Create more useful output for failed invocations#1174
Merged
mvdbeek merged 1 commit intogalaxyproject:masterfrom Jun 7, 2021
Merged
Create more useful output for failed invocations#1174mvdbeek merged 1 commit intogalaxyproject:masterfrom
mvdbeek merged 1 commit intogalaxyproject:masterfrom
Conversation
mvdbeek
added a commit
to mvdbeek/galaxy
that referenced
this pull request
Jun 7, 2021
output_to_cwl_json is used for converting dataset collections into cwl_json when describing workflow outputs. xref galaxyproject/planemo#1174
5 tasks
jmchilton
reviewed
Jun 7, 2021
| "engine": "galaxy", | ||
| "no_dependency_resolution": True, | ||
| "paste_test_data_paths": False, | ||
| "extra_tools": ['$GALAXY_FUNCTIONAL_TEST_TOOLS'], |
jmchilton
approved these changes
Jun 7, 2021
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This should make debugging invocations with failed steps much easier. The core of the change is the try/except AssertionError, which is raised when the step that produces a dataset collection is in error (https://github.com/galaxyproject/galaxy/blob/release_21.01//lib/galaxy/tool_util/cwl/util.py#L447). I'll also remove that on the Galaxy side. Without this change no useful output is produced except that the test failed. With the change we get the regular test structure written out.