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CWL: Fix --no-container & prepull #5188

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merged 3 commits into from
Jan 17, 2025
Merged

CWL: Fix --no-container & prepull #5188

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9111bee
CWL container prepull: no reason to if extensions are enabled, they a…
mr-c Dec 17, 2024
e886b66
CWL container prepull: skip if --no-containers is specified
mr-c Dec 17, 2024
c63334a
Use checksumming revsort test
adamnovak Jan 16, 2025
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2 changes: 1 addition & 1 deletion requirements-cwl.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,4 @@ ruamel.yaml>=0.15,<=0.19
ruamel.yaml.clib>=0.2.6
networkx!=2.8.1,<4
CacheControl[filecache]
cwl-utils>=0.32
cwl-utils>=0.36
11 changes: 2 additions & 9 deletions src/toil/cwl/cwltoil.py
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Expand Up @@ -4252,15 +4252,8 @@ def main(args: Optional[list[str]] = None, stdout: TextIO = sys.stdout) -> int:
raise

# Attempt to prepull the containers
if not options.no_prepull:
if not options.enable_ext:
# The CWL utils parser does not support cwltool extensions and will crash if encountered, so don't prepull if extensions are enabled
# See https://github.com/common-workflow-language/cwl-utils/issues/309
try_prepull(uri, runtime_context, expected_config.batchSystem)
else:
logger.debug(
"Not prepulling containers as cwltool extensions are not supported."
)
if not options.no_prepull and not options.no_container:
try_prepull(uri, runtime_context, expected_config.batchSystem)

options.tool_help = None
options.debug = options.logLevel == "DEBUG"
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5 changes: 5 additions & 0 deletions src/toil/test/cwl/cwlTest.py
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Expand Up @@ -421,6 +421,11 @@ def test_run_revsort_nochecksum(self) -> None:
"revsort.cwl", partial(self._tester, main_args=["--no-compute-checksum"])
)

def test_run_revsort_no_container(self) -> None:
self.revsort_no_checksum(
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"revsort.cwl", partial(self._tester, main_args=["--no-container"])
)

def test_run_revsort2(self) -> None:
self.revsort("revsort2.cwl", self._tester)

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