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This project is work-in-progress and is still in developments. Although we welcome contributions, due to the immature state of this project we recommend raising issues through the Github issues page.


This page has a collection of notes on the development of Janis.


Further information: Testing

Within Janis there is a suite of code-level tests. High quality tests allow fewer bugs to make it out to a production environment and gives you a place to test your function.

All of the tests are placed in: janis/tests/test_*.py. You can create a file in that same directory with tests for your changes.

Running tests

In the terminal you can run the tests and generate a code coverage report with the following bash command.

nosetests -w janis --with-coverage --cover-package=janis


Further Information: Releasing

Releasing is automatic! After you’ve run the tests, simply increment the version number in (with resepect to SemVer), and tag that commit with the same version identifier:

git commit -m "Tag for v0.x.x release"
git tag -a "v0.x.x" -m "Tag message"
git push origin v0.x.x


This project uses a custom logger that can be imported from the root of Janis:

from janis import Logger
  • Logger.mute() stops any output from reaching the console until unmute() is called. This does not affect logging to disk.
  • Logger.unmute() restores the logger’s ability to write to the console if it has been muted. It will restore to the same volume before it was muted.
  • Logging functions:
    • .log(str) - LogLevel.DEBUG
    • .info(str) - LogLevel.INFO
    • .warn(str) - LogLevel.WARNING
    • .critical(str) - LogLevel.CRITICAL
    • .log_exec(exception) - Loglevel.CRITICAL - Prepares exception in standard format

Adding a translation

There are a few things that are super helpful to know before you add a new translation. You should be familiar with Janis’ representation of a workflow.

It’s recommended you use an intermediary library (similar to cwlgen or python-wdlgen) to manage the representation. This allows you to focus on mapping concepts over syntax.


There are a few things you’ll need to keep in mind when you add a

translation, you should understand at least these workflow and janis concepts: | - inputs - outputs - steps + tools - secondary files - command line binding of tools - position, quoted - selectors - input selectors - wildcard glob selectors - cpu and memory selectors - propagated resource overrides


Add a file to the janis/translation with your new language’s name. Create a class called: $LangTranslator that should inherit from TranslatorBase, and provide implementations for those methods.

Please keep your function sizes small and direct, and then write unit tests to cover each component of the translation and then an integration test of the whole translation on the related workflows.

You can find these in /janis/tests/test_translation_*.py)