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Revert "better handle symlinks in Directories (#1462)" #1483

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Merged
mr-c merged 1 commit into from
Aug 16, 2021
Merged

Revert "better handle symlinks in Directories (#1462)" #1483

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21 changes: 6 additions & 15 deletions cwltool/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -356,28 +356,19 @@ def _relocate(src: str, dst: str) -> None:
return

# If the source is not contained in source_directories we're not allowed to delete it
real_src = fs_access.realpath(src)
src = fs_access.realpath(src)
src_can_deleted = any(
os.path.commonprefix([p, real_src]) == p for p in source_directories
os.path.commonprefix([p, src]) == p for p in source_directories
)

_action = "move" if action == "move" and src_can_deleted else "copy"

if _action == "move":
_logger.debug("Moving %s to %s", src, dst)
if fs_access.isdir(src):
if fs_access.isdir(dst):
if len(fs_access.listdir(dst)) > 0:
# merge directories
for dir_entry in scandir(src):
_relocate(
dir_entry.path, fs_access.join(dst, dir_entry.name)
)
else:
os.rmdir(dst)
shutil.move(src, dst)
else:
shutil.move(src, dst)
if fs_access.isdir(src) and fs_access.isdir(dst):
# merge directories
for dir_entry in scandir(src):
_relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
else:
shutil.move(src, dst)

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14 changes: 0 additions & 14 deletions tests/symlinks.cwl
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This file was deleted.

20 changes: 4 additions & 16 deletions tests/test_relocate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,10 @@

from .util import get_data, needs_docker

from io import StringIO
if sys.version_info[0] < 3:
from StringIO import StringIO
else:
from io import StringIO


@needs_docker
Expand All @@ -15,21 +18,6 @@ def test_for_910() -> None:
assert main([get_data("tests/wf/910.cwl")]) == 0


def test_symlinks_with_absolute_paths(tmp_path: Path) -> None:
"""Confirm that absolute paths in Directory types don't cause problems."""
assert (
main(
[
"--debug",
f"--outdir={tmp_path}/result",
f"--tmpdir-prefix={tmp_path}/tmp",
get_data("tests/symlinks.cwl"),
]
)
== 0
)


@needs_docker
def test_for_conflict_file_names(tmp_path: Path) -> None:
stream = StringIO()
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