Metadata-Version: 2.1
Name: termlink
Version: 0.4.4
Summary: Provide an ontology via Terminology Service's API link.
Home-page: https://github.com/lifeomic/termlink
Author: Taylor Steinberg
Author-email: taylor.steinberg@lifeomic.com
License: MIT
Description: # termlink
        
        Prepare an ontology and send it to the Precision Health Cloud.
        
        _Termlink_ is a command line client and library for uploading ontologies to LifeOmic's _Precision Health Cloud_. Its goal is to make uploading standardized ontologies easier and to provide utilities for uploading custom ontologies. It provides a simple command line interface for creating standard ontologies and a Python SDK for building integrations with custom ontologies.
        
        ## Quickstart
        
        Download the following tools:
        
        - [Docker](https://docs.docker.com/install/)
        
        Pull the latest version of _TermLink_ from [Docker Hub](https://hub.docker.com/r/lifeomic/termlink):
        
        ```sh
        docker pull lifeomic/termlink
        ```
        
        Run it.
        
        ```sh
        docker run lifeomic/termlink --help
        ```
        
        Import the output ontology into the [Precision Health Cloud](https://lifeomic.com/products/) using the [LifeOmic CLI](https://github.com/lifeomic/cli):
        
        ```sh
        docker run lifeomic/termlink ... | lo ontologies import <project>
        ```
        
        ## Getting Started
        
        These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
        
        ### Prerequisites
        
        The following tools are required to run _TermLink_:
        
        - [Docker](https://docs.docker.com/install/)
        - [Git](https://git-scm.com/)
        - [Python 3](https://www.python.org/download/releases/3.0/)
        - [Yarn](https://yarnpkg.com/en/)
        
        ### Installing
        
        The following steps will guide you through installing the project locally.
        
        Clone the `git` repository onto your local machine.
        
        ```sh
        git clone git@github.com:lifeomic/termlink.git && cd ./termlink
        ```
        
        Using Python 3, create a `virtualenv` and then activate it.
        
        ```sh
        python3 -m venv venv && source venv/bin/activate
        ```
        
        _Note: Your Python binary may be under a different name._
        
        Check that your local version of Python is at least version 3.7 by running `python --version`.
        
        Once you have verified your version of Python is correct, run the following to download all dependencies.
        
        ```sh
        pip install -r requirements.txt
        ```
        
        ```sh
        pip install -r requirements-dev.txt
        ```
        
        You now have everything you need to start developing on _Termlink_. 
        
        ## Testing
        
        This project uses the Python [`nose`](https://nose.readthedocs.io/en/latest/index.html) framework.
        
        ### Unit Testing
        
        Run unit tests with `yarn`:
        
        ```sh
        yarn test
        ```
        
        ## Deployment
        
        The project is deployed in two locations.
        
        1. [PyPI](https://pypi.org/project/termlink/): Python package. 
        2. [Docker Hub](https://hub.docker.com/r/lifeomic/termlink): Packaged runtime environment.
        
        Publish a new version using the command following command:
        
        ```sh
        yarn deploy
        ```
        
        The deployment will prompt you multiple inputs.
        
        First, you will be promoted to enter a new version, triggered by the `yarn version` command. Please use [SemVer](https://semver.org/) versioning for incrementing versions. To learn more about why SemVer is used, see the section on [_Versioning_](##Versioning) below.
        
        Second, you will be promoted for PyPI credentials. To gain write access to the PyPI package, contact one of the maintainers listed on the project page [here](https://pypi.org/project/termlink/).
        
        Third, `docker push` will run which requires that you have previously logged in using `docker login`. To gain access to the Docker Hub project, contact one of the owners listed on the project page [here](https://hub.docker.com/r/lifeomic/termlink).
        
        ## Built With
        
        - [Docker](https://www.docker.com/): "Build, Ship, and Run Any App, Anywhere."
        - [Python 3](https://www.python.org/): "Python is a programming language that lets you work quickly and integrate systems more effectively."
        - [Requests](http://docs.python-requests.org/en/master/): "Requests is an elegant and simple HTTP library for Python, built for human beings."
        
        ## Contributing
        
        [TODO]
        
        ## Versioning
        
        We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/your/project/tags). 
        
        The following guidelines are provided on the [SemVer]((http://semver.org/)) website:
        
        > Given a version number MAJOR.MINOR.PATCH, increment the:
        >
        > - MAJOR version when you make incompatible API changes,
        > - MINOR version when you add functionality in a backwards-compatible manner, and
        > - PATCH version when you make backwards-compatible bug fixes.
        >
        > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
        
        ## Authors
        
        - **Taylor Steinberg** - *Initial work* - [tdstein](https://github.com/tdstein)
        
        See also the list of [contributors](https://github.com/lifeomic/termlink/contributors) who participated in this project.
        
        ## License
        
        This project is licensed under the MIT - see the [LICENSE](LICENSE.txt) file for details.
        
        ## Acknowledgments
        
        [TODO]
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Natural Language :: English
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Utilities
Description-Content-Type: text/markdown
