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Source code for galaxy.managers.users

Manager and Serializer for Users.
import logging
import random
import socket
from datetime import datetime

from markupsafe import escape
from sqlalchemy import and_, desc, exc, func, true

from galaxy import (
from galaxy.managers import (
from galaxy.security.validate_user_input import validate_email, validate_password, validate_publicname
from galaxy.web import url_for

log = logging.getLogger(__name__)

To reset your Galaxy password for the instance at %s use the following link,
which will expire %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 UserManager(base.ModelManager, deletable.PurgableManagerMixin): foreign_key_name = 'user' # TODO: there is quite a bit of functionality around the user (authentication, permissions, quotas, groups/roles) # most of which it may be unneccessary to have here # TODO: incorp BaseAPIController.validate_in_users_and_groups # TODO: incorp CreatesApiKeysMixin # TODO: incorporate UsesFormDefinitionsMixin?
[docs] def __init__(self, app): self.model_class = app.model.User super(UserManager, self).__init__(app)
[docs] def register(self, trans, email=None, username=None, password=None, confirm=None, subscribe=False): """ Register a new user. """ 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 return None, message if not email or not username or not password or not confirm: return None, "Please provide email, username and password." message = "\n".join([validate_email(trans, email), validate_password(trans, password, confirm), validate_publicname(trans, username)]).rstrip() if message: return None, message email = util.restore_text(email) username = util.restore_text(username) message, status = trans.app.auth_manager.check_registration_allowed(email, username, password) if message: return None, message if subscribe: message = self.send_subscription_email(email) if message: return None, message user = self.create(email=email, username=username, password=password) if self.app.config.user_activation_on: self.send_activation_email(trans, email, username) return user, None
[docs] def create(self, email=None, username=None, password=None, **kwargs): """ Create a new user. """ self._error_on_duplicate_email(email) user = self.model_class(email=email) user.set_password_cleartext(password) user.username = username if self.app.config.user_activation_on: user.active = False else: # Activation is off, every new user is active by default. user.active = True self.session().add(user) try: self.session().flush() # TODO:?? flush needed for permissions below? If not, make optional except exc.IntegrityError as db_err: raise exceptions.Conflict(str(db_err)) # can throw an sqlalx.IntegrityError if username not unique self.app.security_agent.create_private_user_role(user) # We set default user permissions, before we log in and set the default history permissions if hasattr(self.app.config, "new_user_dataset_access_role_default_private"): permissions = self.app.config.new_user_dataset_access_role_default_private self.app.security_agent.user_set_default_permissions(user, default_access_private=permissions) return user
[docs] def delete(self, user): user.deleted = True self.session().add(user) self.session().flush()
def _error_on_duplicate_email(self, email): """ Check for a duplicate email and raise if found. :raises exceptions.Conflict: if any are found """ # TODO: remove this check when unique=True is added to the email column if self.by_email(email) is not None: raise exceptions.Conflict('Email must be unique', email=email) # ---- filters
[docs] def by_email(self, email, filters=None, **kwargs): """ Find a user by their email. """ filters = self._munge_filters(self.model_class.email == email, filters) try: # TODO: use one_or_none return super(UserManager, self).one(filters=filters, **kwargs) except exceptions.ObjectNotFound: return None
[docs] def by_email_like(self, email_with_wildcards, filters=None, order_by=None, **kwargs): """ Find a user searching with SQL wildcards. """ filters = self._munge_filters(self.model_class.email.like(email_with_wildcards), filters) order_by = order_by or (model.User.email, ) return super(UserManager, self).list(filters=filters, order_by=order_by, **kwargs)
# ---- admin
[docs] def is_admin(self, user, trans=None): """Return True if this user is an admin (or session is authenticated as admin). Do not pass trans to simply check if an existing user object is an admin user, pass trans when checking permissions. """ admin_emails = self._admin_emails() if user is None: # Anonymous session or master_api_key used, if master_api_key is detected # return True. rval = bool(trans and trans.user_is_admin) return rval return bool(admin_emails and user.email in admin_emails)
def _admin_emails(self): """ Return a list of admin email addresses from the config file. """ return [email.strip() for email in self.app.config.get("admin_users", "").split(",")]
[docs] def admins(self, filters=None, **kwargs): """ Return a list of admin Users. """ filters = self._munge_filters(self.model_class.email.in_(self._admin_emails()), filters) return super(UserManager, self).list(filters=filters, **kwargs)
[docs] def error_unless_admin(self, user, msg="Administrators only", **kwargs): """ Raise an error if `user` is not an admin. :raises exceptions.AdminRequiredException: if `user` is not an admin. """ # useful in admin only methods if not self.is_admin(user, trans=kwargs.get("trans", None)): raise exceptions.AdminRequiredException(msg, **kwargs) return user
# ---- anonymous
[docs] def is_anonymous(self, user): """ Return True if `user` is anonymous. """ # define here for single point of change and make more readable return user is None
[docs] def error_if_anonymous(self, user, msg="Log-in required", **kwargs): """ Raise an error if `user` is anonymous. """ if user is None: # TODO: code is correct (401) but should be named AuthenticationRequired (401 and 403 are flipped) raise exceptions.AuthenticationFailed(msg, **kwargs) return user
# ---- current
[docs] def current_user(self, trans): # define here for single point of change and make more readable # TODO: trans return trans.user
# ---- api keys
[docs] def create_api_key(self, user): """ Create and return an API key for `user`. """ # TODO: seems like this should return the model return api_keys.ApiKeyManager(self.app).create_api_key(user)
# TODO: possibly move to ApiKeyManager
[docs] def valid_api_key(self, user): """ Return this most recent APIKey for this user or None if none have been created. """ query = (self.session().query(model.APIKeys) .filter_by(user=user) .order_by(desc(model.APIKeys.create_time))) all = query.all() if len(all): return all[0] return None
# TODO: possibly move to ApiKeyManager
[docs] def get_or_create_valid_api_key(self, user): """ Return this most recent APIKey for this user or create one if none have been created. """ existing = self.valid_api_key(user) if existing: return existing return self.create_api_key(self, user)
# ---- preferences
[docs] def preferences(self, user): return dict((key, value) for key, value in user.preferences.items())
# ---- roles and permissions
[docs] def private_role(self, user): return self.app.security_agent.get_private_user_role(user)
[docs] def sharing_roles(self, user): return self.app.security_agent.get_sharing_roles(user)
[docs] def default_permissions(self, user): return self.app.security_agent.user_get_default_permissions(user)
[docs] def quota(self, user, total=False): if total: return self.app.quota_agent.get_quota(user, nice_size=True) return self.app.quota_agent.get_percent(user=user)
[docs] def tags_used(self, user, tag_models=None): """ Return a list of distinct 'user_tname:user_value' strings that the given user has used. """ # TODO: simplify and unify with tag manager if self.is_anonymous(user): return [] # get all the taggable model TagAssociations if not tag_models: tag_models = [v.tag_assoc_class for v in self.app.tag_handler.item_tag_assoc_info.values()] # create a union of subqueries for each for this user - getting only the tname and user_value all_tags_query = None for tag_model in tag_models: subq = (self.session().query(tag_model.user_tname, tag_model.user_value) .filter(tag_model.user == user)) all_tags_query = subq if all_tags_query is None else all_tags_query.union(subq) # if nothing init'd the query, bail if all_tags_query is None: return [] # boil the tag tuples down into a sorted list of DISTINCT name:val strings tags = all_tags_query.distinct().all() tags = [((name + ':' + val) if val else name) for name, val in tags] return sorted(tags)
[docs] def change_password(self, trans, password=None, confirm=None, token=None, id=None, current=None): """ Allows to change a user password with a token. """ if not token and not id: return None, "Please provide a token or a user and password." if token: token_result = trans.sa_session.query(self.app.model.PasswordResetToken).get(token) if not token_result or not token_result.expiration_time > datetime.utcnow(): return None, "Invalid or expired password reset token, please request a new one." user = token_result.user message = self.__set_password(trans, user, password, confirm) if message: return None, message token_result.expiration_time = datetime.utcnow() trans.sa_session.add(token_result) return user, "Password has been changed. Token has been invalidated." else: user = self.by_id(self.app.security.decode_id(id)) if user: message = self.app.auth_manager.check_change_password(user, current) if message: return None, message message = self.__set_password(trans, user, password, confirm) if message: return None, message return user, "Password has been changed." else: return user, "User not found."
def __set_password(self, trans, user, password, confirm): if not password: return "Please provide a new password." if user: # Validate the new password message = validate_password(trans, password, confirm) if message: return message else: # Save new password user.set_password_cleartext(password) # Invalidate all other sessions if trans.galaxy_session: for other_galaxy_session in trans.sa_session.query(self.app.model.GalaxySession) \ .filter(and_(self.app.model.GalaxySession.table.c.user_id == user.id, self.app.model.GalaxySession.table.c.is_valid == true(), self.app.model.GalaxySession.table.c.id != trans.galaxy_session.id)): other_galaxy_session.is_valid = False trans.sa_session.add(other_galaxy_session) trans.sa_session.add(user) trans.sa_session.flush() trans.log_event("User change password") else: return "Failed to determine user, access denied."
[docs] def send_activation_email(self, trans, email, username): """ Send the verification email containing the activation link to the user's email. """ activation_token = self.__get_activation_token(trans, escape(email)) activation_link = url_for(controller='user', action='activate', activation_token=activation_token, email=escape(email), qualified=True) host = self.__get_host(trans) body = ("Hello %s,\n\n" "In order to complete the activation process for %s begun on %s at %s, please click on the following link to verify your account:\n\n" "%s \n\n" "By clicking on the above link and opening a Galaxy account you are also confirming that you have read and agreed to Galaxy's Terms and Conditions for use of this service (%s). This includes a quota limit of one account per user. Attempts to subvert this limit by creating multiple accounts or through any other method may result in termination of all associated accounts and data.\n\n" "Please contact us if you need help with your account at: %s. You can also browse resources available at: %s. \n\n" "More about the Galaxy Project can be found at galaxyproject.org\n\n" "Your Galaxy Team" % (escape(username), escape(email), datetime.utcnow().strftime("%D"), trans.request.host, activation_link, self.app.config.terms_url, self.app.config.error_email_to, self.app.config.instance_resource_url)) to = email frm = self.app.config.email_from or 'galaxy-no-reply@' + host subject = 'Galaxy Account Activation' try: util.send_mail(frm, to, subject, body, self.app.config) return True except Exception: log.debug(body) log.exception('Unable to send the activation email.') return False
def __get_activation_token(self, trans, email): """ Check for the activation token. Create new activation token and store it in the database if no token found. """ user = trans.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == email).first() activation_token = user.activation_token if activation_token is None: activation_token = util.hash_util.new_secure_hash(str(random.getrandbits(256))) user.activation_token = activation_token trans.sa_session.add(user) trans.sa_session.flush() return activation_token
[docs] def send_reset_email(self, trans, payload={}, **kwd): """Reset the user's password. Send an email with token that allows a password change.""" if self.app.config.smtp_server is None: return "Mail is not configured for this Galaxy instance and password reset information cannot be sent. Please contact your local Galaxy administrator." email = payload.get("email") if not email: return "Please provide your email." message = validate_email(trans, email, check_dup=False) if message: return message else: reset_user, prt = self.get_reset_token(trans, email) if prt: host = self.__get_host(trans) reset_url = url_for(controller='root', action='login', token=prt.token) body = PASSWORD_RESET_TEMPLATE % (host, prt.expiration_time.strftime(trans.app.config.pretty_datetime_format), trans.request.host, 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, self.app.config) trans.sa_session.add(reset_user) trans.sa_session.flush() trans.log_event('User reset password: %s' % email) except Exception as e: log.debug(body) return "Failed to submit email. Please contact the administrator: %s" % util.unicodify(e) else: return "Failed to produce password reset token. User not found."
[docs] def get_reset_token(self, trans, email): reset_user = trans.sa_session.query(self.app.model.User).filter(self.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(self.app.model.User).filter(func.lower(self.app.model.User.table.c.email) == func.lower(email)).first() if reset_user: prt = self.app.model.PasswordResetToken(reset_user) trans.sa_session.add(prt) trans.sa_session.flush() return reset_user, prt return None, None
def __get_host(self, trans): host = trans.request.host.split(':')[0] if host in ['localhost', '', '']: host = socket.getfqdn() return host
[docs] def send_subscription_email(self, email): if self.app.config.smtp_server is None: return "Subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." else: body = 'Join Mailing list.\n' to = self.app.config.mailing_join_addr frm = email subject = 'Join Mailing List' try: util.send_mail(frm, to, subject, body, self.app.config) except Exception: log.exception('Subscribing to the mailing list has failed.') return "Subscribing to the mailing list has failed."
[docs]class UserSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin): model_manager_class = UserManager
[docs] def __init__(self, app): """ Convert a User and associated data to a dictionary representation. """ super(UserSerializer, self).__init__(app) self.user_manager = self.manager self.default_view = 'summary' self.add_view('summary', [ 'id', 'email', 'username' ]) self.add_view('detailed', [ # 'update_time', # 'create_time', 'is_admin', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'quota', 'deleted', 'purged', # 'active', 'preferences', # all tags 'tags_used', # all annotations # 'annotations' ], include_keys_from='summary')
[docs] def add_serializers(self): super(UserSerializer, self).add_serializers() deletable.PurgableSerializerMixin.add_serializers(self) self.serializers.update({ 'id' : self.serialize_id, 'create_time' : self.serialize_date, 'update_time' : self.serialize_date, 'is_admin' : lambda i, k, **c: self.user_manager.is_admin(i), 'preferences' : lambda i, k, **c: self.user_manager.preferences(i), 'total_disk_usage' : lambda i, k, **c: float(i.total_disk_usage), 'quota_percent' : lambda i, k, **c: self.user_manager.quota(i), 'quota' : lambda i, k, **c: self.user_manager.quota(i, total=True), 'tags_used' : lambda i, k, **c: self.user_manager.tags_used(i), })
[docs]class UserDeserializer(base.ModelDeserializer): """ Service object for validating and deserializing dictionaries that update/alter users. """ model_manager_class = UserManager
[docs] def add_deserializers(self): super(UserDeserializer, self).add_deserializers() self.deserializers.update({ 'username' : self.deserialize_username, })
[docs] def deserialize_username(self, item, key, username, trans=None, **context): # TODO: validate_user_input requires trans and should(?) raise exceptions # move validation to UserValidator and use self.app, exceptions instead validation_error = validate_publicname(trans, username, user=item) if validation_error: raise base.ModelDeserializingError(validation_error) return self.default_deserializer(item, key, username, trans=trans, **context)
[docs]class CurrentUserSerializer(UserSerializer): model_manager_class = UserManager
[docs] def serialize(self, user, keys, **kwargs): """ Override to return at least some usage info if user is anonymous. """ kwargs['current_user'] = user if self.user_manager.is_anonymous(user): return self.serialize_current_anonymous_user(user, keys, **kwargs) return super(UserSerializer, self).serialize(user, keys, **kwargs)
[docs] def serialize_current_anonymous_user(self, user, keys, trans=None, **kwargs): # use the current history if any to get usage stats for trans' anonymous user # TODO: might be better as sep. Serializer class usage = 0 percent = None history = trans.history if history: usage = self.app.quota_agent.get_usage(trans, history=trans.history) percent = self.app.quota_agent.get_percent(trans=trans, usage=usage) # a very small subset of keys available values = { 'id' : None, 'total_disk_usage' : float(usage), 'nice_total_disk_usage' : util.nice_size(usage), 'quota_percent' : percent, } serialized = {} for key in keys: if key in values: serialized[key] = values[key] return serialized
[docs]class AdminUserFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMixin): model_manager_class = UserManager model_class = model.User def _add_parsers(self): super(AdminUserFilterParser, self)._add_parsers() deletable.PurgableFiltersMixin._add_parsers(self) # PRECONDITION: user making the query has been verified as an admin self.orm_filter_parsers.update({ 'email' : {'op': ('eq', 'contains', 'like')}, 'username' : {'op': ('eq', 'contains', 'like')}, 'active' : {'op': ('eq')}, 'disk_usage' : {'op': ('le', 'ge')} }) self.fn_filter_parsers.update({})