Python 3 fix for reading container elements from job_conf. #5427
Conversation
This file contains 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
nsoranzo
reviewed
Jan 31, 2018
lib/galaxy/jobs/__init__.py
Outdated
| @@ -422,8 +422,10 @@ def __get_params(self, parent): | |||
| key = param.get('id') | |||
| if key in ["container", "container_override"]: | |||
| from galaxy.tools.deps import requirements | |||
| # Get container elements contained within the param. | |||
| # https://docs.python.org/3/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren | |||
| containers = map(requirements.container_from_element, list(param)) | |||
There was a problem hiding this comment.
Can you s|list(param)|param.findall('container')| instead? It's more specific and seems to work for me.
There was a problem hiding this comment.
That is much better - thanks!
- Python 3 fix to martialize iterator into list. - Restrict XML query to just container elements - this is much more correct. Both fixes thanks to @nsoranzo.
nsoranzo
approved these changes
Feb 1, 2018
|
Thanks a lot @jmchilton! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
xref. #1715