diff list_organisms.py @ 3:d4ae83dedb14 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5

--- a/list_organisms.py	Tue May 03 13:48:11 2016 -0400
+++ b/list_organisms.py	Thu Jan 12 11:52:28 2017 -0500
@@ -1,17 +1,19 @@
 #!/usr/bin/env python
 import json
 import argparse
-from webapollo import WebApolloInstance
+from webapollo import WAAuth, WebApolloInstance, AssertUser, accessible_organisms
 
 if __name__ == '__main__':
-    json
     parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
-    parser.add_argument('apollo', help='Complete Apollo URL')
-    parser.add_argument('username', help='WA Username')
-    parser.add_argument('password', help='WA Password')
-
+    WAAuth(parser)
+    parser.add_argument('email', help='User Email')
     args = parser.parse_args()
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
-    print json.dumps(wa.organisms.findAllOrganisms(), indent=2)
+
+    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    all_orgs = wa.organisms.findAllOrganisms()
 
+    orgs = accessible_organisms(gx_user, all_orgs)
+
+    print json.dumps(orgs, indent=2)