import logging
from typing import NamedTuple
from galaxy.util import parse_xml_string
from galaxy.util.tool_shed.common_util import remove_protocol_from_tool_shed_url
from galaxy.util.tool_shed.xml_util import parse_xml
log = logging.getLogger(__name__)
DEFAULT_TOOL_SHEDS_CONF_XML = """<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="Galaxy Main Tool Shed" url="https://toolshed.g2.bx.psu.edu/"/>
</tool_sheds>
"""
[docs]class AUTH_TUPLE(NamedTuple):
username: str
password: str
[docs]class Registry:
[docs] def __init__(self, config=None):
self.tool_sheds = {}
self.tool_sheds_auth = {}
if config:
# Parse tool_sheds_conf.xml
tree, error_message = parse_xml(config)
if tree is None:
log.warning("Unable to load references to tool sheds defined in file %s" % str(config))
return
root = tree.getroot()
else:
root = parse_xml_string(DEFAULT_TOOL_SHEDS_CONF_XML)
config = "internal default config"
log.debug('Loading references to tool sheds from %s' % config)
for elem in root.findall('tool_shed'):
try:
name = elem.get('name', None)
url = elem.get('url', None)
username = elem.get('user', None)
password = elem.get('pass', None)
if name and url:
self.tool_sheds[name] = url
self.tool_sheds_auth[name] = None
log.debug('Loaded reference to tool shed: %s' % name)
if name and url and username and password:
self.tool_sheds_auth[name] = AUTH_TUPLE(username, password)
except Exception as e:
log.warning('Error loading reference to tool shed "{}", problem: {}'.format(name, str(e)))
[docs] def url_auth(self, url):
"""
If the tool shed is using external auth, the client to the tool shed must authenticate to that
as well. This provides access to the six.moves.urllib.request.HTTPPasswordMgrWithdefaultRealm() object for the
url passed in.
Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at
some stage...
"""
url_sans_protocol = remove_protocol_from_tool_shed_url(url)
for shed_name, shed_url in self.tool_sheds.items():
shed_url_sans_protocol = remove_protocol_from_tool_shed_url(shed_url)
if url_sans_protocol.startswith(shed_url_sans_protocol):
return self.tool_sheds_auth[shed_name]
log.debug("Invalid url '%s' received by tool shed registry's url_auth method." % str(url))
return None