diff env/lib/python3.7/site-packages/ephemeris/workflow_install.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/ephemeris/workflow_install.py	Sat May 02 07:14:21 2020 -0400
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+#!/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()