managed to reproduce this problem with two parallel imports (as described) and an empty database; subsequent imports worked as expected. I. e. very specific setup, is it therefore really a blocker?
Also for some reason this problem seems to be fixed in the develop branch, just occures in dev_5_0.

comment:10 Changed 5 years ago by mtbcarroll

Parallel imports aren't unlikely; I guess it depends how sure we are that it only happens with an empty database. The 5.0/5.1 difference is curious.

comment:11 Changed 5 years ago by pwalczysko

Yes, but empty db is highly unlikely. That is why I never saw this.

comment:12 Changed 5 years ago by dlindner

Sorry, the empty database was coincidence, the problem also occurs when there are already screens in the database; hard to trace, because it happens quite randomly.

comment:13 Changed 5 years ago by pwalczysko

That is quite serious then indeed.

comment:14 Changed 5 years ago by mtbcarroll

I just managed to reproduce this under Linux (starting with an empty database) in testing ​https://github.com/openmicroscopy/openmicroscopy/pull/2445.

comment:15 Changed 5 years ago by jburel

  • Resolution set to fixed
  • Status changed from new to closed

PR opened ​https://github.com/openmicroscopy/openmicroscopy/pull/2473

comment:16 Changed 5 years ago by jamoore

"Bugfix: Prevent user/group deletion (rebased onto dev_5_0)" ?

comment:17 Changed 5 years ago by jburel

sorry I put the wrong PR: correct one ​https://github.com/openmicroscopy/openmicroscopy/pull/2474

Last edited 5 years ago by jburel (previous) (diff)
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