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Task #10272 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: Imaris Big image

Reported by: wmoore Owned by:
Priority: critical Milestone: OMERO-4.4.9
Component: Import Version: 4.4.8
Keywords: FS Cc: fs@…, cxallan, ux@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

The image at /imaris/jake/p75Cherry M2 010-3~B.ims (8.7 GB, 63104 x 147328) imports OK in FS, but doesn't display in a big image viewer (except in Insight when zoomed out several levels). This is partly due to the tile size being reported as 63104 x 147328 (same size at the image).

Don't know what the main issue is here. The image is currently on gretzky, user-5:

https://gretzky.openmicroscopy.org.uk/omero/webclient/?show=image-116

Attachments (2)

imaris - tiles are bars in Insight.png (515.7 KB) - added by pwalczysko 11 years ago.
imaris in web - horizontal bars .png (19.8 KB) - added by pwalczysko 11 years ago.

Download all attachments as: .zip

Change History (18)

comment:1 Changed 11 years ago by pwalczysko

  • Cc fs@… ux@… added; jmoore removed

I thought this is a "must have" for the demo. How is it with the prospects of having it on Thursday for the big images import testing ? (if not, I will put it off the list).
@mlinkert-x, @jburel: what is the correct procedure to put this one into test_images_good ?

comment:2 Changed 11 years ago by mlinkert

I have a fix for this in the works and should have a PR open in time for testing on Thursday.

In terms of getting this into test_images_good, the best thing to do would be to make a 'qbi' folder under test_images_good/imaris/ and then copy from_skyking/imaris/jake/*.ims and from_skyking/imaris/jake/.bioformats into the 'qbi' folder. (For any other files, just copy to a relevant location under test_images_good and then send a message out so that Roger or I can make sure that everything is fine for the automated tests to pass.)

comment:3 Changed 11 years ago by mlinkert

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

Fixed as part of: https://github.com/openmicroscopy/bioformats/pull/375

You may want to reduce the compression level when viewing in Insight, otherwise the full-resolution images are likely to look a bit blocky.

comment:4 Changed 11 years ago by pwalczysko

@rleigh @mlinkert : I have copied the imaris file to test_images_good exaclty as indicated in the comment by mlinkert above.

comment:5 Changed 11 years ago by pwalczysko

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:6 follow-up: Changed 11 years ago by pwalczysko

During testing on 14-02-13 found out following:

Import okay (around 1 hour)

Thumbnails okay in Web and Insight

Viewing okay in Insight

Viewing not okay in Web - too slow (more than 5 mins when zoomed out for new tiles to upload) - not usable.
This might be connected to the fact, that the shape of the tiles is not square as usual.
Instead, the tiles appear as horizontal bars over the whole image length (both Web and Insight, only in Insight it is faster) - this means that much more information is uploaded to create the view in question, which takes then unsupportably long time to render.
See screenshot

Changed 11 years ago by pwalczysko

Changed 11 years ago by pwalczysko

comment:7 in reply to: ↑ 6 Changed 11 years ago by pwalczysko

Replying to pwalczysko:

During testing on 14-02-13 found out following:

Import okay (around 1 hour)

Thumbnails okay in Web and Insight

Viewing okay in Insight

Viewing not okay in Web - too slow (more than 5 mins when zoomed out for new tiles to upload) - not usable.
This might be connected to the fact, that the shape of the tiles is not square as usual.
Instead, the tiles appear as horizontal bars over the whole image length (both Web and Insight, only in Insight it is faster) - this means that much more information is uploaded to create the view in question, which takes then unsupportably long time to render.
See screenshot

Correction: also in Insight, the rendering takes just too long to be usable - strangely, it helps when the slidebar is moved a bit - the "tiles" are loaded up faster after you have moved the slide bar a bit

comment:8 Changed 11 years ago by mlinkert

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

New PR opened: https://github.com/openmicroscopy/bioformats/pull/384

The tile access time isn't changed much, but the sizes are now such that you only need to wait for ~2-8 tiles to load (instead of 30+), so it should look faster.

comment:9 Changed 11 years ago by mtbcarroll

It seems to work reasonably, but in the web view if I drag the bird's eye somewhere else, it's some minutes before I see any tiles at all.

comment:10 Changed 11 years ago by jmoore

Mark: I'd think the delay times for drag-n-drop are generally covered by #6850, perhaps multiplied by any general perf. issues on develop.

comment:11 Changed 11 years ago by pwalczysko

  • Priority changed from major to critical
  • Resolution fixed deleted
  • Status changed from closed to reopened

Imaris file failed to import on Windows (server mortar).
test_images_good/imaris/qbi/...


java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]", stacktrace=java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1698)
	at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:381)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:267)
	at omero.cmd.HandleI.steps(HandleI.java:435)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor255.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at $Proxy65.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:416)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at ome.services.util.Executor$Impl$1.call(Executor.java:447)
	at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	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._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:172)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:254)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:226)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1682)
	... 34 more
}

	at ome.formats.importer.ImportLibrary.getImportResponse(ImportLibrary.java:469)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:411)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6664)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6646)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1272)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6716)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6646)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1272)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]", stacktrace=java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1698)
	at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(ManagedImportRequestI.java:381)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:267)
	at omero.cmd.HandleI.steps(HandleI.java:435)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor255.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at $Proxy65.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:416)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at ome.services.util.Executor$Impl$1.call(Executor.java:447)
	at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:663)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy65.doWork(Unknown Source)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:416)

                        	at ome.services.util.Executor$Impl.execute(Executor.java:360)

                        	at ome.services.throttling.Adapter.run(Adapter.java:51)

                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)

                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:164)

                        	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

                        	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

                        	at java.lang.reflect.Method.invoke(Unknown Source)

                        	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:59)

                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

                        	at $Proxy95.saveToDB_async(Unknown Source)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:223)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:371)

                        	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.ValidationException"
    message = "No row with the given identifier exists: [ome.model.containers.Dataset#4]; nested exception is org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [ome.model.containers.Dataset#4]"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	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._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:172)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:254)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:226)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1682)
	... 34 more
}

	at ome.formats.importer.ImportLibrary.getImportResponse(ImportLibrary.java:469)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:411)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6664)
	... 12 more

comment:12 Changed 11 years ago by pwalczysko

  • Summary changed from Bug: Imaris Big image to RFE: Dataset disappeared - import failed

@ jmoore has advised this is a problem with a disappearance of Dataset 4. Not aware of deleting consciously any dataset, but cannot exclude some irregularities, as many actions were performed in preparations of the demo.

It would be good to have a procedure in place when a trivial mistake occurs like this, to import the data anyway (import should not fail because of this).

comment:13 Changed 11 years ago by mlinkert

  • Component changed from Bio-Formats to Import
  • Owner mlinkert deleted
  • Status changed from reopened to accepted

This latest issue is entirely different from what this ticket originally covered, though, right? If I understand correctly, it's not a Bio-Formats issue, so I'm changing the component and ownership.

comment:14 Changed 11 years ago by jamoore

  • Cc ux@… added; ux@… removed
  • Version set to 4.4.8

comment:15 Changed 11 years ago by jburel

  • Keywords FS removed
  • Summary changed from RFE: Dataset disappeared - import failed to Bug: Dataset disappeared - import failed

comment:16 Changed 11 years ago by jamoore

  • Keywords FS added
  • Resolution set to fixed
  • Status changed from accepted to closed
  • Summary changed from Bug: Dataset disappeared - import failed to Bug: Imaris Big image

Note: this ticket is very hard to understand. I'm rolling this back to being strictly an Imaris ticket and re-closing it. I've created a new ticket (#11430) where we can discuss Petr's second issue.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

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