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Fixed lockfile check when using a Docker read-only filesystem #3832

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merged 6 commits into from
Oct 26, 2022
Merged

Fixed lockfile check when using a Docker read-only filesystem #3832

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c7fa13e
Added OSError
jfennick Sep 16, 2022
41342f6
Check OSError errno
jfennick Sep 18, 2022
51e3b75
re-raise exception properly
jfennick Sep 18, 2022
186fbfe
Added to package/AUTHORS
jfennick Oct 26, 2022
f08e1c3
Merge branch 'develop' into develop
IAlibay Oct 26, 2022
5b5ec9d
Update CHANGELOG
IAlibay Oct 26, 2022
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2 changes: 1 addition & 1 deletion package/MDAnalysis/coordinates/XDR.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ def _load_offsets(self):
try:
with fasteners.InterProcessLock(lock_name) as filelock:
pass
except PermissionError:
except (PermissionError, OSError):
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A reproducer for the original handled PermissionError is straightforward, like below, I wonder if we could cook something up for the other error? May not be worth much energy though.

--- a/testsuite/MDAnalysisTests/coordinates/test_xdr.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_xdr.py
@@ -904,3 +904,14 @@ class TestTRRReader_offsets(_GromacsReader_offsets):
         9155712, 10300176
     ])
     _reader = mda.coordinates.TRR.TRRReader
+
+
+def test_offset_readonly_handle(tmpdir):
+    with tmpdir.as_cwd():
+        curr_path = os.getcwd()
+        new_gro = os.path.join(curr_path, os.path.basename(GRO))
+        new_xtc = os.path.join(curr_path, os.path.basename(XTC))
+        shutil.copyfile(GRO, new_gro)
+        shutil.copyfile(XTC, new_xtc)
+        os.chmod(curr_path, 0o555)
+        u = mda.Universe(new_gro, new_xtc)

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@zemanj zemanj Sep 18, 2022 •
edited
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According to the Python docs, PermissionError is a subclass of OSError, so your code is currently equivalent to only checking for OSError.
I'd advise against a simple check for OSError only, though, as this exception class covers many kinds of OS-related errors.
To narrow down the cause of the exception, it might be better to catch OSError, then check if it's a PermissionError or the errno member of the exception is the one you encountered. If so, raise the warning as before, otherwise just raise for the exception to bubble up.
For checking the errno, there should be a suitable constant in the errno module of the standard library so you don't have to hard-code numbers here.

EDIT: It's errno.EROFS.

warnings.warn(f"Cannot write lock/offset file in same location as "
"{self.filename}. Using slow offset calculation.")
self._read_offsets(store=True)
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