Scipion Portal

http://calm-shelf-73264.herokuapp.com

http://scipion.i2pc.es

Set up

Dependencies

$ cd scipion-portal
$ virtualenv --python /usr/bin/python2 env
$ env/bin/pip install -r requirements.txt

Development server

$ export DATABASE_URL=postgres://user:password@localhost:5432/scipion
$ env/bin/python manage.py runserver

Production server (Apache)

<VirtualHost *:80>
  ServerName scipion.i2pc.es
  Alias /static /home/ubuntu/scipion-portal/staticfiles

  <Directory /home/ubuntu/scipion-portal/staticfiles>
    Require all granted
  </Directory>

  <Directory /home/ubuntu/scipion-portal/main>
    <Files wsgi.py>
      Require all granted
    </Files>
  </Directory>

  WSGIDaemonProcess scipion-portal python-home=/home/ubuntu/scipion-portal/env python-path=/home/ubuntu/scipion-portal
  WSGIProcessGroup scipion-portal
  WSGIScriptAlias / /home/ubuntu/scipion-portal/main/wsgi.py

  SetEnv DATABASE_URL postgres://scipion:j6rUtd8Y6qW@localhost:5432/scipion
</VirtualHost>

Downloads

Files in section Download are stored in static/install and its contents described by the file static/install/downloadables.json. See static/install/downloadables.json.template in the repository for reference.

Database: Postgres

$ createdb scipion
$ pg_restore scipion_usage_bd_20170620.backup | psql scipion
$ psql scipion
$ echo "ALTER TABLE django_content_type ADD COLUMN name character varying(50) NOT NULL DEFAULT 'someName';" | psql scipion

Set the environment variable DATABASE_URL. Example: postgres://user:password@localhost:5432/scipion.

$ export DATABASE_URL=postgres://user:password@localhost:5432/scipion
$ python manage.py migrate --fake-initial

Database: Convert old sqlite3 database to postgres

Install the dependencies:

$ env/bin/pip install records

And execute the utilities script passing source and target database path/url. An example:

$ env/bin/python utilities/convert_db_sqlite_to_postgres.py \
  downloads.sqlite3 \
  postgres://user:password@localhost:5432/scipion

Admin interface (requires password)

http://scipion.i2pc.es/admin/

Details of usage data collection

You can find them here https://github.com/I2PC/scipion/wiki/Collecting-Usage-Statistics-for-Scipion

Test: Query from command line:

$ curl http://scipion.i2pc.es/report_protocols/api/workflow/protocol/?name=ProtMonitorSystem
$ curl http://scipion.i2pc.es/report_protocols/api/workflow/workflow/?project_uuid=b9a2d873-53d2-42fb-aa69-a5002f2f08e9