diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 4b023851374..b83b3b214ea 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -28,7 +28,7 @@ from galaxy.web.base.controller import CreatesUsersMixin from galaxy.web.base.controller import CreatesApiKeysMixin from galaxy.web.form_builder import CheckboxField from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from datetime import datetime, timedelta from galaxy.util import hash_util, biostar @@ -164,7 +164,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat user_openid.provider = openid_provider if trans.user: if user_openid.user and user_openid.user.id != trans.user.id: - message = "The OpenID %s is already associated with another Galaxy account, %s. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + message = "The OpenID %s is already associated with another Galaxy account, %s. Please disassociate it from that account before attempting to associate it with a new account." % ( escape( display_identifier ), escape( user_openid.user.email ) ) if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. @@ -179,23 +179,23 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat user_openid.session = trans.galaxy_session if not openid_provider_obj.never_associate_with_user: if not auto_associate and ( user_openid.user and user_openid.user.id == trans.user.id ): - message = "The OpenID %s is already associated with your Galaxy account, %s." % ( display_identifier, trans.user.email ) + message = "The OpenID %s is already associated with your Galaxy account, %s." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "warning" else: - message = "The OpenID %s has been associated with your Galaxy account, %s." % ( display_identifier, trans.user.email ) + message = "The OpenID %s has been associated with your Galaxy account, %s." % ( escape( display_identifier ), escape( trans.user.email ) ) status = "done" user_openid.user = trans.user trans.sa_session.add( user_openid ) trans.sa_session.flush() trans.log_event( "User associated OpenID: %s" % display_identifier ) else: - message = "The OpenID %s cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % ( openid_provider_obj.name ) + message = "The OpenID %s cannot be used to log into your Galaxy account, but any post authentication actions have been performed." % escape( openid_provider_obj.name ) status = "info" openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if redirect: - message = '%s
Click here to return to the page you were previously viewing.' % ( message, redirect ) + message = '%s
Click here to return to the page you were previously viewing.' % ( message, escape( self.__get_redirect_url( redirect ) ) ) if redirect and status != "error": - return trans.response.send_redirect( redirect ) + return trans.response.send_redirect( self.__get_redirect_url( redirect ) ) return trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -208,6 +208,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) if not redirect: redirect = url_for( '/' ) + redirect = self.__get_redirect_url( redirect ) return trans.response.send_redirect( redirect ) trans.sa_session.add( user_openid ) trans.sa_session.flush() @@ -448,18 +449,9 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat @web.expose def login( self, trans, refresh_frames=[], **kwd ): - """Handle Galaxy login""" - redirect = kwd.get( 'redirect', trans.request.referer ).strip() - root_url = url_for( '/', qualified=True ) - # Always start with redirect_url being empty. - redirect_url = '' - # Compare urls, to prevent a redirect from pointing (directly) - # outside of galaxy or to enter a logout/login loop. - if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): - redirect = root_url - if kwd.get( 'noredirect', False ): - # The referrer is explicitly asking not to redirect. - redirect = '' + '''Handle Galaxy Log in''' + redirect = self.__get_redirect_url( kwd.get( 'redirect', trans.request.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' ) @@ -910,7 +902,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat username = util.restore_text( params.get( 'username', '' ) ) if not username: username = user.username - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) if trans.webapp.name == 'galaxy': user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) @@ -1146,7 +1138,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. Click here to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) + message = "Password has been reset and emailed to: %s. Click here to return to the login form." % ( escape( email ), web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: status = 'error' message = 'Failed to reset password: %s' % str( e ) @@ -1371,17 +1363,20 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) + @web.require_login( "to add addresses" ) @web.expose def new_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) institution = util.restore_text( params.get( 'institution', '' ) ) @@ -1432,10 +1427,10 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat phone=phone ) trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) has been added' % user_address.desc + message = 'Address (%s) has been added' % escape( user_address.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1453,24 +1448,29 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat postal_code=postal_code, country=country, phone=phone, - message=message, + message=escape(message), status=status ) + @web.require_login( "to edit addresses" ) @web.expose def edit_address( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) is_admin = cntrller == 'admin' and trans.user_is_admin() - user_id = params.get( 'user_id', False ) - if not user_id: - # User must be logged in to create a new address - return trans.show_error_message( "You must be logged in to create a new address." ) - user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + user_id = params.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to add a new address to." ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user address_id = params.get( 'address_id', None ) if not address_id: - return trans.show_error_message( "No address id received for editing." ) + return trans.show_error_message( "Invalid address id." ) address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) + if address_obj.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) if params.get( 'edit_address_button', False ): short_desc = util.restore_text( params.get( 'short_desc', '' ) ) name = util.restore_text( params.get( 'name', '' ) ) @@ -1518,10 +1518,10 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat address_obj.phone = phone trans.sa_session.add( address_obj ) trans.sa_session.flush() - message = 'Address (%s) has been updated.' % address_obj.desc + message = 'Address (%s) has been updated.' % escape( address_obj.desc ) new_kwd = dict( message=message, status=status ) if is_admin: - new_kwd[ 'user_id' ] = trans.security.encode_id( user.id ) + new_kwd[ 'id' ] = trans.security.encode_id( user.id ) return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, @@ -1531,45 +1531,44 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat cntrller=cntrller, user=user, address_obj=address_obj, - message=message, + message=escape( message ), status=status ) + @web.require_login( "to delete addresses" ) @web.expose - def delete_address( self, trans, cntrller, address_id=None, user_id=None ): + def delete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'delete', address_id=address_id, **kwd ) + + @web.require_login( "to undelete addresses" ) + @web.expose + def undelete_address( self, trans, cntrller, address_id=None, **kwd ): + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + + def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): + is_admin = cntrller == 'admin' and trans.user_is_admin() + user_id = kwd.get( 'id', False ) + if is_admin: + if not user_id: + return trans.show_error_message( "You must specify a user to %s an address from." % op ) + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: - message = 'Invalid address is (%s)' % address_id - status = 'error' + return trans.show_error_message( "Invalid address id." ) if user_address: - user_address.deleted = True + if user_address.user_id != user.id: + return trans.show_error_message( "Invalid address id." ) + user_address.deleted = True if op == 'delete' else False trans.sa_session.add( user_address ) trans.sa_session.flush() - message = 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) %sd' % ( escape( user_address.desc ), op ) status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', cntrller=cntrller, - user_id=user_id, - message=message, - status=status ) ) - - @web.expose - def undelete_address( self, trans, cntrller, address_id=None, user_id=None ): - try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) - except: - message = 'Invalid address is (%s)' % address_id - status = 'error' - if user_address: - user_address.deleted = False - trans.sa_session.flush() - message = 'Address (%s) undeleted' % user_address.desc - status = 'done' - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_user_info', - cntrller=cntrller, - user_id=user_id, + id=trans.security.encode_id( user.id ), message=message, status=status ) ) @@ -1729,7 +1728,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat @web.require_login() def api_keys( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + 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 ) @@ -1741,6 +1740,18 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat message=message, status=status ) + def __get_redirect_url( self, redirect ): + root_url = url_for( '/', qualified=True ) + redirect_url = '' # always start with redirect_url being empty + # compare urls, to prevent a redirect from pointing (directly) outside of galaxy + # or to enter a logout/login loop + if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + log.warning('Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: %s', redirect) + redirect = root_url + elif util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): + redirect = root_url + return redirect + # ===== Methods for building SelectFields ================================ def __build_user_type_fd_id_select_field( self, trans, selected_value ): # Get all the user information forms diff --git a/lib/galaxy/webapps/galaxy/controllers/userskeys.py b/lib/galaxy/webapps/galaxy/controllers/userskeys.py index fbcbc3d7b86..4cba3086f12 100644 --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -3,12 +3,11 @@ Contains the user interface in the Universe class """ import logging -import pprint from galaxy import web from galaxy import util, model from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from inspect import getmembers @@ -21,65 +20,46 @@ require_login_template = """

""" -class UserOpenIDGrid( grids.Grid ): - use_panels = False - title = "OpenIDs linked to your account" - model_class = model.UserOpenID - template = '/user/openid_manage.mako' - default_filter = { "openid" : "All" } - default_sort_key = "-create_time" - columns = [ - grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), - ] - operations = [ - grids.GridOperation( "Delete", async_compatible=True ), - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) +# FIXME: This controller is using unencoded IDs, but I am not going to address +# this now since it is admin-side and should be reimplemented in the API +# anyway. + class User( BaseUIController, UsesFormDefinitionsMixin ): - user_openid_grid = UserOpenIDGrid() - installed_len_files = None - - @web.expose @web.require_login() @web.require_admin def index( self, trans, cntrller, **kwd ): return trans.fill_template( 'webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller ) - - @web.expose @web.require_login() @web.require_admin def admin_api_keys( self, trans, cntrller, uid, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) uid = params.get('uid', uid) - pprint.pprint(uid) if params.get( 'new_api_key_button', False ): new_key = trans.app.model.APIKeys() new_key.user_id = uid new_key.key = trans.app.security.get_new_guid() trans.sa_session.add( new_key ) trans.sa_session.flush() - message = "Generated a new web API key" + message = "A new web API key has been generated for (%s)" % escape( new_key.user.email ) status = "done" - return trans.fill_template( 'webapps/galaxy/user/ok_admin_api_keys.mako', - cntrller=cntrller, - message=message, - status=status ) - - + return trans.response.send_redirect( web.url_for( controller='userskeys', + action='all_users', + cntrller=cntrller, + message=message, + status=status ) ) + @web.expose @web.require_login() @web.require_admin def all_users( self, trans, cntrller="userskeys", **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = escape( util.restore_text( params.get( 'message', '' ) ) ) status = params.get( 'status', 'done' ) users = [] for user in trans.sa_session.query( trans.app.model.User ) \ diff --git a/lib/tool_shed/util/basic_util.py b/lib/tool_shed/util/basic_util.py index 3a3a01f881f..18497640206 100644 --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -4,7 +4,7 @@ import shutil import sys from string import Template -from galaxy.util import unicodify +from galaxy.util import unicodify, nice_size from galaxy import eggs @@ -13,10 +13,10 @@ import markupsafe log = logging.getLogger( __name__ ) -CHUNK_SIZE = 2**20 # 1Mb +CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. -NO_OUTPUT_TIMEOUT = 1200.0 +NO_OUTPUT_TIMEOUT = 3600.0 MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 @@ -48,6 +48,7 @@ SELECTED_REPOSITORIES_TEMPLATE = ''' RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}" ''' + def evaluate_template( text, install_environment ): """ Substitute variables defined in XML blocks from dependencies file. The value of the received @@ -57,6 +58,7 @@ def evaluate_template( text, install_environment ): """ return Template( text ).safe_substitute( get_env_var_values( install_environment ) ) + def get_env_var_values( install_environment ): """ Return a dictionary of values, some of which enable substitution of reserved words for the values. @@ -73,6 +75,7 @@ def get_env_var_values( install_environment ): env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict + def get_file_type_str( changeset_revision, file_type ): if file_type == 'zip': file_type_str = '%s.zip' % changeset_revision @@ -84,6 +87,7 @@ def get_file_type_str( changeset_revision, file_type ): file_type_str = '' return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) @@ -98,6 +102,7 @@ def move_file( current_dir, source, destination, rename_to=None ): os.makedirs( destination_directory ) shutil.move( source_path, destination_path ) + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if dir: @@ -107,18 +112,21 @@ def remove_dir( dir ): except: pass + def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( size ) + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size( size ) raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' + def stringify( list ): if list: return ','.join( list ) return '' + def strip_path( fpath ): """Attempt to strip the path from a file name.""" if not fpath: @@ -129,6 +137,7 @@ def strip_path( fpath ): file_name = fpath return file_name + def to_html_string( text ): """Translates the characters in text to an html string""" if text: diff --git a/templates/admin/forms/create_form.mako b/templates/admin/forms/create_form.mako index 7cb981bc162..8d55b642457 100644 --- a/templates/admin/forms/create_form.mako +++ b/templates/admin/forms/create_form.mako @@ -9,7 +9,7 @@

Create a new form definition
%for label, input in inputs:
- + ${input.get_html()}
diff --git a/templates/admin/forms/edit_form_definition.mako b/templates/admin/forms/edit_form_definition.mako index c080e843eeb..d4ea953e61d 100644 --- a/templates/admin/forms/edit_form_definition.mako +++ b/templates/admin/forms/edit_form_definition.mako @@ -96,14 +96,14 @@ $(document).ready(function(){
-
Edit form definition "${form_definition.name}" (${form_definition.type})
+
Edit form definition "${form_definition.name | h}" (${form_definition.type | h})
%if response_redirect: %endif %for label, input in form_details:
%if label != 'Type': - + %endif
${input.get_html()} diff --git a/templates/admin/request_type/common.mako b/templates/admin/request_type/common.mako index 01149003ff7..afb28830971 100644 --- a/templates/admin/request_type/common.mako +++ b/templates/admin/request_type/common.mako @@ -2,7 +2,7 @@
- + ## Do not show remove button for the first state %if element_count > 0: @@ -10,7 +10,7 @@
- +
optional
diff --git a/templates/admin/request_type/create_request_type.mako b/templates/admin/request_type/create_request_type.mako index 5809751e179..cd0bfb1da6e 100644 --- a/templates/admin/request_type/create_request_type.mako +++ b/templates/admin/request_type/create_request_type.mako @@ -23,7 +23,7 @@
Create a new request type
%for rt_info in rt_info_widgets:
- +
${rt_info['widget'].get_html()}
diff --git a/templates/admin/request_type/edit_request_type.mako b/templates/admin/request_type/edit_request_type.mako index 88cfd5e84cf..e3444576bfa 100644 --- a/templates/admin/request_type/edit_request_type.mako +++ b/templates/admin/request_type/edit_request_type.mako @@ -32,26 +32,26 @@
-
"Edit ${request_type.name}" request type
+
"Edit ${request_type.name | h}" request type
- +
- +
- ${request_type.request_form.name} + ${request_type.request_form.name | h} ## Hidden field needed by the __save_request_type() method
- ${request_type.sample_form.name} + ${request_type.sample_form.name | h} ## Hidden field needed by the __save_request_type() method
@@ -63,11 +63,11 @@
- +
- +
optional
diff --git a/templates/admin/request_type/request_type_permissions.mako b/templates/admin/request_type/request_type_permissions.mako index 377a31ff96b..8aa486e9b5a 100644 --- a/templates/admin/request_type/request_type_permissions.mako +++ b/templates/admin/request_type/request_type_permissions.mako @@ -48,7 +48,7 @@ %endif
-
Manage access permissions on request type "${request_type.name}"
+
Manage access permissions on request type "${request_type.name | h}"
@@ -65,13 +65,13 @@ in_roles.add( a.role ) out_roles = filter( lambda x: x not in in_roles, all_roles ) %> - ${action.description}

+ ${action.description | h}

Roles associated:

@@ -80,7 +80,7 @@ Roles not associated:

diff --git a/templates/admin/request_type/view_request_type.mako b/templates/admin/request_type/view_request_type.mako index 10a0a763a0c..cc659097f29 100644 --- a/templates/admin/request_type/view_request_type.mako +++ b/templates/admin/request_type/view_request_type.mako @@ -30,24 +30,24 @@ %endif
-
"${request_type.name}" request type
+
"${request_type.name | h}" request type
- ${request_type.name} + ${request_type.name | h}
- ${request_type.desc} + ${request_type.desc | h}
- ${request_type.request_form.name} + ${request_type.request_form.name | h}
- ${request_type.sample_form.name} + ${request_type.sample_form.name | h}

@@ -55,8 +55,8 @@

Sample states defined for this request type
%for state in request_type.states:
- - ${state.desc} + + ${state.desc | h}
%endfor @@ -67,8 +67,8 @@ %if request_type.external_services: %for index, external_service in enumerate( request_type.external_services ):
- - ${external_service.get_external_service_type( trans ).name} + + ${external_service.get_external_service_type( trans ).name | h}
%endfor %else: diff --git a/templates/admin/requests/reject.mako b/templates/admin/requests/reject.mako index 50243700e21..d742b9f7a26 100644 --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -15,7 +15,7 @@
-
Reject sequencing request "${request.name}"
+
Reject sequencing request "${request.name | h}"
Rejecting this request will move the request state to Rejected. diff --git a/templates/admin/requests/rename_datasets.mako b/templates/admin/requests/rename_datasets.mako index d849a34cce2..c9d6174abca 100644 --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,7 +3,7 @@ <% from galaxy.webapps.galaxy.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -

Rename datasets for Sample "${sample.name}"

+

Rename datasets for Sample "${sample.name | h}"

  • Browse datasets
    • @@ -35,7 +35,7 @@ ${rename_datasets_for_sample_select_field.get_html()} - + ${sample_dataset.file_path} diff --git a/templates/admin/requests/view_sample_dataset.mako b/templates/admin/requests/view_sample_dataset.mako index 52b6e9f9e69..6b16824211e 100644 --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -21,19 +21,19 @@
-
"${sample.name}" Dataset
+
"${sample.name | h}" Dataset
- ${sample_dataset.name} + ${sample_dataset.name | h}
- ${sample_dataset.external_service.name} (${sample_dataset.external_service.get_external_service_type( trans ).name}) + ${sample_dataset.external_service.name | h} (${sample_dataset.external_service.get_external_service_type( trans ).name | h})
diff --git a/templates/user/edit_address.mako b/templates/user/edit_address.mako index 430c967e356..6f27d5e1aaa 100644 --- a/templates/user/edit_address.mako +++ b/templates/user/edit_address.mako @@ -10,17 +10,17 @@
Edit address
- +
- +
Required
@@ -28,7 +28,7 @@
- +
Required
@@ -36,7 +36,7 @@
- +
Required
@@ -44,7 +44,7 @@
- +
Required
@@ -52,7 +52,7 @@
- +
Required
@@ -60,7 +60,7 @@
- +
Required
@@ -68,7 +68,7 @@
- +
Required
@@ -76,7 +76,7 @@
- +
Required
@@ -84,7 +84,7 @@
- +
diff --git a/templates/user/index.mako b/templates/user/index.mako index ed56148b599..df27c61499b 100644 --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -1,9 +1,4 @@ <%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif %if trans.user:

${_('User preferences')}

diff --git a/templates/user/info.mako b/templates/user/info.mako index 1415bcc4465..20ae4744ae0 100644 --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -90,7 +90,7 @@
Login Information
- +
If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it.
@@ -99,13 +99,13 @@ %if t.webapp.name == 'tool_shed': %if user.active_repositories: - - ${username} + + ${username | h}
You cannot change your public name after you have created a repository in this tool shed.
%else: - +
Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least four characters in length and contain only lower-case letters, numbers, @@ -114,7 +114,7 @@
%endif %else: - +
Your public name is an optional identifier that will be used to generate addresses for information you share publicly. Public names must be at least four characters in length and contain only lower-case diff --git a/templates/user/new_address.mako b/templates/user/new_address.mako index f9e8d5e8c63..c80f613cdcc 100644 --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -10,18 +10,18 @@
Add new address
- +
- +
Required
@@ -29,7 +29,7 @@
- +
Required
@@ -37,7 +37,7 @@
- +
Required
@@ -45,7 +45,7 @@
- +
Required
@@ -53,7 +53,7 @@
- +
Required
@@ -61,7 +61,7 @@
- +
Required
@@ -69,7 +69,7 @@
- +
Required
@@ -77,7 +77,7 @@
- +
Required
@@ -85,7 +85,7 @@
- +
diff --git a/templates/webapps/galaxy/requests/common/common.mako b/templates/webapps/galaxy/requests/common/common.mako index 401ba04057c..dd012a3d03c 100644 --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -257,18 +257,18 @@ %endif - +
- ${' (required)' } + (required)
%if display_bar_code: %if is_admin and is_submitted: - + %else: - ${sample_widget['bar_code']} - + ${sample_widget['bar_code'] | h} + %endif %endif @@ -416,7 +416,7 @@ transferred_dataset_files = [] %>
%if can_select_datasets: @@ -439,11 +439,11 @@ %endif
%else: - ${sample_widget_name} + ${sample_widget_name | h} %endif %if display_bar_code: - ${sample_widget_bar_code} + ${sample_widget_bar_code | h} %endif %if is_unsubmitted: Unsubmitted @@ -451,12 +451,12 @@ ${render_sample_state( sample )} %endif %if sample_widget_library and library_cntrller is not None: - ${sample_widget_library.name} + ${sample_widget_library.name | h} %else: %endif %if sample_widget_folder: - ${sample_widget_folder.name} + ${sample_widget_folder.name | h} %else: %endif @@ -464,11 +464,11 @@ %if trans.user == sample_widget_history.user: - ${sample_widget_history.name} + ${sample_widget_history.name | h} %else: - ${sample_widget_history.name} + ${sample_widget_history.name | h} %endif %else: @@ -477,11 +477,11 @@ %if trans.user == sample_widget_workflow.stored_workflow.user: - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} %else: - ${sample_widget_workflow.name} + ${sample_widget_workflow.name | h} %endif %else: @@ -519,7 +519,7 @@ <%def name="render_sample_form( index, sample_name, sample_values, fields_dict, display_only )"> - ${sample_name} + ${sample_name | h} %for field_index, field in fields_dict.items(): <% field_type = field[ 'type' ] @@ -532,17 +532,17 @@ %if field_type == 'WorkflowField': %if str( field_value ) != 'none': <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int( field_value ) ) %> - ${workflow.name} + ${workflow.name | h} %endif %else: - ${field_value} + ${field_value | h} %endif %else: None %endif %else: %if field_type == 'TextField': - + %elif field_type == 'SelectField': ${request.user.email} (sequencing request owner) + ${request.user.email | h} (sequencing request owner)
- +
Enter one email address per line
diff --git a/templates/webapps/galaxy/requests/common/find_samples.mako b/templates/webapps/galaxy/requests/common/find_samples.mako index 36974dbbb49..02f1c33bc31 100644 --- a/templates/webapps/galaxy/requests/common/find_samples.mako +++ b/templates/webapps/galaxy/requests/common/find_samples.mako @@ -72,7 +72,7 @@ %if samples: %for sample in samples:
- Sample: ${sample.name} | Barcode: ${sample.bar_code}
+ Sample: ${sample.name | h} | Barcode: ${sample.bar_code | h}
%if sample.request.is_new or not sample.state: State: Unsubmitted
%else: @@ -85,10 +85,10 @@ %> Datasets: ${len( sample.datasets )}
%if is_admin: - User: ${sample.request.user.email} + User: ${sample.request.user.email | h} %endif
- Sequencing request: ${sample.request.name} | Type: ${sample.request.type.name} | State: ${sample.request.state} + Sequencing request: ${sample.request.name | h} | Type: ${sample.request.type.name} | State: ${sample.request.state}

diff --git a/templates/webapps/galaxy/requests/common/view_request.mako b/templates/webapps/galaxy/requests/common/view_request.mako index 8ceab0c739a..98fdc644a8b 100644 --- a/templates/webapps/galaxy/requests/common/view_request.mako +++ b/templates/webapps/galaxy/requests/common/view_request.mako @@ -58,7 +58,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)}
-
Sequencing request "${request.name}"
+
Sequencing request "${request.name | h}"
@@ -67,12 +67,12 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)}
- ${request.desc} + ${request.desc | h}
- ${request.user.email} + ${request.user.email | h}
@@ -94,7 +94,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} %>
- ${field_value} + ${field_value | h}
%endfor @@ -116,7 +116,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)} else: emails = '' %> - ${emails} + ${emails | h}
diff --git a/templates/webapps/galaxy/requests/common/view_request_history.mako b/templates/webapps/galaxy/requests/common/view_request_history.mako index e46d465a0a6..89faaaafd48 100644 --- a/templates/webapps/galaxy/requests/common/view_request_history.mako +++ b/templates/webapps/galaxy/requests/common/view_request_history.mako @@ -36,7 +36,7 @@ ${render_msg( message, status )} %endif -

History of sequencing request "${request.name}"

+

History of sequencing request "${request.name | h}"

@@ -52,7 +52,7 @@ - + %endfor diff --git a/templates/webapps/galaxy/requests/common/view_sample.mako b/templates/webapps/galaxy/requests/common/view_sample.mako index 93fcb0df7d7..8d4eede464f 100644 --- a/templates/webapps/galaxy/requests/common/view_sample.mako +++ b/templates/webapps/galaxy/requests/common/view_sample.mako @@ -6,7 +6,7 @@ %if external_service:

-
Available External Service Actions for ${sample.name} at ${external_service.name}
+
Available External Service Actions for ${sample.name | h} at ${external_service.name | h}
%for item in external_service.actions: @@ -25,7 +25,7 @@
- ${external_service_group.label} + ${external_service_group.label | h}
@@ -54,7 +54,7 @@ target = 'galaxy_main' %>
- ${external_service_action.label} + ${external_service_action.label | h}
@@ -75,38 +75,38 @@ %endif
-
Sample "${sample.name}"
+
Sample "${sample.name | h}"
- ${sample.name} + ${sample.name | h}
- ${sample.desc} + ${sample.desc | h}
- ${sample.bar_code} + ${sample.bar_code | h}
%if sample.library:
- ${sample.library.name} + ${sample.library.name | h}
- ${sample.folder.name} + ${sample.folder.name | h}
%endif
- ${sample.request.name} + ${sample.request.name | h}
diff --git a/templates/webapps/galaxy/requests/common/view_sample_history.mako b/templates/webapps/galaxy/requests/common/view_sample_history.mako index 196c0be8aea..902fcffecf0 100644 --- a/templates/webapps/galaxy/requests/common/view_sample_history.mako +++ b/templates/webapps/galaxy/requests/common/view_sample_history.mako @@ -12,7 +12,7 @@ ${render_msg( message, status )} %endif -

History of sample "${sample.name}"

+

History of sample "${sample.name | h}"

${event.state} ${time_ago( event.update_time )}${event.comment}${event.comment | h}
@@ -27,10 +27,10 @@ %for event in sample.events: - - + + - + %endfor diff --git a/templates/webapps/galaxy/user/list_users.mako b/templates/webapps/galaxy/user/list_users.mako index b6968c3868c..e5638b9448c 100644 --- a/templates/webapps/galaxy/user/list_users.mako +++ b/templates/webapps/galaxy/user/list_users.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> %if message: ${render_msg( message, status )} diff --git a/templates/webapps/galaxy/user/manage_info.mako b/templates/webapps/galaxy/user/manage_info.mako index e3c3f2f399a..8b1a747b662 100644 --- a/templates/webapps/galaxy/user/manage_info.mako +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -42,7 +42,7 @@ ${render_user_info()}

- +
User Addresses
%if user.addresses: @@ -53,9 +53,9 @@ ${render_user_info()} | %endif %if show_filter == filter: - ${filter} + ${filter} %else: - ${filter} + ${filter} %endif %endfor
@@ -73,10 +73,10 @@ ${render_user_info()} diff --git a/templates/webapps/galaxy/user/ok_admin_api_keys.mako b/templates/webapps/galaxy/user/ok_admin_api_keys.mako deleted file mode 100644 index e7eb97be5a1..00000000000 --- a/templates/webapps/galaxy/user/ok_admin_api_keys.mako +++ /dev/null @@ -1,28 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -

- - -%if message: - ${render_msg( message, status )} -%endif - -
-
- SUCCESS. A new API key has been generated. -
- - -
- An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password. -
-
${event.state.name}${event.state.desc}${event.state.name | h}${event.state.desc | h} ${time_ago( event.update_time )}${event.comment}${event.comment | h}