Merge pull request #907 from dannon/quota_bugfix

Quota bugfixes

lib/galaxy/jobs/__init__.py

@@ -1322,14 +1322,14 @@ def path_rewriter( path ):
                              tool=self.tool, stdout=job.stdout, stderr=job.stderr )
         job.command_line = self.command_line
 
-        bytes = 0
+        collected_bytes = 0
         # Once datasets are collected, set the total dataset size (includes extra files)
         for dataset_assoc in job.output_datasets:
             dataset_assoc.dataset.dataset.set_total_size()
-            bytes += dataset_assoc.dataset.dataset.get_total_size()
+            collected_bytes += dataset_assoc.dataset.dataset.get_total_size()
 
         if job.user:
-            job.user.total_disk_usage += bytes
+            job.user.adjust_total_disk_usage(collected_bytes)
 
         # Empirically, we need to update job.user and
         # job.workflow_invocation_step.workflow_invocation in separate

lib/galaxy/managers/hdas.py

@@ -160,7 +160,7 @@ def purge( self, hda, flush=True):
         super( HDAManager, self ).purge( hda, flush=flush )
         # decrease the user's space used
         if quota_amount_reduction:
-            user.total_disk_usage -= quota_amount_reduction
+            user.adjust_total_disk_usage(-quota_amount_reduction)
         return hda
 
     # .... states

lib/galaxy/model/__init__.py

@@ -204,6 +204,9 @@ def set_disk_usage( self, bytes ):
 
     total_disk_usage = property( get_disk_usage, set_disk_usage )
 
+    def adjust_total_disk_usage( self, amount ):
+        self.disk_usage = func.coalesce(self.table.c.disk_usage, 0) + amount
+
     @property
     def nice_total_disk_usage( self ):
         """
@@ -1103,7 +1106,7 @@ def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid=True,
             if set_hid:
                 dataset.hid = self._next_hid()
         if quota and self.user:
-            self.user.total_disk_usage += dataset.quota_amount( self.user )
+            self.user.adjust_total_disk_usage(dataset.quota_amount(self.user))
         dataset.history = self
         if genome_build not in [None, '?']:
             self.genome_build = genome_build

lib/galaxy/web/framework/webapp.py

@@ -603,7 +603,7 @@ def handle_user_login( self, user ):
                     if prev_galaxy_session.user is None:
                         # Increase the user's disk usage by the amount of the previous history's datasets if they didn't already own it.
                         for hda in history.datasets:
-                            user.total_disk_usage += hda.quota_amount( user )
+                            user.adjust_total_disk_usage(hda.quota_amount(user))
             elif self.galaxy_session.current_history:
                 history = self.galaxy_session.current_history
             if (not history and users_last_session and

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -899,7 +899,7 @@ def _purge( self, trans, dataset_id ):
             # HDA is purgeable
             # Decrease disk usage first
             if user:
-                user.total_disk_usage -= hda.quota_amount( user )
+                user.adjust_total_disk_usage(-hda.quota_amount(user))
             # Mark purged
             hda.purged = True
             trans.sa_session.add( hda )

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -350,7 +350,7 @@ def _list_delete( self, trans, histories, purge=False ):
                 if purge and trans.app.config.allow_user_dataset_purge:
                     for hda in history.datasets:
                         if trans.user:
-                            trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+                            trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user))
                         hda.purged = True
                         trans.sa_session.add( hda )
                         trans.log_event( "HDA id %s has been purged" % hda.id )
@@ -1112,7 +1112,7 @@ def purge_deleted_datasets( self, trans ):
                 if not hda.deleted or hda.purged:
                     continue
                 if trans.user:
-                    trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+                    trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user))
                 hda.purged = True
                 trans.sa_session.add( hda )
                 trans.log_event( "HDA id %s has been purged" % hda.id )
@@ -1142,7 +1142,7 @@ def delete_current( self, trans, purge=False ):
         if purge and trans.app.config.allow_user_dataset_purge:
             for hda in history.datasets:
                 if trans.user:
-                    trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+                    trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user))
                 hda.purged = True
                 trans.sa_session.add( hda )
                 trans.log_event( "HDA id %s has been purged" % hda.id )

scripts/cleanup_datasets/cleanup_datasets.py

@@ -483,7 +483,7 @@ def _purge_dataset( app, dataset, remove_from_disk, info_only=False ):
                                 if hda.history.user is not None and hda.history.user not in usage_users:
                                     usage_users.append( hda.history.user )
                         for user in usage_users:
-                            user.total_disk_usage -= dataset.get_total_size()
+                            user.adjust_total_disk_usage(-dataset.get_total_size())
                             app.sa_session.add( user )
                     print "Purging dataset id", dataset.id
                     dataset.purged = True

test/unit/test_galaxy_mapping.py

@@ -230,6 +230,17 @@ def test_collections_in_library_folders(self):
         # self.assertEquals(len(loaded_dataset_collection.datasets), 2)
         # assert loaded_dataset_collection.collection_type == "pair"
 
+    def test_default_disk_usage( self ):
+        model = self.model
+
+        u = model.User( email="disk_default@test.com", password="password" )
+        self.persist( u )
+        u.adjust_total_disk_usage( 1 )
+        u_id = u.id
+        self.expunge()
+        user_reload = model.session.query( model.User ).get( u_id )
+        assert user_reload.disk_usage == 1
+
     def test_basic( self ):
         model = self.model