[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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