[ome-users] access problems

[Ilya Goldberg]

Hi Bernd
This probably doesn't have to do with access rights.
The *.info file was apparently successfully opened, and the header  
information successfully read.  The "Incompatible file type" error is  
reported when omeis doesn't recognize what it reads in the header.
The problem probably stemmed from the move to a different file-system  
and/or a different machine architecture running the omeis binary.
Where did your OMEIS repository start from and where did it end up   
(hardware/OS+Version/OME version)?  What program/commands did you use  
to move the repository?  Did the omeis binary move to a different  
machine as well sometime between having it running and having it not  
running?

One thing that's probably worth doing with your shared-repository  
setup is to run:
src/C/omeis/t/test-concurrent-write
This test doesn't require an internet connection, or any special  
users - you can run it as any user.
You need to first create OMEIS-TEST, OMEIS-TEST/Pixels and OMEIS-TEST/ 
Files directories in the same directory where the test-concurrent- 
write executable lives (you can put it wherever you want).  You  
should run this test locally on your omeis host (the computer that  
has the omeis binary in its cgi-bin).
This test will generally fail if the NFS implementation does not  
properly support POSIX file locking, which is fairly common in NFS  
implementations, unfortunately.  This test is most informative when  
run on multi-core/multi-CPU machines.

Instead of mounting a shared drive, its a much better setup to run  
the omeis binary locally on the machine connected to your drives/ 
RAID.  This machine doesn't need any other pieces of OME - just the  
omeis binary in its cgi-bin, as well as the actual OMEIS repository  
of course.

-Ilya


On Sep 12, 2007, at 7:41 PM, bernd wrote:

> Hi there,
> I have a problem with OMEIS. I guess it is related to access
> rights... I am mounting an NTFS filesystem via NFS. In order to get
> things working I had to change the apache user to something with a
> password. So I created a new account and assigned the user in the
> apache config and during ome installation. I restored a previous
> OMEIS database that was locally mounted before and the corresponding
> OME database. I can see those images through the web page.
> Now the problem: I want to import new images and for the three
> folders I tried so far I always get the same error messages:
> [Wed Sep 12 13:47:17 2007] /usr/local/bin/ome[7168]: Error Error
> calling PixelsSHA1 with PixelsID=18774: GetPixelsRep failed.
> OMEIS Error: Incompatible file type.
> Incompatible file type. Update failed.
> Unable to open Header File
> Could not open pixels file (ID=18774). Result=-1
> importing image: OME::ImportEngine::INCellRunXML HASH(0x1f03974)
> image Name: 0501027_6done_5_5_0_0
> [Wed Sep 12 13:47:33 2007] /usr/local/bin/ome[7168]: Error Error
> calling PixelsSHA1 with PixelsID=18775: GetPixelsRep failed.
> OMEIS Error: Incompatible file type.
> Incompatible file type. Update failed.
> Unable to open Header File
> Could not open pixels file (ID=18775). Result=-1
> importing image: OME::ImportEngine::INCellRunXML HASH(0x1f3b344)
> DBD::Pg::db commit failed: ERROR:  insert or update on table
> "actual_inputs" violates foreign key constraint
> "actual_inputs_module_execution_id_fkey"
> DETAIL:  Key (module_execution_id)=(58969) is not present in table
> "module_executions".
> DBD::Pg::db commit failed: ERROR:  insert or update on table
> "actual_inputs" violates foreign key constraint
> "actual_inputs_module_execution_id_fkey"
> DETAIL:  Key (module_execution_id)=(58969) is not present in table
> "module_executions".
> Exiting...
> Exiting...
>
>
>
> I assume this has something to do with access rights. Maybe it has
> something to do with the postgres database that been loaded as well
> and it restored the www user or something like that is not valid any
> more...
>
>  From the error message it is difficult for me to judge where to
> start debugging.
>
> I would appreciate any help you might be able to give.
>
> thanks,
>
> Bernd
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