Mercurial > repos > shellac > guppy_basecaller

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

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #!/usr/bin/env python
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2 '''Tool to install workflows on a Galaxy instance.'''
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3 import argparse
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4 import json
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5 import os
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6
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7 from . import get_galaxy_connection
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8 from .common_parser import get_common_args
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9
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10
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11 def import_workflow(gi, path, publish_wf=False):
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12 """
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13 Given a connection to a Galaxy Instance (gi) and a path to a Galaxy workflow file,
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14 this function will import the worklfow into Galaxy.
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15 """
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16 with open(path, 'r') as wf_file:
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17 import_uuid = json.load(wf_file).get('uuid')
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18 existing_uuids = [d.get('latest_workflow_uuid') for d in gi.workflows.get_workflows()]
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19 if import_uuid not in existing_uuids:
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20 gi.workflows.import_workflow_from_local_path(path, publish=publish_wf)
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22
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23 def _parser():
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24 parent = get_common_args()
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25 parser = argparse.ArgumentParser(parents=[parent])
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26 parser.add_argument("-w", "--workflow_path",
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27 required=True,
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28 help='Path to a workflow file or a directory with multiple workflow files ending with ".ga"')
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29 parser.add_argument("--publish_workflows",
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30 required=False,
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31 action='store_true',
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32 help='Flag to publish all imported workflows, so that they are viewable by other users')
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33 return parser
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34
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35
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36 def main():
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37 """
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38 This script uses bioblend to import .ga workflow files into a running instance of Galaxy
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39 """
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40 args = _parser().parse_args()
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41 gi = get_galaxy_connection(args)
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42
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43 if os.path.isdir(args.workflow_path):
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44 for file_path in os.listdir(args.workflow_path):
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45 if file_path.endswith('.ga'):
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46 import_workflow(gi, os.path.join(args.workflow_path, file_path), args.publish_workflows)
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47 else:
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48 import_workflow(gi, args.workflow_path, args.publish_workflows)
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49
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50
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51 if __name__ == '__main__':
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52 main()