comparison alveo_get_item_list.py @ 14:a38315ecf593 draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty

13:be3fd14899a1

from __future__ import print_function
import json
import argparse
import pyalveo
import sys
import os
from fnmatch import fnmatch

API_URL = 'https://app.alveo.edu.au' # TODO: export constants to a separate module

def parser():
    parser = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
    parser.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
    parser.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download")
    parser.add_argument('--output', required=True, action="store", type=str, help="output file name")
    return parser.parse_args()

def main():
    args = parser()
    try:
        api_key = open(args.api_key, 'r').read().strip()

        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()

14:a38315ecf593

from __future__ import print_function
import argparse
import pyalveo
import sys
from util import API_URL


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")
    return p.parse_args()


def main():
    args = parser()
    try:
        api_key = open(args.api_key, 'r').read().strip()

        with open(args.output, 'w') as out:
            out.write("ItemURL\n")
            for item in item_list:
                out.write(item + "\n")

    except pyalveo.APIError as e:
        print("ERROR: " + str(e), file=sys.stderr)
        sys.exit(1)


if __name__ == '__main__':
    main()