comparison data_manager/data_manager_refgenie_pull.py @ 0:aec9bc48cdb7 draft

"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"

0:aec9bc48cdb7

#!/usr/bin/env python


import argparse
import logging
from base64 import urlsafe_b64encode
from urllib.parse import urljoin

import refgenconf
import requests


log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull")


def galaxy_code_get_refgenie_assets(refgenie_config_file):
    rgc = refgenconf.RefGenConf(refgenie_config_file)
    rval = []
    for urlname, genomes in rgc.listr().items():
        urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')
        ul = []
        for genome, assets in genomes.items():
            al = []
            for name in assets:
                al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False})
            ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False})
        rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False})
    return rval


if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload')
    parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload')
    parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key')

    args = parser.parse_args()
    if not args.names:
        tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json()
        args.names = [d.get('name') for d in tables]
    for name in args.names:
        print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json())