A toolkit for ETL curation for the tranSMART data warehouse.
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
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 setup.py install
or if you want to run the tool from code in development mode:
pip install -r requirements.txt python setup.py 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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