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Task #10180 (closed)

Opened 7 years ago

Closed 7 years ago

Freeze while importing Olympus ScanR

Reported by: rkferguson Owned by: jburel
Priority: major Milestone: OMERO-4.4.7
Component: Insight Version: n.a.
Keywords: FS Cc: fs@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2013-02-12 (5)

Description

User-8

Gretzky

OMERO.insight-4.4.4-823-b02a128-dirty-ice33-b116-mac

Affected: test_images_good /scanr

Importing screen by itself (other images already successfully imported).

From within CLS using images on local HD.

Import completed successfully in import window.
Clicked "View" - taken to Screen tab.
When initially selected screen - no thumbnails rendered - just showing as blank.
Double clicked on blank thumbnail about in the middle of row G1 (not exactly sure which one) - got viewer opening progress bar.
Stalled like that for about a minute, then rendered thumbnails down to first image in G1 row and showed 50% on progress bar at bottom of middle pane.
Clicked Cancel on the viewer opening window and tried double clicking on thumbnail that had rendered (first image in row A1).
Had a flash of a dialog warning but only for a fraction of a second before it disappeared - may have been connection interruption - too fast to read.
Insight froze and only action I could do was switch to Projects tab which then froze as well and I could do nothing.
Had to Force Quit Insight.
Error message from log below.
Restarted Insight and logged in again.
Behaving as normal - opened Screens tab - thumbnails still only 50% rendered (up to G1 first image) i.e. where it had crashed. Progress bar active.
Waited about 1 minute and rendering of rest of thumbnails completed.
Checks of all images show expected thumbnails, rendering and behaviour, so import and final rendering appears to be normal and unaffected.

2013-01-16 09:23:40,939 INFO [ ome.formats.importer.ImportConfig] (Thread-105) Bioformats version: 4.5-DEV revision: fb46c88 date: 16 January 2013
2013-01-16 09:36:37,803 DEBUG [copy.shoola.env.data.DataServicesFactory] (Thread-115) Connection ErrorIce.SocketException
    error = 0
 at IceInternal.Selector.setInterrupt(Selector.java:347)
 at IceInternal.Selector.remove(Selector.java:107)
 at IceInternal.ThreadPool.finish(ThreadPool.java:183)
 at Ice.ConnectionI.setState(ConnectionI.java:1454)
 at Ice.ConnectionI.setState(ConnectionI.java:1351)
 at Ice.ConnectionI.sendRequest(ConnectionI.java:383)
 at IceInternal.ConnectionRequestHandler.sendRequest(ConnectionRequestHandler.java:36)
 at IceInternal.Outgoing.invoke(Outgoing.java:66)
 at omero.api._IMetadataDelM.loadAnnotations(_IMetadataDelM.java:260)
 at omero.api.IMetadataPrxHelper.loadAnnotations(IMetadataPrxHelper.java:320)
 at omero.api.IMetadataPrxHelper.loadAnnotations(IMetadataPrxHelper.java:292)
 at org.openmicroscopy.shoola.env.data.OMEROGateway.loadAnnotations(OMEROGateway.java:2739)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredAnnotations(OmeroMetadataServiceImpl.java:1022)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:707)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:811)
 at org.openmicroscopy.shoola.env.data.views.calls.StructuredAnnotationLoader$6.doCall(StructuredAnnotationLoader.java:211)
 at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
 at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
 at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
 at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
 at java.lang.Thread.run(Thread.java:680)
Caused by: java.nio.channels.ClosedByInterruptException
 at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:184)
 at sun.nio.ch.SinkChannelImpl.write(SinkChannelImpl.java:153)
 at IceInternal.Selector.setInterrupt(Selector.java:343)
 ... 22 more
Connection ErrorIce.SocketException
    error = 0
 at IceInternal.Selector.setInterrupt(Selector.java:347)
 at IceInternal.Selector.remove(Selector.java:107)
 at IceInternal.ThreadPool.finish(ThreadPool.java:183)
 at Ice.ConnectionI.setState(ConnectionI.java:1454)
 at Ice.ConnectionI.setState(ConnectionI.java:1351)
 at Ice.ConnectionI.sendRequest(ConnectionI.java:383)
 at IceInternal.ConnectionRequestHandler.sendRequest(ConnectionRequestHandler.java:36)
 at IceInternal.Outgoing.invoke(Outgoing.java:66)
 at omero.api._IMetadataDelM.loadAnnotations(_IMetadataDelM.java:260)
 at omero.api.IMetadataPrxHelper.loadAnnotations(IMetadataPrxHelper.java:320)
 at omero.api.IMetadataPrxHelper.loadAnnotations(IMetadataPrxHelper.java:292)
 at org.openmicroscopy.shoola.env.data.OMEROGateway.loadAnnotations(OMEROGateway.java:2739)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredAnnotations(OmeroMetadataServiceImpl.java:1022)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:707)
 at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.loadStructuredData(OmeroMetadataServiceImpl.java:811)
 at org.openmicroscopy.shoola.env.data.views.calls.StructuredAnnotationLoader$6.doCall(StructuredAnnotationLoader.java:211)
 at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
 at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
 at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
 at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
 at java.lang.Thread.run(Thread.java:680)
Caused by: java.nio.channels.ClosedByInterruptException
 at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:184)
 at sun.nio.ch.SinkChannelImpl.write(SinkChannelImpl.java:153)
 at IceInternal.Selector.setInterrupt(Selector.java:343)
 ... 22 more
Exception in thread "Thread-115"

Change History (2)

comment:1 Changed 7 years ago by jmoore

This is the same error message in Petr's log for #10116. Linking this there.

comment:2 Changed 7 years ago by jmoore

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

Closing in favor of #10116

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