python-ohdsi

Python wrappers for (some) OHDSI tools. This project has been initiated for supporting OMOP data sources in vantage6.

Make sure you have a working R environment with the OHDSI packages installed.

Installation

Python binding

Interact with the OMOP database using a python interface.

Install Java JDK.
Install R: sudo apt-get install r-base (set R_HOME)
Install R packages

pip install ohdsi-common
pip install ohdsi-sqlrender
pip install ohdsi-circe
pip install ohdsi-database-connector
pip install ohdsi-feature-extraction
pip install ohdsi-cohort-generator
pip install ohdsi-cohort-diagnostics

API service

Spin up a small webserver next to the OMOP database to allow HTTP requests to the OMOP database. You can use the prebuild image from dockerhub:

docker pull ...
docker run ...

Or you can build the image yourself:

docker build -t ohdsi-api .
docker run -p 5000:5000 ohdsi-api

Or you can run the API service directly from the source code:

pip install -r requirements.txt
python api.py

Building documentation

cd docs
export IGNORE_R_IMPORTS=True
make html

cd docs
Set-Item -Path Env:IGNORE_R_IMPORTS -Value True
make html

or you can use make livehtml to automatically rebuild the documentation when a file is changed.

You can set the IGNORE_R_IMPORTS environment variable to ignore the R imports in the documentation. This is useful when you don't have the R packages installed but want to build the documentation anyway.

Release

make set-version VERSION=x.x.x

If you created a new package add it to the Maketools
Create release on Github

User Documentation

The user documentation can be found at readthedocs.