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
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