kids-first / kf-omop-imports

🚧 Imports into the experimental Kids First OMOP Database

Kids First OMOP Imports

This repository is primarily meant to store configurations for importing study datasets into the experimental Kids First OMOP Database.

Note

Currently, the repository also contains a basic library (source code in common) with command line interface for running the ingestions in OMOP Postgres database. This is in place of the soon to be complete Kids First Data Ingest library. Once the Kids First Data Ingest library is complete, the common package will go away and the new library can be used.

There are only two datasets that have ingest configurations implemented: Vilain 2015 and CBTTC Proteomics.

Getting Started

Install

 # Git clone this repository
git clone [email protected]:kids-first/kf-omop-imports.git

# Setup and activate virtual env
python3 -m venv venv
source venv/bin/activate

# Install requirements
pip install -e .
pip install -r requirements.txt

Set Environment Variables

The import tool loads data into the OMOP database by connecting directly to it. It uses the following environment variables to make the connection URL. Change these to control the database connection.

1. PG_HOST - if not set will default to localhost
2. PG_NAME - if not set will default to omop
3. PG_USER - if not set will default to postgres
4. PG_PASS - if not set will default to empty string

Usage

$ cd kf-omop-imports
$ omop ingest <path to folder containing extract configs>

Example

$ omop ingest cbttc_proteomics