cegid: An HTML repository from vsoch

Center for Genomic Immune Diseases Docker

under construction

Setup for Local Development

Installing dependencies

Fork the main repository
Clone your fork to your computer: git clone https://github.com/<your_username>/cegid

Warning: if you are using OS X you have to clone the repository to a subfolder in your home folder - /Users/<your_username/... - otherwise boot2docker will not be able to mount code directories and will fail silently.

Install docker >= 1.6 (If you are using OS X you'll also need boot2docker)
Install docker-compose >= 1.2
If you are using OS X and homebrew steps 3 and 4 can be achieved by: brew update && brew install docker boot2docker docker-compose
Make sure your docker daemon is running (on OS X: boot2docker init && boot2docker up)

Running the server

To run the server in detached mode, do:

  docker-compose up -d

The webpage will be available at 127.0.0.1 (unless you are using boot2docker - then run boot2docker ip to figure out which IP address you need to use). You can also run the server in non-detached mode, which shows all the logs in realtime.

  docker-compose up

Stopping the server

To stop the server:

  docker-compose stop

Restarting the server

After making changes to the code you need to restart the server (but just the uwsgi component):

  docker-compose restart uwsgi worker nginx

Reseting the server

If you would like to reset the server and clean the database:

  docker-compose stop
  docker-compose rm
  docker-compose up

Running Django shell

If you want to interactively develop, it can be helpful to do so in the Django shell. Thank goodness we can still connect to it in the floaty Docker container with the following!

  docker-compose run --rm uwsgi python manage.py shell

Connecting to Running container

It can be helpful to debug by connecting to a running container. First you need to find the id of the uwsgi container:

  docker ps

Then you can connect:

  docker exec -i -t [container_id] bash

Updating docker image

Any change to the python code needs to update the docker image, which could be adding a new package to requirements.txt. If there is any reason that you would need to modify the Dockerfile or rebuild the image, do:

 docker build -t vanessa/cegid .

Getting Started

Before bringing up your container, you must create a file secrets.py in the cegid folder with the following:

  SECRET_KEY = "xxxx"

You can generate a secret key here. You will also need to define a SendMail username and password for sending results to email:

  EMAIL_HOST_USER = 'sendmail_username'
  EMAIL_HOST_PASSWORD = 'sendmail_password

Note that this API will let you use their SMTP server, giving you 12K emails per month. Then you can bring up the container (see steps at beginning of README), essentially:

  docker-compose up -d

You will then need to log into the container to create the superuser. First do docker ps to get the container id of the uwsgi that is running vanessa/expfactory image, and then connect to the running container:

  docker ps
  docker exec -it [container_id] bash

Then you will want to make sure migrations are done, and then you can interactively generate a superuser:

  python manage.py makemigrations
  python manage.py migrate
  python manage.py shell

Then to create your superuser, for example:

  from django.contrib.auth.models import User
  User.objects.create_superuser(username='ADMINUSER', password='ADMINPASS', email='')

and replace ADMINUSER and ADMINPASS with your chosen username and password, respectively.

Site Name

Use the script scripts/name_site.py to name the site. You will need to log into the instance and run this to do so. When it's running (after docker-compose up -d first find the id of the container that has the /code directory:

  docker ps

Then connect to it interactively:

  docker exec -it CONTAINERID bash

and run the script. You can also copy paste the code into the interactive shell generated with python manage.py shell.

Encrypted database connection

If your provider (eg aws) provides you with a certificate, you can add it to /etc/ssl/certs on the server, and this path is already mapped in the docker-compose for the nginx container. You then need to specify to use SSL in the database connection in your settings.py or local_settings.py:

  DATABASES = {
      'default': {
          'ENGINE': 'django.db.backends.postgresql_psycopg2',
          'NAME': 'dbname',
          'USER': 'dbuser',
          'PASSWORD':'dbpassword',
          'HOST': 'dbhost',
          'PORT': '5432',
          'OPTIONS': {
                  'sslmode': 'require',
                  'sslrootcert':'/etc/ssl/certs/rds-cert.pem'
          },
      }
  }

vsoch/cegid