Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #12676 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: Connection lost - Import As

Reported by: pwalczysko Owned by: jburel
Priority: critical Milestone: 5.1.0
Component: Insight Version: 5.1.0-m1
Keywords: n.a. Cc: ux@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

After change of user which you are importing as, you will get connection lost message.

  • login as admin to octopus
  • Import from_skyking/mias/frans/siRNA_PRIM1_03102008/ into read-only-1 as user-3 (target the import into a screen)
  • start import
  • while the import for user-3 is still running, import the same plate for user-4
  • error occurs (see below)


Slight varioation:

  • import into private-1 as user-1 and user-2, targeting the import into a project
  • observe message "connection destroyed, application will now exit"
  • Insight exits after clicking on OK 
omero.ClientError: Call createSession() to login.
	at omero.client.getSession(client.java:522)
	at omero.model.DetailsI.<init>(DetailsI.java:61)
	at omero.model.DetailsI$1.create(DetailsI.java:38)
	at IceInternal.BasicStream$EncapsDecoder.newInstance(BasicStream.java:2854)
	at IceInternal.BasicStream$EncapsDecoder10.readInstance(BasicStream.java:3279)
	at IceInternal.BasicStream$EncapsDecoder10.readPendingObjects(BasicStream.java:3235)
	at IceInternal.BasicStream.readPendingObjects(BasicStream.java:584)
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:198)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:581)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:553)
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:111)
	at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6676)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1284)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6707)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1284)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)
Caused by: omero.ClientError: Call createSession() to login.
	at omero.client.getSession(client.java:522)
	at omero.model.DetailsI.<init>(DetailsI.java:61)
	at omero.model.DetailsI$1.create(DetailsI.java:38)
	at IceInternal.BasicStream$EncapsDecoder.newInstance(BasicStream.java:2854)
	at IceInternal.BasicStream$EncapsDecoder10.readInstance(BasicStream.java:3279)
	at IceInternal.BasicStream$EncapsDecoder10.readPendingObjects(BasicStream.java:3235)
	at IceInternal.BasicStream.readPendingObjects(BasicStream.java:584)
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:198)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:581)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:553)
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:111)
	at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6676)
	... 12 more

Change History (6)

comment:1 Changed 9 years ago by pwalczysko

In another variation of the workflow, I get after importing for user-3 and immediately for user-4 first the dialog "trying to reconnect", then import failure with 

org.openmicroscopy.shoola.env.data.DSOutOfServiceException: Cannot access the Import service.
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportStore(OMEROGateway.java:1309)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6655)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1284)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6707)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1284)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)
Caused by: org.openmicroscopy.shoola.env.data.DSOutOfServiceException: Cannot access the Import service.
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportStore(OMEROGateway.java:1309)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6655)
	... 12 more

comment:2 Changed 9 years ago by jburel

  • Milestone changed from 5.0.7 to 5.1.0
  • Priority changed from major to critical

Moving to 5.1 as a critical. Won't be doable for 5.0.7

comment:3 Changed 9 years ago by pwalczysko

  • Version changed from 5.0.6 to 5.1.0-m1

comment:4 Changed 9 years ago by pwalczysko

I cannot repeat it. It seems to work fine on trout merge.

comment:5 Changed 9 years ago by jburel

I cannot reproduce the error. The only problem I noticed is a black thumbnail
see

Error retrieving Pixels id:24307. Pixels set does not exist or the user id:7 has insufficient permissions to retrieve it.
                        	at ome.services.ThumbnailCtx.getPixels(ThumbnailCtx.java:444)
                        	at ome.services.ThumbnailBean.setPixelsId(ThumbnailBean.java:278)
                        	at sun.reflect.GeneratedMethodAccessor1020.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

I am going to see if I can fix the problem but not a blocker.

comment:6 Changed 9 years ago by jburel

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

see ​https://github.com/openmicroscopy/openmicroscopy/pull/3657

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

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.64141 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!