[ome-users] omero.cli error

[Simon Li]

Hi John

What version of Java are you using? We've come across a similar error before on our daily test servers but it seemed to fix itself after we updated to Java 1.7.0_51:
http://trac.openmicroscopy.org.uk/ome/ticket/11081

Balaji's just done some testing today on importing large numbers of images, he managed to reproduce your error with 1.7.0_11-b21 but not with 1.7.0_51-b13.

Thanks

Simon


On 26 Mar 2014, at 09:10, "John Webber (NBI)" <John.Webber at nbi.ac.uk<mailto:John.Webber at nbi.ac.uk>>
 wrote:

Hi Simon,

Thanks for the quick response.

My problem is that I have a bulk upload to perform and the omero.cli is now consistently failing!  I can upload 60+ images to Omero before I see this error, so switching debug on might be omerous!  However, I do have the cli.err from an example of this fail – I have attached it to this email.

I have also amended my code to work around this issue so that, if it sees this error, it attempts the upload again before crashing out:

    try:
        cli.invoke(import_args, strict=True)

    except omero.cli.NonZeroReturnCode, err:
        logging.warning('%s: Omero CLI has had a NonZeroReturnCode, trying again' % (self))

        try:
            cli.invoke(import_args, strict=True)

        except:
            logging.error('%s: Omero CLI has failed twice - exiting.' % (self))
            sys.exit(7)

Not a particularly elegant work around – but it works.

Thanks
John



From: Simon Li [mailto:s.p.li at dundee.ac.uk<http://dundee.ac.uk>]
Sent: 25 March 2014 16:40
To: John Webber (NBI)
Cc: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] omero.cli error

Hi John

Could you try adding --debug DEBUG to your import command, and see if it gives any more information? If that doesn't help could you send us cli.err and cli.out?

Many thanks

Simon

On 25 Mar 2014, at 15:46, "John Webber (NBI)" <John.Webber at nbi.ac.uk<mailto:John.Webber at nbi.ac.uk>>
 wrote:


Hi,

I’m currently experiencing an issue with a bulk upload of images to Omero.  This is being run from the command line.

I am seeing the following errors, and my bulk upload fails:

    cli.invoke(import_args, strict=True)
  File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 749, in invoke
    self.assertRC()
  File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 738, in assertRC
    raise NonZeroReturnCode(self.rv, "assert failed")
omero.cli.NonZeroReturnCode: assert failed

The bulk upload failed while writing an image, with the following arguments:

['import', '-s', 'localhost', '-u', 'upload', '-w', '<password removed>', '-p', '4064', '-d', '1687', '-n', '11_03_14_krp4_1130_b1_boundaries.inr.gz', '---errs=cli.err', '---file=cli.out', '--', '/tmp/tmpB3u1Gn/11_03_14_krp4_1130_b1/11_03_14_krp4_1130_b1_boundaries.inr.gz']

When I try to run the upload again, it fails for a different image – it does not fail on the same one upload time!

I am unable to see much additional information:  I have checked in the omero logs, (/opt/Omero/var/log), but am not able to see any additional logging.  I have checked filesystem sizes, and nothing seems to have filled up!

Please can you point me in the right direction as to how I can debug this issue further?

Thanks
John



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John Webber
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