Metadata-Version: 2.1
Name: mcl.sickbay
Version: 0.0.6
Summary: 🤢 Sickbay: Clinical data model for the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions.
Home-page: https://github.com/MCLConsortium/mcl.sickbay
Author: Sean Kelly
Author-email: sean.kelly@jpl.nasa.gov
License: ALv2
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](https://mcl.nci.nih.gov/).
        
        
        ## 🏃‍♀️ Getting Started
        
        The "Sickbay" software provides a [Python](https://python.org/) based API into a data model (a series of related classes) and takes advantage of [SQLAlchemy](https://www.sqlalchemy.org/) as the object-relational mapper. This section will help you get started.
        
        
        ### 📀 The Database
        
        For this project, we're using [PostgreSQL](https://www.postgresql.org). You can create a PostgreSQL database to use with this software as follows:
        
        ```console
        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:
        
        ```console
        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](https://twine.readthedocs.io/).
        
        
        ### 🔢 Versioning
        
        We use the [SemVer](https://semver.org/) philosophy for versioning this software. For versions available, see the [release history](https://pypi.org/project/mcl.sickbay/#history).
        
        
        ## 📦 Additional Resources
        
        Some resources that provide further context for this software are as follows:
        
        -   [Sample data, presentations, mockups, etc.](https://drive.google.com/drive/folders/1oXqRl-Aw2TSF70D9sPJaW99F9hyPiFHY?usp=sharing)
        -   [Common Data Elements](https://mcl.nci.nih.gov/resources/standards/mcl-cdes)
        
        
        ## 👥 Contributing
        
        Well it's wide open right now, but later you might look at [open issues](https://github.com/MCLConsortium/mcl.sickbay/issues), forking the project, and submitting a pull request.
        
        
        ## 📃 License
        
        The project is licensed under the [Apache version 2](LICENSE.txt) license.
        
        
        
        ## 📜 Changelog
        
        This documents the changes from release to release.
        
        
        ### 0.0.6
        
        In this release:
        
        -   Base metadata for all classes now includes:
            -   `consortium`, a nullable string that can be used to contain an RDF URI to the consortium that originated the data, such as `https://mcl.nci.nih.gov/` for the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions.
            -   `protocolID`, a nullable integer that tells the research protocol that generated the data.
        -   Kristen's sample data (`--add-sample-data`) includes these consortium and protocol IDs
        
        
        ### 0.0.5
        
        This release fixes:
        
        -   In `BreastOrgan`, the field `her2_in_situ_hybridization` was the wrong enumerated type. It should've been `HER2InSituHybridization`.
        -   In the enums, add the type `HER2InSituHybridization`.
        -   Add test data from `12_78_BreastCore_20200625_0`.
        -   Removed foreign key constraint from `Biospecimen.specimen_parent_ID` because the parent ID may be either another biospecimen or could be a participant (clinical core) object.
        -   New class `AdjacentSpecimen` to work around circular dependency problem of having adjacent specimens directly on `Biospeciment`.
        -   New JSON serialization for `adjacent_specimens` on `Biospecimen`
        -   Misspelled enumeration `AnatomicalSite`: `pancrease` → `pancreas`
        -   Change `create-demo-db` to `create-clinical-db` since this is no longer a demo but the real deal
        -   Transition from old style `setup.py` to everything in `setup.cfg`
        
        In this release, 0.0.5, we also finally start keeping a changelog 😮
        
Keywords: rest api web clinical data lesions cancer orm model database
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Web Environment
Classifier: Framework :: Buildout
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Database
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
