diff data_manager/fetch_artic_primers.py @ 1:59b3556d9ec8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

--- a/data_manager/fetch_artic_primers.py	Thu Apr 16 14:06:59 2020 +0000
+++ b/data_manager/fetch_artic_primers.py	Thu Apr 16 20:45:35 2020 +0000
@@ -19,13 +19,16 @@
         }
 
     if not os.path.isdir(output_directory):
-        os.makedirs(output_directory)    
-    data_manager_dict = json.load(open(output_filename))
+        os.makedirs(output_directory)
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = json.load(open(output_filename)).get('data_tables', {})
     data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
     data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, [])
     
     data = []
     for name, url in primer_sets.items():
+        if name not in primers:
+            continue
         response = requests.get(url)
         if response.status_code != 200:
             print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)