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119
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1 import argparse
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2 import os
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3 import subprocess
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4 import sys
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5 import urllib.request
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6
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7 from bioblend import galaxy
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8
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9 WF = "https://drive.google.com/uc?export=download&id=13xE8o7tucHGNA0qYkEP98FfUGl2wdOU5"
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10 HIST = (
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11 "https://drive.google.com/uc?export=download&id=1V0ZN9ZBuqcGJvt2AP7s3g0q11uYEhdDB"
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12 )
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13 WF_FILE = "tf_workflow.ga"
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14 HIST_FILE = "tf_history.tgz"
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15
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16
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17 def _parser():
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18 parser = argparse.ArgumentParser()
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19 parser.add_argument(
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20 "-g", "--galaxy", help="URL of target galaxy", default="http://localhost:9090"
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21 )
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22 parser.add_argument("-a", "--key", help="Galaxy admin key", default=None)
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23 return parser
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24
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25
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26 def main():
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27 """
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28 load the planemo tool_factory demonstration history and tool generating workflow
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29 fails in planemo served galaxies because there seems to be no user in trans?
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30 """
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31 args = _parser().parse_args()
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32 urllib.request.urlretrieve(WF, WF_FILE)
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33 urllib.request.urlretrieve(HIST, HIST_FILE)
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34 assert args.key, "Need an administrative key for the target Galaxy supplied please"
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35 wfp = os.path.abspath(WF_FILE)
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36 hp = os.path.abspath(HIST_FILE)
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37 gi = galaxy.GalaxyInstance(
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38 url=args.galaxy, key=args.key, email="planemo@galaxyproject.org"
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39 )
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40 x = gi.workflows.import_workflow_from_local_path(WF_FILE, publish=True)
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41 print(f"installed {WF_FILE} Returned = {x}\n")
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42 x = gi.histories.import_history(file_path=HIST_FILE)
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43 print(f"installed {HIST_FILE} Returned = {x}\n")
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44
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45
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46 if __name__ == "__main__":
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47 main()
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