- Move api.helpers to base.populators.
- Refactor helper subclasses adapted to use bioblend instead of test framework stuff into base.populators for greater visibility.
- Refactor workflow format 2 testing stuff for reuse by Selenium.
This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework).
This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change.
In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways:
- 'steps' must now be explicit (previously converted auto-convert list to dict).
- Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'.
This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly).
Fill out the dataset collection parameter test and add a new test for a workflow that includes subcollection mapping. Move toward orchestrating jobs in this file via a high-level YAML description of steps and test data as well as some higher-level methods for testing various stuff about extracted workflows (step counts, input types, tools used, connected-ness, etc...).
Allow ordering jobs index API by create_time instead of update_time.
test_workflows.py was pretty unwieldy and the workflow extraction tests were very different than the other tests in that file (e.g. very different helper functions).
Nicola Soranzo