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Bugfix --preserve-environment and add --preserve-entire-environment. #199

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Merged
merged 1 commit into from
Sep 29, 2016
Merged

Bugfix --preserve-environment and add --preserve-entire-environment. #199

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2 changes: 2 additions & 0 deletions cwltool/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
vars_to_preserve = kwargs.get("preserve_environment")
if kwargs.get("preserve_entire_environment"):
vars_to_preserve = os.environ
if vars_to_preserve is not None:
for key, value in os.environ.items():
if key in vars_to_preserve and key not in env:
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13 changes: 9 additions & 4 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,12 +50,17 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
help="Do not execute jobs in a Docker container, even when specified by the CommandLineTool",
dest="use_container")

parser.add_argument("--preserve-environment", type=Text, nargs='+',
help="Preserve specified environment variables when running CommandLineTools",
metavar=("VAR1,VAR2"),
default=("PATH",),
parser.add_argument("--preserve-environment", type=Text, action="append",
help="Preserve specific environment variable when running CommandLineTools. May be provided multiple times.",
metavar="ENVVAR",
default=["PATH"],
dest="preserve_environment")

parser.add_argument("--preserve-entire-environment", action="store_true",
help="Preserve entire parent environment when running CommandLineTools.",
default=False,
dest="preserve_entire_environment")

exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--rm-container", action="store_true", default=True,
help="Delete Docker container used by jobs after they exit (default)",
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