Open Microscopy Environment

Hi all,

I am tying to install omero server (beta 4.1.1) on cent OS 5.5
I installed all packages without problem, and I got diagnostic table as follows.

Code: Select all

==================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================
       
Commands:   java -version                  1.6.0     (/develop/software/java/jdk1.6.0_21/bin/java -- 2 others)
Commands:   python -V                      2.4.3     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.1.22    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 15634, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FSServer                       inactive (disabled)
Server:     Indexer-0                      active (pid = 15664, enabled)
Server:     OMERO.Glacier2                 active (pid = 15662, enabled)
Server:     OMERO.IceStorm                 active (pid = 15665, enabled)
Server:     Processor-0                    active (pid = 15666, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     Web                            inactive (enabled)

Log dir:    /home/omerouser/omero/omero_dist/var/log exists

Log files:  Blitz-0.log                    342.0 KB      errors=0    warnings=4   
Log files:  DropBox.log                    1.0 KB        errors=4    warnings=0   
Log files:  FSServer.log                   1.0 KB        errors=2    warnings=0   
Log files:  Indexer-0.log                  209.0 MB      errors=49785 warnings=4   
Log files:  OMEROweb.log                   0.0 KB        errors=1    warnings=1   
Log files:  OMEROweb.log.2011-03-02        0.0 KB        errors=2    warnings=2   
Log files:  Processor-0.log                2.0 KB        errors=0    warnings=1   
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     2.0 KB        errors=0    warnings=4   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     209.84 MB


but, when I run 'bin/omero web setting', it generates a couple of error messages.
It said that I need to install 'pysqlite2' package, but I have no idea what this lib is, and
how I can download this lib ? I got error messages as follows.

It would be very helpful if you guys give me any suggestions !!!
Thanks in advance.

Code: Select all

Database synchronization...
Traceback (most recent call last):
  File "manage.py", line 42, in ?
    execute_manager(settings)
  File "/home/omerouser/omero/omero_dist/lib/python/django/core/management/__init__.py", line 340, in execute_manager
    utility.execute()
  File "/home/omerouser/omero/omero_dist/lib/python/django/core/management/__init__.py", line 295, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File "/home/omerouser/omero/omero_dist/lib/python/django/core/management/base.py", line 77, in run_from_argv
    self.execute(*args, **options.__dict__)
  File "/home/omerouser/omero/omero_dist/lib/python/django/core/management/base.py", line 87, in execute
    translation.activate('en-us')
  File "/home/omerouser/omero/omero_dist/lib/python/django/utils/translation/__init__.py", line 73, in activate
    return real_activate(language)
  File "/home/omerouser/omero/omero_dist/lib/python/django/utils/translation/__init__.py", line 43, in delayed_loader
    return g['real_%s' % caller](*args, **kwargs)
  File "/home/omerouser/omero/omero_dist/lib/python/django/utils/translation/trans_real.py", line 209, in activate
    _active[currentThread()] = translation(language)
  File "/home/omerouser/omero/omero_dist/lib/python/django/utils/translation/trans_real.py", line 198, in translation
    default_translation = _fetch(settings.LANGUAGE_CODE)
  File "/home/omerouser/omero/omero_dist/lib/python/django/utils/translation/trans_real.py", line 181, in _fetch
    app = getattr(__import__(appname[:p], {}, {}, [appname[p+1:]]), appname[p+1:])
  File "/home/omerouser/omero/omero_dist/lib/python/django/contrib/admin/__init__.py", line 1, in ?
    from django.contrib.admin.options import ModelAdmin, HORIZONTAL, VERTICAL
  File "/home/omerouser/omero/omero_dist/lib/python/django/contrib/admin/options.py", line 5, in ?
    from django.contrib.contenttypes.models import ContentType
  File "/home/omerouser/omero/omero_dist/lib/python/django/contrib/contenttypes/models.py", line 1, in ?
    from django.db import models
  File "/home/omerouser/omero/omero_dist/lib/python/django/db/__init__.py", line 16, in ?
    backend = __import__('%s%s.base' % (_import_path, settings.DATABASE_ENGINE), {}, {}, [''])
  File "/home/omerouser/omero/omero_dist/lib/python/django/db/backends/sqlite3/base.py", line 26, in ?
    raise ImproperlyConfigured, "Error loading %s module: %s" % (module, e)
django.core.exceptions.ImproperlyConfigured: Error loading pysqlite2 module: No module named pysqlite2


We'd strongly encourage you to upgrade to the latest release (Beta 4.2.2). That said, pysqlite2 can be installed via easy_install or by downloading the package itself, extracting it and running python setup.py install.

Is there a big difference between beta 4.1.1 and 4.2.2 ?
Do I need to uninstall all applications including postgreSQL to upgrade beta 4.2.2 ?
I prefer to download pysqlite2 package manually if it works fine.
could you let me know where I can download psyqlite2 package ?
thanks for your suggestion, though.

Yes, there is a big difference between 4.1.1 and 4.2.2. The feature lists for 4.2.0, 4.2.1 and 4.2.2 are available here:

https://trac.openmicroscopy.org.uk/ome/ ... RO-Beta4.2
https://trac.openmicroscopy.org.uk/ome/ ... -Beta4.2.1
https://trac.openmicroscopy.org.uk/ome/ ... -Beta4.2.2

Most of the requirements are the same, so there's no need to uninstall anything. You can download pysqlite2 here:

http://code.google.com/p/pysqlite/downloads/list

There is detailed documentation about pysqlite2 and how to install it on the Trac Wiki:

http://trac.edgewall.org/wiki/PySqlite

Thanks for your answer.
I installed 4.2 version of omero, and executed omero.web without problems.
But, error messages pops up like " error: connection not available. please check your user name and password"
I tried all possible ID and password, but it seems doesn't work.

I found some comments that said " I need to set up environment like DYLD_LIBRARY_PATH".
Is it critical issue to set up this path ? I am stuck with this path issue for a long time.
It would be great help to give me any suggestion.
Thanks in advance.

DYLD_LIBRARY_PATH is only for Mac OS X, its equivalent on Linux is LD_LIBRARY_PATH. Have you enabled debugging for your OMERO.web and looked at the log? Can you attach it here so we can see if you have the same problem?

Thanks for your response.
Could you let me know how I can debug omero.web and where the log file is in the system ?
I will post it as soon as possible after debugging..
Thanks.

All that information is in the other thread:

viewtopic.php?f=5&t=624

Specifically you need set the omero.web.debug configuration property and look for OMEROweb-DEBUG.log in var/log.

thanks for your reply.
I uploaded log zip file in here as you recommended.
let me know if you find some solutions for this issue.

Steve Oh

Hi cxallan,

Could you let me know what's the problem in the log file ?
I tried all possible ID and password while logging in the omen.web.
But, it seems not work...

Thanks in advance,
Steve Oh