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A toolkit for ETL curation for the tranSMART data warehouse.

Project description


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`_.

Some features:
- create a transmart-batch ready study from clinical data files.
- load an existing study and validate its contents.
- edit the transmart concept tree in The Arborist graphical editor.
- create chromosomal region annotation files.


tmtk is a ``python3`` package meant to be run in ``Jupyter notebooks``.
Results for other setups may vary.

For documentation visit `readthedocs`_.


Step 1: Opening a notebook

First open a Jupyter Notebook, open a shell and change directory to some
place where your data is. Then start the notebook server:

.. code:: sh

cd /path/to/studies/
jupyter notebook

This should open your browser to Jupyters file browser, create a new
notebook for here.

Step 2: Using tmtk

.. code:: py

# First import the toolkit into your environment
import tmtk

# Then create a <tmtk.Study> object by pointing to study.params of a transmart-batch study
study = tmtk.Study('~/studies/a_tm_batch_ready_study/study.params')
# Or, by using the study wizard on a directory with correctly structured, clinical data files.
# (Visit the transmart-batch documentation to find out what is expected.)
study = tmtk.wizard.create_study('~/studies/dir_with_some_clinical_data_files/')

Now we have loaded the study as a ``tmtk.Study`` object we have some
interesting functions available:

.. code:: py

# Check whether transmart-batch will find any issues with the way your study is setup

# Graphically manipulate the concept tree in this study by using The Arborist

For more, see the `examples`_.


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

.. code:: sh

$ pip3 install tmtk


.. code:: sh

$ pip3 install -r requirements.txt
$ python3 install

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

.. code:: sh
$ pip3 install -r requirements.txt
$ python3 develop
$ jupyter-nbextension install --py tmtk.arborist
$ jupyter-serverextension enable tmtk.arborist


These dependencies will have to be installed:
- pandas>=0.19.2
- ipython>=5.3.0
- jupyter>=1.0.0
- jupyter-client>=5.0.0
- jupyter-core>=4.3.0
- jupyter-console>=5.1.0
- notebook>=4.2.0
- requests>=2.13.0
- tqdm>=4.11.0
- mygene>=3.0.0


.. _transmart-batch:
.. _readthedocs:
.. _examples: examples

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