OMERO.qa

OMERO.qa is the web application which helps support community by OMERO team.

Requirements

• PostgreSQL 8.2+
• Python 2.6+

Development Installation

1. Clone the repository

    git clone git@github.com:openmicroscopy/stats.git
   

2. Set up a virtualenv (http://www.pip-installer.org/) and activate it

    pip install virtualenv
    virtualenv --system-site-packages stats-virtualenv
    source stats-virtualenv/bin/activate
   

3. Install dependencies

    pip install matplotlib
    pip install psycopg2
    pip install mercurial
    pip install -r requirements.txt
   

4. Dump and restore database.

5. Download and extract GeoIP databases

    GeoIP2-Domain.mmdb, GeoIPOrg.dat, GeoLite2-City.mmdb
   

Configuration

• Create new settings-prod.py and import default settings

    from settings import *
  

• Set DEBUG

    DEBUG=False
    TEMPLATE_DEBUG = DEBUG
  

• Set ADMINS

    ADMINS = (
        ('Full Name', 'email@example.com'),
    )
  

• Change database settings

    DATABASES = {
        'default': {
            'ENGINE': 'django.db.backends.postgresql_psycopg2',
                                            # Add 'postgresql_psycopg2', 'mysql', 'sqlite3' or 'oracle'.
            'NAME': 'stats_database',       # Or path to database file if using sqlite3.
            'USER': 'stats_user',           # Not used with sqlite3.
            'PASSWORD': 'secret',           # Not used with sqlite3.
            'HOST': 'localhost',            # Set to empty string for localhost. Not used with sqlite3.
            'PORT': '5432',                 # Set to empty string for default. Not used with sqlite3.
        }
    }
  

• Set up email server

    # Application allows to notify user
    EMAIL_HOST = 'localhost'
    EMAIL_HOST_PASSWORD = ''
    EMAIL_HOST_USER = ''
    EMAIL_PORT = 25
    EMAIL_SUBJECT_PREFIX = '[OMERO.stats] '
    EMAIL_USE_TLS = False
    SERVER_EMAIL = 'email@example.com' # email address
  

• WSGI config file for virtual environment (omerostats/django.wsgi):

    import os
    import sys
    import site
  
    # Add the site-packages of the chosen virtualenv to work with
    site.addsitedir('/path/to/stats-virtualenv/lib64/python2.6/site-packages')
  
    # Add the app's directory to the PYTHONPATH
    sys.path.append('/path/to/stats.git/')
    sys.path.append('/path/to/stats.git/omerostats')
  
    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "omerostats.settings-prod")
  
    # Activate your virtual env
    activate_env=os.path.expanduser('/path/to/stats-virtualenv/bin/activate_this.py')
    execfile(activate_env, dict(__file__=activate_env))
  
    import django.core.handlers.wsgi
    application = django.core.handlers.wsgi.WSGIHandler()
  

• Synchronise the database

    export DJANGO_SETTINGS_MODULE=omerostats.settings-prod
    python manage.py syncdb
    python manage.py sqlcustom registry | python manage.py dbshell
  

• Populated GEO details about IPs python upgrade/ip.py

• Collect statics

    python manage.py collectstatic
  

• Setup apache

  <VirtualHost *:80>

    ServerAlias stats.openmicroscopy.org
    ServerName stats.openmicroscopy.org
    ServerAdmin sysadmin@openmicroscopy.org
  
    ErrorLog /var/log/httpd/stats.openmicroscopy.org.err
    CustomLog /var/log/httpd/stats.openmicroscopy.org.log combined
  
    DocumentRoot /home/omero-stats/stats.git
  
    WSGIDaemonProcess omerostats processes=2 threads=15 display-name=%{GROUP} python-path=/home/omero-stats/stats.git:/home/omero-stats/reg-virtualenv/lib/python2.6/site-packages
    WSGIProcessGroup omerostats
  
    WSGIScriptAlias / /home/omero-stats/stats.git/omerostats/django.wsgi
  
    <Directory /home/omero-stats/stats.git/omerostats/>
        Order allow,deny
        Allow from all
    </Directory>
  
    Alias /static /home/omero-stats/stats.git/static
    <Location "/static/">
        Options -Indexes
    </Location>
  

  WSGISocketPrefix run/wsgi

Legal

The source for OMERO.stats is released under the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

OMERO.stats is Copyright (C) 2015 University of Dundee