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Fix --tmp-outdir-prefix for CommandLineTools. #244

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Merged
tetron merged 3 commits into from
Dec 6, 2016
Merged

Fix --tmp-outdir-prefix for CommandLineTools. #244

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22bba2c
Fix --tmp-outdir-prefix for CommandLineTools. Clean up initializatio…
Dec 6, 2016
f91978e
tmp_outdir_prefix optional.
Dec 6, 2016
71e591f
Use setattr so mypy doesn't complain.
Dec 6, 2016
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37 changes: 16 additions & 21 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@ def output_callback(out, processStatus):

output_dirs = set()
finaloutdir = kwargs.get("outdir")
kwargs["outdir"] = tempfile.mkdtemp()
kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get("tmp_outdir_prefix") else tempfile.mkdtemp()
output_dirs.add(kwargs["outdir"])

jobReqs = None
Expand Down Expand Up @@ -678,20 +678,22 @@ def main(argsl=None, # type: List[str]
if isinstance(tool, int):
return tool

if args.tmp_outdir_prefix != 'tmp':
# Use user defined temp directory (if it exists)
setattr(args, 'tmp_outdir_prefix',
os.path.abspath(args.tmp_outdir_prefix))
if not os.path.exists(args.tmp_outdir_prefix):
_logger.error("Intermediate output directory prefix doesn't exist.")
return 1
for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
if getattr(args, dirprefix) and getattr(args, dirprefix) != 'tmp':
sl = "/" if getattr(args, dirprefix).endswith("/") or dirprefix == "cachedir" else ""
setattr(args, dirprefix,
os.path.abspath(getattr(args, dirprefix))+sl)
if not os.path.exists(os.path.dirname(getattr(args, dirprefix))):
try:
os.makedirs(os.path.dirname(getattr(args, dirprefix)))
except Exception as e:
_logger.error("Failed to create directory: %s", e)
return 1

if args.tmpdir_prefix != 'tmp':
# Use user defined prefix (if the folder exists)
setattr(args, 'tmpdir_prefix', os.path.abspath(args.tmpdir_prefix))
if not os.path.exists(args.tmpdir_prefix):
_logger.error("Temporary directory prefix doesn't exist.")
return 1
if args.cachedir:
if args.move_outputs == "move":
setattr(args, 'move_outputs', "copy")
setattr(args, "tmp_outdir_prefix", args.cachedir)

if job_order_object is None:
job_order_object = load_job_order(args, tool, stdin,
Expand All @@ -703,14 +705,7 @@ def main(argsl=None, # type: List[str]
if isinstance(job_order_object, int):
return job_order_object

if args.cachedir:
setattr(args, 'cachedir', os.path.abspath(args.cachedir))
if args.move_outputs == "move":
setattr(args, 'move_outputs', "copy")

try:
setattr(args, 'tmp_outdir_prefix',
args.cachedir if args.cachedir else args.tmp_outdir_prefix)
setattr(args, 'basedir', job_order_object[1])
del args.workflow
del args.job_order
Expand Down