# HG changeset patch
# User iuc
# Date 1606049156 0
# Node ID 19b6a2f0dbe23d60e3403122e892304abd94cd01
# Parent  edacc4bcd3cbcdeb04ede3aee1aafab4990ca39d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

diff -r edacc4bcd3cb -r 19b6a2f0dbe2 data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Sun Dec 22 11:57:46 2019 -0500
+++ b/data_manager/kraken2_build_database.py	Sun Nov 22 12:45:56 2020 +0000
@@ -292,14 +292,15 @@
     parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
     args = parser.parse_args()
 
-    data_manager_input = json.loads(open(args.data_manager_json).read())
+    with open(args.data_manager_json) as fh:
+        data_manager_input = json.load(fh)
 
     target_directory = data_manager_input['output_data'][0]['extra_files_path']
 
     try:
-        os.mkdir( target_directory )
+        os.mkdir(target_directory)
     except OSError as exc:
-        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
             pass
         else:
             raise
@@ -354,7 +355,8 @@
     else:
         sys.exit("Invalid database type")
 
-    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True))
+    with open(args.data_manager_json, 'w') as fh:
+        json.dump(data_manager_output, fh, sort_keys=True)
 
 
 if __name__ == "__main__":