Merge pull request #727 from girder/suppress-some-warnings

Suppress some warnings

girder/girder_large_image/__init__.py

@@ -16,6 +16,7 @@
 
 import datetime
 import json
+import warnings
 
 from girder_jobs.constants import JobStatus
 from girder_jobs.models.job import Job
@@ -49,6 +50,11 @@
     pass
 
 
+# Girder 3 is pinned to use pymongo < 4; its warnings aren't relevant until
+# that changes.
+warnings.filterwarnings('ignore', category=UserWarning, module='pymongo')
+
+
 def _postUpload(event):
     """
     Called when a file is uploaded. We check the parent item to see if it is

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -29,7 +29,6 @@
 import types
 
 import bioformats
-import bioformats.log4j
 import javabridge
 import numpy
 from pkg_resources import DistributionNotFound, get_distribution
@@ -75,6 +74,28 @@ def _monitor_thread():
     _stopJavabridge()
 
 
+def _reduceLogging():
+    # As of bioformat 4.0.0, org.apache.log4j isn't in the bundled
+    # jar file, so setting log levels just produces needless warnings.
+    # bioformats.log4j.basic_config()
+    # javabridge.JClassWrapper('loci.common.Log4jTools').setRootLevel(
+    #     logging.getLevelName(logger.level))
+    #
+    # This is taken from
+    # https://github.com/pskeshu/microscoper/blob/master/microscoper/io.py
+    try:
+        rootLoggerName = javabridge.get_static_field(
+            'org/slf4j/Logger', 'ROOT_LOGGER_NAME', 'Ljava/lang/String;')
+        rootLogger = javabridge.static_call(
+            'org/slf4j/LoggerFactory', 'getLogger',
+            '(Ljava/lang/String;)Lorg/slf4j/Logger;', rootLoggerName)
+        logLevel = javabridge.get_static_field(
+            'ch/qos/logback/classic/Level', 'WARN', 'Lch/qos/logback/classic/Level;')
+        javabridge.call(rootLogger, 'setLevel', '(Lch/qos/logback/classic/Level;)V', logLevel)
+    except Exception:
+        pass
+
+
 def _startJavabridge(logger):
     global _javabridgeStarted
 
@@ -85,11 +106,7 @@ def _startJavabridge(logger):
         monitor.start()
         try:
             javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
-            # As of bioformat 4.0.0, org.apache.log4j isn't in the bundled
-            # jar file, so setting log levels just produces needless warnings.
-            # bioformats.log4j.basic_config()
-            # javabridge.JClassWrapper('loci.common.Log4jTools').setRootLevel(
-            #     logging.getLevelName(logger.level))
+            _reduceLogging()
             atexit.register(_stopJavabridge)
             logger.info('Started JVM for Bioformats tile source.')
             _javabridgeStarted = True