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Source code for galaxy.webapps.tool_shed.controllers.user
import logging
import socket
from markupsafe import escape
from sqlalchemy import func
from galaxy import (
util,
web
)
from galaxy.security.validate_user_input import (
transform_publicname,
validate_email,
validate_publicname
)
from galaxy.web import url_for
from galaxy.web.form_builder import CheckboxField
from galaxy.webapps.galaxy.controllers.user import User as BaseUser
log = logging.getLogger(__name__)
REQUIRE_LOGIN_TEMPLATE = """
<p>
This %s has been configured such that only users who are logged in may use it.%s
</p>
"""
PASSWORD_RESET_TEMPLATE = """
To reset your Galaxy password for the instance at %s use the following link,
which will expire %s.
%s
If you did not make this request, no action is necessary on your part, though
you may want to notify an administrator.
If you're having trouble using the link when clicking it from email client, you
can also copy and paste it into your browser.
"""
[docs]class User(BaseUser):
[docs] @web.expose
def index(self, trans, cntrller='user', **kwd):
return trans.fill_template('/webapps/tool_shed/user/index.mako', cntrller=cntrller)
[docs] @web.expose
def login(self, trans, refresh_frames=[], **kwd):
'''Handle Galaxy Log in'''
referer = trans.request.referer or ''
redirect = self.__get_redirect_url(kwd.get('redirect', referer).strip())
redirect_url = '' # always start with redirect_url being empty
use_panels = util.string_as_bool(kwd.get('use_panels', False))
message = kwd.get('message', '')
status = kwd.get('status', 'done')
header = ''
user = trans.user
success = False
login = kwd.get('login', '')
if user:
# Already logged in.
redirect_url = redirect
message = 'You are already logged in.'
status = 'info'
elif kwd.get('login_button', False):
response = self.__validate_login(trans, **kwd)
if trans.response.status == 400:
trans.response.status = 200
message = response.get("err_msg")
status = "error"
elif response.get("expired_user"):
change_password_url = url_for(controller='user', action='change_password', id=response.get("expired_user"))
message = "%s<br>Click <a href='%s'>here</a> to change your password." % (response.get("message"), change_password_url)
status = "warning"
else:
success = True
if success:
redirect_url = redirect
if not success and not user and trans.app.config.require_login:
if trans.app.config.allow_user_creation:
create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \
web.url_for(controller='user', action='create', cntrller='user')
header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", create_account_str)
else:
header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", "")
return trans.fill_template('/webapps/tool_shed/user/login.mako',
login=login,
header=header,
use_panels=use_panels,
redirect_url=redirect_url,
redirect=redirect,
refresh_frames=refresh_frames,
message=message,
status=status,
form_input_auto_focus=True,
active_view="user")
[docs] @web.expose
def create(self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd):
params = util.Params(kwd)
# If the honeypot field is not empty we are dealing with a bot.
honeypot_field = params.get('bear_field', '')
if honeypot_field != '':
return trans.show_error_message("You've been flagged as a possible bot. If you are not, please try registering again and fill the form out carefully. <a target=\"_top\" href=\"%s\">Go to the home page</a>.") % url_for('/')
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
use_panels = util.string_as_bool(kwd.get('use_panels', True))
email = util.restore_text(params.get('email', ''))
# Do not sanitize passwords, so take from kwd
# instead of params ( which were sanitized )
password = kwd.get('password', '')
confirm = kwd.get('confirm', '')
username = util.restore_text(params.get('username', ''))
subscribe = params.get('subscribe', '')
subscribe_checked = CheckboxField.is_checked(subscribe)
referer = trans.request.referer or ''
redirect = kwd.get('redirect', referer).strip()
is_admin = trans.user_is_admin
success = False
show_user_prepopulate_form = False
if not trans.app.config.allow_user_creation and not trans.user_is_admin:
message = 'User registration is disabled. Please contact your local Galaxy administrator for an account.'
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
status = 'error'
else:
# check user is allowed to register
message, status = trans.app.auth_manager.check_registration_allowed(email, username, password)
if not message:
# Create the user, save all the user info and login to Galaxy
if params.get('create_user_button', False):
# Check email and password validity
message = self.__validate(trans, email, password, confirm, username)
if not message:
# All the values are valid
message, status, user, success = self.__register(trans, subscribe_checked=subscribe_checked, **kwd)
if success and not is_admin:
# The handle_user_login() method has a call to the history_set_default_permissions() method
# (needed when logging in with a history), user needs to have default permissions set before logging in
trans.handle_user_login(user)
trans.log_event("User created a new account")
trans.log_event("User logged in")
else:
status = 'error'
registration_warning_message = trans.app.config.registration_warning_message
if success:
if is_admin:
redirect_url = web.url_for('/admin/users?status=success&message=Created new user account.')
else:
redirect_url = web.url_for('/')
return trans.fill_template('/webapps/tool_shed/user/register.mako',
cntrller=cntrller,
email=email,
username=transform_publicname(trans, username),
subscribe_checked=subscribe_checked,
show_user_prepopulate_form=show_user_prepopulate_form,
use_panels=use_panels,
redirect=redirect,
redirect_url=redirect_url,
refresh_frames=refresh_frames,
registration_warning_message=registration_warning_message,
message=message,
status=status)
def __register(self, trans, email=None, username=None, password=None, subscribe_checked=False, **kwd):
"""Registers a new user."""
email = util.restore_text(email)
username = util.restore_text(username)
status = None
message = None
is_admin = trans.user_is_admin
user = self.user_manager.create(email=email, username=username, password=password)
if subscribe_checked:
# subscribe user to email list
if trans.app.config.smtp_server is None:
status = "error"
message = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. <br>Please contact your local Galaxy administrator."
else:
body = 'Join Mailing list.\n'
to = trans.app.config.mailing_join_addr
frm = email
subject = 'Join Mailing List'
try:
util.send_mail(frm, to, subject, body, trans.app.config)
except Exception:
log.exception('Subscribing to the mailing list has failed.')
status = "warning"
message = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed."
if status != "error":
if not is_admin:
# The handle_user_login() method has a call to the history_set_default_permissions() method
# (needed when logging in with a history), user needs to have default permissions set before logging in
trans.handle_user_login(user)
trans.log_event("User created a new account")
trans.log_event("User logged in")
if trans.app.config.user_activation_on:
is_activation_sent = self.user_manager.send_activation_email(trans, email, username)
if is_activation_sent:
message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target="_top" href="%s">Return to the home page.</a>' % (escape(user.email), url_for('/'))
else:
status = "error"
message = 'Unable to send activation email, please contact your local Galaxy administrator.'
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
else:
# User activation is OFF, proceed without sending the activation email.
message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % (escape(user.email), url_for('/'))
return message, status, user, status is None
[docs] @web.expose
def reset_password(self, trans, email=None, **kwd):
"""Reset the user's password. Send an email with token that allows a password change."""
if trans.app.config.smtp_server is None:
return trans.show_error_message("Mail is not configured for this Galaxy instance "
"and password reset information cannot be sent. "
"Please contact your local Galaxy administrator.")
message = None
status = 'done'
if kwd.get('reset_password_button', False):
message = validate_email(trans, email, check_dup=False)
if not message:
# Default to a non-userinfo-leaking response message
message = ("Your reset request for %s has been received. "
"Please check your email account for more instructions. "
"If you do not receive an email shortly, please contact an administrator." % (escape(email)))
reset_user = trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).first()
if not reset_user:
# Perform a case-insensitive check only if the user wasn't found
reset_user = trans.sa_session.query(trans.app.model.User).filter(func.lower(trans.app.model.User.table.c.email) == func.lower(email)).first()
if reset_user:
prt = trans.app.model.PasswordResetToken(reset_user)
trans.sa_session.add(prt)
trans.sa_session.flush()
host = trans.request.host.split(':')[0]
if host in ['localhost', '127.0.0.1', '0.0.0.0']:
host = socket.getfqdn()
reset_url = url_for(controller='user',
action="change_password",
token=prt.token, qualified=True)
body = PASSWORD_RESET_TEMPLATE % (host, prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
reset_url)
frm = trans.app.config.email_from or 'galaxy-no-reply@' + host
subject = 'Galaxy Password Reset'
try:
util.send_mail(frm, email, subject, body, trans.app.config)
trans.sa_session.add(reset_user)
trans.sa_session.flush()
trans.log_event("User reset password: %s" % email)
except Exception:
log.exception('Unable to reset password.')
return trans.fill_template('/webapps/tool_shed/user/reset_password.mako',
message=message,
status=status)
[docs] @web.expose
def manage_user_info(self, trans, cntrller, **kwd):
'''Manage a user's login, password, public username, type, addresses, etc.'''
params = util.Params(kwd)
user_id = params.get('id', None)
if user_id:
user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
else:
user = trans.user
if not user:
raise AssertionError("The user id (%s) is not valid" % str(user_id))
email = util.restore_text(params.get('email', user.email))
username = util.restore_text(params.get('username', ''))
if not username:
username = user.username
message = escape(util.restore_text(params.get('message', '')))
status = params.get('status', 'done')
return trans.fill_template('/webapps/tool_shed/user/manage_info.mako',
cntrller=cntrller,
user=user,
email=email,
username=username,
message=message,
status=status)
[docs] @web.expose
@web.require_login()
def api_keys(self, trans, cntrller, **kwd):
params = util.Params(kwd)
message = escape(util.restore_text(params.get('message', '')))
status = params.get('status', 'done')
if params.get('new_api_key_button', False):
self.create_api_key(trans, trans.user)
message = "Generated a new web API key"
status = "done"
return trans.fill_template('/webapps/tool_shed/user/api_keys.mako',
cntrller=cntrller,
user=trans.user,
message=message,
status=status)
# For REMOTE_USER, we need the ability to just edit the username
[docs] @web.expose
@web.require_login("to manage the public name")
def edit_username(self, trans, cntrller, **kwd):
params = util.Params(kwd)
is_admin = cntrller == 'admin' and trans.user_is_admin
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
user_id = params.get('user_id', None)
if user_id and is_admin:
user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
else:
user = trans.user
if user and params.get('change_username_button', False):
username = kwd.get('username', '')
if username:
message = validate_publicname(trans, username, user)
if message:
status = 'error'
else:
user.username = username
trans.sa_session.add(user)
trans.sa_session.flush()
message = 'The username has been updated with the changes.'
return trans.fill_template('/webapps/tool_shed/user/username.mako',
cntrller=cntrller,
user=user,
username=user.username,
message=message,
status=status)
[docs] @web.expose
def edit_info(self, trans, cntrller, **kwd):
"""
Edit user information = username, email or password.
"""
params = util.Params(kwd)
is_admin = cntrller == 'admin' and trans.user_is_admin
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
user_id = params.get('user_id', None)
if user_id and is_admin:
user = trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(user_id))
elif user_id and (not trans.user or trans.user.id != trans.security.decode_id(user_id)):
message = 'Invalid user id'
status = 'error'
user = None
else:
user = trans.user
if user and params.get('login_info_button', False):
# Editing email and username
email = util.restore_text(params.get('email', ''))
username = util.restore_text(params.get('username', '')).lower()
# Validate the new values for email and username
message = validate_email(trans, email, user)
if not message and username:
message = validate_publicname(trans, username, user)
if message:
status = 'error'
else:
if (user.email != email):
# The user's private role name must match the user's login ( email )
private_role = trans.app.security_agent.get_private_user_role(user)
private_role.name = email
private_role.description = 'Private role for ' + email
# Change the email itself
user.email = email
trans.sa_session.add_all((user, private_role))
trans.sa_session.flush()
if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on:
user.active = False
trans.sa_session.add(user)
trans.sa_session.flush()
is_activation_sent = self.user_manager.send_activation_email(trans, user.email, user.username)
if is_activation_sent:
message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.'
else:
message = 'Unable to send activation email, please contact your local Galaxy administrator.'
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
if (user.username != username):
user.username = username
trans.sa_session.add(user)
trans.sa_session.flush()
message = 'The login information has been updated with the changes.'
elif user and params.get('edit_user_info_button', False):
# Edit user information - webapp MUST BE 'galaxy'
user_type_fd_id = params.get('user_type_fd_id', 'none')
if user_type_fd_id not in ['none']:
user_type_form_definition = trans.sa_session.query(trans.app.model.FormDefinition).get(trans.security.decode_id(user_type_fd_id))
elif user.values:
user_type_form_definition = user.values.form_definition
else:
# User was created before any of the user_info forms were created
user_type_form_definition = None
if user_type_form_definition:
values = self.get_form_values(trans, user, user_type_form_definition, **kwd)
else:
values = {}
flush_needed = False
if user.values:
# Editing the user info of an existing user with existing user info
user.values.content = values
trans.sa_session.add(user.values)
flush_needed = True
elif values:
form_values = trans.model.FormValues(user_type_form_definition, values)
trans.sa_session.add(form_values)
user.values = form_values
flush_needed = True
if flush_needed:
trans.sa_session.add(user)
trans.sa_session.flush()
message = "The user information has been updated with the changes."
if user and trans.webapp.name == 'galaxy' and is_admin:
kwd['user_id'] = trans.security.encode_id(user.id)
kwd['id'] = user_id
if message:
kwd['message'] = util.sanitize_text(message)
if status:
kwd['status'] = status
return trans.response.send_redirect(web.url_for(controller='user',
action='manage_user_info',
cntrller=cntrller,
**kwd))
[docs] @web.expose
def change_password(self, trans, token=None, id=None, **kwd):
"""
Provides a form with which one can change their password. If token is
provided, don't require current password.
"""
if kwd.get('change_password_button', False):
password = kwd.get('password', '')
confirm = kwd.get('confirm', '')
current = kwd.get('current', '')
user, message = self.user_manager.change_password(trans, password=password,
current=current, token=token, confirm=confirm, id=id)
if not user:
return trans.show_error_message(message)
return trans.show_ok_message('The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).')
return trans.fill_template('/webapps/tool_shed/user/change_password.mako', token=token, id=id)
[docs] @web.expose
def logout(self, trans, logout_all=False, **kwd):
trans.handle_user_logout(logout_all=logout_all)
message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % \
(url_for('/'))
if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
trans.response.send_redirect(trans.app.config.remote_user_logout_href)
else:
return trans.fill_template('/webapps/tool_shed/user/logout.mako',
refresh_frames=['masthead'],
message=message,
status='done',
active_view="user")
def __validate(self, trans, email, password, confirm, username):
# If coming from the tool shed webapp, we'll require a public user name
if not username:
return "A public user name is required in the tool shed."
if username in ['repos']:
return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a public user name." % escape(username)
return super(User, self).__validate(trans, email, password, confirm, username)