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Expressiontool timer #1681

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Merged
merged 7 commits into from
Jun 23, 2022
Merged

Expressiontool timer #1681

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cb18326
increase default eval_timeout value
douglowe Jun 9, 2022
158b930
Increase eval-timeout default to 60 seconds
douglowe Jun 9, 2022
73f03c3
Add log information when eval-timeout is exceeded
douglowe Jun 9, 2022
cfd88b2
cleanup using make format
douglowe Jun 10, 2022
8913810
Add eval_timeout control to validate_js_expressions
douglowe Jun 23, 2022
d9dc958
Merge branch 'main' into expressiontool_timer
douglowe Jun 23, 2022
807323b
make format; add missing defaults
mr-c Jun 23, 2022
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4 changes: 2 additions & 2 deletions cwltool/argparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,9 +226,9 @@ def arg_parser() -> argparse.ArgumentParser:
parser.add_argument(
"--eval-timeout",
help="Time to wait for a Javascript expression to evaluate before giving "
"an error, default 20s.",
"an error, default 60s.",
type=float,
default=20,
default=60,
)

provgroup = parser.add_argument_group(
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2 changes: 1 addition & 1 deletion cwltool/context.py
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Expand Up @@ -164,7 +164,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
self.js_console = False # type: bool
self.job_script_provider = None # type: Optional[DependenciesConfiguration]
self.select_resources = None # type: Optional[select_resources_callable]
self.eval_timeout = 20 # type: float
self.eval_timeout = 60 # type: float
self.postScatterEval = (
None
) # type: Optional[Callable[[CWLObjectType], Optional[CWLObjectType]]]
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14 changes: 11 additions & 3 deletions cwltool/sandboxjs.py
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Expand Up @@ -285,12 +285,20 @@ def process_finished() -> bool:
pipes[1].write(buf)
except OSError:
break
timer.cancel()

stdin_buf.close()
stdoutdata = stdout_buf.getvalue()[: -len(PROCESS_FINISHED_STR) - 1]
stderrdata = stderr_buf.getvalue()[: -len(PROCESS_FINISHED_STR) - 1]

if not timer.is_alive():
_logger.info("Expression Tool stopped because time limit has been exceeded.")
_logger.info("Time limit is {} seconds. This can be increased using the --eval-timeout flag.\n".format(timeout))
stdoutdata = stdout_buf.getvalue()
stderrdata = stderr_buf.getvalue()
else:
stdoutdata = stdout_buf.getvalue()[: -len(PROCESS_FINISHED_STR) - 1]
stderrdata = stderr_buf.getvalue()[: -len(PROCESS_FINISHED_STR) - 1]

timer.cancel()

nodejs.poll()

if nodejs.poll() not in (None, 0):
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