Orphapacket Data Importer

This Python script imports Orphapacket data from JSON files into a PostgreSQL database. The JSON files can be downloaded from the Orphanet Orphapacket repository.

Features

• Inserts Orphapacket data, including genes, phenotypes, synonyms, text sections, average age of onset, type of inheritances, and prevalences.
• Handles relationships between Orphapackets and external references.

Schema

Setup

Clone this repository and navigate to the project directory. Create a .env file in the root of the project directory with the following content:

DB_NAME=<database_name>
DB_USER=<database_user>
DB_PASSWORD=<database_password>
DB_HOST=<database_host>
DB_PORT=<database_port>

Create the tables in the database by running the following command:

source .env
psql -h $DB_HOST -p $DB_PORT -U $DB_USER -d $DB_NAME -f orphapacket.sql

Running the Script

1. Ensure you have your PostgreSQL database running and accessible.

2. Download the JSON files from the Orphanet Orphapacket repository and place them in a folder named json within the project directory.

   mkdir json
   rm json/* # Remove any existing files in the json folder (if the folder already exists)
   git clone git@github.com:Orphanet/orphapacket.git
   mkdir json
   cp orphapacket/json/* json/

3. Run the script to import data into the database:

   python import_orphapacket.py

   The script will automatically detect all JSON files in the json folder and begin importing them into the PostgreSQL database. Progress will be displayed with a progress bar.