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Avoid relink if not having permissions #1045

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Avoid relink if not having permissions #1045

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3c4263f
Avoid relink if not having permissions
Jan 24, 2019
8725472
Try remove and symlink if succeded
Jan 24, 2019
1868d74
Try remove and symlink if succeded
Jan 24, 2019
48f5f74
Comment fix
Jan 24, 2019
67706fe
Bare except to work on all python versions
Jan 25, 2019
9027bbd
Merge branch 'master' into fix/1042
mr-c Apr 22, 2019
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13 changes: 9 additions & 4 deletions cwltool/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,14 +138,18 @@ def relink_initialworkdir(pathmapper, # type: PathMapper
("WritableFile", "WritableDirectory"))):
if not vol.target.startswith(container_outdir):
# this is an input file written outside of the working
# directory, so therefor ineligable for being an output file.
# directory, so therefore ineligible for being an output file.
# Thus, none of our business
continue
host_outdir_tgt = os.path.join(
host_outdir, vol.target[len(container_outdir) + 1:])
# Try to remove and relink only if remove is permitted
if os.path.islink(host_outdir_tgt) \
or os.path.isfile(host_outdir_tgt):
os.remove(host_outdir_tgt)
try:
os.remove(host_outdir_tgt)
except:
pass
elif os.path.isdir(host_outdir_tgt) \
and not vol.resolved.startswith("_:"):
shutil.rmtree(host_outdir_tgt)
Expand All @@ -157,8 +161,9 @@ def relink_initialworkdir(pathmapper, # type: PathMapper
shutil.copy(vol.resolved, host_outdir_tgt)
elif vol.type in ("Directory", "WritableDirectory"):
copytree_with_merge(vol.resolved, host_outdir_tgt)
elif not vol.resolved.startswith("_:"):
os.symlink(vol.resolved, host_outdir_tgt)
elif not vol.resolved.startswith("_:") \
and not os.path.exists(host_outdir_tgt):
os.symlink(vol.resolved, host_outdir_tgt)


class JobBase(with_metaclass(ABCMeta, HasReqsHints)):
Expand Down