Factory: also parse command-line options #2060
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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Outdated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) |
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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 <[email protected]>
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Re-do of #1099