Merge pull request #1405 from girder/report-jar-version

Get bioformats jar version if bioformats was started

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Improve checks for formats we shouldn't read ([#1399](../../pull/1399))
 - Support negative x, y in addTile ([#1401](../../pull/1401))
 - Add a utility function for getting loggers ([#1403](../../pull/1403))
+- Get bioformats jar version if bioformats was started ([#1405](../../pull/1405))
 
 ### Changes
 - Use an enum for priority constants ([#1400](../../pull/1400))

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -26,10 +26,12 @@
 import logging
 import math
 import os
+import pathlib
 import re
 import threading
 import types
 import weakref
+import zipfile
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
@@ -53,6 +55,7 @@
 javabridge = None
 
 _javabridgeStarted = None
+_bioformatsVersion = None
 _openImages = []
 
 
@@ -110,14 +113,23 @@ def _reduceLogging():
 
 
 def _startJavabridge(logger):
-    global _javabridgeStarted
+    global _javabridgeStarted, _bioformatsVersion
 
     if _javabridgeStarted is None:
         # Only import these when first asked.  They are slow to import.
         global bioformats
         global javabridge
         if bioformats is None:
             import bioformats
+            try:
+                _bioformatsVersion = zipfile.ZipFile(
+                    pathlib.Path(bioformats.__file__).parent /
+                    'jars/bioformats_package.jar',
+                ).open('META-INF/MANIFEST.MF').read(8192).split(
+                    b'Implementation-Version: ')[1].split()[0].decode()
+                logger.info('Bioformats.jar version: %s', _bioformatsVersion)
+            except Exception:
+                pass
         if javabridge is None:
             import javabridge
 

test/test_source_bioformats.py

@@ -25,3 +25,10 @@ def testInternalMetadata():
     source = large_image_source_bioformats.open(imagePath)
     metadata = source.getInternalMetadata()
     assert 'sizeColorPlanes' in metadata
+
+
+def testBioformatsJarVersion():
+    import large_image_source_bioformats
+
+    datastore.fetch('HENormalN801.czi')
+    assert '.' in large_image_source_bioformats._bioformatsVersion