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A toolkit for ETL curation for the tranSMART data warehouse.

Project description

Master: Documentation Status


Anaconda Cloud latest package:

A toolkit for ETL curation for the tranSMART data warehouse. The TranSMART curation toolkit (tmtk) can be used to edit and validate studies prior to loading them with transmart-batch.

For general documentation visit readthedocs.


Installing via Anaconda Cloud or Pip package managers


conda install -c conda-forge tmtk


pip install tmtk

Installing manually

Initialize a virtualenv

python3 -m venv env
source env/bin/activate

Installation from source

To install tmtk and all dependencies into your Python environment, and enable the Arborist Jupyter notebook extension, run:

pip install -r requirements.txt
python install

or if you want to run the tool from code in development mode:

pip install -r requirements.txt
python develop
jupyter-nbextension install --py tmtk.arborist
jupyter-serverextension enable tmtk.arborist


The dependencies are in requirements.txt, optional dependencies are in requirements-dev.txt.



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