Mercurial > repos > recetox > msmetaenhancer

diff msmetaenhancer_wrapper.py @ 5:1d649315904c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit fc4fc95ed79d03b2f8d075d0df27d75eb93c58ea"
author recetox
date Mon, 25 Apr 2022 06:29:11 +0000
parents b48c57453a25
children f30b5c473b65
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line diff
--- a/msmetaenhancer_wrapper.py	Fri Apr 08 06:34:08 2022 +0000
+++ b/msmetaenhancer_wrapper.py	Mon Apr 25 06:29:11 2022 +0000
@@ -2,7 +2,7 @@
 import asyncio
 import sys
 
-
+from matchms import set_matchms_logger_level
 from MSMetaEnhancer import Application
 
 
@@ -16,9 +16,14 @@
 
     app = Application(log_file=args.log_file)
 
+    # set matchms logging level to avoid extensive messages in stdout while reading file
+    set_matchms_logger_level("ERROR")
     # import .msp file
     app.load_spectra(args.input_file, file_format='msp')
 
+    # set matchms logging level back to warning
+    set_matchms_logger_level("WARNING")
+
     # curate given metadata
     app.curate_spectra()