Mercurial > repos > blankenberglab > data_manager_refgenie_pull
view data_manager/data_manager_refgenie_pull.py @ 3:b2fa406276e7 draft default tip
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
author | blankenberglab |
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date | Fri, 01 Apr 2022 16:14:13 +0000 |
parents | 2cb1863cd236 |
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#!/usr/bin/env python import argparse import logging from base64 import urlsafe_b64encode from html import escape 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): try: rval = [] rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True) 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 except Exception as e: log.debug("Failed to access refgenie server: %s", e) return[{'name': escape(str(e)), 'value': 'ERROR', 'options': [], 'selected': False}] 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') parser.add_argument('-g', '--graceful', dest='graceful', action='store_true', help='Fail gracefully') args = parser.parse_args() try: 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()) except Exception as e: if args.graceful: print("Failed to reload data tables:\n%s" % (e)) else: raise e