Skip to content

Makes publishing of imported workflows available. #74

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mvdbeek merged 2 commits into from
Feb 1, 2018
Merged

Makes publishing of imported workflows available. #74

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1e95530
Makes publishing of imported workflows available.
pcm32 Feb 1, 2018
4f85519
Avoids conflict with existing option
pcm32 Feb 1, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions ephemeris/workflow_install.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from .common_parser import get_common_args


def import_workflow(gi, path):
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.
Expand All @@ -17,7 +17,7 @@ def import_workflow(gi, path):
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)
gi.workflows.import_workflow_from_local_path(path, publish=publish_wf)


def _parser():
Expand All @@ -26,6 +26,10 @@ def _parser():
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


Expand All @@ -39,9 +43,9 @@ def main():
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))
import_workflow(gi, os.path.join(args.workflow_path, file_path), args.publish_workflows)
else:
import_workflow(gi, args.workflow_path)
import_workflow(gi, args.workflow_path, args.publish_workflows)


if __name__ == '__main__':
Expand Down
⚡