Open Microscopy Environment

Hi,

I am having a problem getting Omero.web up and running. I am following the walkthrough, but the db.sqlite3 file is missing and i cannot do the following step.
"Copy the db.sqlite3 from {OMERO_HOME}/Current/lib/python/omeroweb/ to /var/lib/omero/webdb/" but this file is missing I simply untarred the file and searched it and cannot find it, is this file made during the installation?

I receive the following error when doing executing bin/omero web syncdb

omero> web syncdb
Database synchronization...
Traceback (most recent call last):
File "manage.py", line 42, in <module>
execute_manager(settings)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 362, in execute_manager
utility.execute()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 303, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/base.py", line 195, in run_from_argv
self.execute(*args, **options.__dict__)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/base.py", line 213, in execute
translation.activate('en-us')
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/translation/__init__.py", line 73, in activate
return real_activate(language)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/translation/__init__.py", line 43, in delayed_loader
return g['real_%s' % caller](*args, **kwargs)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/translation/trans_real.py", line 205, in activate
_active[currentThread()] = translation(language)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/translation/trans_real.py", line 194, in translation
default_translation = _fetch(settings.LANGUAGE_CODE)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/translation/trans_real.py", line 180, in _fetch
app = import_module(appname)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/importlib.py", line 35, in import_module
__import__(name)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/contrib/admin/__init__.py", line 1, in <module>
from django.contrib.admin.helpers import ACTION_CHECKBOX_NAME
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/contrib/admin/helpers.py", line 2, in <module>
from django import forms
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/forms/__init__.py", line 17, in <module>
from models import *
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/forms/models.py", line 8, in <module>
from django.utils.text import get_text_list, capfirst
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/text.py", line 179, in <module>
ustring_re = re.compile(u"([\u0080-\uffff])")
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/re.py", line 190, in compile
return _compile(pattern, flags)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/re.py", line 243, in _compile
p = sre_compile.compile(pattern, flags)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 510, in compile
code = _code(p, flags)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 495, in _code
_compile(code, p.data, flags)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 107, in _compile
_compile(code, av[1], flags)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 63, in _compile
_compile_charset(av, flags, code, fixup)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 189, in _compile_charset
for op, av in _optimize_charset(charset, fixup):
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 232, in _optimize_charset
return _optimize_unicode(charset, fixup)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sre_compile.py", line 352, in _optimize_unicode
mapping = array.array('b', mapping).tostring()
AttributeError: 'module' object has no attribute 'array'
omero>

Any help is greatly appreciated
-Brandon

Hi Brandon,

Which version of the server are you trying to install?

4.1

Did you succeed in running bin/omero web settings? There should really be no reason to run syncdb.

I have succeeded in the first two steps of the web settings, but the database sync is the last step and is where i am getting the error. So i just specified the web syncdb in my error.

I'm still confused then as to what stage you are at and what is going wrong. Can you please paste the entire console content here?

Heres what I get when trying to setup the web admin,

adam-hoppes-mac-pro:Current omero$ bin/omero web settings
/Library/Omero/Versions/4.1.1/lib/python/omeroweb/custom_settings.py already exist. Do you want to ovewrite it? (yes/no)yes
Please enter the domain you want to run OMERO.web on (http://www.domain.com:8000/):http://137.216.143.58:8000/
Please enter the Email address you want to send from (omero_admin@example.com): brandon.scott1@sdstate.edu
Please enter the SMTP server host you want to send from (smtp.example.com): smtp.sdstate.edu
Optional: please enter the SMTP server port (default 25):
Optional: Please enter the SMTP server username:
Optional: Password:
Optional: TSL? (yes/no):
Saved to /Library/Omero/Versions/4.1.1/lib/python/omeroweb/custom_settings.py


/Library/Omero/Versions/4.1.1/lib/python/omeroweb/initial_data.json already exist. Do you want to ovewrite it? (yes/no)yes
Please enter Username for OMERO.web administrator: root
Please enter Email address: brandon.scott1@sdstate.edu
Please enter password for OMERO.web administrator:
Please re-enter password for OMERO.web administrator:
<string>:36: DeprecationWarning: the sha module is deprecated; use the hashlib module instead
Saved to /Library/Omero/Versions/4.1.1/lib/python/omeroweb/initial_data.json


Database synchronization...
Traceback (most recent call last):
File "manage.py", line 42, in <module>
execute_manager(settings)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 438, in execute_manager
utility.execute()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 379, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 261, in fetch_command
klass = load_command_class(app_name, subcommand)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/__init__.py", line 67, in load_command_class
module = import_module('%s.management.commands.%s' % (app_name, name))
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/utils/importlib.py", line 35, in import_module
__import__(name)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/commands/syncdb.py", line 7, in <module>
from django.core.management.sql import custom_sql_for_model, emit_post_sync_signal
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/core/management/sql.py", line 5, in <module>
from django.contrib.contenttypes import generic
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/contrib/contenttypes/generic.py", line 6, in <module>
from django.db import connection
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/db/__init__.py", line 77, in <module>
connection = connections[DEFAULT_DB_ALIAS]
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/db/utils.py", line 91, in __getitem__
backend = load_backend(db['ENGINE'])
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/OmeroPython/django/db/utils.py", line 49, in load_backend
raise ImproperlyConfigured(error_msg)
django.core.exceptions.ImproperlyConfigured: 'django.db.backends.postgresql_psycopg2' isn't an available database backend.
Try using django.db.backends.XXX, where XXX is one of:
'dummy', 'mysql', 'oracle', 'postgresql', 'postgresql_psycopg', 'sqlite3'
Error was: No module named postgresql_psycopg2.base
adam-hoppes-mac-pro:Current omero$


Thanks for your help,
Brandon

Is there any other information that i didnt post that would be a major help for this problem

-Brandon

I never thought this day would come, but I have finally installed the server. Just wanted to thank the helpful suggestions that i received along the way.

-Now the bigger question is how do I use this thing...but that's another time and place.

-Brandon

Brandon,
How did you get around the missing "db.sqlite3" in the step
"Copy the db.sqlite3 from {OMERO_HOME}/Current/lib/python/omeroweb/ to /var/lib/omero/webdb/" .

Thanks,
Jeff Lary.