Mercurial > repos > stevecassidy > alveoimport
view alveo_data_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 |
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from __future__ import print_function import argparse import pyalveo import sys from util import API_URL, write_key def parser(): p = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List") p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key") p.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download") p.add_argument('--output', required=True, action="store", type=str, help="output file name") p.add_argument('--outputkey', required=True, action="store", type=str, help="output file name for API Key") return p.parse_args() def main(): args = parser() try: write_key(args.api_key, args.outputkey) client = pyalveo.Client(api_key=args.api_key, api_url=API_URL, use_cache=False) item_list = client.get_item_list(args.item_list_url) with open(args.output, 'w') as out: out.write("ItemURL\n") for item in item_list: out.write(item + "\n") print(item) except pyalveo.APIError as e: print("ERROR: " + str(e), file=sys.stderr) sys.exit(1) if __name__ == '__main__': main()