from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime now = datetime.datetime.utcnow import sys, logging # Need our custom types, but don't import anything else from model from galaxy.model.custom_types import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) format = "%(name)s %(levelname)s %(asctime)s %(message)s" formatter = logging.Formatter( format ) handler.setFormatter( formatter ) log.addHandler( handler ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "" print "========================================" print """This script creates a job_to_output_library_dataset table for allowing library uploads to run as regular jobs. To support this, a library_folder_id column is added to the job table, and library_folder/output_library_datasets relations are added to the Job object. An index is also added to the dataset.state column.""" print "========================================" JobToOutputLibraryDatasetAssociation_table = Table( "job_to_output_library_dataset", metadata, Column( "id", Integer, primary_key=True ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), Column( "name", String(255) ) ) def upgrade(): display_migration_details() # Load existing tables metadata.reflect() # Create the job_to_output_library_dataset table try: JobToOutputLibraryDatasetAssociation_table.create() except Exception, e: print "Creating job_to_output_library_dataset table failed: %s" % str( e ) log.debug( "Creating job_to_output_library_dataset table failed: %s" % str( e ) ) # Create the library_folder_id column try: Job_table = Table( "job", metadata, autoload=True ) except NoSuchTableError: Job_table = None log.debug( "Failed loading table job" ) if Job_table: try: col = Column( "library_folder_id", Integer, index=True ) col.create( Job_table ) assert col is Job_table.c.library_folder_id except Exception, e: log.debug( "Adding column 'library_folder_id' to job table failed: %s" % ( str( e ) ) ) try: LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) except NoSuchTableError: LibraryFolder_table = None log.debug( "Failed loading table library_folder" ) # Add 1 foreign key constraint to the job table if Job_table and LibraryFolder_table: try: cons = ForeignKeyConstraint( [Job_table.c.library_folder_id], [LibraryFolder_table.c.id], name='job_library_folder_id_fk' ) # Create the constraint cons.create() except Exception, e: log.debug( "Adding foreign key constraint 'job_library_folder_id_fk' to table 'library_folder' failed: %s" % ( str( e ) ) ) # Create the ix_dataset_state index try: Dataset_table = Table( "dataset", metadata, autoload=True ) except NoSuchTableError: Dataset_table = None log.debug( "Failed loading table dataset" ) i = Index( "ix_dataset_state", Dataset_table.c.state ) try: i.create() except Exception, e: print str(e) log.debug( "Adding index 'ix_dataset_state' to dataset table failed: %s" % str( e ) ) def downgrade(): metadata.reflect() # Drop the library_folder_id column try: Job_table = Table( "job", metadata, autoload=True ) except NoSuchTableError: Job_table = None log.debug( "Failed loading table job" ) if Job_table: try: col = Job_table.c.library_folder_id col.drop() except Exception, e: log.debug( "Dropping column 'library_folder_id' from job table failed: %s" % ( str( e ) ) ) # Drop the job_to_output_library_dataset table try: JobToOutputLibraryDatasetAssociation_table.drop() except Exception, e: print str(e) log.debug( "Dropping job_to_output_library_dataset table failed: %s" % str( e ) ) # Drop the ix_dataset_state index try: Dataset_table = Table( "dataset", metadata, autoload=True ) except NoSuchTableError: Dataset_table = None log.debug( "Failed loading table dataset" ) i = Index( "ix_dataset_state", Dataset_table.c.state ) try: i.drop() except Exception, e: print str(e) log.debug( "Dropping index 'ix_dataset_state' from dataset table failed: %s" % str( e ) )