Skip to main content

IRIDA uploader: upload NGS data to IRIDA system

Project description

IRIDA Uploader

Integration Tests Documentation Status install with bioconda

Download / Installation

The IRIDA Uploader is available via pip and bioconda

Installation instructions can be found in our documentation.

ReadTheDocs

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 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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

iridauploader-0.9.5.tar.gz (122.2 kB view details)

Uploaded Source

Built Distribution

iridauploader-0.9.5-py3-none-any.whl (182.2 kB view details)

Uploaded Python 3

File details

Details for the file iridauploader-0.9.5.tar.gz.

File metadata

  • Download URL: iridauploader-0.9.5.tar.gz
  • Upload date:
  • Size: 122.2 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.11.5

File hashes

Hashes for iridauploader-0.9.5.tar.gz
Algorithm Hash digest
SHA256 fa2781ae005f9f194e8fc9c668ff893dceb1ba9f7139b57b141983362e99b3c0
MD5 d1ec90705c0eda68da99fd06403e58bf
BLAKE2b-256 225e1091a3e67893e74159cd6a110392a3a84d0b623b3ffc28fb24423e38ea74

See more details on using hashes here.

File details

Details for the file iridauploader-0.9.5-py3-none-any.whl.

File metadata

  • Download URL: iridauploader-0.9.5-py3-none-any.whl
  • Upload date:
  • Size: 182.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.11.5

File hashes

Hashes for iridauploader-0.9.5-py3-none-any.whl
Algorithm Hash digest
SHA256 2959665fd9df71e3f0053aa81d7c3dee04b1eb9f584096d6ad56c3646397e67e
MD5 c601fd56a0bef4e133a6615bf0db6b10
BLAKE2b-256 f31b9f7f6495373888d42e6df122bb26fe9b4e250f1539718c5298725312739f

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page