Mercurial > repos > stevecassidy > alveoimport
view alveo_item_list_importer.py @ 14:a38315ecf593 draft
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author | stevecassidy |
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date | Wed, 01 Nov 2017 01:18:15 -0400 |
parents | 56fda3d161f0 |
children |
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from __future__ import print_function import argparse import sys from util import get_item_lists def parser(): p = argparse.ArgumentParser(description="Retrieves Alveo Item Lists") p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key") p.add_argument('--output', required=True, action="store", type=str, help="Path to output file") return p.parse_args() def write_table(item_lists, filename): with open(filename, 'w') as outfile: for list_set in item_lists.values(): for item_list in list_set: outfile.write("%s (%d)\t%s\n" % (item_list['name'], item_list['num_items'], item_list['item_list_url'])) def main(): args = parser() try: api_key = open(args.api_key, 'r').read().strip() item_lists = get_item_lists(api_key) if item_lists: write_table(item_lists, args.output) except Exception as e: print("ERROR: " + str(e), file=sys.stderr) sys.exit(1) if __name__ == '__main__': main()