fix(dataset): ensure proper handling of LMDB read environment and prevent access errors

Signed-off-by: R. Garcia-Dias <rafaelagd@gmail.com>

Author: garciadias

monai/data/dataset.py

@@ -609,7 +609,7 @@ def __init__(
         # the cache is created without multi-threading
         self._read_env: Any | None = None
         # this runs on the primary thread/process
-        self._fill_cache_start_reader(show_progress=self.progress)
+        self._read_env = self._fill_cache_start_reader(show_progress=self.progress)
         print(f"Accessing lmdb file: {self.db_file.absolute()}.")
 
     def set_data(self, data: Sequence):
@@ -637,6 +637,12 @@ def _fill_cache_start_reader(self, show_progress=True):
         Args:
             show_progress: whether to show the progress bar if possible.
         """
+        # Close any open read environment before attempting write-mode access
+        # to prevent "environment already open" errors when multiple LMDBDataset
+        # instances target the same db file
+        if self._read_env is not None:
+            self._read_env.close()
+            self._read_env = None
         # create cache
         self.lmdb_kwargs["readonly"] = False
         env = lmdb.open(path=f"{self.db_file}", subdir=False, **self.lmdb_kwargs)
@@ -664,7 +670,7 @@ def _fill_cache_start_reader(self, show_progress=True):
                         size = env.info()["map_size"]
                         new_size = size * 2
                         warnings.warn(
-                            f"Resizing the cache database from {int(size) >> 20}MB" f" to {int(new_size) >> 20}MB."
+                            f"Resizing the cache database from {int(size) >> 20}MB to {int(new_size) >> 20}MB."
                         )
                         env.set_mapsize(new_size)
                     except lmdb.MapResizedError:

tests/transforms/test_spacing.py

@@ -36,6 +36,7 @@ def _template_5_expected_output(device: torch.device) -> torch.Tensor:
         return _TEMPLATE_5_COMPILED
     return _TEMPLATE_5_NATIVE
 
+
 all_template_parts = [
     [
         {"pixdim": (1.0, 1.5), "padding_mode": "zeros", "dtype": float},

versioneer.py

@@ -429,9 +429,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
     return stdout, process.returncode
 
 
-LONG_VERSION_PY[
-    "git"
-] = r'''
+LONG_VERSION_PY["git"] = r'''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build