Initial fix for concurrent update db issue (still using psycopg). Commented out "job requeued" log statement. Changed error reporting email in config.

lib/galaxy/jobs/__init__.py

@@ -134,7 +134,7 @@ class JobQueue( object ):
                 job_state = job.check_if_ready_to_run()
                 if job_state == JOB_WAIT: 
                     new_waiting.append( job )
-                    log.debug( "job has been requeued" )
+                    #log.debug( "job has been requeued" )
                 elif job_state == JOB_ERROR:
                     log.info( "job %d ended with an error" %job.job_id )
                 elif job_state == JOB_READY:

lib/galaxy/model/mapping.py

@@ -2,6 +2,8 @@
 Details of how the data model objects are mapped onto the relational database
 are encapsulated here. 
 """
+import logging
+log = logging.getLogger( __name__ )
 
 import pkg_resources
 pkg_resources.require( "pysqlite>=2", "sqlalchemy>=0.3" )
@@ -252,9 +254,24 @@ def init( file_path, url, **kwargs ):
                 table.columns['create_time'].type = TIMESTAMP()
             if table.columns.has_key( "update_time" ):
                 table.columns['update_time'].type = TIMESTAMP()
-                table.columns['update_time'].type = TIMESTAMP()
-    # Connect the metadata the database. 
-    metadata.connect( url, **kwargs )
+    # Connect the metadata to the database. 
+    if url.find( "sqlite" ) < 0 and url.find( '///' ) >= 0:
+        import psycopg
+        try:
+            dbconn = url.split('///')
+            dbtype = dbconn[0]
+            dbname = dbconn[1]
+            def connect():
+                connection = psycopg.connect( 'dbname=%s' %dbname )
+                connection.set_isolation_level(1)
+                return connection
+            engine = create_engine('%s///' %dbtype, creator=connect)
+            metadata.connect( engine )
+        except:
+            log.exception( "error connecting to database using connection: '%s'." % url )
+            metadata.connect( url, **kwargs )
+    else:
+        metadata.connect( url, **kwargs )
     ## metadata.engine.echo = True
     # Create tables if needed
     if create_tables:

test/functional/test_history_functions.py

@@ -7,7 +7,7 @@ class TestHistory( TwillTestCase ):
         self.logout()    #Ensure we are not logged in
         self.history_options()
         self.check_page_for_string( 'logged in</a> to store or switch histories.' )
-        self.login( email='test2@bx.psu.edu' ) #Just to make sure we hav created this account since it is used to share histories
+        self.login( email='test2@bx.psu.edu' ) #Just to make sure we have created this account since it is used to share histories
         self.logout()
     def test_05_new_history_then_delete( self ):
         """Testing creating a new history and then deleting it"""

universe_wsgi.ini.sample

@@ -80,7 +80,7 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
 
 # Mail
 smtp_server = coltrane.bx.psu.edu
-error_email_to = james@bx.psu.edu
+error_email_to = galaxy_bugs@bx.psu.edu
 
 # Use the new iframe / javascript based layout
 use_new_layout = true