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Escape messages passed in through kwd.

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This commit is contained in:
Dave Bouvier
2014-12-11 11:10:30 -05:00
parent b0827d8b20
commit 0b29252374
14 changed files with 140 additions and 126 deletions
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lib/galaxy/web/base/controllers/admin.py
+3 -2
View File
@@ -7,6 +7,7 @@ from galaxy.util import inflector
from galaxy.web.form_builder import CheckboxField
from string import punctuation as PUNCTUATION
import galaxy.queue_worker
from markupsafe import escape
from tool_shed.util import shed_util_common as suc
@@ -28,7 +29,7 @@ class Admin( object ):
@web.expose
@web.require_admin
def index( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if trans.webapp.name == 'galaxy':
installed_repositories = trans.install_model.context.query( trans.install_model.ToolShedRepository ).first()
@@ -46,7 +47,7 @@ class Admin( object ):
@web.expose
@web.require_admin
def center( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if trans.webapp.name == 'galaxy':
return trans.fill_template( '/webapps/galaxy/admin/center.mako',
lib/galaxy/webapps/demo_sequencer/controllers/common.py
+3 -2
View File
@@ -4,6 +4,7 @@ from galaxy import util
import time, socket, urllib, urllib2, base64, copy
from galaxy.util.json import *
from urllib import quote_plus, unquote_plus
from markupsafe import escape
import logging
log = logging.getLogger( __name__ )
@@ -16,7 +17,7 @@ class CommonController( BaseUIController ):
titles = util.listify( titles )
JobId = util.restore_text( kwd.get( 'JobId', '' ) )
sample_id = util.restore_text( kwd.get( 'sample_id', '' ) )
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
status = kwd.get( 'status', 'done' )
redirect_delay = trans.app.sequencer_actions_registry.redirect_delay
sequencer_redirects = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_redirects )
@@ -144,7 +145,7 @@ class CommonController( BaseUIController ):
titles = util.restore_text( kwd.get( 'titles', '' ) )
JobId = util.restore_text( kwd.get( 'JobId', '' ) )
sample_id = util.restore_text( kwd.get( 'sample_id', '' ) )
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
status = kwd.get( 'status', 'done' )
url, http_method, request_params, response_type = request_tup
url = unquote_plus( url )
lib/galaxy/webapps/galaxy/controllers/admin.py
+4 -3
View File
@@ -17,6 +17,7 @@ from galaxy.web.framework.helpers import grids, time_ago
from galaxy.web.params import QuotaParamParser
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from markupsafe import escape
log = logging.getLogger( __name__ )
@@ -838,7 +839,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
@web.expose
@web.require_admin
def review_tool_migration_stages( self, trans, **kwd ):
message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
migration_stages_dict = odict()
migration_modules = []
@@ -870,13 +871,13 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
@web.expose
@web.require_admin
def view_datatypes_registry( self, trans, **kwd ):
message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_datatypes_registry.mako', message=message, status=status )
@web.expose
@web.require_admin
def view_tool_data_tables( self, trans, **kwd ):
message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status )
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+22 -21
View File
@@ -8,6 +8,7 @@ from galaxy import util
from galaxy.web.form_builder import CheckboxField
from galaxy.util import json
from galaxy.model.orm import or_
from markupsafe import escape
import tool_shed.repository_types.util as rt_util
@@ -72,7 +73,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def browse_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
@@ -169,7 +170,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def browse_tool_dependency( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
@@ -197,7 +198,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def browse_tool_sheds( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
message=message,
@@ -230,7 +231,7 @@ class AdminToolshed( AdminGalaxy ):
require the same entry. For now we'll never delete entries from config.shed_tool_data_table_config,
but we may choose to do so in the future if it becomes necessary.
"""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
remove_from_disk = kwd.get( 'remove_from_disk', '' )
remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk )
@@ -442,7 +443,7 @@ class AdminToolshed( AdminGalaxy ):
@web.require_admin
def import_workflow( self, trans, workflow_name, repository_id, **kwd ):
"""Import a workflow contained in an installed tool shed repository into Galaxy."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if workflow_name:
workflow_name = encoding_util.tool_shed_decode( workflow_name )
@@ -479,7 +480,7 @@ class AdminToolshed( AdminGalaxy ):
tool shed repository.
"""
# Get the tool_shed_repository from one of the tool_dependencies.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
err_msg = ''
tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
@@ -512,7 +513,7 @@ class AdminToolshed( AdminGalaxy ):
@web.require_admin
def install_latest_repository_revision( self, trans, **kwd ):
"""Install the latest installable revision of a repository that has been previously installed."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
if repository_id is not None:
@@ -589,7 +590,7 @@ class AdminToolshed( AdminGalaxy ):
updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
if 'install_tool_dependencies_with_update_button' in kwd:
@@ -665,7 +666,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def manage_repositories( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
if 'operation' in kwd:
@@ -744,7 +745,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def manage_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
if repository_id is None:
@@ -808,7 +809,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def manage_repository_tool_dependencies( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
if tool_dependency_ids:
@@ -890,7 +891,7 @@ class AdminToolshed( AdminGalaxy ):
def manage_tool_dependencies( self, trans, **kwd ):
# This method is called when tool dependencies are being installed. See the related manage_repository_tool_dependencies
# method for managing the tool dependencies for a specified installed tool shed repository.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
repository_id = kwd.get( 'repository_id', None )
@@ -978,7 +979,7 @@ class AdminToolshed( AdminGalaxy ):
message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
message += 'Shed wiki for all of the details.'
return trans.show_error_message( message )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
shed_tool_conf = kwd.get( 'shed_tool_conf', None )
tool_shed_url = kwd.get( 'tool_shed_url', '' )
@@ -1314,7 +1315,7 @@ class AdminToolshed( AdminGalaxy ):
and tool dependencies of the repository.
"""
rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd[ 'id' ]
tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id )
@@ -1450,7 +1451,7 @@ class AdminToolshed( AdminGalaxy ):
Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as
each repository's tool dependencies.
"""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
if not repository_id:
@@ -1715,7 +1716,7 @@ class AdminToolshed( AdminGalaxy ):
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd )
else:
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repositories_select_field = irmm.build_repository_ids_select_field()
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
@@ -1852,7 +1853,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def uninstall_tool_dependencies( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
if not tool_dependency_ids:
@@ -1897,7 +1898,7 @@ class AdminToolshed( AdminGalaxy ):
@web.require_admin
def update_to_changeset_revision( self, trans, **kwd ):
"""Update a cloned repository to the latest revision possible."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
tool_shed_url = kwd.get( 'tool_shed_url', '' )
# Handle protocol changes over time.
@@ -2070,7 +2071,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def update_tool_shed_status_for_installed_repository( self, trans, all_installed_repositories=False, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if all_installed_repositories:
success_count = 0
@@ -2112,7 +2113,7 @@ class AdminToolshed( AdminGalaxy ):
@web.expose
@web.require_admin
def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id )
repository_metadata = repository.metadata
@@ -2146,7 +2147,7 @@ class AdminToolshed( AdminGalaxy ):
@web.require_admin
def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ):
"""Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if workflow_name:
workflow_name = encoding_util.tool_shed_decode( workflow_name )
lib/galaxy/webapps/galaxy/controllers/library_admin.py
+3 -2
View File
@@ -5,8 +5,9 @@ import galaxy.util
from galaxy import web
from galaxy.web.base.controller import BaseUIController
from galaxy.web.framework.helpers import escape, grids, time_ago
from galaxy.web.framework.helpers import grids, time_ago
from library_common import get_comptypes, lucene_search, whoosh_search
from markupsafe import escape
# from galaxy.model.orm import *
log = logging.getLogger( __name__ )
@@ -148,7 +149,7 @@ class LibraryAdmin( BaseUIController ):
@web.expose
@web.require_admin
def create_library( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if kwd.get( 'create_library_button', False ):
name = kwd.get( 'name', 'No name' )
lib/galaxy/webapps/galaxy/controllers/library_common.py
+27 -27
View File
@@ -20,7 +20,7 @@ from galaxy.util.json import dumps, loads
from galaxy.util.streamball import StreamBall
from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field
from galaxy.web.framework.helpers import escape
from markupsafe import escape
from galaxy.model.orm import and_, eagerload_all
# Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled.
@@ -93,7 +93,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
@web.expose
def browse_library( self, trans, cntrller='library', **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
# If use_panels is True, the library is being accessed via an external link
# which did not originate from within the Galaxy instance, and the library will
@@ -121,7 +121,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
hidden_folder_ids = util.listify( kwd.get( 'hidden_folder_ids', '' ) )
if created_ldda_ids and not message:
message = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \
( len( created_ldda_ids.split( ',' ) ), library.name )
( len( created_ldda_ids.split( ',' ) ), escape( library.name ) )
message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the "
message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset."
status = "info"
@@ -152,7 +152,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
message=escape( message ),
status=escape( status ) )
except Exception, e:
message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) )
message = 'Error attempting to display contents of library (%s): %s.' % ( escape( str( library.name ) ), str( e ) )
status = 'error'
default_action = kwd.get( 'default_action', None )
@@ -164,7 +164,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=status ) )
@web.expose
def library_info( self, trans, cntrller, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
@@ -223,7 +223,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def library_permissions( self, trans, cntrller, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
@@ -269,7 +269,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -345,7 +345,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def folder_info( self, trans, cntrller, id, library_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -401,7 +401,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def folder_permissions( self, trans, cntrller, id, library_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -450,7 +450,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -505,7 +505,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
old_name = ldda.name
new_name = kwd.get( 'name', '' )
new_info = kwd.get( 'info', '' )
new_message = kwd.get( 'message', '' )
new_message = escape( kwd.get( 'message', '' ) )
if not new_name:
message = 'Enter a valid name'
status = 'error'
@@ -602,7 +602,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
show_associated_hdas_and_lddas = util.string_as_bool( kwd.get( 'show_associated_hdas_and_lddas', False ) )
@@ -650,7 +650,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -787,9 +787,9 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
ldda_message = kwd.get( 'ldda_message', '' )
ldda_message = escape( kwd.get( 'ldda_message', '' ) )
deleted = util.string_as_bool( kwd.get( 'deleted', False ) )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1046,7 +1046,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
dataset_upload_inputs.append( input )
# Library-specific params
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
server_dir = kwd.get( 'server_dir', '' )
if replace_dataset not in [ None, 'None' ]:
@@ -1256,9 +1256,9 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
@web.expose
def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
ldda_message = kwd.get( 'ldda_message', '' )
ldda_message = escape( kwd.get( 'ldda_message', '' ) )
show_deleted = kwd.get( 'show_deleted', False )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
replace_id = kwd.get( 'replace_id', None )
@@ -1547,7 +1547,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status='error' ) )
@web.expose
def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1595,7 +1595,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1642,7 +1642,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status=escape( status ) )
@web.expose
def make_library_item_public( self, trans, cntrller, library_id, item_type, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1703,7 +1703,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
rval += '%s %i %s%s %s\r\n' % ( crc, size, self.url_base, quoted_fname, relpath )
return rval
# Perform an action on a list of library datasets.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1979,7 +1979,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
# - a select list option for acting on multiple selected datasets within a library
# ( ldda_ids is a comma separated string of ldda ids )
# - a menu option for a library dataset search result set ( ldda_ids is a comma separated string of ldda ids )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -2102,7 +2102,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
current_user_roles = trans.get_current_user_roles()
@@ -2152,7 +2152,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
# 'ldda' and item_id is a comma separated string of ldda ids )
# - a menu option for a library dataset search result set ( item_type is 'ldda' and item_id is a
# comma separated string of ldda ids )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -2723,7 +2723,7 @@ def sort_by_attr( seq, attr ):
return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
"""Return display of results from a full-text lucene search of data libraries."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
full_url = "%s/find?%s" % ( search_url, urllib.urlencode( { "kwd" : search_term } ) )
response = urllib2.urlopen( full_url )
@@ -2733,7 +2733,7 @@ def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
return status, message, get_sorted_accessible_library_items( trans, cntrller, lddas, 'name' )
def whoosh_search( trans, cntrller, search_term, **kwd ):
"""Return display of results from a full-text whoosh search of data libraries."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
ok = True
if whoosh_search_enabled:
lib/galaxy/webapps/galaxy/controllers/user.py
+6 -5
View File
@@ -28,9 +28,10 @@ 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, escape
from galaxy.web.framework.helpers import time_ago, grids
from datetime import datetime, timedelta
from galaxy.util import hash_util, biostar
from markupsafe import escape
log = logging.getLogger( __name__ )
@@ -254,7 +255,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
if not trans.app.config.enable_openid:
return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' )
use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
email = kwd.get( 'email', '' )
username = kwd.get( 'username', '' )
@@ -502,7 +503,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
"""
Function validates numerous cases that might happen during the login time.
"""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'error' )
email = kwd.get( 'email', '' )
password = kwd.get( 'password', '' )
@@ -719,7 +720,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
email = util.restore_text( kwd.get( 'email', '' ) )
password = kwd.get( 'password', '' )
username = util.restore_text( kwd.get( 'username', '' ) )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
is_admin = cntrller == 'admin' and trans.user_is_admin()
user = self.create_user( trans=trans, email=email, username=username, password=password )
@@ -1093,7 +1094,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
def reset_password( self, trans, email=None, **kwd ):
if trans.app.config.smtp_server is None:
return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." )
message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) ))
message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) )
status = kwd.get( 'status', 'done' )
if kwd.get( 'reset_password_button', False ):
reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
lib/galaxy/webapps/galaxy/controllers/workflow.py
+3 -2
View File
@@ -22,7 +22,7 @@ from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
from galaxy.web.framework.formbuilder import form
from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape
from galaxy.web.framework.helpers import grids, time_ago, to_unicode
from galaxy.workflow.modules import WorkflowModuleInjector
from galaxy.workflow.modules import MissingToolException
from galaxy.workflow.modules import module_factory, is_tool_module_type
@@ -37,6 +37,7 @@ from galaxy.workflow.steps import (
order_workflow_steps_with_levels,
)
from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING
from markupsafe import escape
class StoredWorkflowListGrid( grids.Grid ):
@@ -1021,7 +1022,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
"""
url = kwd.get( 'url', '' )
workflow_text = kwd.get( 'workflow_text', '' )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
import_button = kwd.get( 'import_button', False )
# The special Galaxy integration landing page's URL on myExperiment
lib/galaxy/webapps/reports/controllers/users.py
+8 -6
View File
@@ -9,17 +9,19 @@ import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
import logging
from markupsafe import escape
log = logging.getLogger( __name__ )
class Users( BaseUIController ):
@web.expose
def registered_users( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
num_users = trans.sa_session.query( galaxy.model.User ).count()
return trans.fill_template( '/webapps/reports/registered_users.mako', num_users=num_users, message=message )
@web.expose
def registered_users_per_month( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ),
sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ),
from_obj = [ galaxy.model.User.table ],
@@ -36,7 +38,7 @@ class Users( BaseUIController ):
message=message )
@web.expose
def specified_month( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
specified_month = specified_date[ :7 ]
@@ -66,7 +68,7 @@ class Users( BaseUIController ):
message=message )
@web.expose
def specified_date( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
# If specified_date is not received, we'll default to the current month
specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
year, month, day = map( int, specified_date.split( "-" ) )
@@ -95,7 +97,7 @@ class Users( BaseUIController ):
message=message )
@web.expose
def last_access_date( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
not_logged_in_for_days = kwd.get( 'not_logged_in_for_days', 90 )
if not not_logged_in_for_days:
not_logged_in_for_days = 0
@@ -120,7 +122,7 @@ class Users( BaseUIController ):
@web.expose
def user_disk_usage( self, trans, **kwd ):
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
user_cutoff = int( kwd.get( 'user_cutoff', 60 ) )
# disk_usage isn't indexed
users = sorted( trans.sa_session.query( galaxy.model.User ).all(), key=operator.attrgetter( 'disk_usage' ), reverse=True )
lib/galaxy/webapps/tool_shed/controllers/admin.py
+11 -10
View File
@@ -3,6 +3,7 @@ import logging
from galaxy import util
from galaxy.util import inflector
from galaxy import web
from markupsafe import escape
from galaxy.web.base.controller import BaseUIController
from galaxy.web.base.controllers.admin import Admin
@@ -121,7 +122,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def create_category( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
name = kwd.get( 'name', '' ).strip()
description = kwd.get( 'description', '' ).strip()
@@ -154,7 +155,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def delete_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
@@ -197,7 +198,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def delete_repository_metadata( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
@@ -221,7 +222,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def edit_category( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if not id:
@@ -306,7 +307,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def regenerate_statistics( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'regenerate_statistics_button' in kwd:
trans.app.shed_counter.generate_statistics()
@@ -352,7 +353,7 @@ class AdminController( BaseUIController, Admin ):
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
else:
message = util.restore_text( kwd.get( 'message', '' ) )
message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
status = kwd.get( 'status', 'done' )
repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids',
multiple=True,
@@ -366,7 +367,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def undelete_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
@@ -417,7 +418,7 @@ class AdminController( BaseUIController, Admin ):
# TODO: We should probably eliminate the Category.deleted column since it really makes no
# sense to mark a category as deleted (category names and descriptions can be changed instead).
# If we do this, and the following 2 methods can be eliminated.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
@@ -445,7 +446,7 @@ class AdminController( BaseUIController, Admin ):
# This method should only be called for a Category that has previously been deleted.
# Purging a deleted Category deletes all of the following from the database:
# - RepoitoryCategoryAssociations where category_id == Category.id
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
@@ -473,7 +474,7 @@ class AdminController( BaseUIController, Admin ):
@web.expose
@web.require_admin
def undelete_category( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
lib/galaxy/webapps/tool_shed/controllers/repository.py
+32 -31
View File
@@ -6,6 +6,7 @@ from time import gmtime
from time import strftime
from datetime import date
from datetime import datetime
from markupsafe import escape
from galaxy import util
from galaxy import web
@@ -385,7 +386,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
action='reviewed_repositories_i_own' ) )
elif operation == "repositories_by_category":
category_id = kwd.get( 'id', None )
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories_in_category',
@@ -721,9 +722,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def browse_repository( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
# Update repository files for browsing.
@@ -891,7 +892,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def check_for_updates( self, trans, **kwd ):
"""Handle a request from a local Galaxy instance."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
# If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url.
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
@@ -976,7 +977,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def contact_owner( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app,
@@ -995,7 +996,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def create_galaxy_docker_image( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_ids = util.listify( kwd.get( 'id', '' ) )
if 'operation' in kwd:
@@ -1051,7 +1052,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def create_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
categories = suc.get_categories( trans )
if not categories:
@@ -1108,7 +1109,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset
# revisions that may be associated with the repository. Revisions are not marked as not downlaodable
# because those that have installed the repository must be allowed to get updates.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -1164,7 +1165,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
tv = tool_validator.ToolValidator( trans.app )
@@ -1229,7 +1230,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def export( self, trans, repository_id, changeset_revision, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
export_repository_dependencies = kwd.get( 'export_repository_dependencies', '' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -1309,7 +1310,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def find_tools( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if 'operation' in kwd:
@@ -1400,7 +1401,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def find_workflows( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if 'operation' in kwd:
@@ -2020,13 +2021,13 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def help( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd )
@web.expose
def import_capsule( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
capsule_file_name = kwd.get( 'capsule_file_name', None )
encoded_file_path = kwd.get( 'encoded_file_path', None )
@@ -2069,7 +2070,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def index( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
# See if there are any RepositoryMetadata records since menu items require them.
repository_metadata = trans.sa_session.query( trans.model.RepositoryMetadata ).first()
@@ -2151,7 +2152,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'error' )
render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
tv = tool_validator.ToolValidator( trans.app )
@@ -2203,7 +2204,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "manage email alerts" )
def manage_email_alerts( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
new_repo_alert = kwd.get( 'new_repo_alert', '' )
new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert )
@@ -2234,7 +2235,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "manage repository" )
def manage_repository( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository_type = kwd.get( 'repository_type', str( repository.type ) )
@@ -2500,7 +2501,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "manage repository administrators" )
def manage_repository_admins( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
@@ -2558,7 +2559,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "multi select email alerts" )
def multi_select_email_alerts( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
@@ -2607,7 +2608,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -2714,7 +2715,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "rate repositories" )
def rate_repository( self, trans, **kwd ):
""" Rate a repository and return updated rating data. """
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if not id:
@@ -2787,7 +2788,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
else:
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids',
multiple=True,
@@ -2800,9 +2801,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def select_files_to_delete( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
@@ -3145,7 +3146,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def upload_capsule( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
url = kwd.get( 'url', '' )
if 'upload_capsule_button' in kwd:
@@ -3175,7 +3176,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def view_changelog( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3210,7 +3211,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def view_changeset( self, trans, id, ctx_str, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3302,7 +3303,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def view_repository( self, trans, id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3390,7 +3391,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -3471,7 +3472,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ):
"""Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
if workflow_name:
lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+13 -12
View File
@@ -2,6 +2,7 @@ import logging
import os
from sqlalchemy.sql.expression import func
from markupsafe import escape
from galaxy import util
from galaxy import web
@@ -40,7 +41,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "approve repository review" )
def approve_repository_review( self, trans, **kwd ):
# The value of the received id is the encoded review id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
encoded_review_id = kwd[ 'id' ]
review = review_util.get_review( trans.app, encoded_review_id )
@@ -74,7 +75,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "browse review" )
def browse_review( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
review = review_util.get_review( trans.app, kwd[ 'id' ] )
repository = review.repository
@@ -105,7 +106,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "create component" )
def create_component( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
name = kwd.get( 'name', '' )
description = kwd.get( 'description', '' )
@@ -136,7 +137,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "create review" )
def create_review( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
changeset_revision = kwd.get( 'changeset_revision', None )
@@ -201,7 +202,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "edit component" )
def edit_component( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if not id:
@@ -232,7 +233,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "edit review" )
def edit_review( self, trans, **kwd ):
# The value of the received id is the encoded review id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
review_id = kwd.get( 'id', None )
review = review_util.get_review( trans.app, review_id )
@@ -408,7 +409,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "manage repositories reviewed by me" )
def manage_repositories_reviewed_by_me( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'operation' in kwd:
kwd[ 'mine' ] = True
@@ -475,7 +476,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "manage repository reviews" )
def manage_repository_reviews( self, trans, mine=False, **kwd ):
# The value of the received id is the encoded repository id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
if repository_id:
@@ -524,7 +525,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "manage repository reviews of revision" )
def manage_repository_reviews_of_revision( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
changeset_revision = kwd.get( 'changeset_revision', None )
@@ -547,7 +548,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "repository reviews by user" )
def repository_reviews_by_user( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'operation' in kwd:
@@ -573,7 +574,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "reviewed repositories i own" )
def reviewed_repositories_i_own( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
# The value of the received id is the encoded repository id.
if 'operation' in kwd:
@@ -592,7 +593,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.require_login( "select previous review" )
def select_previous_review( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
changeset_revision = kwd.get( 'changeset_revision', None )
lib/galaxy/webapps/tool_shed/controllers/upload.py
+3 -2
View File
@@ -9,6 +9,7 @@ from galaxy import util
from galaxy import web
from galaxy.datatypes import checkers
from galaxy.web.base.controller import BaseUIController
from markupsafe import escape
from tool_shed.dependencies import attribute_handlers
from tool_shed.galaxy_install import dependency_display
@@ -34,9 +35,9 @@ class UploadController( BaseUIController ):
@web.expose
@web.require_login( 'upload', use_panels=True )
def upload( self, trans, **kwd ):
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = kwd.get( 'commit_message', 'Uploaded' )
commit_message = escape( kwd.get( 'commit_message', 'Uploaded' ) )
category_ids = util.listify( kwd.get( 'category_id', '' ) )
categories = suc.get_categories( trans.app )
repository_id = kwd.get( 'repository_id', '' )
lib/tool_shed/util/repository_util.py
+2 -1
View File
@@ -7,6 +7,7 @@ from galaxy import util
from galaxy import web
from galaxy.web.form_builder import build_select_field
from galaxy.webapps.tool_shed.model import directory_hash_id
from markupsafe import escape
from tool_shed.dependencies.repository import relation_builder
@@ -256,7 +257,7 @@ def get_role_by_id( app, role_id ):
def handle_role_associations( app, role, repository, **kwd ):
sa_session = app.model.context.current
message = kwd.get( 'message', '' )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_owner = repository.user
if kwd.get( 'manage_role_associations_button', False ):