/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 48 lines · 36 code · 5 blank · 7 comment · 2 complexity · 661f256c2ab8d7adbb89d51aa4dd1da6 MD5 · raw file
- """
- This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
- allowing existing metadata files to be written when using external metadata and a cluster
- set up with read-only access to database/files
- """
- from sqlalchemy import *
- from sqlalchemy.orm 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()
- def display_migration_details():
- print "========================================"
- print "This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,"
- print" allowing existing metadata files to be written when using external metadata and a cluster"
- print "set up with read-only access to database/files"
- print "========================================"
- def upgrade(migrate_engine):
- metadata.bind = migrate_engine
- display_migration_details()
- # Load existing tables
- metadata.reflect()
- try:
- job_external_output_metadata = Table( "job_external_output_metadata", metadata, autoload=True )
- col = Column( "filename_override_metadata", String( 255 ) )
- col.create( job_external_output_metadata )
- assert col is job_external_output_metadata.c.filename_override_metadata
- except Exception, e:
- log.debug( "Adding column 'filename_override_metadata' to job_external_output_metadata table failed: %s" % ( str( e ) ) )
- def downgrade(migrate_engine):
- metadata.bind = migrate_engine
- pass