BDD

AddInDatabase

In this directory is presented the tool AddInDatabase, which allows to fill a database implemented with Postgresql.

Database Schema :

To launch this tool, you need to have the folder containing the results of the Nextflow analyser and a folder with the global information (author and information about the workflow from github)

1. The folder containing the results of the Nextflow analyser must contain all the workflow results folder :

Obtain with the command :

NFanalyzer --input "/home/clemence/AnalyseDonneesNextflow/bddFiles" --results_directory "/home/clemence/AnalyseDonneesNextflow"  --name 'Result_Nfanalyser' --mode 'multi'

• A workflow written in DSL1 must contain in it repository 7 files:

• And a DSL2 workflow contain only 1 file :

2. The global information folder must contain at least 2 files : one with the wf in it name and a second with the word author. Warning : not two distinct files in this directory must contain in their names wf or author

Install and Run

To install and run this tool, you first need to be in this directory.

Postgrsql Connection file configuration :

This file is located in the resources folder. How find the information to complete the documentation :

• In a terminal open a postgresql session: psql
• Then type the command: \conninfo
• To finish, put your parameters in the config file and add your password.

To install :

sudo python3 setup.py install

Before running :

In the postgresql session launch the script to create the tables :

Command : \i address_to_the_script_if_not_in_the_same_directory/createTables.sql

To run :

• The option --system : 'N' (Nextflow)

AddInDatabase --system 'N' --results_directory 'address/to_folder/to_result' --json_directory 'address/to_folder/to_json_information'

Requirements

Your software environment needs the following Python packages :

• configparser
• argparse
• psycopg
• pathlib
• datetime
• glob
• json
• os