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Task #10287 (closed)

Opened 11 years ago

Closed 11 years ago

BUG: Error on display of .ndpi

Reported by: pwalczysko Owned by:
Priority: critical Milestone: 5.0.0-beta1
Component: Import Version: n.a.
Keywords: FS Cc: fs@…, ux@…,
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: FS Demo 2

Description

Gretzky, build OMERO.insight-4.4.4-1196-a8163de-dirty-ice33-b153-mac.
Importing test_images_good/hamamatsu/david/2009-12-18 09.20.56.ndpi .
Import failed.

Ice.CommunicatorDestroyedException
	at IceInternal.Instance.objectAdapterFactory(Instance.java:122)
	at Ice.ObjectPrxHelperBase.createDelegate(ObjectPrxHelperBase.java:997)
	at Ice.ObjectPrxHelperBase.__getDelegate(ObjectPrxHelperBase.java:946)
	at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:593)
	at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:567)
	at ome.formats.importer.ImportLibrary.cleanupUpload(ImportLibrary.java:333)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:323)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:380)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6645)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6628)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1263)
	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:6692)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6628)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1263)
	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: Ice.CommunicatorDestroyedException
	at IceInternal.Instance.objectAdapterFactory(Instance.java:122)
	at Ice.ObjectPrxHelperBase.createDelegate(ObjectPrxHelperBase.java:997)
	at Ice.ObjectPrxHelperBase.__getDelegate(ObjectPrxHelperBase.java:946)
	at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:593)
	at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:567)
	at ome.formats.importer.ImportLibrary.cleanupUpload(ImportLibrary.java:333)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:323)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:380)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6645)
	... 12 more

Change History (5)

comment:1 Changed 11 years ago by jmoore

This points to your client losing its connection. Possibly related to gretzky hanging (OutOfMemory?).

comment:2 Changed 11 years ago by pwalczysko

Just found out that import of /Volumes/ome/data_repo/test_images_good/hamamatsu/david/2009-12-18 09.20.56.ndpi went fine on Gretzky. The viewing was not possible though - the tiles were replaced by horizontal lines in Inishgth. When viewing this image in Web, a stacktrace appears. After refreshing of the browser, Internal server error appears.

Identical problem occurred with
/Volumes/ome/data_repo/test_images_good/hamamatsu/david/2009-12-18 09.27.02.ndpi

and (the same display problems, but did not cause a stack trace in Web)
/Volumes/ome/data_repo/test_images_good/hamamatsu/david/2009-12-18 09.33.21.ndpi

Last edited 11 years ago by pwalczysko (previous) (diff)

comment:3 Changed 11 years ago by pwalczysko

  • Keywords import removed
  • Milestone changed from OMERO-4.5 to OMERO-5
  • Sprint changed from 2013-02-12 (5) to FS Demo 2
  • Summary changed from BUG: Error on import of .ndpi to BUG: Error on display of .ndpi

comment:4 Changed 11 years ago by mlinkert

As mentioned in the meeting, if this PR wasn't in the build: https://github.com/openmicroscopy/bioformats/pull/159

then it's expected that .ndpi display will be wrong.

comment:5 Changed 11 years ago by jmoore

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

Added to #10381 as a duplicate. If we decide that we need to handle the CommunicatorDestroyedException differently than the CommunicatorLostException we may want to re-open.

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