[ome-users] Upload problem
Woodbridge, Mark R
m.woodbridge at imperial.ac.uk
Mon May 12 17:24:16 BST 2014
No problem installing a new version. Or sending you the database and my folder (via the QA system?).
From: Josh Moore [josh at glencoesoftware.com]
Sent: 12 May 2014 17:04
To: Woodbridge, Mark R
Cc: ome-users at lists.openmicroscopy.org.uk; Aleksandra Tarkowska
Subject: Re: [ome-users] Upload problem
On May 12, 2014, at 4:57 PM, Woodbridge, Mark R wrote:
> I have set up a new OMERO server with a blank filesystem/database and successfully imported an image. Then I shut down our old non-functioning server, pointed the new server at the old filesystem/database and have reproduced the import error. So it does appear that some inconsistency between the database and the filesystem is preventing new imports. I guess this could have been due to an unclean shutdown, an out-of-memory error (of which we have had a few recently) or perhaps an NFS issue.
> Is there any way to verify/reconcile the filesystem and database so that we can repair the server?
There's nothing automatic in place, but I don't think it will be a complicated fix once we know what's going wrong. Would you be up for trying out a merge build (after taking a DB dump) or possibly send a DB dump along with your OMERO user's directory?
> Thanks for all your help so far,
> From: Josh Moore [josh at glencoesoftware.com]
> Sent: 09 May 2014 15:16
> To: Woodbridge, Mark R
> Cc: Aleksandra Tarkowska; ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Upload problem
> Hi Mark,
> On May 9, 2014, at 4:07 PM, Mark Woodbridge wrote:
>> I did try creating a file inside that folder as the OMERO user and it was successful, so not sure what the issue is. Will keep looking though.
> Could you try the same import from the CLI and see if more of the stracktrace is printed?
> What I think is happening is that somehow there's a de-synchronization between your /OMERO/ManagedRepository directory and the values in the DB. If import notices that either a directory exists that isn't listed in the DB OR an entry is in the DB but doesn't exist on disk, it will complain.
>> On 09/05/14 14:54, Aleksandra Tarkowska wrote:
>>> Hi Mark,
>>> From what I can see in the codebase
>>> 2014-05-09 14:06:43,253 INFO [ ome.services.util.ServiceHandler]
>>> (l.Server-8) Excp: ome.services.blitz.repo.RepositoryDaoImpl$Rethrow:
>>> is thrown when is trying to create a nested path in the repository.
>>> Creates each directory in the path if it doen't already exist.
>>> Does it give you any clue?
>>> Kind regards
>>> On 09/05/2014 14:12, "Mark Woodbridge" <m.woodbridge at imperial.ac.uk> wrote:
>>>> For some reason we can't upload images to our OMERO at the moment and I
>>>> can't figure out why! The only log with any recent entries is
>>>> Blitz-0.log, so I've attached the complete Insight session where I tried
>>>> to upload a jpeg. The disk isn't full and I have tried restarting the
>>>> Clicking 'View Exception' and 'Submit' in the client doesn't seem to do
>>>> much, so I don't have anything else to go on.
>>>> Any ideas would be really appreciated,
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