Mercurial > repos > stevecassidy > alveoimport

annotate alveo_item_list_importer.py @ 14:a38315ecf593 draft

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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author stevecassidy
date Wed, 01 Nov 2017 01:18:15 -0400
parents 56fda3d161f0
children
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1 from __future__ import print_function
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2 import argparse
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3 import sys
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a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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4 from util import get_item_lists
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7 def parser():
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8 p = argparse.ArgumentParser(description="Retrieves Alveo Item Lists")
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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9 p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
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10 p.add_argument('--output', required=True, action="store", type=str, help="Path to output file")
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11 return p.parse_args()
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14 def write_table(item_lists, filename):
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15 with open(filename, 'w') as outfile:
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16 for list_set in item_lists.values():
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17 for item_list in list_set:
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18 outfile.write("%s (%d)\t%s\n" % (item_list['name'], item_list['num_items'], item_list['item_list_url']))
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21 def main():
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22 args = parser()
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23 try:
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24 api_key = open(args.api_key, 'r').read().strip()
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25 item_lists = get_item_lists(api_key)
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26 if item_lists:
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27 write_table(item_lists, args.output)
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28 except Exception as e:
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29 print("ERROR: " + str(e), file=sys.stderr)
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30 sys.exit(1)
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33 if __name__ == '__main__':
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34 main()