omero server installation - web setting error

[toh2]

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


[cxallan]

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.

[toh2]

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.

[cxallan]

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

[toh2]

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.

[cxallan]

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?

[toh2]

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.

[cxallan]

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.

[toh2]

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

[toh2]

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