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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

#!/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()