comparison toolfactory/install_tf_demos.py @ 4:2a46da701dde draft

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author fubar
date Mon, 26 Apr 2021 05:25:26 +0000
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3:c4f192ec521c 4:2a46da701dde
1 import argparse
2 import urllib.request
3
4 from bioblend import galaxy
5
6 WF = "https://drive.google.com/uc?export=download&id=13xE8o7tucHGNA0qYkEP98FfUGl2wdOU5"
7 HIST = (
8 "https://drive.google.com/uc?export=download&id=1V0ZN9ZBuqcGJvt2AP7s3g0q11uYEhdDB"
9 )
10 WF_FILE = "tf_workflow.ga"
11 HIST_FILE = "tf_history.tgz"
12
13
14 def _parser():
15 parser = argparse.ArgumentParser()
16 parser.add_argument(
17 "-g", "--galaxy", help="URL of target galaxy", default="http://localhost:9090"
18 )
19 parser.add_argument("-a", "--key", help="Galaxy admin key", default=None)
20 return parser
21
22
23 def main():
24 """
25 load the planemo tool_factory demonstration history and tool generating workflow
26 fails in planemo served galaxies because there seems to be no user in trans?
27 """
28 args = _parser().parse_args()
29 urllib.request.urlretrieve(WF, WF_FILE)
30 urllib.request.urlretrieve(HIST, HIST_FILE)
31 assert args.key, "Need an administrative key for the target Galaxy supplied please"
32 gi = galaxy.GalaxyInstance(
33 url=args.galaxy, key=args.key, email="planemo@galaxyproject.org"
34 )
35 x = gi.workflows.import_workflow_from_local_path(WF_FILE, publish=True)
36 print(f"installed {WF_FILE} Returned = {x}\n")
37 x = gi.histories.import_history(file_path=HIST_FILE)
38 print(f"installed {HIST_FILE} Returned = {x}\n")
39
40
41 if __name__ == "__main__":
42 main()