[ome-users] Upload problem

[Mark Woodbridge]

We've now solved this issue with the help of the OMERO team (esp. Josh). 
Very grateful for their advice (and patience!).

It turned out that due to a poorly executed server migration we had 
ended up with two data repositories and a database that matched neither. 
Definitely not an issue with OMERO itself.

Mark.


On 14/05/14 20:19, Josh Moore wrote:
>
> On May 12, 2014, at 6:24 PM, Woodbridge, Mark R wrote:
>
>> No problem installing a new version. Or sending you the database and my folder (via the QA system?).
>
> Thanks for the upload, Mark. 5.0.1 is unfortunately swallowing the error.
> With the upcoming 5.0.2, this is printed:
>
>    Directory exists but is not registered: CheckedPath(mwoodbri_2)
>
> If you had OOMs and other similar issues, then that would likely explain
> the problem. In the zip you sent me, no data was imported to your
> 'mwoodbri_2' directory, so it should be safe to remove. We can look into
> doing the same check: "if empty, then simply register".
>
> Sorry for the trouble!
> ~Josh.
>
>
>> ________________________________________
>> 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:
>>
>>> Hi,
>>
>> Hi Mark,
>>
>>> 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,
>>> Mark.
>>
>> Cheers,
>> ~Josh.
>>
>>
>>> ________________________________________
>>> 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.
>>>
>>> Cheers,
>>> ~Josh.
>>>
>>>> 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:
>>>>> 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
>>>>> Ola
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 09/05/2014 14:12, "Mark Woodbridge" <m.woodbridge at imperial.ac.uk> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> 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
>>>>>> server.
>>>>>>
>>>>>> 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,
>>>>>>
>>>>>> Mark.
>