Introduction

This project is the backend part of omop-mapper.fgh.ovh

How to install ?

database

• path for the csv : ln -s local_csv_file csv/omop

• make postgres-create to create de db

• set db with config.py file in app conf_files: postgres auth

# To generate a new secret key:
# >>> import random, string
# >>> result = "".join([random.choice(string.printable) for _ in range(24)])
SECRET_KEY = result

SQLALCHEMY_TRACK_MODIFICATIONS = False
PROPAGATE_EXCEPTIONS = True
JWT_BLACKLIST_ENABLED = True
JWT_BLACKLIST_TOKEN_CHECKS = ['access', 'refresh']

POSTGRES = {
    'user': 'omop-mapper',
    'pwd': 'omop-mapper',
    'db': 'omop-mapper',
    'host': 'localhost',
    'port': '5432',

}
SQLALCHEMY_DATABASE_URI = 'postgresql://%(user)s:%(pwd)s\
@%(host)s:%(port)s/%(db)s' % POSTGRES

run app

• dev mode (no synchronisation with solr, no need to install solr)

  • virtualenv -p python3.7 venv
  • source venv/bin/activate
  • pip install -r app/equirements.txt
  • mv app/server.py .
  • mv conf_files/config.py app/.
  • python server.py

• production mode : uwsgi/proxy/flask (should install solr before)

  • docker-compose build
  • docker-compose up

Languages

See ISO_OMOP_LANGUAGES in share/macros.py

Frontend

The frontend part is here

TODO

Put Solr and Livy in docker

Remark : Create Standardized vocabulary tables

• https://github.com/MIT-LCP/mimic-omop/tree/master/omop/build-omop/postgresql
• https://github.com/OHDSI/CommonDataModel/tree/master/PostgreSQL