1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/dd4786c5b4e4/
changeset: dd4786c5b4e4
user: greg
date: 2012-11-06 14:38:52
summary: Per James Johnson, handle files with a .tar extension when installing tool dependencies along with a tool shed repository.
affected #: 1 file
diff -r b996950ffcf2342f1211dc49e6ca75c4dfd7050f -r dd4786c5b4e48db780f6ec5da42dfafec19538f4 lib/galaxy/tool_shed/tool_dependencies/common_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py
@@ -93,7 +93,7 @@
def tar_extraction_directory( file_path, file_name ):
"""Try to return the correct extraction directory."""
file_name = file_name.strip()
- extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.zip' ]
+ extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.tar', '.zip' ]
for extension in extensions:
if file_name.find( extension ) > 0:
dir_name = file_name[ :-len( extension ) ]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9d6a61f060d3/
changeset: 9d6a61f060d3
user: dannon
date: 2012-11-05 21:30:44
summary: Cloud Launch: Fix non-keyboard paste detection for cluster lookup step.
affected #: 1 file
diff -r 4d0bfc13fd582083eb2caec31029a3b4664da4ce -r 9d6a61f060d359a0289b3163990f6a8ba122d253 templates/cloud/index.mako
--- a/templates/cloud/index.mako
+++ b/templates/cloud/index.mako
@@ -76,7 +76,7 @@
}
});
//When id_secret and id_key are complete, submit to get_account_info
- $("#id_secret, #id_key_id").bind("change paste keyup", function(){
+ $("#id_secret, #id_key_id").bind("change paste keyup input propertychange", function(){
secret_el = $("#id_secret");
key_el = $("#id_key_id");
if (secret_el.val().length === 40 && key_el.val().length === 20){
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4d0bfc13fd58/
changeset: 4d0bfc13fd58
user: dannon
date: 2012-11-05 21:21:05
summary: Security: Prevent potential reflected XSS via MessageException (possible in the case of invalid/malicious id lookups, for instance). Cleanup imports.
affected #: 1 file
diff -r 873dba0459da52335fab1dab38de88a92d44a264 -r 4d0bfc13fd582083eb2caec31029a3b4664da4ce lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -4,19 +4,19 @@
import pkg_resources
-import os, sys, time, socket, random, string
+import os, time, socket, random, string
import inspect
from Cookie import CookieError
pkg_resources.require( "Cheetah" )
from Cheetah.Template import Template
import base
-import pickle
from functools import wraps
from galaxy import util
from galaxy.exceptions import MessageException
from galaxy.util.json import to_json_string, from_json_string
from galaxy.util.backports.importlib import import_module
+from galaxy.util.sanitize_html import sanitize_html
pkg_resources.require( "simplejson" )
import simplejson
@@ -240,11 +240,11 @@
output_encoding = 'utf-8' )
def handle_controller_exception( self, e, trans, **kwargs ):
+ if isinstance( e, MessageException ):
+ #In the case of a controller exception, sanitize to make sure unsafe html input isn't reflected back to the user
+ return trans.show_message( sanitize_html(e.err_msg), e.type )
- if isinstance( e, MessageException ):
- return trans.show_message( e.err_msg, e.type )
def make_body_iterable( self, trans, body ):
-
if isinstance( body, FormBuilder ):
body = trans.show_form( body )
return base.WebApplication.make_body_iterable( self, trans, body )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/873dba0459da/
changeset: 873dba0459da
user: dan
date: 2012-11-05 17:09:50
summary: Add a message about tools that will not be enabled during migration due to not being in the tool_conf.xml.
affected #: 1 file
diff -r 8afb981f46c11886a6106fa317936e709c311791 -r 873dba0459da52335fab1dab38de88a92d44a264 lib/galaxy/tool_shed/install_manager.py
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -143,6 +143,8 @@
tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
for k, v in tool_panel_dict_for_tool_config.items():
tool_panel_dict_for_display[ k ] = v
+ else:
+ print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=self.app,
repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b3585fb0c986/
changeset: b3585fb0c986
user: smcmanus
date: 2012-11-04 07:49:43
summary: The input datatype for display changed from LibraryDataset to Dataset, causing permission-checking issues. They've been fixed.
affected #: 2 files
diff -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef -r b3585fb0c98639a57d8934f09f4553a3ad69e80b lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -275,11 +275,12 @@
# then the returned permissions will not carry an entry for the dataset.
ret_permissions = {}
if ( len( permission_items ) > 0 ):
+ # SM: NB: LibraryDatasets became Datasets for some odd reason.
if ( isinstance( permission_items[0], trans.model.LibraryDataset ) ):
ids = [ item.library_dataset_id for item in permission_items ]
permissions = trans.sa_session.query( trans.model.LibraryDatasetPermissions ) \
.filter( and_( trans.model.LibraryDatasetPermissions.library_dataset_id.in_( ids ),
- trans.model.LibraryDatasetPermissions.action == action ) ) \
+ trans.model.LibraryDatasetPermissions.action == action.action ) ) \
.all()
# Massage the return data. We will return a list of permissions
@@ -292,6 +293,23 @@
ret_permissions[ item.library_dataset_id ] = []
for permission in permissions:
ret_permissions[ permission.library_dataset_id ].append( permission )
+ elif ( isinstance( permission_items[0], trans.model.Dataset ) ):
+ ids = [ item.id for item in permission_items ]
+ permissions = trans.sa_session.query( trans.model.DatasetPermissions ) \
+ .filter( and_( trans.model.DatasetPermissions.dataset_id.in_( ids ),
+ trans.model.DatasetPermissions.action == action.action ) ) \
+ .all()
+
+ # Massage the return data. We will return a list of permissions
+ # for each library dataset. So we initialize the return list to
+ # have an empty list for each dataset. Then each permission is
+ # appended to the right lib dataset.
+ # TODO: Consider eliminating the initialization and just return
+ # empty values for each library dataset id.
+ for item in permission_items:
+ ret_permissions[ item.id ] = []
+ for permission in permissions:
+ ret_permissions[ permission.dataset_id ].append( permission )
# Test that we get the same response from get_item_actions each item:
test_code = False
@@ -333,14 +351,13 @@
LDDAs.
"""
all_items_actions = self.get_actions_for_items( trans, action, items )
+ ret_allow_action = {}
- ret_allow_action = {}
# Change item to lib_dataset or vice-versa.
for item in items:
if all_items_actions.has_key( item.id ):
item_actions = all_items_actions[ item.id ]
- # For access, all of the dataset's
if self.permitted_actions.DATASET_ACCESS == action:
ret_allow_action[ item.id ] = True
for item_action in item_actions:
diff -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef -r b3585fb0c98639a57d8934f09f4553a3ad69e80b lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -131,7 +131,17 @@
comptypes = get_comptypes( trans )
try:
if self.app.config.new_lib_browse:
- pass
+ return trans.fill_template( 'library/common/browse_library_opt.mako',
+ cntrller=cntrller,
+ use_panels=use_panels,
+ library=library,
+ created_ldda_ids=created_ldda_ids,
+ hidden_folder_ids=hidden_folder_ids,
+ show_deleted=show_deleted,
+ comptypes=comptypes,
+ current_user_roles=current_user_roles,
+ message=message,
+ status=status )
else:
return trans.fill_template( 'library/common/browse_library.mako',
cntrller=cntrller,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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