diff update_organism.py @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update_organism.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+import json
+import argparse
+from webapollo import WebApolloInstance
+
+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('organismId', help='Organism ID #')
+    parser.add_argument('email', help='User Email')
+
+    parser.add_argument('--commonName', help='Organism Common Name')
+    parser.add_argument('--jbrowse', help='JBrowse Data Directory')
+    parser.add_argument('--blatdb', help='BlatDB Directory')
+    parser.add_argument('--genus', help='Organism Genus')
+    parser.add_argument('--species', help='Organism Species')
+    parser.add_argument('--public', action='store_true', help='Make organism public')
+
+    args = parser.parse_args()
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+    data = wa.organisms.updateOrganismInfo(
+        args.organismId,
+        args.commonName,
+        args.jbrowse,
+        # mandatory
+        blatdb=args.blatdb,
+        genus=args.genus,
+        species=args.species,
+        public=args.public
+    )
+    # Need to filter data
+    wanted_data = [x for x in data if str(x['id']) == str(args.organismId)]
+    print json.dumps(wanted_data, indent=2)