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deployment.md

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Depoyment on bioce (vm on mozzarella)

  1. Apache should be installed from webmin, one still needs to install mod_wsgi module:
sudo apt-get install apache2
sudo apt-get install python3-pip
sudo apt-get install libapache2-mod-wsgi-py3
sudo apt-get install supervisor
sudo apt-get install libgsl-dev
sudo apt-get install swig
  1. Now clone the BioCE webserver repo and register the app with apache and make a few folders:
git clone github.com/Andre-lab/bioce_webserver.git
mkdir logs
mkdir failedAnalyses
mkdir userData
  1. Install all Python packages to native python (Need to change it to requirements file):
pip install flask flask-mail flask-sqlalchemy flask-login flask-security flask-admin flask-migrate requests email_validator seaborn pystan pandas freesas
  1. Compile vbi module
swig -python -c++ -o vbw_sc_wrap.cpp vbw_sc.i
g++ -c VBW_sc.cpp vbw_sc_wrap.cpp -shared -fpic -I/usr/include/python3.8 -fopenmp -O3 -lgsl -lgslcblas -lm -std=c++11
g++ -shared VBW_sc.o vbw_sc_wrap.o -o _vbwSC.so -fopenmp -lgsl -lgslcblas -lm -std=c++11

  1. We want to serve our users through a secure HTTPS connection. This can be done from Webmin interface

  2. Edit config file for Apache:

vi /etc/apache2/sites-enabled/0000-default.conf

Remove what is in the file and copy and paste the following:

<VirtualHost *:80>
 
ServerAdmin [email protected]
ServerName bioce.plantbio.lu.se
DocumentRoot /var/www/html/

#Redirect permanent / http://130.235.135.6

WSGIDaemonProcess frontend user=wojtek group=wojtek processes=1 threads=1
WSGIScriptAlias / /var/www/html/bioce_webserver/frontend/frontend.wsgi process-group=frontend application-group=%{GLOBAL}

<Directory /var/www/html/bioce_webserver/frontend>
WSGIProcessGroup frontend
WSGIApplicationGroup %{GLOBAL}
Require all granted
</Directory>

<Directory /var/www/html/bioce_webserver>
WSGIProcessGroup frontend
WSGIApplicationGroup %{GLOBAL}
Require all granted
</Directory>

#Static Directories
Alias /static /var/www/html/bioce_webserver/frontend/static/
<Location "/static">
SetHandler None
</Location>

</VirtualHost>

It seems that since our access point is running ssl certificate and the server is behind firewall it doesn't require additional SSL setup on bioce

  1. Customize frontend/config_example.py and rename it to frontend/config.py

    1. Generate a secret key for your app like this
    2. Setup the username, email, password for the admin. You can then log in with these credentials and go to the Admin profile from the Profile page. Then you can edit all the tables of the database from online.
    3. Setup mail sending. You can use AWS's SES service if you have a domain name, (that's what I did for CorrMapper and for this demo). Alternatively you can use Gmail also. You'll need to allow less secure apps to use your account for this to work which might not be a great idea. You can also create an app-key.

  2. If you'd like to use Alembic to migrate your database if you update it's schema, then read this blog post and the docs here and do:

./manage.py db init
./manage.py db migrate
./manage.py db upgrade
  1. We are getting close. Let's install SQLite and create the database for the app.
sudo apt-get install sqlite
sudo apt-get install python-tk
python db_create.py
  1. Install RabbitMQ and setup a user with it, add it to config.py
sudo apt-get install rabbitmq-server
sudo rabbitmqctl add_user bioce *********
sudo rabbitmqctl set_permissions -p / bioce ".*" ".*" ".*"

Change config.py to

CELERY_BROKER_URL = 'amqp://bioce:*******@pbioce.andrelab.org:5672//'

Start the service with:

sudo rabbitmq-server

If you get an error saying it's already running, that's OK.

  1. Setup celery

Celery would need to run as a daemon process in the background. For this we'll use the very powerful supervisord package. It can do much more than this so definitely have a look at the docs.

Once supervisor is installed from packages is it should be enough to copy config file:

sudo cp /home/wojtek/public_html/bioce_webserver/supervisor.conf /etc/supervisor/supervisord.conf

The remaining part about celery is deprecated but leaving it for the record in case one wants to run it from pip installable package

Here's a quick tutorial on how to setup supervisor with Celery.

Science Flask repo already has a supervisord.conf file that should work out of the box if you've followed everything till this point.

Let's start supervisord by typing supervisord in science_flask folder.

When you try to start supervisord and get an error like this:

Error: Another program is already listening on a port that one of our HTTP servers is configured to use.

follow this trick

You can restart celeryd process via the supervisorctl like this:

supervisorctl restart celeryd
  1. You can check Apache's logs or from Webmin interface:
less -S /var/log/apache2/error.log
less -S /var/log/apache2/access.log

Celery and Science Flask also logs. These are in ~/bioce_webserver/logs. These are very useful to check on the status of the app.

  1. Restart server and enjoy!
sudo systemctl restart apache2

You should be able to log in with the admin credentials you specified in frontend/config.py. Go to the Profile page and then to the Admin panel (botton right corner).