Package: termlink
TermLinkPrepare an ontology and send it to the Precision Health Cloud.Termlinkis a command line client and library for uploading ontologies to LifeOmic'sPrecision 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.QuickstartDownload the following tools:DockerPull the latest version ofTermLinkfromDocker Hub:dockerpulllifeomic/termlinkRun it.dockerrunlifeomic/termlink--helpImport the output ontology into thePrecision Health Cloudusing theLifeOmic CLI:dockerrunlifeomic/termlink...|loontologiesimport<project>Getting StartedThese 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.PrerequisitesThe following tools are required to runTermLink:DockerGitPython 3YarnInstallingThe following steps will guide you through installing the project locally.Clone thegitrepository onto your local machine.gitclonegit@github.com:lifeomic/termlink.git&&cd./termlinkUsing Python 3, create avirtualenvand then activate it.python3-mvenvvenv&&sourcevenv/bin/activateNote: Your Python binary may be under a different name.Check that your local version of Python is at least version 3.7 by runningpython --version.Once you have verified your version of Python is correct, run the following to download all dependencies.pipinstall-rrequirements.txtpipinstall-rrequirements-dev.txtYou now have everything you need to start developing onTermlink.TestingThis project uses the Pythonnoseframework.Unit TestingRun unit tests withyarn:yarntestTest coverage is enforced using thecoverage.pymodule. Inspect the test
coverage with:yarninspectDeploymentTermLink is published on:PyPI: Python package.Docker Hub: Packaged runtime environment.GitHub: Python package and source files.Documentation is published onGitHub Pages.To publish a new version run the following command:yarnversionYou will be promoted to enter a new version. Please useSemVerversioning for incrementing versions. To learn more about why SemVer is used, see the section onVersioningbelow.This will trigger the deployment pipeline onTravis CI.Built WithDocker: "Build, Ship, and Run Any App, Anywhere."Python 3: "Python is a programming language that lets you work quickly and integrate systems more effectively."Requests: "Requests is an elegant and simple HTTP library for Python, built for human beings."Contributing[TODO]VersioningWe useSemVerfor versioning. For the versions available, see thetags on this repository.The following guidelines are provided on theSemVerwebsite: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, andPATCH 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.AuthorsTaylor Steinberg-Initial work-tdsteinSee also the list ofcontributorswho participated in this project.LicenseThis project is licensed under the MIT - see theLICENSEfile for details.Acknowledgments[TODO]