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Task #12164 (closed)

Opened 10 years ago

Closed 9 years ago

BUG: tagging on import stage

Reported by: pwalczysko Owned by: jburel
Priority: major Milestone: 5.1.0-m4
Component: Insight Version: 5.0.0
Keywords: n.a. Cc: ux@…, spli
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by pwalczysko)

Noted by Simon during 5.0.1-rc1 testing.
See line 32 ​https://docs.google.com/spreadsheet/ccc?key=0AoKiTAl8UOxndDAxRmdETDRFSm44RC0xaEhXd2xsSlE&usp=drive_web#gid=13

Simon:
Import (UI) step 9: Select multiple files from test_images_good/ome (note select individual files, not the folder. Under options create a new tag. Import. The tag is created but not attached to the images. Similarly if a preexisting tag is selected. Note this does work if you select a folder instead of individual images.

PW: Make sure you pick test_images_good/ome-tiff/*.* images to repeat this bug. Appears on Mac as well as Windows.

Change History (8)

comment:1 Changed 10 years ago by jburel

The tagging section of the importer was not modified during the major refactoring.
Gus: could you have a look at it before making any changes?

comment:2 Changed 10 years ago by rkferguson

@jburel - OK

comment:3 Changed 10 years ago by rkferguson

@jburel - I have tested this with 5.0.1 on Gretzky with the following results:


Import 5 test images as folder

  • new project
  • dataset from folder
  • attach existing and new tag
  • Works as expected

Import 5 test images as folder

  • no project
  • dataset from folder
  • attach existing and new tag
  • Works as expected

Import test images as 5 selected images

  • new project
  • dataset from folder
  • attach existing and new tag
  • Works as expected

Import test images as 5 selected images

  • no project
  • dataset from folder
  • attach existing and new tag
  • Works as expected

Import test images as 5 selected images

  • no project
  • new dataset
  • attach existing and new tag
  • Works as expected

Import test images as 1 selected image

  • new project
  • dataset from folder
  • attach existing and new tag
  • Works as expected

Import test image as 1 selected image

  • no project
  • dataset from folder
  • attach existing and new tag
  • Neither tag attached

Repeated - Import test image as 1 selected image

  • no project
  • dataset from folder
  • attach existing and new tag
  • Both tags attached as expected


So it looks as if the bug is intermittent.
Not sure what to do about getting it sorted.
Don't really see what we should be scoping here.

comment:4 Changed 10 years ago by rkferguson

I have had a look at the log and the two single image imports (first successfully attached tags, second failed to attach tags) and the look exactly the same.
However there was a connection error in between.
Don't know if tho is in any way relevant.

rue 
2014-04-08 10:00:31,215 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-151) Cached networkup: true 
2014-04-08 10:00:31,218 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-152) Cached networkup: true 
2014-04-08 10:00:31,229 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-152) Cached networkup: true 
2014-04-08 10:00:31,242 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-153) Cached networkup: true 
2014-04-08 10:00:31,255 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-153) Cached networkup: true 
2014-04-08 10:00:31,263 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-154) Cached networkup: true 
2014-04-08 10:00:31,289 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-154) Cached networkup: true 
2014-04-08 10:00:37,267 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-155) Count: 2  2 
2014-04-08 10:00:37,267 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-156) Count: 2  2 
2014-04-08 10:00:37,267 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-155) Network status: true (in 0 ms.) use cached value: true 
2014-04-08 10:00:37,267 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-156) Network status: true (in 0 ms.) use cached value: true 
2014-04-08 10:01:11,423 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-157) Count: 2  2 
2014-04-08 10:01:11,423 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-157) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:01:27,674 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:01:27,674 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:01:27,868 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-158) Cached networkup: true 
2014-04-08 10:01:28,142 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-158) Cached networkup: true 
2014-04-08 10:01:28,207 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-158) Cached networkup: true 
2014-04-08 10:01:28,216 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:01:28,216 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:01:28,217 INFO  [   ome.formats.importer.ImportCandidates] (Thread-158) Depth: 4 Metadata Level: MINIMUM 
2014-04-08 10:01:28,225 INFO  [                loci.formats.ImageReader] (Thread-158) APNGReader initializing /Users/rkferguson/Documents/1 OME/4 Data/Test Images Small - One/Test Image 01.png 
2014-04-08 10:01:28,227 INFO  [   ome.formats.importer.ImportCandidates] (Thread-158) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 8ms. (10ms total) [0 unknowns] 
2014-04-08 10:01:28,227 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:01:28,228 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:01:28,228 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-158) Cached networkup: true 
2014-04-08 10:01:28,287 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:01:28,287 INFO  [       ome.formats.importer.ImportConfig] (Thread-158) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:01:28,756 INFO  [      o.f.i.transfers.UploadFileTransfer] (Thread-158) Transferring /Users/rkferguson/Documents/1 OME/4 Data/Test Images Small - One/Test Image 01.png... 
2014-04-08 10:01:29,002 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-158) Cached networkup: true 
2014-04-08 10:01:30,902 DEBUG [          o.o.shoola.util.NetworkChecker] (.Client-11) Cached networkup: true 
2014-04-08 10:01:30,902 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-160) Cached networkup: true 
2014-04-08 10:01:31,073 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-161) Cached networkup: true 
2014-04-08 10:01:51,403 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-162) Count: 2  2 
2014-04-08 10:01:51,404 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-162) Network status: true (in 0 ms.) use cached value: true 
2014-04-08 10:01:51,413 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-163) Cached networkup: true 
2014-04-08 10:01:55,914 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-164) Cached networkup: true 
2014-04-08 10:01:56,106 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-164) Cached networkup: true 
2014-04-08 10:01:56,131 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-165) Cached networkup: true 
2014-04-08 10:02:00,363 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Count: 2  2 
2014-04-08 10:02:00,363 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-167) Count: 2  2 
2014-04-08 10:02:00,363 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-168) Count: 2  2 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-168) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-167) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-167) Cached networkup: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-167) Cached networkup: true 
2014-04-08 10:02:00,364 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-167) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,365 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,366 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-166) Cached networkup: true 
2014-04-08 10:02:00,367 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-169) Cached networkup: true 
2014-04-08 10:02:00,392 DEBUG [          o.o.shoola.util.NetworkChecker] (entQueue-0) Cached networkup: true 
2014-04-08 10:02:00,397 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-169) Cached networkup: true 
2014-04-08 10:02:00,402 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-171) Cached networkup: true 
2014-04-08 10:02:00,548 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-171) Cached networkup: true 
2014-04-08 10:02:00,551 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-172) Cached networkup: true 
2014-04-08 10:02:00,572 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-173) Cached networkup: true 
2014-04-08 10:02:00,632 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-170) Cached networkup: true 
2014-04-08 10:02:00,711 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-173) Cached networkup: true 
2014-04-08 10:02:00,729 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-172) Cached networkup: true 
2014-04-08 10:02:27,675 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:02:27,676 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:03:27,678 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:03:27,678 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:03:45,155 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-174) Count: 2  2 
2014-04-08 10:03:45,155 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-174) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:04:27,679 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:04:27,680 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:04:52,208 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-175) Count: 2  2 
2014-04-08 10:04:52,209 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-175) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:04:52,246 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-175) Cached networkup: true 
2014-04-08 10:04:57,833 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-176) Count: 2  2 
2014-04-08 10:04:57,833 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-176) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:05:27,685 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:05:27,685 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:06:27,686 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:06:27,687 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:07:27,688 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:07:27,689 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:08:27,691 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:08:27,692 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 2 ms.) use cached value: false 
2014-04-08 10:09:27,693 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:09:27,693 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:10:27,698 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:10:27,698 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:11:27,700 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:11:27,700 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:12:27,701 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:12:27,702 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:13:27,704 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:13:27,704 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 0 ms.) use cached value: false 
2014-04-08 10:14:27,705 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:14:27,706 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 2 ms.) use cached value: false 
2014-04-08 10:15:27,711 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:15:27,711 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:16:27,713 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:16:27,713 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:17:27,715 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:17:27,715 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:18:27,717 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:18:27,718 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 2 ms.) use cached value: false 
2014-04-08 10:19:27,719 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:19:27,720 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:20:27,725 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:20:27,725 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:21:27,727 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:21:27,727 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:22:27,728 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:22:27,729 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:23:27,730 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:23:27,731 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 2 ms.) use cached value: false 
2014-04-08 10:24:27,732 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 2  2 
2014-04-08 10:24:27,732 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:38:16,702 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  2 
2014-04-08 10:38:16,790 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 89 ms.) use cached value: false 
2014-04-08 10:38:38,665 DEBUG [           o.o.shoola.env.data.Connector] (1-thread-1) Failed encrypted keep alive: Ice.ConnectionLostException
    error = 0
	at IceInternal.Outgoing.invoke(Outgoing.java:158)
	at omero.api._ServiceFactoryDelM.keepAllAlive(_ServiceFactoryDelM.java:1593)
	at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5610)
	at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5569)
	at org.openmicroscopy.shoola.env.data.Connector.keepSessionAlive(Connector.java:675)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.keepSessionAlive(OMEROGateway.java:5291)
	at org.openmicroscopy.shoola.env.data.KeepClientAlive.run(KeepClientAlive.java:64)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
	at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317)
	at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:180)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:204)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)
Caused by: java.io.IOException: Operation timed out
	at sun.nio.ch.FileDispatcher.read0(Native Method)
	at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:21)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:198)
	at sun.nio.ch.IOUtil.read(IOUtil.java:166)
	at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:245)
	at IceSSL.TransceiverI.readNonBlocking(TransceiverI.java:826)
	at IceSSL.TransceiverI.read(TransceiverI.java:309)
	at Ice.ConnectionI.message(ConnectionI.java:996)
	at IceInternal.ThreadPool.run(ThreadPool.java:321)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	... 1 more
 
2014-04-08 10:38:43,673 DEBUG [          o.o.shoola.util.NetworkChecker] (entQueue-0) Count: 1  1 
2014-04-08 10:38:43,673 DEBUG [          o.o.shoola.util.NetworkChecker] (entQueue-0) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:38:43,811 DEBUG [        o.o.shoola.env.data.OMEROGateway] (entQueue-0) joinSession  
2014-04-08 10:38:43,812 DEBUG [          o.o.shoola.util.NetworkChecker] (entQueue-0) Count: 1  1 
2014-04-08 10:38:43,812 DEBUG [          o.o.shoola.util.NetworkChecker] (entQueue-0) Network status: true (in 0 ms.) use cached value: false 
2014-04-08 10:38:43,812 DEBUG [        o.o.shoola.env.data.OMEROGateway] (entQueue-0) joining the session  
2014-04-08 10:39:11,377 DEBUG [        o.o.shoola.env.data.OMEROGateway] (entQueue-0) Failed to join the session Glacier2.PermissionDeniedException
    reason = "Password check failed for '8f1aadf1-35aa-4467-8237-c651e2933144': [user=user-3, created=2014-04-08 09:29:25.668, closed=2014-04-08 10:36:13.618697]"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
	at IceInternal.BasicStream.access$300(BasicStream.java:12)
	at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
	at IceInternal.BasicStream.throwException(BasicStream.java:2077)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
	at Glacier2._RouterDelM.createSession(_RouterDelM.java:52)
	at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:131)
	at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:108)
	at omero.client.createSession(client.java:694)
	at omero.client.joinSession(client.java:623)
	at org.openmicroscopy.shoola.env.data.Connector.joinSession(Connector.java:557)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.joinSession(OMEROGateway.java:2144)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.reconnect(DataServicesFactory.java:401)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory.access$300(DataServicesFactory.java:94)
	at org.openmicroscopy.shoola.env.data.DataServicesFactory$1.propertyChange(DataServicesFactory.java:386)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:297)
	at java.awt.Component.firePropertyChange(Component.java:8327)
	at org.openmicroscopy.shoola.util.ui.ShutDownDialog.cancel(ShutDownDialog.java:253)
	at org.openmicroscopy.shoola.util.ui.ShutDownDialog.actionPerformed(ShutDownDialog.java:270)
	at javax.swing.Timer.fireActionPerformed(Timer.java:291)
	at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
	at java.awt.Dialog$1.run(Dialog.java:1049)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:690)
	at java.awt.EventQueue$3.run(EventQueue.java:688)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
 
2014-04-08 10:39:43,812 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:39:43,813 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:40:43,814 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:40:43,815 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 0 ms.) use cached value: false 
2014-04-08 10:41:43,816 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:41:43,816 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:42:43,818 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:42:43,818 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:43:43,820 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:43:43,820 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:44:43,821 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:44:43,821 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:45:43,830 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:45:43,830 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:46:43,831 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:46:43,831 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 0 ms.) use cached value: false 
2014-04-08 10:47:43,833 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Count: 1  1 
2014-04-08 10:47:43,833 DEBUG [          o.o.shoola.util.NetworkChecker] (1-thread-1) Network status: true (in 1 ms.) use cached value: false 
2014-04-08 10:48:02,044 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Count: 1  1 
2014-04-08 10:48:02,045 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Network status: true (in 1 ms.) use cached value: true 
2014-04-08 10:48:02,160 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:02,223 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:02,246 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:02,349 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:02,392 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:48:02,392 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:48:02,393 INFO  [   ome.formats.importer.ImportCandidates] (Thread-183) Depth: 4 Metadata Level: MINIMUM 
2014-04-08 10:48:02,416 INFO  [                loci.formats.ImageReader] (Thread-183) APNGReader initializing /Users/rkferguson/Documents/1 OME/4 Data/Test Images Small - One/Test Image 01.png 
2014-04-08 10:48:02,417 INFO  [   ome.formats.importer.ImportCandidates] (Thread-183) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 23ms. (24ms total) [0 unknowns] 
2014-04-08 10:48:02,418 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:48:02,418 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:48:02,418 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:02,578 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) OMERO Version: 5.0.1-ice35-b21 
2014-04-08 10:48:02,578 INFO  [       ome.formats.importer.ImportConfig] (Thread-183) Bioformats version: 5.0.1-ice35-b21 revision: b5a33fe date: 3 April 2014 
2014-04-08 10:48:03,070 INFO  [      o.f.i.transfers.UploadFileTransfer] (Thread-183) Transferring /Users/rkferguson/Documents/1 OME/4 Data/Test Images Small - One/Test Image 01.png... 
2014-04-08 10:48:03,557 DEBUG [          o.o.shoola.util.NetworkChecker] (Thread-183) Cached networkup: true 
2014-04-08 10:48:05,259 DEBUG [          o.o.shoola.util.NetworkChecker] (l.Client-1) Cached networkup: true

comment:5 Changed 10 years ago by jburel

The scoping was more about changing how and where the tagging was happening.
I have not been able to reproduce the issue.

comment:6 Changed 10 years ago by pwalczysko

I am reproducing the issue now. The crucial point is to select an test_images_good/ome-tiff/*.* image(s) and tag them on import stage. You can also use Mac for it, no need to go for Win 7 as reported by Simon.
It is an one-tiff specific bug. Also, just as @spli reported originally, it is necessary to pick single images, when the whole one-tiff folder is picked, the workflow is okay.

comment:7 Changed 10 years ago by pwalczysko

  • Description modified (diff)

comment:8 Changed 9 years ago by jburel

  • Cc changed from ux@openmicroscopy.org.uk, spli to ux@openmicroscopy.org.uk, spli
  • Resolution set to fixed
  • Status changed from new to closed

see ​https://github.com/openmicroscopy/openmicroscopy/pull/3445

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