Make activatable_datasets a property of the History object, eliminating the problematic mapper.

lib/galaxy/model/__init__.py

@@ -162,7 +162,6 @@ class History( object ):
         self.user = user
         self.datasets = []
         self.galaxy_sessions = []
-        
     def _next_hid( self ):
         # TODO: override this with something in the database that ensures 
         # better integrity
@@ -174,16 +173,14 @@ class History( object ):
                 if dataset.hid > last_hid:
                     last_hid = dataset.hid
             return last_hid + 1
-
     def add_galaxy_session( self, galaxy_session, association=None ):
         if association is None:
             self.galaxy_sessions.append( GalaxySessionToHistoryAssociation( galaxy_session, self ) )
         else:
             self.galaxy_sessions.append( association )
-
     def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid = True ):
         if isinstance( dataset, Dataset ):
-            dataset = HistoryDatasetAssociation( dataset = dataset )
+            dataset = HistoryDatasetAssociation( dataset = dataset, copied_from = dataset )
             dataset.flush()
         elif not isinstance( dataset, HistoryDatasetAssociation ):
             raise TypeError, "You can only add Dataset and HistoryDatasetAssociation instances to a history ( you tried to add %s )." % str( dataset )
@@ -198,22 +195,28 @@ class History( object ):
         else:
             if set_hid:
                 dataset.hid = self._next_hid()
+        dataset.history = self
         if genome_build not in [None, '?']:
             self.genome_build = genome_build
         self.datasets.append( dataset )
-
-    def copy(self):
-        des = History()
+    def copy( self, target_user = None ):
+        if not target_user:
+            target_user = self.user
+        des = History( user = target_user )
         des.flush()
         des.name = self.name
-        des.user_id = self.user_id
         for data in self.datasets:
-            new_data = data.copy( copy_children = True )
-            des.add_dataset( new_data )
+            new_data = data.copy( copy_children = True, target_history = des )
+            des.add_dataset( new_data, set_hid = False )
             new_data.flush()
         des.hid_counter = self.hid_counter
         des.flush()
         return des
+    @property
+    def activatable_datasets( self ):
+        for hda in self.datasets:
+            if not hda.dataset.purged:
+                yield hda
 
 # class Query( object ):
 #     def __init__( self, name=None, state=None, tool_parameters=None, history=None ):
@@ -656,66 +659,6 @@ class HistoryDatasetAssociation( DatasetInstance ):
             if not metadata_safe or not assoc.metadata_safe:
                 assoc.clear( purge = purge )
 
-class History( object ):
-    def __init__( self, id=None, name=None, user=None ):
-        self.id = id
-        self.name = name or "Unnamed history"
-        self.deleted = False
-        self.purged = False
-        self.genome_build = None
-        # Relationships
-        self.user = user
-        self.datasets = []
-        self.galaxy_sessions = []
-    def _next_hid( self ):
-        # TODO: override this with something in the database that ensures 
-        # better integrity
-        if len( self.datasets ) == 0:
-            return 1
-        else:
-            last_hid = 0
-            for dataset in self.datasets:
-                if dataset.hid > last_hid:
-                    last_hid = dataset.hid
-            return last_hid + 1
-    def add_galaxy_session( self, galaxy_session, association=None ):
-        if association is None:
-            self.galaxy_sessions.append( GalaxySessionToHistoryAssociation( galaxy_session, self ) )
-        else:
-            self.galaxy_sessions.append( association )
-    def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid = True ):
-        if isinstance( dataset, Dataset ):
-            dataset = HistoryDatasetAssociation( dataset = dataset, copied_from = dataset )
-            dataset.flush()
-        elif not isinstance( dataset, HistoryDatasetAssociation ):
-            raise TypeError, "You can only add Dataset and HistoryDatasetAssociation instances to a history."
-        if parent_id:
-            for data in self.datasets:
-                if data.id == parent_id:
-                    dataset.hid = data.hid
-                    break
-            else:
-                if set_hid: dataset.hid = self._next_hid()
-        else:
-            if set_hid: dataset.hid = self._next_hid()
-        dataset.history = self
-        if genome_build not in [None, '?']:
-            self.genome_build = genome_build
-        self.datasets.append( dataset )
-    def copy( self, target_user = None ):
-        if not target_user:
-            target_user = self.user
-        des = History( user = target_user )
-        des.flush()
-        des.name = self.name
-        for data in self.datasets:
-            new_data = data.copy( copy_children = True, target_history = des )
-            des.add_dataset( new_data, set_hid = False )
-            new_data.flush()
-        des.hid_counter = self.hid_counter
-        des.flush()
-        return des
-
 class Library( object ):
     permitted_actions = get_permitted_actions( filter='LIBRARY' )
     def __init__( self, name = None, description = None, root_folder = None ):

lib/galaxy/model/mapping.py

@@ -567,8 +567,7 @@ assign_mapper( context, ImplicitlyConvertedDatasetAssociation, ImplicitlyConvert
 assign_mapper( context, History, History.table,
     properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ),
                      datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ),
-                     active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ),
-                     activatable_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( Dataset.table.c.purged ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=True, viewonly=True )
+                     active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True )
                       ) )
 
 assign_mapper( context, User, User.table, 

lib/galaxy/security/__init__.py

@@ -219,13 +219,6 @@ class GalaxyRBACAgent( RBACAgent ):
                 dup.flush()
         if history:
             for history in user.active_histories:
-                """
-                TODO: instead of user.active_histories, a faster approach would be the following, but we need the 
-                history.activatable_datasets mapper corrected so that eagerload can be used.
-                histories = app.model.History.filter( and_( app.model.History.table.c.user_id==user.id,
-                                                            app.model.History.table.c.purged==False ) ) \
-                                             .options( eagerload( 'activatable_datasets' ) ).all()
-                """
                 self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission )
     def user_get_default_permissions( self, user ):
         permissions = {}

scripts/update_database/update_database_with_security_libraries.py

@@ -187,15 +187,8 @@ def main():
         # Add the new default permissions for the user
         dup = app.model.DefaultUserPermissions( user, default_user_action, private_role )
         dup.flush()
-        # Set DefaultHistoryPermissions on all of the user's active histories and associated datasets
-        # TODO: fix mapping for history.activatable_datasets so it doesn't throw an exception on the
-        # following query when eagerloading activatable_datasets.  Fix all of the queries below that 
-        # call history.active_datasets to be history.activatable_datasets when this works.
-        histories = app.model.History.filter( and_( app.model.History.table.c.user_id==user.id,
-                                                    app.model.History.table.c.purged==False ) ) \
-                                     .options( eagerload( 'active_datasets' ) ).all()
         print "Setting DefaultHistoryPermissions for %d un-purged histories associated with %s" % ( len( histories ), user.email )
-        for history in histories:
+        for history in user.active_histories:
             # Delete all of the current default permissions for the history
             for dhp in history.default_permissions:
                 dhp.delete()
@@ -203,9 +196,9 @@ def main():
             # Add the new default permissions for the history
             dhp = app.model.DefaultHistoryPermissions( history, default_user_action, private_role )
             dhp.flush()
-            print "Setting DatasetPermissionss for %d un-purged datasets in history %d" % ( len( history.active_datasets ), history.id )
+            print "Setting DatasetPermissionss for %d un-purged datasets in history %d" % ( len( history.activatable_datasets ), history.id )
             # Set the permissions on the current history's datasets that are not purged
-            for hda in history.active_datasets:
+            for hda in history.activatable_datasets:
                 dataset = hda.dataset
                 if dataset.library_associations:
                     # Don't change permissions on a dataset associated with a library

templates/root/history.mako

@@ -248,12 +248,7 @@ div#footer {
 
 <%namespace file="history_common.mako" import="render_dataset" />
 
-<%
-    activatable_datasets = []
-    for hda in history.datasets:
-        if not hda.dataset.purged:
-            activatable_datasets.append( hda )
-%>
+<% activatable_datasets = history.activatable_datasets %>
 
 %if ( show_deleted and not activatable_datasets ) or ( not show_deleted and not history.active_datasets ):
     <div class="infomessagesmall" id="emptyHistoryMessage">