MCL Sickbay, a Clinical Data Prototype
Project description
👩⚕️ MCL Sickbay
"MCL Sickbay" is the data model and object-relational mapping for the clinical data application of the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions.
🏃♀️ Getting Started
The "Sickbay" software provides a Python based API into a data model (a series of related classes) and takes advantage of SQLAlchemy as the object-relational mapper. This section will help you get started.
📀 The Database
For this project, we're using PostgreSQL. You can create a PostgreSQL database to use with this software as follows:
dropdb --if-exists clinical_data
dropuser --if-exists mcl
createuser \
--createdb \
--inherit \
--login \
--no-createrole \
--no-superuser \
mcl
createdb --encoding=UTF8 --owner=mcl clinical_data
🖥 The Software
To use this software, simply add mcl.sickbay as a dependency to your project or install it into your Python virtual environment.
You can develop, build, and test the package locally as follows:
python3 bootstrap.py
bin/buildout
bin/test
You can run bin/create-demo-db to populate a PostgreSQL database with the schema of the Sickbay data model. Add -add-test-data to include some test data.
To publish this software, try Twine.
🔢 Versioning
We use the SemVer philosophy for versioning this software. For versions available, see the release history.
📦 Additional Resources
Some resources that provide further context for this software are as follows:
👥 Contributing
Well it's wide open right now, but later you might look at open issues, forking the project, and submitting a pull request.
📃 License
The project is licensed under the Apache version 2 license.
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