OmicsPred backend

Backend part of the OmicsPred Project

• OmicsPred website: https://www.omicspred.org/
• OmicsPred REST API website: https://rest.omicspred.org/

Roles

Manage import, querying and retrieval of the OmicsPred metadata:

• Scripts to import the metadata and generate the genetic scoring files (app imports -> README)
• Scripts to export the metadata and data (app exports)
• Access the databases (apps omicspred, plot) [read & write]
• Provide private (accessible by the website) and public REST APIs (app rest_api) [read only]
• Build and query the search engine (app search_es) using ElasticSearch [read & write]

Softwares / tools

Tool	Role	Version
PostgreSQL	Database to store and query metadata	>= 18
ElasticSearch	Server used as search engine	8.xx (e.g. 8.19)
Django	Python framework to communicate with the database, the ElasticSearch indexes and build a REST API	6.0.x (e.g. 6.0.7)

Setup

Go to root of the repository (e.g. cd .../omicspred_backend)

• Rename app.yaml_template to app.yaml and replace the <values> with your settings

• Install the required Python packages with the commands:

  pip install -r requirements.txt
  pip install -r requirements_local.txt # Only necessary for local deployement

• Create static directory

  python manage.py collectstatic

• Create ElasticSearch indexes

  python manage.py search_index --create

  [!WARNING] The indexing of the scores takes few hours (2-3h)!

  To rebuild existing OmicsPred indexes:

    python manage.py search_index --rebuild -f

• For local deployment, run the command:

  python manage.py runserver

  This will create an instance of the Django apps on your local machine on http://127.0.0.1:8000/

• For cloud deployment (e.g. Google Cloud App Engine), after setting up the Cloud account on your laptop and updating the app.yaml file, run the command:

  gcloud app deploy

Note

You will need to deploy the backend twice:

• One for the Public REST API with the app deployment name service: rest and the variable PUBLIC_SITE: 'True'.
• One for the Private REST API (i.e. the one consumed by the OmicsPred website) with the app deployment name service: rest-private and the variable PUBLIC_SITE: 'False'.
  See the different app.yaml configuration files already set in the Group Google Drive directory Website -> Systems/Settings -> REST API (back-end)

Tests

Tests have been written for the metadata imports and the REST API. To run the tests manually, run the command:

python manage.py test

Note

This runs the REST API, exports and imports tests

or to only run one test (e.g. metadata imports):

python manage.py test imports/tests