diff create_or_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/create_or_update_organism.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+import json
+import argparse
+import time
+from webapollo import WebApolloInstance
+import logging
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+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('jbrowse', help='JBrowse Data Directory')
+    parser.add_argument('email', help='User Email')
+    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)
+    # 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")
+
+    log.info("Determining if add or update required")
+    try:
+        org = wa.organisms.findOrganismByCn(args.cn)
+    except Exception:
+        org = None
+
+    if org:
+        log.info("\tUpdating Organism")
+        data = wa.organisms.updateOrganismInfo(
+            org['id'],
+            args.cn,
+            args.jbrowse,
+            # mandatory
+            blatdb=args.blatdb,
+            genus=args.genus,
+            species=args.species,
+            public=args.public
+        )
+    else:
+        # New organism
+        log.info("\tAdding Organism")
+        data = wa.organisms.addOrganism(
+            args.cn,
+            args.jbrowse,
+            blatdb=args.blatdb,
+            genus=args.genus,
+            species=args.species,
+            public=args.public
+        )
+
+        # Must sleep before we're ready to handle
+        time.sleep(1)
+        log.info("Updating permissions for %s on %s", gx_user[0], args.cn)
+        wa.users.updateOrganismPermission(
+            gx_user[0], args.cn,
+            write=True,
+            export=True,
+            read=True,
+        )
+
+    data = [o for o in data if o['commonName'] == args.cn]
+    print json.dumps(data, indent=2)