Factory: also parse command-line options #2060
Open
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
Closed
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2060 +/- ##
==========================================
- Coverage 83.99% 83.97% -0.02%
==========================================
Files 46 46
Lines 8302 8332 +30
Branches 1957 1964 +7
==========================================
+ Hits 6973 6997 +24
- Misses 853 858 +5
- Partials 476 477 +1 ☔ View full report in Codecov by Sentry. |
mr-c
commented
Oct 24, 2024
cwltool/factory.py
Outdated
Comment on lines
98
to
127
| self.runtime_context.find_default_container = functools.partial( | ||
| find_default_container, default_container=None, use_biocontainers=None | ||
| ) | ||
|
|
||
| if sys.platform == "darwin": | ||
| default_mac_path = "/private/tmp/docker_tmp" | ||
| if self.runtimeContext.tmp_outdir_prefix == DEFAULT_TMP_PREFIX: | ||
| self.runtimeContext.tmp_outdir_prefix = default_mac_path | ||
|
|
||
| for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"): | ||
| if ( | ||
| getattr(self.runtime_context, dirprefix) | ||
| and getattr(self.runtime_context, dirprefix) != DEFAULT_TMP_PREFIX | ||
| ): | ||
| sl = ( | ||
| "/" | ||
| if getattr(self.runtime_context, dirprefix).endswith("/") | ||
| or dirprefix == "cachedir" | ||
| else "" | ||
| ) | ||
| setattr( | ||
| self.runtime_context, | ||
| dirprefix, | ||
| os.path.abspath(getattr(self.runtime_context, dirprefix)) + sl, | ||
| ) | ||
| if not os.path.exists(os.path.dirname(getattr(self.runtime_context, dirprefix))): | ||
| try: | ||
| os.makedirs(os.path.dirname(getattr(self.runtime_context, dirprefix))) | ||
| except Exception as e: | ||
| print("Failed to create directory: %s", e) |
There was a problem hiding this comment.
Todo, refactor this and the equivalent code from cwltool/main.py to a shared function. May need to look back to
Line 748 in b0db43e
Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>
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.
Re-do of #1099