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.
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
setup.py (with resepect to
SemVer), and tag that commit with the same
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:
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.
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