diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index f39d33d7657..c4fcef62056 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/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: diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index bfbed5553ff..ad6785a8c66 100644 --- a/lib/galaxy/model/mapping.py +++ b/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: diff --git a/test/functional/test_history_functions.py b/test/functional/test_history_functions.py index 489d0350aff..fae75ba49d3 100644 --- a/test/functional/test_history_functions.py +++ b/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 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""" diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index b114e94a016..19d80bfa4af 100644 --- a/universe_wsgi.ini.sample +++ b/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