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Fixed another symlinking issue with Docker + staged files from InitialWorkDirRequirement #1708

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Fixed another symlinking issue with Docker + staged files from InitialWorkDirRequirement #1708

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9508896
Fixed another symlinking issue with Docker + staged files from Initia…
jfennick Aug 16, 2022
20e3eab
use os.chmod and add write to existing mode
jfennick Aug 16, 2022
08bb056
blasting CI
jfennick Aug 16, 2022
806d695
fix pylint
jfennick Mar 9, 2023
f5a7412
use ensure_writable
jfennick Mar 9, 2023
83b0882
added PermissionError
jfennick Mar 9, 2023
a699296
try setting write bit separately from deletion
mr-c Dec 5, 2023
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2 changes: 1 addition & 1 deletion cwltool/docker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ def add_file_or_directory_volume(
"""Append volume a file/dir mapping to the runtime option list."""
if not volume.resolved.startswith("_:"):
_check_docker_machine_path(volume.resolved)
self.append_volume(runtime, volume.resolved, volume.target)
self.append_volume(runtime, volume.resolved, volume.target, writable=volume.staged)
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What's the goal here? This results in many files that should be mounted read-only to not be..

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The goal overall was to fix a bug I was encountering with a specific CommandLineTool (Yank) which we are no longer using. I still believe there is a bug in cwltool, but I can't seem to simultaneously fix the bug and get the test suite to pass. This is very low priority work for me, so feel free to close if you like.


def add_writable_file_volume(
self,
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7 changes: 6 additions & 1 deletion cwltool/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,11 +101,16 @@
host_outdir_tgt = os.path.join(host_outdir, vol.target[len(container_outdir) + 1 :])
if os.path.islink(host_outdir_tgt) or os.path.isfile(host_outdir_tgt):
try:
ensure_writable(host_outdir_tgt, include_root=True)
os.remove(host_outdir_tgt)
except PermissionError:
pass
elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
shutil.rmtree(host_outdir_tgt)
try:
ensure_writable(host_outdir_tgt, include_root=True)
shutil.rmtree(host_outdir_tgt)
except PermissionError:
pass

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cwltool/job.py#L109-L113 

Added lines #L109 - L113 were not covered by tests
if not vol.resolved.startswith("_:"):
try:
os.symlink(vol.resolved, host_outdir_tgt)
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