diff data_manager/data_manager_eggnog.py @ 1:077cf0a99144 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Fri, 04 Sep 2020 21:38:59 +0000
parents 6d8144eef202
children 3d82020b1e3b
line wrap: on
line diff
--- a/data_manager/data_manager_eggnog.py	Mon Nov 11 11:49:16 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Fri Sep 04 21:38:59 2020 +0000
@@ -11,7 +11,7 @@
 
 
 def _get_db_version(sqlitedb_path):
-    version = '4.5'
+    version = '5.0'
     try:
         query = 'select version from version'
         conn = sqlite3.connect(sqlitedb_path)
@@ -28,7 +28,6 @@
     parser = argparse.ArgumentParser()
     parser.add_argument('--config_file')
     parser.add_argument('--install_path')
-    parser.add_argument('--dbs', default='')
     args = parser.parse_args()
 
     eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
@@ -46,19 +45,9 @@
     data_table_entry = dict(value=db_version, name=db_version,
                             path=args.install_path)
     dm_dict['data_tables'][data_table].append(data_table_entry)
-    data_table = 'eggnog_mapper_hmm_dbs'
-    dm_dict['data_tables'][data_table]\
-        = dm_dict['data_tables'].get(data_table, [])
-    if args.dbs:
-        dbs = [x.strip() for x in args.dbs.split(',')]
-        for db in dbs:
-            key = '%s_%s' % (db_version, db)
-            data_table_entry = dict(key=key, db_version=db_version,
-                                    value=db, name=db, path=db)
-            dm_dict['data_tables'][data_table].append(data_table_entry)
 
     # save info to json file
-    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+    open(args.config_file, 'w').write(json.dumps(dm_dict))
 
 
 if __name__ == "__main__":