Python wrapper for the OHDSI R packages
Project description
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
(setR_HOME
) - Install R packages
pip install python-ohdsi
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.
User Documentation
The user documentation can be found at readthedocs.
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