Development

Note

For linux users, it is necessary to add sudo before all docker commands.

Start dev instance

Step 1 : Open a terminal

Step 2 : Clone project

git clone https://gitlab.com/ifb-elixirfr/covid19/EMERGEN-DB.git
cd EMERGEN-DB

Step 3: Run docker compose

Avertissement

Docker must always be switched on for any installation and use of EMERGEN-DB !

# Run docker-compose
docker-compose up -d --build

# Migrate models into database and
docker-compose exec web python manage.py migrate

# Load data
docker-compose exec web python manage.py load_region
docker-compose exec web python manage.py load_departement
docker-compose exec web python manage.py load_description

# Create materialized view
docker-compose exec web python manage.py generate_mat_view_dep_reg
docker-compose exec web python manage.py generate_mat_view_team_auth_group

# Import GISAID information
docker-compose exec web python manage.py load_gisaid_instruction
docker-compose exec web python manage.py load_ena_instruction

# Create super user
docker-compose exec web python manage.py createsuperuser

EMERGEN-DB is running. You can open a web browser and use it in the following url : [http://localhost:8000/](http://localhost:8000/).

Note

Before submitting data, do not forget to add users. An example file is available with random users (static-apps/datafile/membres-emergen_test.csv) and data working with these users (static-apps/datafile/2021-04-09_IFB-bidon_semaine14_emergen_typage_v1.8.xlsx). This data does not reflect reality and is fictitious.

Useful commands

List of useful command lines in test instance:

  • Close EMERGEN-DB : docker-compose down.

  • Restart EMERGEN-DB : docker-compose up -d.

  • Rebuild EMERGEN-DB: docker-compose up -d --build.

  • Get logs : docker-compose up -d logs -f.

  • Populate with dummy data : bash populate_exemple_test.sh.

  • Generate UML schema : docker-compose exec web python manage.py graph_models -a -o static-apps/img/EMERGEN-DB_models.png.