Merge pull request #27 from galaxyproject/wf_extend

Support directories full of workflows

Author: afgane

ephemeris/workflow_install.py

@@ -1,33 +1,56 @@
 #!/usr/bin/env python
 import argparse
 import json
+import os
+import sys
 
 from bioblend import galaxy
 
 
+def import_workflow(gi, path):
+    """
+    Given a connection to a Galaxy Instance (gi) and a path to a Galaxy workflow file,
+    this function will import the worklfow into Galaxy.
+    """
+    with open(path, 'r') as wf_file:
+        import_uuid = json.load(wf_file).get('uuid')
+    existing_uuids = [d.get('latest_workflow_uuid') for d in gi.workflows.get_workflows()]
+    if import_uuid not in existing_uuids:
+        gi.workflows.import_workflow_from_local_path(path)
+
+
 def main():
     """
         This script uses bioblend to import .ga workflow files into a running instance of Galaxy
     """
     parser = argparse.ArgumentParser()
-    parser.add_argument("-w", "--workflow_path", help='Path to workflow file')
+    parser.add_argument("-w", "--workflow_path",
+                        help='Path to a workflow file or a directory with multiple workflow files ending with ".ga"')
     parser.add_argument("-g", "--galaxy",
-                        dest="galaxy_url",
-                        help="Target Galaxy instance URL/IP address (required "
-                             "if not defined in the tools list file)",)
-    parser.add_argument("-a", "--apikey",
+                        help="Target Galaxy instance URL/IP address.")
+    parser.add_argument("-u", "--user",
+                        help="Galaxy user name")
+    parser.add_argument("-p", "--password",
+                        help="Password for the Galaxy user")
+    parser.add_argument("-a", "--api_key",
                         dest="api_key",
-                        help="Galaxy admin user API key (required if not "
-                             "defined in the tools list file)",)
+                        help="Galaxy admin user API key (required if not defined in the tools list file)")
+
     args = parser.parse_args()
 
-    gi = galaxy.GalaxyInstance(url=args.galaxy_url, key=args.api_key)
+    if args.user and args.password:
+        gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
+    elif args.api_key:
+        gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
+    else:
+        sys.exit('Please specify either a valid Galaxy username/password or an API key.')
 
-    with open(args.workflow_path, 'r') as wf_file:
-        import_uuid = json.load(wf_file).get('uuid')
-    existing_uuids = [d.get('latest_workflow_uuid') for d in gi.workflows.get_workflows()]
-    if import_uuid not in existing_uuids:
-        gi.workflows.import_workflow_from_local_path(args.workflow_path)
+    if os.path.isdir(args.workflow_path):
+        for file_path in os.listdir(args.workflow_path):
+            if file_path.endswith('.ga'):
+                import_workflow(gi, os.path.join(args.workflow_path, file_path))
+    else:
+        import_workflow(gi, args.workflow_path)
 
 
 if __name__ == '__main__':