Open Microscopy Environment

Dear all,

I have successfully installed omero (and just updated to 5.4.0) on a Ubuntu linux system.
The system is running and we have a lot of fun playing around. When we tried to import a Slidebook file, the import failed (as we could have seen in the Omero manual). The problem is that we cannot remove the file from the database. I was of course able to manually remove the file, but I wanted to have a clean solution.

When looking at the CLI, I can see the four occasions where we tried to upload such slidebook files at ID 52,53,61 and 62:

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omero@TERMINALTOR:~/OMERO.server/bin$ ./omero fs sets
Using session 24a033bb-5643-438c-963b-2ad48e8bc14b (root@localhost:4064). Idle timeout: 10 min. Current group: system
# | Id | Prefix                                | Images | Files | Transfer
---+----+---------------------------------------+--------+-------+----------
0 | 62 | Sebastian_52/2017-10/16/15-32-17.714/ | 0      | 1     |         
1 | 61 | Sebastian_52/2017-10/16/15-00-22.555/ | 0      | 1     |         
2 | 60 | Sebastian_52/2017-10/16/10-16-15.123/ | 1      | 1     |         
3 | 56 | Sebastian_52/2017-10/13/17-22-41.234/ | 1      | 1     |         
4 | 55 | Sebastian_52/2017-10/13/17-20-39.931/ | 1      | 1     |         
5 | 53 | Sebastian_52/2017-09/26/15-35-53.025/ | 0      | 1     |         
6 | 52 | Sebastian_52/2017-09/26/15-04-20.220/ | 0      | 1     |         
(7 rows, starting at 0 of approx. 7)

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To check for consistency I wanted to run the omero fs sets --check as root, but it failed with a timeout exception:

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omero@TERMINALTOR:~/OMERO.server/bin$ ./omero fs sets --check
Using session 24a033bb-5643-438c-963b-2ad48e8bc14b (root@localhost:4064). Idle timeout: 10 min. Current group: system
Traceback (most recent call last):
  File "./omero", line 125, in <module>
    rv = omero.cli.argv()
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/cli.py", line 1613, in argv
    cli.invoke(args[1:])
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/cli.py", line 1088, in invoke
    stop = self.onecmd(line, previous_args)
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/cli.py", line 1165, in onecmd
    self.execute(line, previous_args)
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/cli.py", line 1247, in execute
    args.func(args)
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/plugins/fs.py", line 734, in sets
    cb = client.submit(raw)
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/clients.py", line 899, in submit
    closehandle=True)
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/clients.py", line 918, in waitOnCmd
    callback.loop(loops, ms)  # Throw LockTimeout
  File "/home/omero/OMERO.server-5.4.0-ice36-b74/lib/python/omero/callbacks.py", line 256, in loop
    5000L, int(waited))
omero.LockTimeout: exception ::omero::LockTimeout
{
    serverStackTrace = None
    serverExceptionClass = None
    message = Command unfinished after 5.0 seconds
    backOff = 5000
    seconds = 5
}

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If I try to delete the datasets by CLI I get an error:

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omero@TERMINALTOR:~/OMERO.server$ ./bin/omero delete Dataset:53
Using session b677d7ee-68ed-498a-87f5-363152a73320 (root@localhost:4064). Idle timeout: 10 min. Current group: system
omero.cmd.Delete2 Dataset:53 failed: 'graph-fail'
failed: cannot read ome.model.containers.Dataset[53]


I already increased the omero.threads.cancel_timeout and omero.threads.idle_timeout to value=10000, but these don't matter here I think.

So here my questions where I would love to hear any suggestions:
1) How can I get the --check to do the job? Is there a way to increase this timeout?
2) Is there any way to remove the sets that have trouble?

An additional note. The systems does calculate the diskspace correctly, but when hitting the Stats in the client, I get a used space of 49GB (which would be the size if I would not have deleted manually the files that failed to import). How is the used space and the total size in the Stats field calculated?

Thanks a lot for any suggestions,
best,
tobetz

I don't know the answer to your question about timeouts. It's odd that things are taking quite so long for you.

I would guess that the disk size including your manually deleted files may be taking the numbers from the "size" column of the database's "originalfile" table where there is probably still an entry for the file.

I noticed that your "fs sets" output includes Id 53 and you tried deleting Dataset:53 so I thought I should make clear that those Ids are for filesets: i.e. you could try deleting Fileset:53.

Cheers,
Mark