Merge pull request #1375 from girder/harden-bioformats

Harden bioformats shutdown.
girder · Nov 16, 2023 · 329226e · 329226e
2 parents 32b8d01 + 5cee28a
commit 329226e
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@
 ### Changes
 - Update WsiDicomWebClient init call ([#1371](../../pull/1371))
 - Rename DICOMweb AssetstoreImportView ([#1372](../../pull/1372))
+- Harden bioformats shutdown ([#1375](../../pull/1375))
 
 ### Bug Fixes
 - Default to "None" for the DICOM assetstore limit ([#1359](../../pull/1359))

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -74,7 +74,10 @@ def _monitor_thread():
                     source._bioimage.close()
                 except Exception:
                     pass
-                source._bioimage = None
+                try:
+                    source._bioimage = None
+                except Exception:
+                    pass
         except AssertionError:
             pass
         finally:
@@ -128,8 +131,8 @@ def _startJavabridge(logger):
             atexit.register(_stopJavabridge)
             logger.info('Started JVM for Bioformats tile source.')
             _javabridgeStarted = True
-        except RuntimeError as exc:
-            logger.exception('Cannot start JVM for Bioformats tile source.', exc)
+        except RuntimeError:
+            logger.exception('Cannot start JVM for Bioformats tile source.')
             _javabridgeStarted = False
     return _javabridgeStarted
 
@@ -178,7 +181,7 @@ def __init__(self, path, **kwargs):  # noqa
         super().__init__(path, **kwargs)
 
         largeImagePath = str(self._getLargeImagePath())
-        self._ignoreSourceNames('bioformats', largeImagePath, r'\.png$')
+        self._ignoreSourceNames('bioformats', largeImagePath, r'(^[^.]*|\.(png|zarr(\.db|\.zip)))$')
 
         if not _startJavabridge(self.logger):
             msg = 'File cannot be opened by bioformats reader because javabridge failed to start'
@@ -276,6 +279,8 @@ def __del__(self):
                 self._bioimage.close()
                 del self._bioimage
                 _openImages.remove(weakref.ref(self))
+            except Exception:
+                pass
             finally:
                 if javabridge.get_env():
                     javabridge.detach()