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* New PAM AuthProvider for interfacing with the Pluggable Authenticat…

…ion Module system (

* Helper script to allow authenticating against modules as root
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pvanheus committed Jul 14, 2015
1 parent f6b894a commit b9c9f11ce1a433b49fd07f58334a7a24e3008029
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  1. +151 −0 lib/galaxy/auth/providers/
  2. +40 −0 scripts/auth/
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Created on 13/07/2015
Author Peter van Heusden (
import logging
from distutils import spawn
from subprocess import Popen, PIPE
import shlex
from ..providers import AuthProvider
from galaxy.auth import _get_bool
log = logging.getLogger(__name__)
This module provides an AuthProvider for PAM (pluggable authentication module) authentication.
PAM is the Pluggable Authentication Module system (
It relies on python-pam (
Configuration is via config/auth_conf.xml and the following options are supported:
- auto-register: True/False: automatically register an account for an unknown user. Default: False
- maildomain: string: all valid users fall within the specified mail domain. Default: None
- login-use-email: True/False: Parse the email address to get login details. Default: False
- login-use-username: True/False: Use the username argument for login details. Default: False
Technical note: when a user is not found in the database,
their username is the user part of a user@host email
address. After user creation, however, the username is
the user's public name.
- pam-service: string: The service name to use for PAM authentication. Default: galaxy
- use-external-helper: True/False: Run an external helper script as root with sudo to do
authentication. If False authentication is done
by the module directly. Default: False
Technical note: some PAM modules (e.g.
require to be run as root to authenticate users.
- authentication-helper-script: string: Absolute path to helper script to run for authentication. Default: None
There needs to be a config (in /etc/sudoers or /etc/sudoers.d)
that allows the galaxy user to run this as root with no password check
For example:
galaxy ALL=(root) NOPASSWD: /opt/galaxy/scripts/auth/
Configuration example (for internal authentication, use email for user details):
class PAM(AuthProvider):
plugin_type = 'PAM'
def authenticate(self, email, username, password, options):
pam_username = None
auto_register_username = None
auto_register_email = None
force_fail = False
log.debug("use username: {} use email {} email {} username {}".format(options.get('login-use-username'), options.get('login-use-email', False), email, username))
# check email based login first because if email exists in Galaxy DB
# we will be given the "public name" as username
if _get_bool(options, 'login-use-email', False) == True and email is not None:
if '@' in email:
(email_user, email_domain) = email.split('@')
pam_username = email_user
if email_domain == options.get('maildomain', None):
auto_register_email = email
if username is not None:
auto_register_username = username
auto_register_username = email_user
log.debug('PAM authenticate: warning: email does not match configured PAM maildomain')
# no need to fail: if auto-register is not enabled, this
# might still be a valid user
log.debug('PAM authenticate: email must be used to login, but no valid email found')
force_fail = True
elif _get_bool(options, 'login-use-username', False):
# if we get here via authenticate_user then
# user will be "public name" and
# email address will be as per registered user
if username is not None:
pam_username = username
if email is not None:
auto_register_email = email
elif options.get('maildomain', None) is not None:
# we can register a user with this username and mail domain
# if auto registration is enabled
auto_register_email = '{}@{}'.format(username, options['maildomain'])
auto_register_username = username
log.debug('PAM authenticate: username login selected but no username provided')
force_fail = True
log.debug('PAM authenticate: could not find username for PAM')
force_fail = True
if force_fail:
return None, '', ''
pam_service = options.get('pam-service', 'galaxy')
use_helper = _get_bool(options, 'use-external-helper', False)
log.debug("PAM auth: will use external helper: {}".format(use_helper))
authenticated = False
if use_helper:
authentication_helper = options.get('authentication-helper-script', '/bin/false').strip()
log.debug("PAM auth: external helper script: {}".format(authentication_helper))
if not authentication_helper.startswith('/'):
# don't accept relative path
authenticated = False
auth_cmd = shlex.split('/usr/bin/sudo -n {}'.format(authentication_helper))
log.debug("PAM auth: external helper cmd: {}".format(auth_cmd))
proc = Popen(auth_cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE)
message = '{}\n{}\n{}\n'.format(pam_service, pam_username, password)
(output, error) = proc.communicate(message)
status = proc.wait()
if status != 0 and error != '':
log.debug("PAM auth: external authentication script had errors: status {} error {}".format(status, error))
if output.strip() == 'True':
authenticated = True
authenticated = False
import pam
except ImportError:
log.debug('PAM authenticate: could not load pam module, PAM authentication disabled')
return None, '', ''
p_auth = pam.pam()
authenticated = p_auth.authenticate(pam_username, password, service=pam_service)
if authenticated:
log.debug('PAM authentication successful for {}'.format(pam_username))
return True, auto_register_email, auto_register_username
log.debug('PAM authentication failed for {}'.format(pam_username))
return False, '', ''
def authenticate_user(self, user, password, options):
return self.authenticate(, user.username, password, options)[0]
__all__ = ['PAM']
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#!/usr/bin/env python
import sys
import os
import logging
import signal
log = logging.getLogger(__name__)
import pam
except ImportError:
log.debug('PAM auth helper: Could not import pam module')
def handle_timeout(signum, stack):
raise IOError("Timed out reading input")
# set timeout so we don't block on reading stdin
pam_service = sys.stdin.readline().strip()
pam_username = sys.stdin.readline().strip()
pam_password = sys.stdin.readline().strip()
# cancel the alarm
p_auth = pam.pam()
authenticated = p_auth.authenticate(pam_username, pam_password, service=pam_service)
if authenticated:
log.debug('PAM auth helper: authentication successful for {}'.format(pam_username))
log.debug('PAM auth helper: authentication failed for {}'.format(pam_username))

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