diff env/lib/python3.7/site-packages/ephemeris/workflow_install.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/ephemeris/workflow_install.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-#!/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()