iris-django-template

Description

This is a template for an Django application that can be deployed in IRIS as an native Web Application.

Installation

1. Clone the repository
2. Create a virtual environment
3. Install the requirements
4. Run the docker-compose file

git clone
cd iris-django-template
python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
docker-compose up

Usage

The base URL is http://localhost:53795/django/.

Endpoints

• /iris - Returns a JSON object with the top 10 classes present in the IRISAPP namespace.
• /interop - A ping endpoint to test the interoperability framework of IRIS.
• /api/patients - A list endpoint for a Patient object.
• /api/patients/<pk></pk> - A retrieve endpoint for a Patient object.
• /api/genomes/<pk> - A retrieve endpoint for a Genome object.
• /api/pharmacogenomics/get-pharmacogenomics-from-genome/ - API for retrieve pharmacogenomics from an array of genes

Code presentation

The Django application is structured as follows:

• app - Django project folder
  • app - Django app folder for configuration
    • settings.py - Django settings file
    • urls.py - Django URL configuration file to connect the views to the URLs
    • wsgi.py - Django WSGI file
    • asgi.py - Django ASGI file
  • community - Django app folder for the community app, crud on Post, Comment, Patient, Genome and Pharmacogenomics objects
    • models.py - Django models file for the Post, Comment, Patient, Genome and Pharmacogenomics objects
    • views.py - Django views file to access the Post, Comment, Patient, Genome and Pharmacogenomics objects
    • serializers.py - Django serializers file for the Post, Comment, Patient, Genome and Pharmacogenomics objects
    • admin.py - Django admin file add crud to the admin interface
    • migrations - Django migrations folder to build the database
    • fixtures - Django fixtures folder demo data
  • sqloniris - Django app folder for the SQL on IRIS app
    • views.py - Django views file to query the IRISAPP namespace
    • apps.py - Django app configuration file
  • interop - Django app folder for the interoperability app
    • views.py - Django views file to test the interoperability framework
    • apps.py - Django app configuration file
  • manage.py - Django management file

Troubleshooting

How to run the Django application in a standalone mode

To run the Django application in a standalone mode, we can use the following command:

cd /irisdev/app/app
python3 manage.py runserver 0.0.0.0:8001

This will run the Django application on the default port 8001.

NB : You must be inside of the container to run this command.

NOTE: This projects starts the Django server by default for easy debug. (You don't have the rebuild the image when you make changes to the Django code)

docker exec -it iris-django-template-iris-1 bash

Restart the application in IRIS

Be in DEBUG mode make multiple calls to the application, and the changes will be reflected in the application.

How to access the IRIS Management Portal

You can access the IRIS Management Portal by going to http://localhost:53795/csp/sys/UtilHome.csp.

Run this template locally

For this you need to have IRIS installed on your machine.

Next you need to create a namespace named IRISAPP.

Install the requirements.

# Move to the app directory
cd /irisdev/app/app

# python manage.py flush --no-input
python3 manage.py migrate
# create superuser
export DJANGO_SUPERUSER_PASSWORD=SYS
python3 manage.py createsuperuser --no-input --username SuperUser --email [email protected]

# load demo data
python3 manage.py loaddata community/fixtures/demo.json

# collect static files
python3 manage.py collectstatic --no-input --clear

# init iop
iop --init

# load production
iop -m /irisdev/app/app/interop/settings.py

# start production
iop --start Python.Production

How to serve static files

To serve the static files in the Django application, we can use the following command:

cd /irisdev/app
python3 manage.py collectstatic

This will collect the static files from the Django application and serve them in the /irisdev/app/static directory.

To publish the static files in IRIS, configure the Security->Applications->Web Applications section.