[ome-users] Unable to import image files

Josh Moore josh at glencoesoftware.com
Tue Mar 24 11:24:16 GMT 2015


Hi José,


On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres
<josator at ebi.ac.uk> wrote:
> Sorry, I can not execute the second command, I do not have root permissions on the OMERO machine.

Hmmm....do you have access to the server logs? Can you put us in
contact with your server administrator?

Thanks,
~Josh

> (I had to build and manually install every dependency).
>
> omero admin diagnostics
>
> ================================================================================
> OMERO Diagnostics 5.1.0-m2-ice35-SNAPSHOT
> ================================================================================
>
> Commands:   java -version                  1.6.0     (/usr/bin/java)
> Commands:   python -V                      2.6.6     (/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin/python -- 2 others)
> Commands:   icegridnode --version          3.5.1     (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridnode)
> Commands:   icegridadmin --version         3.5.1     (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridadmin)
> Commands:   psql --version                 8.4.20    (/usr/bin/psql)
>
> Server:     icegridnode                    running
> Server:     Blitz-0                        active (pid = 4104, enabled)
> Server:     DropBox                        active (pid = 4116, enabled)
> Server:     FileServer                     active (pid = 4123, enabled)
> Server:     Indexer-0                      active (pid = 4125, enabled)
> Server:     MonitorServer                  active (pid = 4124, enabled)
> Server:     OMERO.Glacier2                 active (pid = 4126, enabled)
> Server:     OMERO.IceStorm                 inactive (disabled)
> Server:     PixelData-0                    active (pid = 4129, enabled)
> Server:     Processor-0                    active (pid = 4127, enabled)
> Server:     Tables-0                       inactive (disabled)
> Server:     TestDropBox                    inactive (enabled)
>
> Log dir:    /nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/log exists
>
> Log files:  Blitz-0.log                    17.0 MB       errors=1    warnings=912
> Log files:  Blitz-0.log.1                  524.0 MB      errors=65   warnings=9855
> Log files:  Blitz-0.log.2                  524.0 MB      errors=3900 warnings=6595
> Log files:  DropBox.log                    41.0 KB       errors=20   warnings=19
> Log files:  FileServer.log                 7.0 KB        errors=2    warnings=0
> Log files:  Indexer-0.log                  2.0 MB        errors=162  warnings=590
> Log files:  MonitorServer.log              20.0 KB       errors=3    warnings=0
> Log files:  OMEROweb.log                   1.0 MB        errors=316  warnings=294
> Log files:  OMEROweb_request.log           176.0 KB      errors=205  warnings=290
> Log files:  PixelData-0.log                419.0 KB      errors=23   warnings=290
> Log files:  Processor-0.log                109.0 KB      errors=46   warnings=30
> Log files:  Tables-0.log                   n/a
> Log files:  TestDropBox.log                n/a
> Log files:  master.err                     78.0 KB       errors=53   warnings=53
> Log files:  master.out                     0.0 KB        errors=1    warnings=0
> Log files:  Total size                     1070.65 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_TEMPDIR=(unset)
> Environment:PATH=/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin:/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/bin:/nfs/public/rw/pdbe/mol2cell/software/bin:/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/bin:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/bin:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/net/isilonP/public/rw/homes/pdb_em/bin
> Environment:PYTHONPATH=/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/lib/python:/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/lib/python2.6:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/python::/net/isilonP/public/rw/homes/pdb_em/python-2.6-libraries
> Environment:ICE_HOME=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1
> Environment:LD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/lib:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib64:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/lib:
> Environment:DYLD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib:
>
> OMERO SSL port:4064
> OMERO TCP port:4063
> OMERO data dir:'/nfs/public/rw/pdbe/mol2cell/omero/development/var/OMERO.data' Exists? True     Is writable? True
> OMERO temp dir:'/net/isilonP/public/rw/homes/pdb_em/omero/tmp' Exists? True     Is writable? True   (Size: 0)
>
> JVM settings: Blitz                         -Xmx602m -XX:MaxPermSize=512m
> JVM settings: Indexer                       -Xmx401m -XX:MaxPermSize=512m
> JVM settings: Pixeldata                     -Xmx602m -XX:MaxPermSize=512m
> JVM settings: Repository                    -Xmx401m -XX:MaxPermSize=512m
>
> OMERO.web status... [RUNNING] (PID 4375)
>
>
>
>
>
>> On 23 Mar 2015, at 18:54, Josh Moore <josh at glencoesoftware.com> wrote:
>>
>> Hi José,
>>
>> On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <josator at ebi.ac.uk> wrote:
>>> Dear OMERO users:
>>>
>>> I was able to do the import before but now without changing configuration or anything it fails from any machine (even localhost). However Romero insight is working properly. Can you help me?:
>> ...
>>> 2015-03-23 10:40:43,444 2219       [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import
>>> java.lang.RuntimeException: Cannot exclusively use the managed repository.
>>>        at ome.formats.importer.ImportLibrary.checkManagedRepo(ImportLibrary.java:709) ~[blitz.jar:na]
>>>        at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:316) ~[blitz.jar:na]
>>>        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:465) ~[blitz.jar:na]
>>>        at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]
>>>        at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
>>>        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:752) [blitz.jar:na]
>>> 2015-03-23 10:40:43,444 2219       [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error
>>
>> This looks like there is some server error. Could you provide use the output of:
>>
>> $ bin/omero admin diagnostics
>>
>> as well as:
>>
>>
>> $ bin/omero -s root at localhost fs repos
>>
>> e.g.
>>
>> # | Id    | UUID                                 | Type    | Path
>> ---+-------+--------------------------------------+---------+-------------------------------------------------------------------
>> 0 | 17    | ce1e2766-089f-4555-a52a-f75746fd44da | Public  |
>> /repositories/OMERO-5.0-latest-deploy
>> 1 | 18    | ScriptRepo                           | Script  |
>> /opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/scripts
>> 2 | 10901 | a5a2b4b3-d146-4ccc-98fa-7353a1ba023b | Managed |
>> /repositories/OMERO-5.1-merge-deploy/ManagedRepository
>> 3 | 18651 | 34b38044-0ff6-4019-8f97-4e0093f5a3c3 | Public  |
>> /repositories/OMERO-5.0-latest-deploy
>> 4 | 18701 | 640d985e-0ba5-47a6-bacb-42b7cf60354b | Public  |
>> /repositories/OMERO-5.1-merge-deploy
>> (5 rows)
>>
>> Cheers,
>> ~Josh
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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