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‎README.md‎

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# Microbetrace
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![image](https://user-images.githubusercontent.com/33426295/150403131-0468f0be-2539-4f2d-88ee-0fb7d4fd411c.png)
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This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 7.0.0.
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## Development Environment
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Angular CLI: 7.3.10<br />
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Node: 12.22.12<br />
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Npm: 6.14.16<br />
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OS: darwin x64<br />
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Angular: 7.2.16<br />
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... animations, common, compiler, compiler-cli, core, forms<br />
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... language-service, platform-browser, platform-browser-dynamic<br />
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... router<br />
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Package Version
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-----------------------------------------------------------
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@angular-devkit/architect 0.13.10<br />
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@angular-devkit/build-angular 0.13.10<br />
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@angular-devkit/build-optimizer 0.13.10<br />
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@angular-devkit/build-webpack 0.13.10<br />
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@angular-devkit/core 7.3.10<br />
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@angular-devkit/schematics 7.3.10<br />
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@angular/cdk 7.3.2<br />
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@angular/cli 7.3.10<br />
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@angular/material 7.3.2<br />
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@ngtools/webpack 7.3.10<br />
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@schematics/angular 7.3.10<br />
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@schematics/update 0.13.10<br />
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rxjs 6.3.3<br />
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typescript 3.2.4<br />
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webpack 4.29.0
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## Development server
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Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The app will automatically reload if you change any of the source files.
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## Code scaffolding
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Run `ng generate component component-name` to generate a new component. You can also use `ng generate directive|pipe|service|class|guard|interface|enum|module`.
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## Build
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Run `ng build` to build the project. The build artifacts will be stored in the `dist/` directory. Use the `--prod` flag for a production build.
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## Running unit tests
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Run `ng test` to execute the unit tests via [Karma](https://karma-runner.github.io).
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## Running end-to-end tests
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Run `ng e2e` to execute the end-to-end tests via [Protractor](http://www.protractortest.org/).
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## Build angular app on personal github account using gh-pages
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1. Fork repo to personal account.
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2. Navigate to settings of forked repo.
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3. Go to pages in the sidebar.
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4. Source should be gh-pages branch and the root folder.
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## Update angular web app
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1. Checkout angularMigration branch of forked repo.
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2. Run npm i angular-cli-ghpages --save-dev (Only if you dont already have it. This will install globally)
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3. Run an npm install to get node modules if not done yet.
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4. Make changes to the webapp and test locally.
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5. Run ng build --prod --optimization=false --base-href "https://YOURusername.github.io/MicrobeTrace/"
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6. Run npx ngh --dir dist/Microbetrace
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7. Updates will be visible in 5-10 minutes.
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IMPORTANT before building dist folder - If adding new assets that are loaded via filepath in the app (.ie src="assets/images/Logo.png"), follow these steps:
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1. Add the asset filepath to the "assets" array in the angular.json file.
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2. When referencing the asset in the code, modify the filepath to use the appRootUrl() function, which depending on whether the app is running locally or online, generates the correct path to the root where the assets are located. For example, when loading a newly imported image, I should make the "src" value [src]="appRootUrl() + 'assets/images/Logo.png'", instead of src="assets/images/Logo.png".
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## Further help
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To get more help on the Angular CLI use `ng help` or go check out the [Angular CLI README](https://github.com/angular/angular-cli/blob/master/README.md).
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# MicrobeTrace [![MicrobeTrace DOI](https://img.shields.io/badge/DOI-10.1101%2F2020.07.22.216275-blue)](https://doi.org/10.1101/2020.07.22.216275)
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*The Visualization Multitool for Molecular Epidemiology and Bioinformatics*
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Developed By ([some folks](https://github.com/CDCgov/MicrobeTrace/blob/master/humans.txt) at) CDC.
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## To Use MicrobeTrace:
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* **[Launch MicrobeTrace](https://microbetrace.cdc.gov/MicrobeTrace/)**
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* [Download Sample Data](https://github.com/CDCgov/MicrobeTrace/raw/master/demo/MicrobetraceDemoData.zip)
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* [Download Sample COVID Data](https://github.com/CDCgov/MicrobeTrace/raw/master/demo/COVID%20Dummy%20Data.zip)
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* [View the Help Wiki](https://github.com/CDCgov/MicrobeTrace/wiki)
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* [Read the Latest Manual](https://github.com/CDCgov/MicrobeTrace/raw/master/docs/MicrobeTrace_Manual.pdf)
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* [Watch and follow along with the webinar](https://www.youtube.com/watch?v=5E-_Kb7yvHU)
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* [Watch how to use MicrobeTrace for COVID-19](https://www.youtube.com/watch?v=he0Yq5yvToc)
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* [Cite MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/Cite-MicrobeTrace)
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## To Spread the Word:
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* [View the MicrobeTrace Flyer](https://github.com/CDCgov/MicrobeTrace/blob/master/docs/MicrobeTrace%20Flyer_Sept_2019.pdf)
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* [Read our Reports](https://medium.com/microbetrace-reports/latest)
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* [Connect with our User Community](https://www.reddit.com/r/MicrobeTrace/)
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## To Help Us Build:
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* [Report Bugs or Request Features](https://github.com/CDCgov/MicrobeTrace/issues)
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* [Request Access to Our Slack](mailto:microbetrace@cdc.gov?subject=Slack%20Request&body=Hello!%0AI'd%20like%20an%20invitation%20to%20join%20the%20MicrobeTrace%20Slack%20Channel%2C%20please.%0AThank%20you!)
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* [Deploy Your Own Instance of MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/z-Deployment)
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* [Help us Develop MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/z-Development)
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## Public Domain
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This project constitutes a work of the United States Government and is not
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subject to domestic copyright protection under 17 USC § 105. This project is in
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the public domain within the United States, and copyright and related rights in
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the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
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All contributions to this project will be released under the CC0 dedication. By
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submitting a pull request you are agreeing to comply with this waiver of
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copyright interest.
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## License
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The project utilizes code licensed under the terms of the Apache Software
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License and therefore is licensed under ASL v2 or later.
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This program is free software: you can redistribute it and/or modify it under
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the terms of the Apache Software License version 2, or (at your option) any
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later version.
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This program is distributed in the hope that it will be useful, but WITHOUT ANY
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WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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PARTICULAR PURPOSE. See the Apache Software License for more details.
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You should have received a copy of the Apache Software License along with this
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program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
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## Privacy
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This project contains only non-sensitive, publicly available data and
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information. All material and community participation is covered by the
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Surveillance Platform [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
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and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
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For more information about CDC's privacy policy, please visit [http://www.cdc.gov/privacy.html](http://www.cdc.gov/privacy.html).
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## Contributing
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Anyone is encouraged to contribute to the project by [forking](https://help.github.com/articles/fork-a-repo)
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and submitting a pull request. (If you are new to GitHub, you might start with a
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[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
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to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
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non-exclusive, transferable license to all users under the terms of the
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[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
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later.
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Before you get started, please read the [Developer's Guide to MicrobeTrace.](https://github.com/CDCgov/MicrobeTrace/wiki/z-Development)
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All comments, messages, pull requests, and other submissions received through
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CDC including this GitHub page are subject to the [Presidential Records Act](http://www.archives.gov/about/laws/presidential-records.html)
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and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
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## Records
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This project is not a source of government records, but is a copy to increase
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collaboration and collaborative potential. All government records will be
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published through the [CDC web site](http://www.cdc.gov).
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## Notices
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Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
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for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
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[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
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and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).

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