Mercurial > repos > blankenberglab > data_manager_refgenie_pull

comparison data_manager/data_manager_refgenie_pull.py @ 3:b2fa406276e7 draft default tip

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"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
author blankenberglab
date Fri, 01 Apr 2022 16:14:13 +0000
parents 2cb1863cd236
children
comparison
equal deleted inserted replaced
2:2cb1863cd236 3:b2fa406276e7
2 2
3 3
4 import argparse 4 import argparse
5 import logging 5 import logging
6 from base64 import urlsafe_b64encode 6 from base64 import urlsafe_b64encode
7 from html import escape
7 from urllib.parse import urljoin 8 from urllib.parse import urljoin
8 9
9 import refgenconf 10 import refgenconf
10 import requests 11 import requests
11 12
13 log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull") 14 log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull")
14 15
15 16
16 def galaxy_code_get_refgenie_assets(refgenie_config_file): 17 def galaxy_code_get_refgenie_assets(refgenie_config_file):
17 try: 18 try:
19 rval = []
18 rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True) 20 rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True)
19 except refgenconf.exceptions.RefgenconfError as e: 21 for urlname, genomes in rgc.listr().items():
20 return[{'name': str(e), 'value': 'ERROR', 'options': [], 'selected': False}] 22 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')
21 rval = [] 23 ul = []
22 for urlname, genomes in rgc.listr().items(): 24 for genome, assets in genomes.items():
23 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8') 25 al = []
24 ul = [] 26 for name in assets:
25 for genome, assets in genomes.items(): 27 al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False})
26 al = [] 28 ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False})
27 for name in assets: 29 rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False})
28 al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False}) 30 return rval
29 ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False}) 31 except Exception as e:
30 rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False}) 32 log.debug("Failed to access refgenie server: %s", e)
31 return rval 33 return[{'name': escape(str(e)), 'value': 'ERROR', 'options': [], 'selected': False}]
32 34
33 35
34 if __name__ == '__main__': 36 if __name__ == '__main__':
35 parser = argparse.ArgumentParser() 37 parser = argparse.ArgumentParser()
36 parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload') 38 parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload')
37 parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload') 39 parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload')
38 parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key') 40 parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key')
41 parser.add_argument('-g', '--graceful', dest='graceful', action='store_true', help='Fail gracefully')
39 42
40 args = parser.parse_args() 43 args = parser.parse_args()
41 if not args.names: 44 try:
42 tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json() 45 if not args.names:
43 args.names = [d.get('name') for d in tables] 46 tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json()
44 for name in args.names: 47 args.names = [d.get('name') for d in tables]
45 print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json()) 48 for name in args.names:
49 print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json())
50 except Exception as e:
51 if args.graceful:
52 print("Failed to reload data tables:\n%s" % (e))
53 else:
54 raise e