Genomicus

Contributors :

• Ambre Baumann
• Lindsay Goulet
• George Marchment
• Clémence Sebe

This repository contains :

• The Genomicus source code
• The Documentation
• Step by step guides to run Genomicus on a local work environnement or as a Docker container
• Visual representation of the database and how to generate it

Supervisors :

• Bryan Brancotte
• Olivier Lespinet

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Steps to run Genomicus on a 'local' work environnement

Install the necessary python modules

• We first have to start by installing the necessary python modules. Simply run the command :

pip install -r requirements.txt

To Fill Database with the .fa data

• We have chosen to load the application with some prototype data, to create the database and fill it with the prototype data, run the command :

./create_DB.sh

To fill the database we have decided to use (json) fixtures which we create by parsing the .fa files, with a dedicated python script. This is not an optimal solution, but since this project consists of only a 'small' application and that we do not have a large amount of data, we felt that running these commands to create and destroy the database was a suitable option.

To run the application

• To run the Genomicus application simply run the following command

./run.sh

• To access the application, go to the following address : http://127.0.0.1:8000/

• To access the different users :

Type	email	password
'lecteur'	clemence.sebe@universite-paris-saclay.fr	clemence
'annotateur'	ambre.baumann@universite-paris-saclay.fr	ambre
'validateur'	lindsay.goulet@universite-paris-saclay.fr	lindsay
'administrateur'	george.marchment@universite-paris-saclay.fr	george

To empty and delete the Database

Warning : When pushing any changes to the git make sure to destroy the DB

• To destroy the database, simply run the command

./destroy_DB.sh

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Steps to run Genomicus in a docker container

Warning : When using docker, you might have to use sudo

The Dockerfile and the create_site.sh script can be found in the folder elements_docker.

Pulling Docker image

• We first have to start by pulling the corresponding Docker image, run the command :

docker pull marchment/genomicus:v3.0

Running the application

• To guarantee the docker container is up to date with the current version of the genomicus project, we access the containers terminal. Simply run the following command :

docker run -it -p 8000:8000 --entrypoint bash  -t -i marchment/genomicus:v3.0

• Now we need to create the database, fill it and run the application. Simply run the following command :

./create_site.sh

• Now to access the application, go to the following address : http://localhost:8000/

Note : To access the users, the same rule applies as above.

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Visual representation of the Database

Here is a UML class diagram of the genomicus data base :

Steps to generate the diagram

• The first step is to install graphviz if it is not installed already. Simply run the following command (for Debian or Debian-based Linux distributions) :

sudo apt install graphviz

• Then we need to generate the diagram using the command manage.py graph_models, simply run the following commands :

python3 genomicus/manage.py graph_models -a --dot -o diagram.dot
dot -Tpng diagram.dot -o diagram.png

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