Mercurial > repos > stevecassidy > alveoimport
annotate 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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14
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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1 from __future__ import print_function |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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2 import argparse |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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3 import pyalveo |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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4 import sys |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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5 from util import API_URL, write_key |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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6 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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7 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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8 def parser(): |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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9 p = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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10 p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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11 p.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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12 p.add_argument('--output', required=True, action="store", type=str, help="output file name") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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13 p.add_argument('--outputkey', required=True, action="store", type=str, help="output file name for API Key") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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14 return p.parse_args() |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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15 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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16 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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17 def main(): |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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18 args = parser() |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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19 try: |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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20 write_key(args.api_key, args.outputkey) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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21 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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22 client = pyalveo.Client(api_key=args.api_key, api_url=API_URL, use_cache=False) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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23 item_list = client.get_item_list(args.item_list_url) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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24 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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25 with open(args.output, 'w') as out: |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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26 out.write("ItemURL\n") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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27 for item in item_list: |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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28 out.write(item + "\n") |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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29 print(item) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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30 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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diff
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31 except pyalveo.APIError as e: |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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32 print("ERROR: " + str(e), file=sys.stderr) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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33 sys.exit(1) |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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34 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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35 |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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36 if __name__ == '__main__': |
a38315ecf593
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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37 main() |