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Indentation and typo fixes.

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This commit is contained in:
Nicola Soranzo
2015-07-05 19:45:11 +01:00
parent fca6854ac0
commit f14ed0317b
3 changed files with 19 additions and 11 deletions
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lib/galaxy/managers/collections_util.py
+1 -1
View File
@@ -79,7 +79,7 @@ def dictify_dataset_collection_instance( dataset_collection_instance, parent, se
collection = dataset_collection_instance.collection
dict_value[ 'elements' ] = map( dictify_element, collection.elements )
dict_value[ 'populated' ] = collection.populated
security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this.
security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recursive formulation of this.
return dict_value
lib/galaxy/managers/libraries.py
+14 -7
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@@ -119,13 +119,20 @@ class LibraryManager( object ):
# Nonadmins can't see deleted libraries
current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ]
library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action
restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions )
.filter( trans.model.LibraryPermissions.table.c.action == library_access_action )
.distinct() ) ]
accessible_restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions )
.filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action,
trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ) ]
query = query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) )
restricted_library_ids = [ lp.library_id for lp in (
trans.sa_session.query( trans.model.LibraryPermissions ).filter(
trans.model.LibraryPermissions.table.c.action == library_access_action
).distinct() ) ]
accessible_restricted_library_ids = [ lp.library_id for lp in (
trans.sa_session.query( trans.model.LibraryPermissions ).filter(
and_(
trans.model.LibraryPermissions.table.c.action == library_access_action,
trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids )
) ) ) ]
query = query.filter( or_(
not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ),
trans.model.Library.table.c.id.in_( accessible_restricted_library_ids )
) )
return query
def secure( self, trans, library, check_accessible=True ):
lib/galaxy/managers/workflows.py
+4 -3
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@@ -455,9 +455,10 @@ class WorkflowContentsManager(UsesAnnotations):
if module.type == 'tool':
pja_dict = {}
for pja in step.post_job_actions:
pja_dict[pja.action_type + pja.output_name] = dict( action_type=pja.action_type,
output_name=pja.output_name,
action_arguments=pja.action_arguments )
pja_dict[pja.action_type + pja.output_name] = dict(
action_type=pja.action_type,
output_name=pja.output_name,
action_arguments=pja.action_arguments )
step_dict[ 'post_job_actions' ] = pja_dict
# Data inputs
step_dict['inputs'] = module.get_runtime_input_dicts( annotation_str )