diff env/lib/python3.9/site-packages/ephemeris/workflow_install.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/ephemeris/workflow_install.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+'''Tool to install workflows on a Galaxy instance.'''
+import argparse
+import json
+import os
+
+from . import get_galaxy_connection
+from .common_parser import get_common_args
+
+
+def import_workflow(gi, path, publish_wf=False):
+    """
+    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, publish=publish_wf)
+
+
+def _parser():
+    parent = get_common_args()
+    parser = argparse.ArgumentParser(parents=[parent])
+    parser.add_argument("-w", "--workflow_path",
+                        required=True,
+                        help='Path to a workflow file or a directory with multiple workflow files ending with ".ga"')
+    parser.add_argument("--publish_workflows",
+                        required=False,
+                        action='store_true',
+                        help='Flag to publish all imported workflows, so that they are viewable by other users')
+    return parser
+
+
+def main():
+    """
+        This script uses bioblend to import .ga workflow files into a running instance of Galaxy
+    """
+    args = _parser().parse_args()
+    gi = get_galaxy_connection(args)
+
+    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), args.publish_workflows)
+    else:
+        import_workflow(gi, args.workflow_path, args.publish_workflows)
+
+
+if __name__ == '__main__':
+    main()