More performance improvements in checking security on datasets and generatng HTML for libraries, and a bit of code cleanup in these areas.

lib/galaxy/model/__init__.py

@@ -709,9 +709,9 @@ class LibraryFolder( object ):
         folder.order_id = self.item_count
         self.item_count += 1
     def get_info_association( self, restrict=False ):
-        # If restrict is True, we will return this folder's info_association whether it
-        # exists or not.  If restrict is False, we'll return the next available info_association
-        # in the inheritable hierarchy
+        # If restrict is True, we will return this folder's info_association, not inheriting.
+        # If restrict is False, we'll return the next available info_association in the
+        # inheritable hierarchy
         if self.info_association:
             return self.info_association[0]
         if restrict:
@@ -722,9 +722,6 @@ class LibraryFolder( object ):
             return self.library_root[0].get_info_association()
         return None
     @property
-    def active_components( self ):
-        return list( self.active_folders ) + list( self.active_library_datasets )
-    @property
     def active_library_datasets( self ):
          # This needs to be a list
         return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
@@ -736,10 +733,6 @@ class LibraryFolder( object ):
     def active_datasets( self ):
          # This needs to be a list
         return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
-    @property #make this a relation
-    def activatable_folders( self ):
-        # This needs to be a list
-        return [ folder for folder in self.folders if not folder.purged ]
 
 class LibraryDataset( object ):
     # This class acts as a proxy to the currently selected LDDA
@@ -1062,17 +1055,11 @@ class Request( object ):
                 return s
         return False
     def submitted(self):
-        if self.state == self.states.SUBMITTED:
-            return True
-        return False
+        return self.state == self.states.SUBMITTED
     def unsubmitted(self):
-        if self.state == self.states.UNSUBMITTED:
-            return True
-        return False
+        return self.state == self.states.UNSUBMITTED
     def complete(self):
-        if self.state == self.states.COMPLETE:
-            return True
-        return False
+        return self.state == self.states.COMPLETE
         
 class RequestType( object ):
     def __init__(self, name=None, desc=None, request_form=None, sample_form=None):

lib/galaxy/model/mapping.py

@@ -233,10 +233,10 @@ LibraryDataset.table = Table( "library_dataset", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected
     Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
-    Column( "order_id", Integer ),
+    Column( "order_id", Integer ), #not currently being used, but for possible future use
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "name", TrimmedString( 255 ), key="_name" ), #when not None/null this will supercede display in library (but not when imported into user's history?)
+    Column( "name", TrimmedString( 255 ), key="_name", index=True ), #when not None/null this will supercede display in library (but not when imported into user's history?)
     Column( "info", TrimmedString( 255 ),  key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?)
     Column( "deleted", Boolean, index=True, default=False ) )
 
@@ -248,7 +248,7 @@ LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_associa
     Column( "update_time", DateTime, default=now, onupdate=now ),
     Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ),
     Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ),
-    Column( "name", TrimmedString( 255 ) ),
+    Column( "name", TrimmedString( 255 ), index=True ),
     Column( "info", TrimmedString( 255 ) ),
     Column( "blurb", TrimmedString( 255 ) ),
     Column( "peek" , TEXT ),
@@ -276,9 +276,9 @@ LibraryFolder.table = Table( "library_folder", metadata,
     Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "name", TEXT ),
+    Column( "name", TEXT, index=True ),
     Column( "description", TEXT ),
-    Column( "order_id", Integer ),
+    Column( "order_id", Integer ), #not currently being used, but for possible future use
     Column( "item_count", Integer ),
     Column( "deleted", Boolean, index=True, default=False ),
     Column( "purged", Boolean, index=True, default=False ),
@@ -823,15 +823,16 @@ assign_mapper( context, LibraryFolder, LibraryFolder.table,
         folders=relation( 
             LibraryFolder, 
             primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ),
+            order_by=asc( LibraryFolder.table.c.name ),
             backref=backref( "parent", primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), remote_side=[LibraryFolder.table.c.id] ) ),
         active_folders=relation( LibraryFolder, 
             primaryjoin=( ( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolder.table.c.deleted ) ) ), 
-            order_by=asc( LibraryFolder.table.c.order_id ), 
+            order_by=asc( LibraryFolder.table.c.name ), 
             lazy=True, #"""sqlalchemy.exceptions.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship."""
             viewonly=True ),
         datasets=relation( LibraryDataset,
             primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ), 
-            order_by=asc( LibraryDataset.table.c.order_id ), 
+            order_by=asc( LibraryDataset.table.c._name ), 
             lazy=False, 
             viewonly=True )
     ) )

lib/galaxy/model/migrate/versions/0017_library_item_indexes.py

@@ -0,0 +1,53 @@
+"""
+This script adds 3 indexes to table columns: library_folder.name,
+library_dataset.name, library_dataset_dataset_association.name.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+import sys, logging
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+LibraryFolder_table = Table( "library_folder", metadata, autoload=True )
+LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
+LibraryDataset_table = Table( "library_dataset", metadata, autoload=True )
+          
+def display_migration_details():
+    print "========================================"
+    print "This script adds 3 indexes to table columns: library_folder.name,"
+    print "library_dataset.name, library_dataset_dataset_association.name."
+    print "========================================"
+        
+def upgrade():
+    display_migration_details()
+    # Load existing tables
+    metadata.reflect()
+    # Add 1 index to the library_folder table
+    i = Index( 'ix_library_folder_name', LibraryFolder_table.c.name )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_library_folder_name' to library_folder table failed: %s" % ( str( e ) ) )
+    # Add 1 index to the library_dataset_dataset_association table
+    i = Index( 'ix_library_dataset_dataset_association_name', LibraryDatasetDatasetAssociation_table.c.name )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_library_dataset_dataset_association_name' to library_dataset_dataset_association table failed: %s" % ( str( e ) ) )
+    # Add 1 index to the library_dataset table
+    i = Index( 'ix_library_dataset_name', LibraryDataset_table.c.name )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_library_dataset_name' to library_dataset table failed: %s" % ( str( e ) ) )
+def downgrade():
+    log.debug( "Downgrade is not possible." )

lib/galaxy/security/__init__.py

@@ -33,12 +33,20 @@ class RBACAgent:
     def get_actions( self ):
         """Get all permitted actions as a list of Action objects"""
         return self.permitted_actions.__dict__.values()
-    def allow_action( self, user, roles, action, **kwd ):
-        raise 'No valid method of checking action (%s) on %s for user %s.' % ( action, kwd, user )
     def get_item_action( self, action, item ):
         raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item )
     def guess_derived_permissions_for_datasets( self, datasets = [] ):
         raise "Unimplemented Method"
+    def can_access_dataset( self, roles, dataset ):
+        raise "Unimplemented Method"
+    def can_manage_dataset( self, roles, dataset ):
+        raise "Unimplemented Method"
+    def can_add_library_item( self, user, roles, item ):
+        raise "Unimplemented Method"
+    def can_modify_library_item( self, user, roles, item ):
+        raise "Unimplemented Method"
+    def can_manage_library_item( self, user, roles, item ):
+        raise "Unimplemented Method"
     def associate_components( self, **kwd ):
         raise 'No valid method of associating provided components: %s' % kwd
     def create_private_user_role( self, user ):
@@ -89,36 +97,20 @@ class GalaxyRBACAgent( RBACAgent ):
         to allow migration toward a more SQLAlchemy 0.4 style of use.
         """
         return self.model.context.current
-    def allow_action( self, user, roles, action, **kwd ):
-        if 'dataset' in kwd:
-            return self.allow_dataset_action( user, roles, action, kwd[ 'dataset' ] )
-        elif 'library_item' in kwd:
-            return self.allow_library_item_action( user, roles, action, kwd[ 'library_item' ] )
-        raise 'No valid method of checking action (%s) for user %s using kwd %s' % ( action, str( user ), str( kwd ) )
-    def allow_dataset_action( self, user, roles, action, dataset ):
-        """Returns true when user has permission to perform an action"""
-        if not user:
-            if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in dataset.actions ]:
-                # anons only get access, and only if there are no roles required for the access action
-                # Other actions (or if the dataset has roles defined for the access action) fall through
-                # to the false below for anons
-                return True
-        elif action.action not in [ dp.action for dp in dataset.actions ]:
-            if action.model == 'restrict':
-                # Implicit access to restrict-style actions if the dataset does not have the action
-                # Grant style actions fall through to the false below
-                return True
-        else:
-            perms = self.get_dataset_permissions( dataset )
-            if action in perms.keys():
-                # The filter() returns a list of the dataset's role ids of which the user is not a member,
-                # so an empty list means the user has all of the required roles.
-                if not filter( lambda x: x not in roles, [ r for r in perms[ action ] ] ):
-                    # User has all of the roles required to perform the action
-                    return True
-        # The user is missing at least one required role
-        return False
-    def allow_library_item_action( self, user, roles, action, library_item ):
+    def allow_dataset_action( self, roles, action, dataset ):
+        """
+        Returns true when user has permission to perform an action on an
+        instance of Dataset.
+        """
+        dataset_action = self.get_item_action( action, dataset )
+        if dataset_action is None:
+            return action.model == 'restrict'
+        return dataset_action.role in roles
+    def can_access_dataset( self, roles, dataset ):
+        return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset )
+    def can_manage_dataset( self, roles, dataset ):
+        return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset )
+    def allow_library_item_action( self, user, roles, action, item ):
         """
         Method for checking a permission for the current user to perform a
         specific library action on a library item, which must be one of:
@@ -127,30 +119,22 @@ class GalaxyRBACAgent( RBACAgent ):
         if user is None:
             # All permissions are granted, so non-users cannot have permissions
             return False
-        # Check to see if user has access to any of the roles
-        allowed_role_assocs = []
-        for item_class, permission_class in self.library_item_assocs:
-            if isinstance( library_item, item_class ):
-                if permission_class == self.model.LibraryPermissions:
-                    allowed_role_assocs = permission_class.filter_by( action=action.action,
-                                                                      library=library_item ).all()
-                elif permission_class == self.model.LibraryFolderPermissions:
-                    allowed_role_assocs = permission_class.filter_by( action=action.action,
-                                                                      folder=library_item ).all()
-                elif permission_class == self.model.LibraryDatasetPermissions:
-                    allowed_role_assocs = permission_class.filter_by( action=action.action,
-                                                                      library_dataset=library_item ).all()
-                elif permission_class == self.model.LibraryDatasetDatasetAssociationPermissions:
-                    allowed_role_assocs = permission_class.filter_by( action=action.action,
-                                                                      library_dataset_dataset_association=library_item ).all()
-        for allowed_role_assoc in allowed_role_assocs:
-            if allowed_role_assoc.role in roles:
-                return True
-        return False
+        # Check to see if user has access to any of the roles associated with action
+        item_action = self.get_item_action( action, item )
+        if item_action is None:
+            # All permissions are granted, so item must have action
+            return False
+        return item_action.role in roles
+    def can_add_library_item( self, user, roles, item ):
+        return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item )
+    def can_modify_library_item( self, user, roles, item ):
+        return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item )
+    def can_manage_library_item( self, user, roles, item ):
+        return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item )
     def get_item_action( self, action, item ):
         # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
         for permission in item.actions:
-            if permission.action == action:
+            if permission.action == action.action:
                 return permission
         return None
     def guess_derived_permissions_for_datasets( self, datasets=[] ):
@@ -282,10 +266,7 @@ class GalaxyRBACAgent( RBACAgent ):
                 if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]:
                     # Don't change permissions on a dataset associated with a history not owned by the user
                     continue
-                if bypass_manage_permission or self.allow_action( user,
-                                                                  user.all_roles(),
-                                                                  self.permitted_actions.DATASET_MANAGE_PERMISSIONS,
-                                                                  dataset=dataset ):
+                if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ):
                     self.set_all_dataset_permissions( dataset, permissions )
     def history_get_default_permissions( self, history ):
         permissions = {}
@@ -445,7 +426,7 @@ class GalaxyRBACAgent( RBACAgent ):
         the string, True is returned if the current user has permission to perform any 1 of actions_to_check
         on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets
         this criteria, if it exists.
-        """
+        """        
         for action in actions_to_check:
             if self.allow_library_item_action( user, roles, action, library_item ):
                 return True, hidden_folder_ids
@@ -515,7 +496,7 @@ class GalaxyRBACAgent( RBACAgent ):
         with the string, True is returned if the current user has permission to access folder. Otherwise,
         cycle through all sub-folders in folder until one is found that meets this criteria, if it exists.
         """
-        action = self.permitted_actions.DATASET_ACCESS.action
+        action = self.permitted_actions.DATASET_ACCESS
         lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \
             .join( "library_dataset" ) \
             .filter( self.model.LibraryDataset.folder == folder ) \

lib/galaxy/tools/actions/__init__.py

@@ -48,10 +48,7 @@ class DefaultToolAction( object ):
                             assoc.flush()
                             data = new_data
                 user, roles = trans.get_user_and_roles()
-                if data and not trans.app.security_agent.allow_action( user,
-                                                                       roles,
-                                                                       data.permitted_actions.DATASET_ACCESS,
-                                                                       dataset=data.dataset ):
+                if data and not trans.app.security_agent.can_access_dataset( roles, data.dataset ):
                     raise "User does not have permission to use a dataset (%s) provided for input." % data.id
                 return data
             if isinstance( input, DataToolParameter ):
@@ -267,10 +264,7 @@ class DefaultToolAction( object ):
         user, roles = trans.get_user_and_roles()
         for name, dataset in inp_data.iteritems():
             if dataset:
-                if not trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              dataset.permitted_actions.DATASET_ACCESS,
-                                                              dataset=dataset.dataset ):
+                if not trans.app.security_agent.can_access_dataset( roles, dataset.dataset ):
                     raise "User does not have permission to use a dataset (%s) provided for input." % data.id
                 job.add_input_dataset( name, dataset )
             else:

lib/galaxy/tools/parameters/basic.py

@@ -1149,19 +1149,11 @@ class DataToolParameter( ToolParameter ):
                     hid = str( hda.hid )
                 if not hda.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED] and \
                     hda.visible and \
-                    trans.app.security_agent.allow_action( user,
-                                                           roles,
-                                                           hda.permitted_actions.DATASET_ACCESS,
-                                                           dataset=hda.dataset ):
+                    trans.app.security_agent.can_access_dataset( roles, hda.dataset ):
                     # If we are sending data to an external application, then we need to make sure there are no roles
-                    # associated with the dataset that restrict it's access from "public".  We determine this by sending
-                    # None as the user to the allow_action method.
-                    if self.tool and self.tool.tool_type == 'data_destination':
-                        if not trans.app.security_agent.allow_action( None,
-                                                                      None,
-                                                                      hda.permitted_actions.DATASET_ACCESS,
-                                                                      dataset=hda.dataset ):
-                            continue
+                    # associated with the dataset that restrict it's access from "public".
+                    if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ):
+                        continue
                     if self.options and hda.get_dbkey() != filter_value:
                         continue
                     if isinstance( hda.datatype, self.formats):
@@ -1172,10 +1164,7 @@ class DataToolParameter( ToolParameter ):
                         if target_ext:
                             if converted_dataset:
                                 hda = converted_dataset
-                            if not trans.app.security_agent.allow_action( user,
-                                                                          roles,
-                                                                          trans.app.security_agent.permitted_actions.DATASET_ACCESS,
-                                                                          dataset=hda.dataset ):
+                            if not trans.app.security_agent.can_access_dataset( roles, hda.dataset ):
                                 continue
                             selected = ( value and ( hda in value ) )
                             field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected )

lib/galaxy/web/controllers/admin.py

@@ -2001,7 +2001,6 @@ class Admin( BaseController ):
                                         show_deleted=False,
                                         msg=msg,
                                         messagetype=messagetype )
-
     def _save_request_type(self, trans, **kwd):
         params = util.Params( kwd )
         num_states = int( util.restore_text( params.get( 'num_states', 0 ) ))
@@ -2031,7 +2030,6 @@ class Admin( BaseController ):
             ss.flush()
         msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states)
         return rt, msg
-
     @web.expose
     @web.require_admin
     def delete_request_type( self, trans, **kwd ):
@@ -2045,7 +2043,6 @@ class Admin( BaseController ):
                                                           action='manage_request_types',
                                                           msg='Request type <b>%s</b> has been deleted' % rt.name,
                                                           messagetype='done') )
-        
     @web.expose
     @web.require_admin
     def undelete_request_type( self, trans, **kwd ):

lib/galaxy/web/controllers/dataset.py

@@ -109,10 +109,7 @@ class DatasetInterface( BaseController ):
         if not data:
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         user, roles = trans.get_user_and_roles()
-        if trans.app.security_agent.allow_action( user,
-                                                  roles,
-                                                  data.permitted_actions.DATASET_ACCESS,
-                                                  dataset=data.dataset ):
+        if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
             if data.state == trans.model.Dataset.states.UPLOAD:
                 return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." )
             if filename is None or filename.lower() == "index":
@@ -147,12 +144,9 @@ class DatasetInterface( BaseController ):
             return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' )
         redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] )
         user, roles = trans.get_user_and_roles()
-        if trans.app.security_agent.allow_action( None, None, data.permitted_actions.DATASET_ACCESS, dataset=data.dataset ):
+        if trans.app.security_agent.dataset_is_public( data.dataset ):
             return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac
-        if trans.app.security_agent.allow_action( user,
-                                                  roles,
-                                                  data.permitted_actions.DATASET_ACCESS,
-                                                  dataset=data.dataset ):
+        if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
             trans.app.host_security_agent.set_dataset_permissions( data, trans.user, site )
             return trans.response.send_redirect( redirect_url )
         else:

lib/galaxy/web/controllers/history.py

@@ -443,15 +443,9 @@ class HistoryController( BaseController ):
                     for hda in history.activatable_datasets:
                         # If the current dataset is not public, we may need to perform an action on it to
                         # make it accessible by the other user.
-                        if not trans.app.security_agent.allow_action( send_to_user,
-                                                                      send_to_user.all_roles(),
-                                                                      trans.app.security_agent.permitted_actions.DATASET_ACCESS, 
-                                                                      dataset=hda.dataset ):
+                        if not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
                             # The user with which we are sharing the history does not have access permission on the current dataset
-                            if trans.app.security_agent.allow_action( user,
-                                                                      user_roles,
-                                                                      trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, 
-                                                                      dataset=hda.dataset ) and not hda.dataset.library_associations:
+                            if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations:
                                 # The current user has authority to change permissions on the current dataset because
                                 # they have permission to manage permissions on the dataset and the dataset is not associated 
                                 # with a library.
@@ -556,15 +550,9 @@ class HistoryController( BaseController ):
                                 no_change_needed[ send_to_user ][ history ] = [ hda ]
                             else:
                                 no_change_needed[ send_to_user ][ history ].append( hda )
-                        elif not trans.app.security_agent.allow_action( send_to_user,
-                                                                        send_to_user.all_roles(),
-                                                                        trans.app.security_agent.permitted_actions.DATASET_ACCESS, 
-                                                                        dataset=hda.dataset ):
+                        elif not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
                             # The user with which we are sharing the history does not have access permission on the current dataset
-                            if trans.app.security_agent.allow_action( user,
-                                                                      user_roles,
-                                                                      trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, 
-                                                                      dataset=hda.dataset ) and not hda.dataset.library_associations:
+                            if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations:
                                 # The current user has authority to change permissions on the current dataset because
                                 # they have permission to manage permissions on the dataset and the dataset is not associated 
                                 # with a library.

lib/galaxy/web/controllers/library.py

@@ -2,6 +2,7 @@ from galaxy.web.base.controller import *
 from galaxy.model.orm import *
 from galaxy.datatypes import sniff
 from galaxy import util
+from galaxy.util.odict import odict
 from galaxy.web.controllers.forms import get_all_forms, get_form_widgets
 from galaxy.util.streamball import StreamBall
 import logging, tempfile, zipfile, tarfile, os, sys
@@ -74,7 +75,7 @@ class Library( BaseController ):
         # The folders that should not be displayed may not be a complete list, but it is ultimately passed
         # to the browse_library() method and the browse_library.mako template to keep from re-checking the
         # same folders when the library is rendered.
-        authorized_libraries = {}
+        authorized_libraries = odict()
         for library in all_libraries:
             can_access, hidden_folder_ids = trans.app.security_agent.check_folder_contents( user, roles, library.root_folder )
             if can_access:
@@ -283,10 +284,7 @@ class Library( BaseController ):
             user, roles = trans.get_user_and_roles()
             for id in ldda_ids:
                 ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id )
-                if not ldda or not trans.app.security_agent.allow_action( user,
-                                                                          roles,
-                                                                          trans.app.security_agent.permitted_actions.DATASET_ACCESS,
-                                                                          dataset = ldda.dataset ):
+                if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ):
                     continue
                 path = ""
                 parent_folder = ldda.library_dataset.folder
@@ -384,10 +382,7 @@ class Library( BaseController ):
         user, roles = trans.get_user_and_roles()
         if action == 'information':
             if params.get( 'edit_attributes_button', False ):
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                          library_item=library_dataset ):
+                if trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ):
                     if params.get( 'edit_attributes_button', False ):
                         old_name = library_dataset.name
                         new_name = util.restore_text( params.get( 'name', '' ) )
@@ -411,10 +406,7 @@ class Library( BaseController ):
                                         messagetype=messagetype )
         elif action == 'permissions':
             if params.get( 'update_roles_button', False ):
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                          library_item=library_dataset ):
+                if trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ):
                     # The user clicked the Save button on the 'Associate With Roles' form
                     permissions = {}
                     for k, v in trans.app.model.Library.permitted_actions.items():
@@ -501,14 +493,8 @@ class Library( BaseController ):
             if action == 'permissions':
                 if params.get( 'update_roles_button', False ):
                     # The user clicked the Save button on the 'Associate With Roles' form
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                              library_item=ldda ) and \
-                        trans.app.security_agent.allow_action( user,
-                                                               roles,
-                                                               trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS,
-                                                               dataset=ldda.dataset ):
+                    if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
+                        trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
                         permissions = {}
                         for k, v in trans.app.model.Dataset.permitted_actions.items():
                             in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
@@ -547,10 +533,7 @@ class Library( BaseController ):
             elif action == 'edit_info':
                 if params.get( 'change', False ):
                     # The user clicked the Save button on the 'Change data type' form
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                              library_item=ldda ):
+                    if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
                         if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
                             trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
                             trans.app.model.flush()
@@ -571,10 +554,7 @@ class Library( BaseController ):
                                                 messagetype=messagetype )
                 elif params.get( 'save', False ):
                     # The user clicked the Save button on the 'Edit Attributes' form
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                              library_item=ldda ):
+                    if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
                         old_name = ldda.name
                         new_name = util.restore_text( params.get( 'name', '' ) )
                         new_info = util.restore_text( params.get( 'info', '' ) )
@@ -613,10 +593,7 @@ class Library( BaseController ):
                                                 messagetype=messagetype )
                 elif params.get( 'detect', False ):
                     # The user clicked the Auto-detect button on the 'Edit Attributes' form
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                              library_item=ldda ):
+                    if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
                         for name, spec in ldda.datatype.metadata_spec.items():
                             # We need to be careful about the attributes we are resetting
                             if name not in [ 'name', 'info', 'dbkey' ]:
@@ -638,10 +615,7 @@ class Library( BaseController ):
                                                 msg=msg,
                                                 messagetype=messagetype )
                 elif params.get( 'delete', False ):
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                              library_item=folder ):
+                    if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
                         ldda.deleted = True
                         ldda.flush()
                         msg = 'Dataset %s has been removed from this library' % ldda.name
@@ -656,10 +630,7 @@ class Library( BaseController ):
                                                 widgets=widgets,
                                                 msg=msg,
                                                 messagetype=messagetype )
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                          library_item=ldda ):
+                if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
                     ldda.datatype.before_edit( ldda )
                     if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey:
                         # Copy dbkey into metadata, for backwards compatability
@@ -697,14 +668,8 @@ class Library( BaseController ):
                                                            messagetype='error' ) )
             if action == 'permissions':
                 if params.get( 'update_roles_button', False ):
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                              library_item=ldda ) and \
-                        trans.app.security_agent.allow_action( user,
-                                                               roles,
-                                                               trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS,
-                                                               dataset=ldda.dataset ):
+                    if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
+                        trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
                         permissions = {}
                         for k, v in trans.app.model.Dataset.permitted_actions.items():
                             in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
@@ -735,14 +700,8 @@ class Library( BaseController ):
                                                 library_id=library_id,
                                                 msg=msg,
                                                 messagetype=messagetype )
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                          library_item=ldda ) and \
-                    trans.app.security_agent.allow_action( user,
-                                                           roles,
-                                                           trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS,
-                                                           dataset=ldda.dataset ):
+                if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
+                    trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
                     # Ensure that the permissions across all library items are identical, otherwise we can't update them together.
                     check_list = []
                     for ldda in lddas:
@@ -774,14 +733,8 @@ class Library( BaseController ):
                                             library_id=library_id,
                                             msg=msg,
                                             messagetype=messagetype )
-        if trans.app.security_agent.allow_action( user,
-                                                  roles,
-                                                  trans.app.security_agent.permitted_actions.LIBRARY_ADD,
-                                                  library_item=folder ) or \
-             ( replace_dataset and trans.app.security_agent.allow_action( user,
-                                                                          roles,
-                                                                          trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
-                                                                          library_item=replace_dataset ) ):
+        if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \
+             ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ):
             if params.get( 'new_dataset_button', False ):
                 upload_option = params.get( 'upload_option', 'upload_file' )
                 created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans,
@@ -804,10 +757,7 @@ class Library( BaseController ):
                     # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
                     # to check one of them to see if the current user can manage permissions on them.
                     check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] )
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                              library_item=check_ldda ):
+                    if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
                         if replace_dataset:
                             default_action = ''
                         else:
@@ -929,10 +879,7 @@ class Library( BaseController ):
                     # to check one of them to see if the current user can manage permissions on them.
                     check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] )
                     user, roles = trans.get_user_and_roles()
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              trans.app.security_agent.permitted_actions.LIBRARY_MANAGE,
-                                                              library_item=check_ldda ):
+                    if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
                         if replace_dataset:
                             default_action = ''
                         else:
@@ -1033,10 +980,7 @@ class Library( BaseController ):
             else:
                 widgets = []
             if params.get( 'rename_folder_button', False ):
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, 
-                                                          library_item=folder ):
+                if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
                     old_name = folder.name
                     new_name = util.restore_text( params.name )
                     new_description = util.restore_text( params.description )
@@ -1077,10 +1021,7 @@ class Library( BaseController ):
         elif action == 'permissions':
             if params.get( 'update_roles_button', False ):
                 # The user clicked the Save button on the 'Associate With Roles' form
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, 
-                                                          library_item=folder ):
+                if trans.app.security_agent.can_manage_library_item( user, roles, folder ):
                     permissions = {}
                     for k, v in trans.app.model.Library.permitted_actions.items():
                         in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
@@ -1202,3 +1143,41 @@ class Library( BaseController ):
                                                           edit_info=True,
                                                           msg=util.sanitize_text( msg ),
                                                           messagetype='done' ) )
+
+# ---- Utility methods -------------------------------------------------------
+
+def active_folders( trans, folder ):
+    # Much faster way of retrieving all active sub-folders within a given folder than the
+    # performance of the mapper.  This query also eagerloads the permissions on each folder.
+    return trans.sa_session.query( trans.app.model.LibraryFolder ) \
+                           .filter_by( parent=folder, deleted=False ) \
+                           .options( eagerload_all( "actions" ) ) \
+                           .order_by( trans.app.model.LibraryFolder.table.c.name ) \
+                           .all()
+def activatable_folders( trans, folder ):
+    return trans.sa_session.query( trans.app.model.LibraryFolder ) \
+                           .filter_by( parent=folder, purged=False ) \
+                           .options( eagerload_all( "actions" ) ) \
+                           .order_by( trans.app.model.LibraryFolder.table.c.name ) \
+                           .all()
+def active_folders_and_lddas( trans, folder ):
+    folders = active_folders( trans, folder )
+    # This query is much faster than the folder.active_library_datasets property
+    lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
+                            .filter_by( deleted=False ) \
+                            .join( "library_dataset" ) \
+                            .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
+                            .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
+                            .all()
+    return folders, lddas
+def activatable_folders_and_lddas( trans, folder ):
+    folders = activatable_folders( trans, folder )
+    # This query is much faster than the folder.activatable_library_datasets property
+    lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
+                            .join( "library_dataset" ) \
+                            .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
+                            .join( "dataset" ) \
+                            .filter( trans.app.model.Dataset.table.c.deleted==False ) \
+                            .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
+                            .all()
+    return folders, lddas

lib/galaxy/web/controllers/requests.py

@@ -4,6 +4,7 @@ from galaxy.model.orm import *
 from galaxy.datatypes import sniff
 from galaxy import util
 from galaxy.util.streamball import StreamBall
+from galaxy.util.odict import odict
 import logging, tempfile, zipfile, tarfile, os, sys
 from galaxy.web.form_builder import * 
 from datetime import datetime, timedelta
@@ -470,7 +471,7 @@ class Requests( BaseController ):
         # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids
         # so that you do not need to check those same folders yet again when populating the select list.
         #
-        libraries = {}
+        libraries = odict()
         for library in all_libraries:
             can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
             if can_show:

lib/galaxy/web/controllers/root.py

@@ -153,10 +153,7 @@ class RootController( BaseController ):
                 return "Dataset id '%s' is invalid" %str( id )
         if data:
             user, roles = trans.get_user_and_roles()
-            if trans.app.security_agent.allow_action( user,
-                                                      roles,
-                                                      data.permitted_actions.DATASET_ACCESS,
-                                                      dataset = data.dataset ):
+            if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
                 mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() )
                 trans.response.set_content_type(mime)
                 if tofile:
@@ -189,10 +186,7 @@ class RootController( BaseController ):
                 child = data.get_child_by_designation( designation )
                 if child:
                     user, roles = trans.get_user_and_roles()
-                    if trans.app.security_agent.allow_action( user,
-                                                              roles,
-                                                              child.permitted_actions.DATASET_ACCESS,
-                                                              dataset = child ):
+                    if trans.app.security_agent.can_access_dataset( roles, child ):
                         return self.display( trans, id=child.id, tofile=tofile, toext=toext )
                     else:
                         return "You are not privileged to access this dataset."
@@ -209,10 +203,7 @@ class RootController( BaseController ):
             authz_method = kwd['authz_method']
         if data:
             user, roles = trans.get_user_and_roles()
-            if authz_method == 'rbac' and trans.app.security_agent.allow_action( user,
-                                                                                 roles,
-                                                                                 data.permitted_actions.DATASET_ACCESS,
-                                                                                 dataset = data ):
+            if authz_method == 'rbac' and trans.app.security_agent.can_access_dataset( roles, data ):
                 trans.response.set_content_type( data.get_mime() )
                 trans.log_event( "Formatted dataset id %s for display at %s" % ( str( id ), display_app ) )
                 return data.as_display_type( display_app, **kwd )
@@ -262,10 +253,7 @@ class RootController( BaseController ):
         if id is not None and data.history.user is not None and data.history.user != trans.user:
             return trans.show_error_message( "This instance of a dataset (%s) in a history does not belong to you." % ( data.id ) )
         user, roles = trans.get_user_and_roles()
-        if trans.app.security_agent.allow_action( user,
-                                                  roles,
-                                                  data.permitted_actions.DATASET_ACCESS,
-                                                  dataset=data.dataset ):
+        if trans.app.security_agent.can_access_dataset( roles, data.dataset ):
             if data.state == trans.model.Dataset.states.UPLOAD:
                 return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to edit its metadata." )
             params = util.Params( kwd, safe=False )
@@ -331,10 +319,7 @@ class RootController( BaseController ):
             elif params.update_roles_button:
                 if not trans.user:
                     return trans.show_error_message( "You must be logged in if you want to change permissions." )
-                if trans.app.security_agent.allow_action( user,
-                                                          roles,
-                                                          data.dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS,
-                                                          dataset = data.dataset ):
+                if trans.app.security_agent.can_manage_dataset( roles, data.dataset ):
                     permissions = {}
                     for k, v in trans.app.model.Dataset.permitted_actions.items():
                         in_roles = params.get( k + '_in', [] )

lib/galaxy/web/framework/__init__.py

@@ -503,7 +503,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         if user:
             roles = user.all_roles()
         else:
-            roles = None
+            roles = []
         return user, roles
 
     def user_is_admin( self ):

templates/admin/library/browse_library.mako

@@ -1,18 +1,16 @@
 <%inherit file="/base.mako"/>
-<%namespace file="common.mako" import="render_dataset" />
 <%namespace file="/message.mako" import="render_msg" />
-<% from galaxy import util %>
+<%
+    from time import strftime
+    from galaxy import util
+    from galaxy.web.controllers.library import active_folders_and_lddas, activatable_folders_and_lddas
+%>
 
 <%def name="stylesheets()">
     <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
     <link href="${h.url_for('/static/style/library.css')}" rel="stylesheet" type="text/css" />
 </%def>
 
-<%
-def name_sorted( l ):
-    return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) )
-%>
-
 <script type="text/javascript">
     $( document ).ready( function () {
         // Hide all the folder contents
@@ -72,24 +70,77 @@ def name_sorted( l ):
     }
 </script>
 
-<%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id )">
+<%def name="render_dataset( ldda, library_dataset, selected, library, folder, deleted, show_deleted )">
+    <%
+        ## The received data must always be a LibraryDatasetDatasetAssociation object.  The object id passed to methods
+        ## from the drop down menu should be the ldda id to prevent id collision ( which could happen when displaying
+        ## children, which are always lddas ).  We also need to make sure we're displaying the latest version of this
+        ## library_dataset, so we display the attributes from the ldda.
+        if ldda.user:
+            uploaded_by = ldda.user.email
+        else:
+            uploaded_by = 'anonymous'
+        if ldda == library_dataset.library_dataset_dataset_association:
+            current_version = True
+        else:
+            current_version = False
+    %>
+    <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}">
+        ## Header row for library items (name, state, action buttons)
+        <div class="historyItemTitleBar">     
+            <table cellspacing="0" cellpadding="0" border="0" width="100%">
+                <tr>
+                    <td width="*">
+                        %if selected:
+                            <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/>
+                        %else:
+                            <input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
+                        %endif
+                        <span class="libraryItemDeleted-${ldda.deleted}">
+                            <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a>
+                        </span>
+                        <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
+                        %if not library.deleted and not folder.deleted and not library_dataset.deleted:
+                            <div popupmenu="dataset-${ldda.id}-popup">
+                                <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
+                                ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
+                                ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
+                                <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
+                                %if current_version:
+                                    <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
+                                %endif
+                                %if ldda.has_data:
+                                    <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a>
+                                %endif
+                                <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a>
+                            </div>
+                        %elif not library.deleted and not folder.deleted and library_dataset.deleted:
+                            <div popupmenu="dataset-${ldda.id}-popup">
+                                <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a>
+                            </div>
+                        %endif
+                    </td>
+                    <td width="300">${ldda.message}</td>
+                    <td width="150">${uploaded_by}</td>
+                    <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
+                </tr>
+            </table>
+        </div>
+    </div>
+</%def>
+
+<%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id, root_folder=False )">
     <%
-        root_folder = not folder.parent
         if root_folder:
             pad = folder_pad
-        else:
-            pad = folder_pad + 20
-        if folder_pad == 0:
             expander = "/static/images/silk/resultset_bottom.png"
             folder_img = "/static/images/silk/folder_page.png"
-            subfolder = False
         else:
+            pad = folder_pad + 20
             expander = "/static/images/silk/resultset_next.png"
             folder_img = "/static/images/silk/folder.png"
-            subfolder = True
-        created_ldda_id_list = util.listify( created_ldda_ids )
-        if created_ldda_id_list:
-           created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ]
+        if created_ldda_ids:
+            created_ldda_ids = [ int( ldda_id ) for ldda_id in util.listify( created_ldda_ids ) ]
     %>
     %if not root_folder:
         <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;">
@@ -104,10 +155,6 @@ def name_sorted( l ):
                 </div>
             %endif
             %if not folder.deleted:
-                <%
-                    library_item_ids = {}
-                    library_item_ids[ 'folder' ] = folder.id
-                %>
                 <div popupmenu="folder-${folder.id}-popup">
                     <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
                     <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
@@ -130,30 +177,31 @@ def name_sorted( l ):
             %endif
         </li>
     %endif
-    %if subfolder:
+    %if pad > 0:
         <ul id="subFolder">
     %else:
         <ul>
     %endif
         %if show_deleted:
             <%
-                parent_folders = folder.activatable_folders
-                parent_datasets = folder.activatable_library_datasets
+                sub_folders, lddas = activatable_folders_and_lddas( trans, folder )
             %>
         %else:
             <%
-                parent_folders = folder.active_folders
-                parent_datasets = folder.active_library_datasets
+                sub_folders, lddas = active_folders_and_lddas( trans, folder )
             %>
         %endif
-        %for folder in name_sorted( parent_folders ):
-            ${render_folder( folder, pad, deleted, show_deleted, created_ldda_ids, library_id )}
-        %endfor    
-        %for library_dataset in name_sorted( parent_datasets ):
+        %for sub_folder in sub_folders:
+            ${render_folder( sub_folder, pad, deleted, show_deleted, created_ldda_ids, library_id )}
+        %endfor 
+        %for ldda in lddas:
             <%
-                selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids
+                library_dataset = ldda.library_dataset
+                selected = created_ldda_ids and ldda.id in created_ldda_ids
             %>
-            <li class="datasetRow" style="padding-left: ${pad + 18}px;">${render_dataset( library_dataset, selected, library, deleted, show_deleted )}</li>
+            <li class="datasetRow" style="padding-left: ${pad + 18}px;">
+                ${render_dataset( ldda, library_dataset, selected, library, folder, deleted, show_deleted )}
+            </li>
         %endfor
     </ul>
 </%def>
@@ -196,10 +244,6 @@ def name_sorted( l ):
                         <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
                         <div popupmenu="library-${library.id}-popup">
                         %if not deleted:
-                            <%
-                                library_item_ids = {}
-                                library_item_ids[ 'library' ] = library.id
-                            %>
                             <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this data library's information</a>
                             ## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition
                             ##%if library.info_association:
@@ -228,7 +272,7 @@ def name_sorted( l ):
             </div>
         </li>
         <ul>
-            ${render_folder( library.root_folder, 0, deleted, show_deleted, created_ldda_ids, library.id )}
+            ${render_folder( library.root_folder, 0, deleted, show_deleted, created_ldda_ids, library.id, root_folder=True )}
         </ul>
         <br/>
     </ul>

templates/admin/library/common.mako

@@ -1,68 +1,3 @@
-<% from time import strftime %>
-
-<%def name="render_dataset( library_dataset, selected, library, deleted, show_deleted )">
-    <%
-        ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu
-        ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always
-        ## lddas ).  We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes
-        ## from the ldda.
-        ldda = library_dataset.library_dataset_dataset_association
-        if ldda.user:
-            uploaded_by = ldda.user.email
-        else:
-            uploaded_by = 'anonymous'
-        if ldda == ldda.library_dataset.library_dataset_dataset_association:
-            current_version = True
-        else:
-            current_version = False
-    %>
-    <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}">
-        ## Header row for library items (name, state, action buttons)
-        <div class="historyItemTitleBar">     
-            <table cellspacing="0" cellpadding="0" border="0" width="100%">
-                <tr>
-                    <td width="*">
-                        %if selected:
-                            <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/>
-                        %else:
-                            <input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
-                        %endif
-                        <span class="libraryItemDeleted-${library_dataset.deleted}">
-                            <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a>
-                        </span>
-                        <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-                        %if not library.deleted and not library_dataset.folder.deleted and not library_dataset.deleted:
-                            <%
-                                library_item_ids = {}
-                                library_item_ids[ 'ldda' ] = ldda.id
-                            %>
-                            <div popupmenu="dataset-${ldda.id}-popup">
-                                <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
-                                ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use
-                                ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a>
-                                <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
-                                %if current_version:
-                                    <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
-                                %endif
-                                %if ldda.has_data:
-                                    <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a>
-                                %endif
-                                <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a>
-                            </div>
-                        %elif not library.deleted and not library_dataset.folder.deleted and library_dataset.deleted:
-                            <div popupmenu="dataset-${ldda.id}-popup">
-                                <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a>
-                            </div>
-                        %endif
-                    </td>
-                    <td width="300">${ldda.message}</td>
-                    <td width="150">${uploaded_by}</td>
-                    <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
-                </tr>
-            </table>
-        </div>
-    </div>
-</%def>
 
 <%def name="render_template_info( library_item, library_id, widgets, editable=True )">
     <%

templates/admin/library/ldda_info.mako

@@ -86,26 +86,14 @@
         <div class="form-row">
             <div>${ldda.blurb}</div>
         </div>
-        <div class="form-row">
-           <div id="info${ldda.id}" class="historyItemBody">
-                %if ldda.peek != "no peek":
+        %if ldda.peek != "no peek":
+            <div class="form-row">
+               <div id="info${ldda.id}" class="historyItemBody">
                     <label>Peek:</label>
                     <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
-                %endif
-                ## Recurse for child datasets
-                %if len( ldda.visible_children ) > 0:
-                    <div>
-                        There are ${len( ldda.visible_children )} secondary datasets.
-                        %for idx, child in enumerate( ldda.visible_children ):
-                            ## TODO: do we need to clarify if the child is deleted?
-                            %if not child.purged:
-                                ${ render_dataset( child, selected, library, False, False ) }
-                            %endif
-                        %endfor
-                    </div>
-                %endif
+                </div>
             </div>
-        </div>
+        %endif
     </div>
     %if widgets:
         ${render_template_info( ldda, library.id, widgets, editable=False )}

templates/dataset/edit_attributes.mako

@@ -190,7 +190,7 @@
 </div>
 <p />
 
-%if trans.app.security_agent.allow_action( user, user_roles, data.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=data.dataset ):
+%if trans.app.security_agent.can_manage_dataset( user_roles, data.dataset ):
     <%namespace file="/dataset/security_common.mako" import="render_permission_form" />
     ${render_permission_form( data.dataset, data.name, h.url_for( controller='root', action='edit', id=data.id ), user_roles )}
 %elif trans.user:

templates/library/browse_library.mako

@@ -2,6 +2,7 @@
 <%namespace file="/message.mako" import="render_msg" />
 <% 
     from galaxy import util
+    from galaxy.web.controllers.library import active_folders
     from time import strftime
     user, roles = trans.get_user_and_roles()
 %>
@@ -13,10 +14,6 @@
 </%def>
 
 <%
-
-def name_sorted( l ):
-    return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) )
-
 class RowCounter( object ):
     def __init__( self ):
         self.count = 0
@@ -82,21 +79,22 @@ class RowCounter( object ):
     });
 </script>
 
-<%def name="render_dataset( library_dataset, selected, library, pad, parent, row_conter )">
+<%def name="render_dataset( ldda, library_dataset, selected, library, folder, pad, parent, row_conter )">
     <%
-        ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu
-        ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always
-        ## lddas ).  We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes
+        ## The id passed to methods from the drop down menu should be the ldda id to prevent id collision
+        ## ( which could happen when displaying children, which are always lddas ).  We also need to make
+        ## sure we're displaying the latest version of this library_dataset, so we display the attributes
         ## from the ldda.
-        ldda = library_dataset.library_dataset_dataset_association
         if ldda.user:
             uploaded_by = ldda.user.email
         else:
             uploaded_by = 'anonymous'
-        if ldda == ldda.library_dataset.library_dataset_dataset_association:
+        if ldda == library_dataset.library_dataset_dataset_association:
             current_version = True
         else:
             current_version = False
+        can_modify_library_dataset = trans.app.security_agent.can_modify_library_item( user, roles, library_dataset )
+        can_manage_library_dataset = trans.app.security_agent.can_manage_library_item( user, roles, library_dataset )
     %>
 
     <tr class="datasetRow"
@@ -111,19 +109,19 @@ class RowCounter( object ):
             %else:
                 <input type="checkbox" name="ldda_ids" value="${ldda.id}"/>
             %endif
-            <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a>
+            <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a>
             <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
             <div popupmenu="dataset-${ldda.id}-popup">
-                %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
-                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
+                %if can_modify_library_dataset:
+                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
                 %else:
-                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
+                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
                 %endif
-                %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ):
-                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
-                %if current_version and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
-                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
+                %if can_manage_library_dataset:
+                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
                 %endif
+                %if current_version and can_modify_library_dataset:
+                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a>
                 %endif
                 %if ldda.has_data:
                     <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a>
@@ -141,7 +139,7 @@ class RowCounter( object ):
     %>
 </%def>
 
-<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None )">
+<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None, root_folder=False )">
     <%
         if str( folder.id ) in hidden_folder_ids:
             return ""
@@ -156,18 +154,15 @@ class RowCounter( object ):
                                                               trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ] )
             if not can_show:
                 return ""
-        root_folder = not folder.parent
         if root_folder:
             pad = folder_pad
         else:
             pad = folder_pad + 20
-        if folder_pad == 0:
-            subfolder = False
-        else:
-            subfolder = True
-        created_ldda_id_list = util.listify( created_ldda_ids )
-        if created_ldda_id_list:
-           created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ]
+        if created_ldda_ids:
+            created_ldda_ids = [ int( ldda_id ) for ldda_id in util.listify( created_ldda_ids ) ]
+        can_add = trans.app.security_agent.can_add_library_item( user, roles, folder )
+        can_modify = trans.app.security_agent.can_modify_library_item( user, roles, folder )
+        can_manage = trans.app.security_agent.can_manage_library_item( user, roles, folder )
         my_row = None
     %>
     %if not root_folder:
@@ -187,21 +182,19 @@ class RowCounter( object ):
                 %endif
                 <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
                 <div popupmenu="folder_img-${folder.id}-popup">
-                    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ):
+                    %if can_add:
                         <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a>
                         <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a>
                     %endif
-                    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ):
+                    %if can_modify:
                         <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a>
                     %else:
                         <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a>
                     %endif
-                    %if forms and not folder.info_association:
-                        %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ):
-                            <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this folder</a>
-                        %endif
+                    %if can_add and forms and not folder.info_association:
+                        <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this folder</a>
                     %endif
-                    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ):
+                    %if can_manage:
                         <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a>
                     %endif
                 </div>
@@ -213,43 +206,48 @@ class RowCounter( object ):
             row_counter.increment()
         %>
     %endif
-    %for child_folder in name_sorted( folder.active_folders ):
-        ${render_folder( child_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, my_row, row_counter )}
+    <% sub_folders = active_folders( trans, folder ) %>
+    %for sub_folder in sub_folders:
+        ${render_folder( sub_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, parent=my_row, row_counter=row_counter )}
     %endfor
-    %for library_dataset in name_sorted( folder.active_library_datasets ):
+    %for library_dataset in folder.active_library_datasets:
         <%
-            selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids
+            ldda = library_dataset.library_dataset_dataset_association
+            can_access = trans.app.security_agent.can_access_dataset( roles, ldda.dataset )
+            selected = created_ldda_ids and ldda.id in created_ldda_ids
         %>
-        %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ):
-            ${render_dataset( library_dataset, selected, library, pad, my_row, row_counter )}
+        %if can_access:
+            ${render_dataset( ldda, library_dataset, selected, library, folder, pad, my_row, row_counter )}
         %endif
     %endfor
 </%def>
 
 <h2>Data Library &ldquo;${library.name}&rdquo;</h2>
 
+<%
+can_add = trans.app.security_agent.can_add_library_item( user, roles, library )
+can_modify = trans.app.security_agent.can_modify_library_item( user, roles, library )
+can_manage = trans.app.security_agent.can_manage_library_item( user, roles, library )
+%>
+
 <ul class="manage-table-actions">
-    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ):
-            %if not deleted:
-                <li>
-                    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a>
-                </li>
-                <li>
-                    <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a>
-                </li>
-            %endif
+    %if can_add and not_deleted:
+        <li>
+            <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a>
+        </li>
+        <li>
+            <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a>
+        </li>
     %endif
-    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ):
+    %if can_modify:
         <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a></li>
     %else:
         <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li>
     %endif
-    %if forms and not library.info_association:
-        %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ):
-            <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a>
-        %endif
+    %if can_add and forms and not library.info_association:
+        <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a>
     %endif
-    %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ):
+    %if can_manage:
         <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li>
     %endif 
 </ul>
@@ -259,10 +257,6 @@ class RowCounter( object ):
 %endif
 
 <form name="import_from_library" action="${h.url_for( controller='library', action='datasets', library_id=library.id )}" method="post">
-    <%
-        library_item_ids = {}
-        library_item_ids[ 'library' ] = library.id
-    %>
     <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid">
         <thead>
             <tr class="libraryTitle">
@@ -273,7 +267,7 @@ class RowCounter( object ):
             </thead>
         </tr>
         <% row_counter = RowCounter() %>
-        ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, hidden_folder_ids, None, row_counter )}
+        ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, hidden_folder_ids, parent=None, row_counter=row_counter, root_folder=True )}
         <tfoot>
             <tr>
                 <td colspan="4" style="padding-left: 42px;">

templates/library/common.mako

@@ -21,7 +21,7 @@
         <div class="toolForm">
             <div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div>
             <div class="toolFormBody">
-                %if editable and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library_item ):
+                %if editable and trans.app.security_agent.can_modify_library_item( user, roles, library_item ):
                     <form name="edit_info" action="${h.url_for( controller='library', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post">
                         <input type="hidden" name="library_item_id" value="${library_item.id}"/>
                         <input type="hidden" name="library_item_type" value="${library_item_type}"/>

templates/library/folder_info.mako

@@ -18,7 +18,7 @@
 <div class="toolForm">
     <div class="toolFormTitle">Edit folder name and description</div>
     <div class="toolFormBody">
-        %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ):
+        %if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
             <form name="folder" action="${h.url_for( controller='library', action='folder', rename=True, id=folder.id, library_id=library_id )}" method="post" >
                 <div class="form-row">
                     <label>Name:</label>

templates/library/folder_permissions.mako

@@ -15,6 +15,6 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ):
+%if trans.app.security_agent.can_manage_library_item( user, roles, folder ):
     ${render_permission_form( folder, folder.name, h.url_for( controller='library', action='folder', id=folder.id, library_id=library_id, permissions=True ), trans.user.all_roles() )}
 %endif

templates/library/ldda_edit_info.mako

@@ -34,7 +34,7 @@
     </select>
 </%def>
 
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
+%if trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ):
     <div class="toolForm">
         <div class="toolFormTitle">Edit attributes of ${ldda.name}</div>
         <div class="toolFormBody">

templates/library/ldda_info.mako

@@ -40,15 +40,15 @@
         Information about ${ldda.name}
         <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
         <div popupmenu="dataset-${ldda.id}-popup">
-            %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
+            %if trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ):
                 <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a>
             %else:
                 <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a>
             %endif
-            %if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ):
+            %if trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ) and trans.app.security_agent.can_manage_library_item( user, roles, ldda.library_dataset ):
                 <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a>
             %endif
-            %if current_version and trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ):
+            %if current_version and trans.app.security_agent.can_modify_library_item( user, roles, ldda.library_dataset ):
                 <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a>
             %endif
             %if ldda.has_data:
@@ -86,28 +86,14 @@
         <div class="form-row">
             <div>${ldda.blurb}</div>
         </div>
-        <div class="form-row">
-           <div id="info${ldda.id}" class="historyItemBody">
-                %if ldda.peek != "no peek":
+        %if ldda.peek != "no peek":
+            <div class="form-row">
+               <div id="info${ldda.id}" class="historyItemBody">
                     <label>Peek:</label>
                     <div><pre id="peek${ldda.id}" class="peek">${ldda.display_peek()}</pre></div>
-                %endif
-                ## Recurse for child datasets
-                ## TODO: eliminate this - child datasets are deprecated, and where does
-                ## render_dataset() come from anyway - it's not imported!
-                %if len( ldda.visible_children ) > 0:
-                    <div>
-                        There are ${len( ldda.visible_children )} secondary datasets.
-                        %for idx, child in enumerate( ldda.visible_children ):
-                            ## TODO: do we need to clarify if the child is deleted?
-                            %if not child.purged:
-                                ${ render_dataset( child, selected, library ) }
-                            %endif
-                        %endfor
-                    </div>
-                %endif
+                </div>
             </div>
-        </div>
+        %endif
     </div>
     %if widgets:
         ${render_template_info( ldda, library_id, widgets, editable=False )}

templates/library/library_dataset_info.mako

@@ -21,7 +21,7 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library_dataset ):
+%if trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ):
     <div class="toolForm">
         <div class="toolFormTitle">Edit attributes of ${library_dataset.name}</div>
         <div class="toolFormBody">

templates/library/library_dataset_permissions.mako

@@ -21,7 +21,7 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, user_roles, trans.app.security_agent.permitted_actions.LIBRARY_manage, library_item=library_dataset ):
+%if trans.app.security_agent.can_manage_library_item( user, user_roles, library_dataset ):
     <%
         roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
     %>

templates/library/library_info.mako

@@ -15,7 +15,7 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ):
+%if trans.app.security_agent.can_modify_library_item( user, roles, library ):
     <div class="toolForm">
         <div class="toolFormTitle">Change library name and description</div>
         <div class="toolFormBody">

templates/library/library_permissions.mako

@@ -15,7 +15,7 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, user_roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ):
+%if trans.app.security_agent.can_manage_library_item( user, user_roles, library ):
     <%
         roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
     %>

templates/mobile/history/detail.mako

@@ -37,7 +37,7 @@
         <div class="secondary">
         ## Body for history items, extra info and actions, data "peek"
         	<% user, roles = trans.get_user_and_roles() %>
-            %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
+            %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ):
                 <div>You do not have permission to view this dataset.</div>
             %elif data_state == "queued":
                 <div>Job is waiting to run</div>

templates/mobile/manage_library.mako

@@ -9,7 +9,7 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ):
+%if trans.app.security_agent.can_modify_library_item( user, roles, library ):
     <div class="toolForm">
         <div class="toolFormTitle">Change library name and description</div>
         <div class="toolFormBody">
@@ -55,7 +55,7 @@
         </div>
     </div>
 %endif
-%if trans.app.security_agent.allow_action( user, roles, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ):
+%if trans.app.security_agent.can_manage_library_item( user, roles, library ):
     <%
         roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
     %>

templates/root/history_common.mako

@@ -8,7 +8,7 @@
     	    data_state = data.state
     	user, roles = trans.get_user_and_roles()
     %>
-    %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
+    %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ):
         <div class="historyItemWrapper historyItem historyItem-${data_state} historyItem-noPermission" id="historyItem-${data.id}">
     %else:
         <div class="historyItemWrapper historyItem historyItem-${data_state}" id="historyItem-${data.id}">
@@ -42,7 +42,7 @@
         ## Body for history items, extra info and actions, data "peek"
         
         <div id="info${data.id}" class="historyItemBody">
-            %if not trans.app.security_agent.allow_action( user, roles, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
+            %if not trans.app.security_agent.can_access_dataset( roles, data.dataset ):
                 <div>You do not have permission to view this dataset.</div>
             %elif data_state == "upload":
                 <div>Dataset is uploading</div>