diff fetch_organism_jbrowse.py @ 3:d4ae83dedb14 draft

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

--- a/fetch_organism_jbrowse.py	Tue May 03 13:48:11 2016 -0400
+++ b/fetch_organism_jbrowse.py	Thu Jan 12 11:52:28 2017 -0500
@@ -1,9 +1,7 @@
 #!/usr/bin/env python
 import os
-import json
 import argparse
-import time
-from webapollo import WebApolloInstance
+from webapollo import WAAuth, WebApolloInstance, GuessOrg, OrgOrGuess
 import logging
 import subprocess
 logging.basicConfig(level=logging.INFO)
@@ -12,23 +10,18 @@
 
 if __name__ == '__main__':
     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 Admin Username')
-    parser.add_argument('password', help='WA Admin Password')
-    parser.add_argument('cn', help='Organism Common Name')
-    parser.add_argument('email', help='User Email')
+    WAAuth(parser)
+    OrgOrGuess(parser)
     parser.add_argument('target_dir', help='Target directory')
 
     args = parser.parse_args()
 
-
     wa = WebApolloInstance(args.apollo, args.username, args.password)
     # User must have an account
-    gx_user = wa.users.loadUsers(email=args.email)
-    if len(gx_user) == 0:
-        raise Exception("Unknown user. Please register first")
-    org = wa.organisms.findOrganismByCn(args.cn)
-
+    org_cn = GuessOrg(args, wa)
+    if isinstance(org_cn, list):
+        org_cn = org_cn[0]
+    org = wa.organisms.findOrganismByCn(org_cn)
 
     if not os.path.exists(args.target_dir):
         os.makedirs(args.target_dir)
@@ -38,5 +31,4 @@
         org['directory'],
         os.path.join(args.target_dir, 'data')
     ]
-    print ' '.join(cmd)
     subprocess.check_call(cmd)