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## How to contribute to metakb | ||
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#### **Did you find a bug?** | ||
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* **Do not open up a GitHub issue if the bug is a security vulnerability**. | ||
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* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/cancervariants/metakb/issues). | ||
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* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/cancervariants/metakb/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring. | ||
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* If possible, use the relevant bug report templates to create the issue. Simply copy the content of the appropriate template into a .rb file, make the necessary changes to demonstrate the issue, and **paste the content into the issue description**: | ||
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#### **Did you write a patch that fixes a bug?** | ||
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* Open a new GitHub pull request with the patch. | ||
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* Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable. | ||
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* Before submitting, please read the codebase to know more about coding conventions and benchmarks. | ||
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#### **Do you intend to add a new feature or change an existing one?** | ||
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* Suggest your change in the [mailing list](todo) and start writing code. | ||
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* Do not open an issue on GitHub until you have collected positive feedback about the change. GitHub issues are primarily intended for bug reports and fixes. | ||
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#### **Do you have questions about the source code?** | ||
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* Ask any question about how to use metakb in the [mailing list](todo). | ||
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#### **Do you want to contribute to the metakb documentation?** | ||
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* Ask any question about how to use metakb in the [mailing list](todo). | ||
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Thanks! :heart: | ||
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metakb Team |
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# metakb | ||
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The intent of the project is to leverage the collective knowledge of the disparate existing resources of the VICC to improve the comprehensiveness of clinical interpretation of genomic variation. An ongoing goal will be to provide and improve upon standards and guidelines by which other groups with clinical interpretation data may make it accessible and visible to the public. We have released a preprint discussing our initial harmonization effort and observed disparities in the structure and content of variant interpretations. | ||
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## Getting Started | ||
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> 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 | ||
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What things you need to install the software and how to install them: | ||
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* python3 | ||
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``` | ||
python3 --version | ||
Python 3.7.1 | ||
``` | ||
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### Installing | ||
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Install requirements | ||
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``` | ||
pip3 install -r requirements.txt | ||
``` | ||
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Install requirements-dev | ||
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``` | ||
pip3 install -r requirements-dev.txt | ||
``` | ||
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> TODO End with an example of getting some data out of the system or using it for a little demo | ||
## Running the tests | ||
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### Unit tests | ||
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Explain how to run the automated tests for this system | ||
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``` | ||
python3 -m pytest | ||
``` | ||
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### Break down into end to end tests | ||
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> TODO Explain what these tests test and why | ||
``` | ||
TODO Give an example | ||
``` | ||
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### And coding style tests | ||
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Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit. | ||
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``` | ||
see .flake8 | ||
``` | ||
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## Deployment | ||
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> TODO Add additional notes about how to deploy this on a live system | ||
## Built With | ||
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* [pre-commit](https://pre-commit.com) - Build chain | ||
* TODO ... add more | ||
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## Contributing | ||
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Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us. | ||
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We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests. | ||
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This ensures: | ||
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* Check code style | ||
* Check for added large files | ||
* Detect AWS Credentials | ||
* Detect Private Key | ||
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Before first commit run: | ||
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``` | ||
pre-commit install | ||
``` | ||
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## Versioning | ||
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We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/cancervariants/metakb/tags). | ||
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## Authors | ||
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* TODO | ||
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See also the list of [contributors](https://github.com/cancervariants/metakb/contributors) who participated in this project. | ||
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## License | ||
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This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details | ||
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## Acknowledgments | ||
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* Hat tip to anyone whose code was used | ||
* Inspiration | ||
* etc |