[ome-users] Unable to import image files

Tue Mar 24 10:59:18 GMT 2015

Sorry, I can not execute the second command, I do not have root permissions on the OMERO machine.
(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