Open Microscopy Environment

Hi all,
i am using OMERO.CLI for importing more than 2000 images at once,but i am getting the error it does not allow even a single image also. please provide sufficient guidance to me

Dear Rahul,

Sorry to hear you've been having a difficult time with OMERO. Did you see our previous replies, e.g., those at http://lists.openmicroscopy.org.uk/pipe ... 05439.html and http://lists.openmicroscopy.org.uk/pipe ... 05442.html -- can you tell us what you type to attempt the import and what the actual error message says? Also, any messages leading up to the error that might be relevant could also help. With enough detail we can probably figure out the issue so that you can start to upload images. If you like, the log files that Josh mentions from var/log, you can zip them up into one file and submit via http://qa.openmicroscopy.org.uk/qa/upload/

Also, I'm curious: if instead of using bin/omero import, if you simply use bin/omero login, does it let you log in, or does that also give an error?

Cheers,
Mark

Dear Rahul,

I should also check: what kinds of image are you attempting to import, into which version of OMERO? If you want to upload one example at the QA link I give above, we would be happy to try importing it at our end to see if it goes smoothly for us.

Cheers,
Mark

Thank you for the response for my problem,
Here iam attaching files to be uploaded and and
omero version : 5.0
i am trying to upload cellomics array scan (.c01 extension)dataset, which contains more than 2000 images one file in the folder is .MBD file ,,

Hi i am unable to add the files so i am just writing the the file names ...


MFGTMP_150618230001.MDB
MFGTMP_150618230001_A01f03d1.C01

rahulmekala wrote:Hi i am unable to add the files so i am just writing the the file names ...
MFGTMP_150618230001.MDB
MFGTMP_150618230001_A01f03d1.C01

The following is the error i am getting ...
Transferring /home/ccbt/Desktop/MFGTMP_150329160001/MFGTMP_150329160001_H05f16d0.C01...
Jun 23, 2015 8:37:29 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 8:39:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
2015-06-23 20:43:18,902 15651937 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/ccbt/Desktop/MFGTMP_150329160001/MFGTMP_150329160001_H05f16d0.C01
Jun 23, 2015 8:46:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 8:46:58 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. and on



Any one of you guys please do let me know where the images are stored in postgres sql(in which table it is stored)


in between processing the service has been blocked suddenly and gives the message as follows


[23/Jun/2015 15:45:24] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:46:24] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:47:25] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:48:24] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:49:24] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:50:24] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 15:53:01] "GET /webclient/keepalive_ping/ HTTP/1.1" 200 2
[23/Jun/2015 16:30:29] "GET /webclient/ HTTP/1.1" 500 178813
Traceback (most recent call last):
File "/usr/lib/python2.7/wsgiref/handlers.py", line 86, in run
self.finish_response()
File "/usr/lib/python2.7/wsgiref/handlers.py", line 128, in finish_response
self.write(data)
File "/usr/lib/python2.7/wsgiref/handlers.py", line 217, in write
self._write(data)
File "/usr/lib/python2.7/socket.py", line 324, in write
self.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 110] Connection timed out
[23/Jun/2015 16:30:29] "GET /webclient/ HTTP/1.1" 500 59
----------------------------------------
Exception happened during processing of request from ('192.168.0.4', 60383)
Traceback (most recent call last):
File "/usr/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock
self.process_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 321, in process_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/django/core/servers/basehttp.py", line 126, in __init__
super(WSGIRequestHandler, self).__init__(*args, **kwargs)
File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
self.wfile.close()
File "/usr/lib/python2.7/socket.py", line 279, in close
self.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------

Hi Rahul,

rahulmekala wrote:MFGTMP_150618230001.MDB
MFGTMP_150618230001_A01f03d1.C01

So this part of the log looks good:

Transferring /home/ccbt/Desktop/MFGTMP_150329160001/MFGTMP_150329160001_H05f16d0.C01...
2015-06-23 20:43:18,902 15651937 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/ccbt/Desktop/MFGTMP_150329160001/MFGTMP_150329160001_H05f16d0.C01

At the moment, I'm not seeing where this goes wrong? Do you have more likes containing "LoggingImporterMonitor" or "ERROR"? Can you upload the whole log file?

Any one of you guys please do let me know where the images are stored in postgres sql(in which table it is stored)

Sure:

Code: Select all

psql omero -c "select * from image order by id desc"


in between processing the service has been blocked suddenly and gives the message as follows

Which processing? Something in the web blocked? What URL were you viewing? Again, the full log file (var/log/OMEROweb.log) would be useful.

~J.

Thank you for the suggestions, i have solved it by putting single image in a separate folder ,how can i rename all those remaining files names among 15,000 images?



"RNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 11:06:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 11:07:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:24:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:29:28 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:29:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:30:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
^Z
"


this is the error log file that i am getting in between the uploading process.....



hope i am cleared your doubts

rahulmekala wrote:Thank you for the suggestions, i have solved it by putting single image in a separate folder ,how can i rename all those remaining files names among 15,000 images?

You''ll likely want to use a shell/python script to edit that many images? Or if the import was fairly fast, you could delete and re-try.

"RNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 11:06:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 23, 2015 11:07:28 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:24:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:29:28 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:29:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jun 24, 2015 12:30:58 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
^Z
"

This is just a Java weirdness, but doesn't really tell us much more.

this is the error log file that i am getting in between the uploading process.....

hope i am cleared your doubts

Hmm.... it doesn't tell me much more, but if things are working for you, I'm glad to hear it. If you don't have anything else in your log files, feel free to attach screenshots.

All the best,
~Josh.

hi i am using the OMERO fine by using COMMAND prompt ...

but now ,i am getting the following error and i am not able to connect the omero server


ERROR:


ccbt@ccbt-OptiPlex-3020:~$ omero
Error loading: /home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/plugins/perf.py
Traceback (most recent call last):
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/cli.py", line 1189, in loadpath
execfile( str(pathobj), loc )
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/plugins/perf.py", line 18, in <module>
import omero.install.perf_test as perf_test
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/install/perf_test.py", line 22, in <module>
import omero.util.temp_files
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 328, in <module>
manager = TempFileManager()
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 52, in __init__
self.userdir = self.tmpdir() / ("%s_%s" % (self.prefix, self.username()))
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 137, in tmpdir
tempprop = tempfile.gettempdir()
File "/usr/lib/python2.7/tempfile.py", line 269, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/lib/python2.7/tempfile.py", line 212, in _get_default_tempdir
("No usable temporary directory found in %s" % dirlist))
IOError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/home/ccbt']
OMERO Python Shell. Version 5.0.2-ice35-b26
Type "help" for more information, "quit" or Ctrl-D to exit
omero> help
usage: /home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/bin/omero <command> [options] args
See 'help <command>' or '<command> -h' for more information on syntax
Type 'quit' to exit

Available commands:
admin, cd, cecog, chgrp, config, db, delete, dir, download, export,
fs, group, help, hql, import, ldap, load, ls, node, obj, pwd,
quit, script, search, server, sessions, shell, tag, testengine,
upload, user, version, web

Other help topics:
debug

For additional information, see:
http://www.openmicroscopy.org/site/supp ... rface.html
Report bugs to <ome-users@lists.openmicroscopy.org.uk>

omero>
omero>
omero>
omero>
[2]+ Stopped omero
ccbt@ccbt-OptiPlex-3020:~$
ccbt@ccbt-OptiPlex-3020:~$
ccbt@ccbt-OptiPlex-3020:~$
ccbt@ccbt-OptiPlex-3020:~$
ccbt@ccbt-OptiPlex-3020:~$ omero
Error loading: /home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/plugins/perf.py
Traceback (most recent call last):
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/cli.py", line 1189, in loadpath
execfile( str(pathobj), loc )
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/plugins/perf.py", line 18, in <module>
import omero.install.perf_test as perf_test
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/install/perf_test.py", line 22, in <module>
import omero.util.temp_files
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 328, in <module>
manager = TempFileManager()
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 52, in __init__
self.userdir = self.tmpdir() / ("%s_%s" % (self.prefix, self.username()))
File "/home/ccbt/apps/OMERO/OMERO.server-5.0.2-ice35-b26/lib/python/omero/util/temp_files.py", line 137, in tmpdir
tempprop = tempfile.gettempdir()
File "/usr/lib/python2.7/tempfile.py", line 269, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/lib/python2.7/tempfile.py", line 212, in _get_default_tempdir
("No usable temporary directory found in %s" % dirlist))
IOError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/home/ccbt']
OMERO Python Shell. Version 5.0.2-ice35-b26
Type "help" for more information, "quit" or Ctrl-D to exit


Please some one help me out.. thank you.