thicham43 / cohort360-back-end

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Modèle de données
5. Contact

About The Project

Portail has the aim of controlling the access to EDS (Entrepôts de Données de Santé) data

The main goals are to allow:

• Users to give access to other users to patient nominative or pseudonymised data
• Users to allow other users to give these accesses
• Cohort360 users to ask for exports of their cohorts and download them as CSV files or transfer them to Jupyter workspaces
• Admins to manage Jupyter and Unix workspaces

Built With

Here is a list of major frameworks used here.

• Django
• Django REST Framework
• PosgreSQL
• Redis
• Celery
• DRF-YASG (Swagger Generator)

Getting Started

Prerequisites

• Python

  sudo apt-get update
  sudo apt-get install python3.8

• PostgreSQL

  sudo apt-get install postgresql postgresql-contrib

• Kerberos authentication development library

  sudo apt-get install -y libkrb5-dev gcc

Installation

1. Clone the repo

   git clone https://gitlab.eds.aphp.fr/dev/console-admin/admin-back-end.git
   cd admin-back-end

2. Prepare a virtual environment

   pip install virtualenv
   virtualenv -p python3.8 venv
   source venv/bin/activate
   pip install -r requirements.txt

3. Prepare your database

   sudo -u postgres psql

   CREATE USER portail_dev_limited_rw PASSWORD 'portail_psswd';
   CREATE DATABASE portail_dev OWNER portail_dev_limited_rw;
   \q
   

4. Configuration :

• create a .env file admin_cohort/.env following .env.example format

5. Now run Django migrations in that order

   source venv/bin/activate
   python manage.py migrate

6. In order to allow Django to run its tests, authorise the user to create a test database

  sudo -u postgres psql

ALTER USER portail_dev_limited_rw CREATEDB;  

7. If you want to run the server locally to try your own new actions, you'll need to give your user access to the schemas

  \c portail_dev
  GRANT ALL PRIVILEGES ON DATABASE portail_dev TO portail_dev_limited_rw;

8. Also, here are a few rows to add so that the whole model could work (adapt with your email address, and the PERIMETER_TYPES you provide in .env):

  \c portail_dev
  -- An admin user
  INSERT INTO "user" (firstname , lastname, provider_id, provider_username, email) VALUES('Cid', 'Kramer', 0, '96214', '[email protected]');
  INSERT INTO accesses_profile(id, user_id, source, is_active, firstname, lastname, email) VALUES(0, '96214', 'Manual', 't', 'Cid', 'Kramer', '[email protected]');

  -- An simple user to play with
  INSERT INTO "user" (firstname , lastname, provider_id, provider_username, email) VALUES('Squall', 'Leonheart', 1, '41269', '[email protected]');
  INSERT INTO accesses_profile(id, user_id, source, is_active, firstname, lastname, email) VALUES(1, '41269', 'Manual', 't', 'Squall', 'Leonheart', '[email protected]');

  -- Basic perimeter tree
  INSERT INTO accesses_perimeter(id, name, local_id, type_source_value, parent_id) 
  VALUES 
      (0, 'AP-HP', 'Local 00', 'AP-HP', null),
      (1, 'Hospital 1', 'Local 01','Hospital', 0),
      (2, 'Hospital 2', 'Local 02','Hospital', 0),
      (3, 'Unit 1', 'Hospital 2','Hospital', 2)
  ;

  -- Full administration role
  INSERT INTO accesses_role(id, name, right_edit_roles, right_add_users, right_edit_users, right_read_users, right_manage_admin_accesses_same_level, right_read_admin_accesses_same_level, right_manage_admin_accesses_inferior_levels, right_read_admin_accesses_inferior_levels, right_manage_data_accesses_same_level, right_read_data_accesses_same_level, right_manage_data_accesses_inferior_levels, right_read_data_accesses_inferior_levels, right_read_patient_nominative, right_search_patient_with_ipp, right_read_patient_pseudo_anonymised, invalid_reason, right_read_logs, right_export_csv_nominative, right_export_csv_pseudo_anonymised, right_manage_export_csv, right_manage_review_export_csv, right_manage_review_transfer_jupyter, right_manage_transfer_jupyter, right_review_export_csv, right_review_transfer_jupyter, right_transfer_jupyter_nominative, right_transfer_jupyter_pseudo_anonymised, right_manage_env_unix_users, right_manage_env_user_links, right_read_env_unix_users) VALUES(0,'FULL_ADMIN','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t','t');
  -- Access to admin profile
  INSERT INTO accesses_access(role_id, perimeter_id, profile_id) VALUES(0, 0, 1);

9. If you want to start using Cohort:

  \c portail_dev
  -- Nominative Data reading role
  INSERT INTO accesses_role(id, name, right_edit_roles, right_add_users, right_edit_users, right_read_users, right_manage_admin_accesses_same_level, right_read_admin_accesses_same_level, right_manage_admin_accesses_inferior_levels, right_read_admin_accesses_inferior_levels, right_manage_data_accesses_same_level, right_read_data_accesses_same_level, right_manage_data_accesses_inferior_levels, right_read_data_accesses_inferior_levels, right_read_patient_nominative, right_search_patient_with_ipp, right_read_patient_pseudo_anonymised, invalid_reason, right_read_logs, right_export_csv_nominative, right_export_csv_pseudo_anonymised, right_manage_export_csv, right_manage_review_export_csv, right_manage_review_transfer_jupyter, right_manage_transfer_jupyter, right_review_export_csv, right_review_transfer_jupyter, right_transfer_jupyter_nominative, right_transfer_jupyter_pseudo_anonymised, right_manage_env_unix_users, right_manage_env_user_links, right_read_env_unix_users) VALUES(1,'Nominative Patient Reader','f','f','f','f','f','f','f','f','f','f','f','f','t','f','f','f','f','f','f','f','f','f','f','f','f','f','f','f','f','f');
  -- Pseudo-anonymised Data reading role
  INSERT INTO accesses_role(id, name, right_edit_roles, right_add_users, right_edit_users, right_read_users, right_manage_admin_accesses_same_level, right_read_admin_accesses_same_level, right_manage_admin_accesses_inferior_levels, right_read_admin_accesses_inferior_levels, right_manage_data_accesses_same_level, right_read_data_accesses_same_level, right_manage_data_accesses_inferior_levels, right_read_data_accesses_inferior_levels, right_read_patient_nominative, right_search_patient_with_ipp, right_read_patient_pseudo_anonymised, invalid_reason, right_read_logs, right_export_csv_nominative, right_export_csv_pseudo_anonymised, right_manage_export_csv, right_manage_review_export_csv, right_manage_review_transfer_jupyter, right_manage_transfer_jupyter, right_review_export_csv, right_review_transfer_jupyter, right_transfer_jupyter_nominative, right_transfer_jupyter_pseudo_anonymised, right_manage_env_unix_users, right_manage_env_user_links, right_read_env_unix_users) VALUES(2,'Pseudo-anonymised Patient Reader','f','f','f','f','f','f','f','f','f','f','f','f','f','f','t','f','f','f','f','f','f','f','f','f','f','f','f','f','f','f');

  -- Access to NominativeDataReader for User 1 on Hospital1
  INSERT INTO accesses_access(role_id, perimeter_id, profile_id) VALUES(1, 1, 1);

Usage

In the initial way to use this back-end server, authentication should be made using connection to APHP jwt server.

If you want to use it fully locally, update admin_cohort/AuthMiddleware.py file.

Run the server to start making request via localhost:8000:

source venv/bin/activate
python manage.py runserver

You can now go on website localhost:8000/docs/ for more details on the API.

Data Models

How to explore data model into your POD

1 - Connection to your POD.

2 - launch the following command:

python3 manage.py shell

3 - import your data models:

from accesses.models import Access, Profile, Role

4 - you can start explore your data models: Exemple

allProfiles = Profile.objects.all()
 firstProfil = allProfiles .first()
firstProfil.provider_id

Testing

Run: python manage.py test

Contact

Alexandre Martin, main developer - @alexandreMartinEcl - [email protected]

Julien Dubiel, project Owner - @j.du - [email protected]