Developer Environment

Prerequisites

To set up the developer environment, first either complete the manual or automatic installation. This step should set up the postgres server, redis server, and nginx server. * Automatic Installation * Manual Installation

You will also need to download the bitbucket repository. Preferrably store this in a separate directory to where the Local EnteroBase installation files are stored, to help avoid confusion. e.g. store it in $HOME/local_enterobase_repo.

After the installation has finished, run the following command:

$ singularity instance stop egp

This stops the server running with the code already inside the container and frees up the port to be used for development.

Running the Application

Entering the Container

To develop the app and run it within the correct environment, you will need to enter the container, binding your Local EnteroBase repository code to override what the container stores. This allows you to avoid having to rebuild the container each time you make changes to the codebase.

$ singularity shell /replace/with/path/to/local_enterobase_repo:/var/www/local_enterobase $HOME/local_enterobase_home/local_enterobase/EGP.sif
$ cd /var/www/local_enterobase
$ source /venvs/gunicorn-env/bin/activate

What the above commands do is enter the shell, cd to the correct directory, and source the python virtual environment.

Development

To run the application in development mode, set STAGING=”development” in manage.py. This is done to make sure the celery worker is connected to the same database as the server.

The following commands are to be run inside the container after following the “Entering the Container” stage

Run Dev Server:

$ python3 manage.py run_app

Run Celery Worker:

$ celery -A manage worker  --loglevel=debug --pidfile=$HOME/celerybeat_myapp_2.pid

Run Celery Beat:

$ celery -A manage beat --loglevel=debug --pidfile=$HOME/celerybeat_myapp.pid -s $HOME/celerybeat-schedule:

Production

To run the application in production mode, set STAGING=”production” in manage.py. This is done to make sure the celery worker is connected to the same database as the server.

The following commands are to be run inside the container after following the “Entering the Container” stage

Run Dev Server:

$ gunicorn -b 0.0.0.0:8000 --timeout 300 --name "local_entero" --log-file=$HOME/logs/gunilog.log --bind=unix:$HOME/sock "manage:create_app_production()"

Run Celery Worker:

$ celery -A manage worker  --loglevel=debug --pidfile=$HOME/celerybeat_myapp_2.pid

Run Celery Beat:

$ celery -A manage beat --loglevel=debug --pidfile=$HOME/celerybeat_myapp.pid -s $HOME/celerybeat-schedule:

Additional Info

Every time you change the code, the dev server will auto-reload, but the Celery Worker, Celery Beat will need to be restarted. If you are running it in production mode you will need to manually restart the gunicorn server as well.