Merge pull request #1491 from girder/bioformats-no-zip

Do not open zip files with bioformats by default

CHANGELOG.md

@@ -11,6 +11,9 @@
 - Guard fetching internal metadata on zarr sources that have less data ([#1481](../../pull/1481))
 - Add a method to list registered extensions and mimetypes ([#1488](../../pull/1488))
 
+### Changes
+- Prohibit bioformats from reading zip directly ([#1491](../../pull/1491))
+
 ### Bug Fixes
 - Fix an issue with single band on multi source with non uniform sources ([#1474](../../pull/1474))
 - Allow alternate name axes in the multi source schema ([#1476](../../pull/1476))

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -61,8 +61,7 @@
 
 
 # Default to ignoring files with no extension and some specific extensions.
-config.ConfigValues['source_bioformats_ignored_names'] = \
-    r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs|zarr(\.db|\.zip)))$'
+config.ConfigValues['source_bioformats_ignored_names'] = r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs|zip|zarr(\.db|\.zip)))$'  # noqa
 
 
 def _monitor_thread():