diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index e00325885f8..054aa4698de 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -1,5 +1,5 @@
-from galaxy.web.base.controller import *
 
+from galaxy.web.base.controller import *
 import logging, sets, time
 
 log = logging.getLogger( __name__ )
@@ -20,51 +20,57 @@ class Admin( BaseController ):
                 msg = self.abandon( **kwd )
         
         users, data = [], []
-        for row in trans.model.User.table.select().execute():
-            users.append(row)
-        for row in trans.model.Dataset.table.select().execute():
-            data.append(row)
-        
+        ut = trans.model.User.table
+        dt = trans.model.Dataset.table
+        for row in ut.select().execute():
+            users.append( row )
+        for row in dt.select().execute():
+            data.append( row )
         qsize = self.app.job_queue.queue.qsize() 
         return trans.fill_template('admin_main.tmpl', toolbox=self.app.toolbox, users=users, data=data, qsize=qsize,msg=msg)
         
-    
     def abandon( self, **kwd ):
+        """
+        'Abandons' userless histories older than the specified number of days by setting the 'deleted'
+        column to 't' in the History table for each History.id whose History.user_id column is null.
+        A list of each of the affected history records is generated during the process.  This list is
+        then used to find all undeleted datasets that are associated with these histories.  Each of
+        these datasets is then deleted by setting the Dataset.deleted column to 't'.  Nothing is removed
+        from the file system.  This function should be executed in preparation for purging datasets using 
+        the purge() function below.
+        """
         params = util.Params(kwd)
         msg = ''
-        if params.days:
+        if params.abandon_days:
             if params.passwd==self.app.config.admin_pass:
                 days = int(params.abandon_days)
-                
                 histories_no_users = []
                 history_count = 0
-                for row in self.app.model.History.table.select().execute():
-                    try:
-                        int(row.user_id)
-                    except:
-                        history = self.app.model.History.get(row.id)
-                        now  = time.time()
-                        last = time.mktime( time.strptime( history.update_time.strftime('%a %b %d %H:%M:%S %Y') )) 
-                        diff = (now - last) /3600/24 # days
-                        if diff>days:
-                            histories_no_users.append(row.id)
-                            if history.deleted: continue #we don't add to history delete count, but we do want to be able to make sure datasets associated with deleted histories are really deleted
+                ht = self.app.model.History.table
+                for row in ht.select( ht.c.user_id==None ).execute():
+                    now  = time.time()
+                    last = time.mktime( time.strptime( row.update_time.strftime( '%a %b %d %H:%M:%S %Y' ) ) ) 
+                    diff = (now-last)/3600/24 # days
+                    if diff > days:
+                        histories_no_users.append( row.id )
+                        if not row.deleted:
+                            log.warn( "Updating history table, setting id %s to deleted" %str( row.id ) )
+                            history = self.app.model.History.get( row.id )
                             history.deleted = True
                             history_count += 1
-                
                 dataset_count = 0
-                for row in self.app.model.Dataset.table.select().execute():
+                dt = self.app.model.Dataset.table
+                for row in dt.select( dt.c.deleted=='f' ).execute():
                     if row.history_id in histories_no_users:
-                        #delete dataset
-                        data = self.app.model.Dataset.get(row.id)
-                        if data.deleted: continue
+                        log.warn( "Updating dataset table, setting id %s to deleted" %str( row.id ) )
+                        data = self.app.model.Dataset.get( row.id )
                         data.deleted = True
                         dataset_count += 1
                 try:
                     self.app.model.flush()
                 except:
                     pass
-                msg = 'deleted %d abandoned histories with %d total datasets' % ( history_count, dataset_count )
+                msg = 'Deleted %d histories (including a total of %d datasets )' % ( history_count, dataset_count )
             else:
                 msg = 'Invalid password'
         return msg
@@ -77,57 +83,28 @@ class Admin( BaseController ):
             if params.passwd==self.app.config.admin_pass:
                 days = int(params.purge_days)
                 count = 0
-                now  = time.time()
-                for row in self.app.model.Dataset.table.select().execute():
-                    data = self.app.model.Dataset.get(row.id)
-                    if data.deleted and not data.purged:
-                        last = time.mktime( time.strptime( data.update_time.strftime('%a %b %d %H:%M:%S %Y') ))
-                        diff = (now - last) /3600/24 # days
-                        if diff>days:
-                            data.purge()
-                            count += 1
-                try:
-                    self.app.model.flush()
-                except:
-                    pass
-                msg = 'Purged %d datasets' % count
-            else:
-                msg = 'Invalid password'
-        return msg
-    
-    def delete( self, **kwd ):
-        params = util.Params(kwd)
-        msg = ''
-        if params.days:
-            if params.passwd==self.app.config.admin_pass:
-                days = int(params.days)
-                values = []
-                for row in self.app.model.Dataset.table.select().execute():
-                    values.append(self.app.model.Dataset.get(row.id))
-                for row in self.app.model.History.table.select().execute():
-                    values.append(self.app.model.History.get(row.id))
-                #for row in self.app.model.User.table.select().execute():
-                #    values.append(self.app.model.User.get(row.id))
-                count = 0
-                for value in values:
-                    now  = time.time()
-                    last = time.mktime( time.strptime( value.update_time.strftime('%a %b %d %H:%M:%S %Y') ))
-                    diff = (now - last) /3600/24 # days
-                    if diff>days:
-                        #value.delete()
-                        value.deleted = True
+                now = time.time()
+                dt = self.app.model.Dataset.table
+                for row in dt.select( ( dt.c.purged=='f' ) & ( dt.c.deleted=='t' ) ).execute():
+                    last = time.mktime( time.strptime( row.update_time.strftime( '%a %b %d %H:%M:%S %Y' ) ) )
+                    diff = (now-last)/3600/24 # days
+                    if diff > days:
+                        log.warn( "Purging dataset id %s" %str( row.id ) )
+                        data = app.model.Dataset.get( row.id )
+                        data.purge()
+                        data.flush()
                         count += 1
                 try:
                     self.app.model.flush()
                 except:
                     pass
-                msg = 'Deleted %d objects' % count
+                msg = 'purged %d datasets' % count
             else:
                 msg = 'Invalid password'
         return msg
 
     def tool_reload( self, **kwd ):
-        params = util.Params(kwd)
+        params = util.Params( kwd )
         if params.passwd==self.app.config.admin_pass:
             tool_id = params.tool_id
             self.app.toolbox.reload( tool_id )
diff --git a/lib/galaxy/webapps/reports/base/controller.py b/lib/galaxy/webapps/reports/base/controller.py
index 4b77b886ad4..956c97d41bf 100644
--- a/lib/galaxy/webapps/reports/base/controller.py
+++ b/lib/galaxy/webapps/reports/base/controller.py
@@ -1,27 +1,15 @@
 """Contains functionality needed in every webapp interface"""
 
 import os, time, logging
-
 # Pieces of Galaxy to make global in every controller
-#from galaxy import config, tools, web, model, util
 from galaxy import web
-
 from Cheetah.Template import Template
 
 log = logging.getLogger( __name__ )
 
 class BaseController( object ):
     """Base class for Galaxy webapp application controllers."""
-    
     beta = False
-
     def __init__( self, app ):
         """Initialize an interface for application 'app'"""
-        self.app = app
-
-    #def get_toolbox(self):
-    #    """Returns the application toolbox"""
-    #    return self.app.toolbox
-        
-#Root = BaseController
-"""Deprecated: `BaseController` used to be available under the name `Root`"""
\ No newline at end of file
+        self.app = app
\ No newline at end of file
diff --git a/lib/galaxy/webapps/reports/controllers/system.py b/lib/galaxy/webapps/reports/controllers/system.py
index 1914dfe54d5..7fb466132be 100644
--- a/lib/galaxy/webapps/reports/controllers/system.py
+++ b/lib/galaxy/webapps/reports/controllers/system.py
@@ -1,15 +1,8 @@
-import sys, sets, string, shutil
-import re, socket
-
-from galaxy import web
-
-from cgi import escape, FieldStorage
-import urllib
 
 import operator, os
 from galaxy.webapps.reports.base.controller import *
 
-import logging, sets, time
+import logging
 log = logging.getLogger( __name__ )
 
 class System( BaseController ):
@@ -23,29 +16,24 @@ class System( BaseController ):
         while True:
             df_line = df_file.readline()
             df_line = df_line.strip()
-            #log.debug("df_line: '%s'" %df_line)
             if df_line:
                 df_line = df_line.lower()
                 if 'filesystem' in df_line or 'proc' in df_line:
                     continue
                 elif is_sym_link:
-                    #log.debug("We have a symlink...")
                     if ':' in df_line and '/' in df_line:
                         mount = df_line
-                        #log.debug("mount: '%s'" %mount)
                     else:
                         try:
                             disk_size, disk_used, disk_avail, disk_cap_pct, file_system = df_line.split()
                             break
                         except:
-                            #log.debug("In symlink try, df_line: '%s'" %df_line)
                             pass
                 else:
                     try:
                         file_system, disk_size, disk_used, disk_avail, disk_cap_pct, mount = df_line.split()
                         break
                     except:
-                        #log.debug("In 2nd try, df_line: '%s'" %df_line)
                         pass
             else:
                 break # EOF
diff --git a/scripts/cleanup_datasets.py b/scripts/cleanup_datasets.py
index e9ef05c38fa..70bb61ae3dd 100644
--- a/scripts/cleanup_datasets.py
+++ b/scripts/cleanup_datasets.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python2.4
 #Dan Blankenberg
-"""
-Allows dataset cleanup.
-"""
 
 import sys, os, time, ConfigParser
 from optparse import OptionParser
@@ -10,79 +7,91 @@ import galaxy.app
 
 def main():
     parser = OptionParser()
-    parser.add_option("-d", "--days", dest="days", action="store", type="int", help="number of days (30)", default=30)
-    parser.add_option("-a", "--abandon", action="store_true", dest="abandon", default=False, help="abandon old, unowned (userless) histories")
-    parser.add_option("-p", "--purge", action="store_true", dest="purge", default=False, help="purge old deleted datasets")
-    (options, args) = parser.parse_args()
+    parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (30)", default=30 )
+    parser.add_option( "-a", "--abandon", action="store_true", dest="abandon", default=False, help="abandon old, unowned (userless) histories" )
+    parser.add_option( "-p", "--purge", action="store_true", dest="purge", default=False, help="purge old deleted datasets" )
+    ( options, args ) = parser.parse_args()
     ini_file = args[0]
     
-    if not (options.purge ^ options.abandon):
+    if not ( options.purge ^ options.abandon ):
         parser.print_help()
         sys.exit(0)
     
-    conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
-    conf_parser.read(ini_file)
+    conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
+    conf_parser.read( ini_file )
     configuration = {}
-    for key, value in conf_parser.items("app:main"): configuration[key] = value
+    for key, value in conf_parser.items("app:main"):
+        configuration[key] = value
     app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
-    msg = None
+    msg = ''
     if options.purge:
-        msg = purge(app, options.days)
+        msg = purge( app, options.days )
     elif options.abandon:
-        msg = abandon(app, options.days)
+        msg = abandon( app, options.days )
     app.shutdown()
     if msg:
-        print
-        print "Number of days buffered: %i" % options.days
-        print msg
+        print "\n%s older than %i days.\n" % ( msg, options.days )
     sys.exit(0)
 
 def abandon( app, days ):
-    """ Abandons userless histories older than specified number of days """
+    """
+    'Abandons' userless histories older than the specified number of days by setting the 'deleted'
+    column to 't' in the History table for each History.id whose History.user_id column is null.
+    A list of each of the affected history records is generated during the process.  This list is
+    then used to find all undeleted datasets that are associated with these histories.  Each of
+    these datasets is then deleted by setting the Dataset.deleted column to 't'.  Nothing is removed
+    from the file system.  This function should be executed in preparation for purging datasets using 
+    the purge() function below.
+    """
     histories_no_users = []
     history_count = 0
-    for row in app.model.History.table.select().execute():
-        try:
-            int(row.user_id)
-        except:
-            history = app.model.History.get(row.id)
-            now  = time.time()
-            last = time.mktime( time.strptime( history.update_time.strftime('%a %b %d %H:%M:%S %Y') )) 
-            diff = (now - last) /3600/24 # days
-            if diff>days:
-                histories_no_users.append(row.id)
-                if history.deleted: continue #we don't add to history delete count, but we do want to be able to make sure datasets associated with deleted histories are really deleted
+    ht = app.model.History.table
+    # Generate a list of userless histories, deleting the histories along the way
+    for row in ht.select( ht.c.user_id==None ).execute():
+        now  = time.time()
+        last = time.mktime( time.strptime( row.update_time.strftime( '%a %b %d %H:%M:%S %Y' ) ) ) 
+        diff = (now-last)/3600/24 # days
+        if diff > days:
+            histories_no_users.append( row.id )
+            if not row.deleted:
+                print "Updating history table, setting id %s to deleted" %str( row.id )
+                history = app.model.History.get( row.id )
                 history.deleted = True
                 history_count += 1
-    
     dataset_count = 0
-    for row in app.model.Dataset.table.select().execute():
+    dt = app.model.Dataset.table
+    # Delete all datasets associated with previously deleted userless histories
+    for row in dt.select( dt.c.deleted=='f' ).execute():
         if row.history_id in histories_no_users:
-            #delete dataset
-            data = app.model.Dataset.get(row.id)
-            if data.deleted: continue
+            print "Updating dataset table, setting id %s to deleted" %str( row.id )
+            data = app.model.Dataset.get( row.id )
             data.deleted = True
             dataset_count += 1
     try:
         app.model.flush()
     except:
         pass
-    msg = 'deleted %d abandoned histories with %d total datasets' % ( history_count, dataset_count )
+    msg = 'Deleted %d histories (including a total of %d datasets )' % ( history_count, dataset_count )
     return msg
 
 def purge( app, days ):
-    """ Purges deleted datasets older than specified number of days """
+    """
+    Purges deleted datasets older than specified number of days by executing the Dataset.purge() function.
+    This will update the Dataset table, setting Dataset.deleted to 't', Dataset.purged to 't', and
+    Dataset.file_size to 0.  The dataset file will then be removed from the file system.
+    """
     count = 0
-    now  = time.time()
-    for row in list(app.model.Dataset.table.select().execute()):
-        data = app.model.Dataset.get(row.id)
-        if data.deleted and not data.purged:
-            last = time.mktime( time.strptime( data.update_time.strftime('%a %b %d %H:%M:%S %Y') ))
-            diff = (now - last) /3600/24 # days
-            if diff>days:
-                data.purge()
-                data.flush()
-                count += 1
+    now = time.time()
+    dt = app.model.Dataset.table
+    for row in dt.select( ( dt.c.purged=='f' ) & ( dt.c.deleted=='t' ) ).execute():
+        last = time.mktime( time.strptime( row.update_time.strftime( '%a %b %d %H:%M:%S %Y' ) ) )
+        diff = (now-last)/3600/24 # days
+        if diff > days:
+            print "Purging dataset id %s" %str( row.id )
+            data = app.model.Dataset.get( row.id )
+            data.purge()
+            data.flush()
+            count += 1
     try:
         app.model.flush()
     except:
@@ -90,6 +99,5 @@ def purge( app, days ):
     msg = 'Purged %d datasets' % count
     return msg
 
-
 if __name__ == "__main__":
     main()
\ No newline at end of file
diff --git a/templates/admin_main.tmpl b/templates/admin_main.tmpl
index b902fcc5070..f28caa5241d 100644
--- a/templates/admin_main.tmpl
+++ b/templates/admin_main.tmpl
@@ -1,61 +1,56 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
 <html>
-
-<head>
-<title>Galaxy Administration</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<link href="$h.url_for('/static/universe.css')" rel="stylesheet" type="text/css" />
-</head>
-
-<body>
-
-<table align="center" width="60%" class="border" cellpadding="5" cellspacing="5">
-   <tr><td>
-      <h3 align="center">Galaxy Administration</h3>
-      #if $msg:
-         <p class="ok_bgr">$msg</p>
-      #end if
-      <p>
-      #set $ulen = len($users)
-      #set $dlen = len($data)
-      <ul>
-         <li>$ulen users</li>
-         <li>$dlen data entries</li>
-         <li>$qsize jobs in the queue</li>
-      </ul>
-      </p>
-   </td></tr>
-   <tr><td>
-      <form method="post" action="admin">
-         <p>Admin password: <input type="password" name="passwd" size="8"> </p>
-         <p>
-         Purge deleted datasets older than <input type="textfield" value="30" size="3" name="purge_days"> days.
-         <button name="action" value="purge">Purge</button>
-         </p>
-#*
-         <p>
-         Delete objects older than <input type="textfield" value="120" size="3" name="days"> days.
-         <button name="action" value="delete">Delete</button>
-         </p>
-*#
-         <p>
-         Delete abandoned histories older than <input type="textfield" value="14" size="3" name="abandon_days"> days.
-         <button name="action" value="abandon">Abandon</button>
-         </p>
-         <p>
-         Reload tool: <select name="tool_id">
-                        #for $i, $section in enumerate( $toolbox.sections )
-                            <optgroup label="$section.name">
-                            #for $t in $section.tools
-                                <option value="$t.id">$t.name</option>
-                            #end for
-                        #end for
-                     </select>
-         <button name="action" value="tool_reload">Reload</button>
-         </p>
-      </form>
-   </td></tr>
-</table>
-
-</body>
+  <head>
+    <title>Galaxy Administration</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+    <link href="$h.url_for('/static/universe.css')" rel="stylesheet" type="text/css" />
+  </head>
+  <body>
+    <table align="center" width="60%" class="border" cellpadding="5" cellspacing="5">
+      <tr>
+        <td>
+          <h3 align="center">Galaxy Administration</h3>
+          #if $msg:
+            <p class="ok_bgr">$msg</p>
+          #end if
+          <p>
+            #set $ulen = len($users)
+            #set $dlen = len($data)
+            <ul>
+              <li>$ulen users</li>
+              <li>$dlen data entries</li>
+              <li>$qsize jobs in the queue</li>
+            </ul>
+          </p>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <form method="post" action="admin">
+            <p>Admin password: <input type="password" name="passwd" size="8"></p>
+            <p>
+              Purge deleted datasets older than <input type="textfield" value="30" size="3" name="purge_days"> days.
+              <button name="action" value="purge">Purge</button>
+            </p>
+            <p>
+              Delete abandoned histories older than <input type="textfield" value="30" size="3" name="abandon_days"> days.
+              <button name="action" value="abandon">Abandon</button>
+            </p>
+            <p>
+              Reload tool: 
+              <select name="tool_id">
+                #for $i, $section in enumerate( $toolbox.sections )
+                  <optgroup label="$section.name">
+                  #for $t in $section.tools
+                    <option value="$t.id">$t.name</option>
+                  #end for
+                #end for
+              </select>
+              <button name="action" value="tool_reload">Reload</button>
+            </p>
+          </form>
+        </td>
+      </tr>
+    </table>
+  </body>
 </html>
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 75e17cf85d7..47ded80faa2 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -35,6 +35,10 @@ job_queue_cleanup_interval = 30
 database_file = database/universe.sqlite
 # You may use a SQLAlchemy connection string to specify an external database instead
 ## database_connection = postgres:///galaxy_test
+## database_engine_option_echo = true
+## database_engine_option_echo_pool = true
+## database_engine_option_pool_size = 10
+## database_engine_option_max_overflow = 20
 
 # Where dataset files are saved
 file_path = database/files