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irida-uploader
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Sequence file uploader for IRIDA
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irida-uploader
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IRIDA Uploader ============== [](https://github.com/phac-nml/irida-uploader/actions?query=branch%3Adevelopment) [](https://irida-uploader.readthedocs.io/en/stable/?badge=stable) [](http://bioconda.github.io/recipes/irida-uploader/README.html) Download / Installation -------------------- The IRIDA Uploader is available via `pip` and `bioconda` Installation instructions can be found in our documentation. [ReadTheDocs](https://irida-uploader.readthedocs.io/en/stable/) Tutorial -------- You can find a walkthrough and tutorial on the phac-nml github https://github.com/phac-nml/irida-uploader-tutorial Running the project from source code -------------------------- You can build an environment and run the uploader from source code with the following commands: $ make $ source .virtualenv/bin/activate $ irida-uploader --help You can also build and run the GUI with: $ make gui $ source .virtualenv/bin/activate $ irida-uploader-gui Creating the Windows installer from source code ------------------------------ A new windows installer can be built on linux, so first see the installation instructions for installing on linux in our documentation. You will also need `nsis` installed to create the windows installer. $ sudo apt install nsis Then run the command: $ make windows This will create a new installer in the folder `build/nsis/` with a name similar to `IRIDA_Uploader_GUI_0.X.X.exe` Running Tests ------------- #### Unit tests Running the unittests can be done with the command: $ make unittests #### Integration tests To run integration tests You will need to download and install chromedriver http://chromedriver.chromium.org/downloads You will need to grant the IRIDA instance access to the mysql database needed for the tests $ mysql -e "CREATE USER 'test'@'localhost' IDENTIFIED BY 'test'; GRANT ALL ON irida_uploader_test.* to 'test'@'localhost';" Running the IRIDA integration tests can be done with the command: $ make integrationtests branch=<IRIDA github branch to test against> Example: $ make integrationtests branch=development Tests will be logged to `~/.cache/irida_uploader_test/log/irida-uploader.log` #### PEP8 tests You can run pep8 tests with: $ make pep8 #### Test Coverage You can run the entire test suite and generate a coverage report with the following command: $ make coverage To view the detailed report, open the generated `htmlcov/index.html` with your web browser. Documentation ------------------------------ You can [ReadTheDocs](https://irida-uploader.readthedocs.io/en/stable/) here. Alternatively, documentation is built locally using `mkdocs`. It can be built with the command: $ make docs Or you can install mkdocs to your system: $ sudo apt install mkdocs $ mkdocs build HTML docs will be generated to `site/` for local browsing
