[2] | 1 | """ |
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| 2 | This migration script changes certain values in the history_dataset_association.extension |
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| 3 | column, specifically 'qual' is chaged to be 'qual454'. |
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| 4 | """ |
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| 5 | from sqlalchemy import * |
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| 6 | from sqlalchemy.orm import * |
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| 7 | from migrate import * |
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| 8 | import sys, logging |
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| 9 | |
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| 10 | log = logging.getLogger( __name__ ) |
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| 11 | log.setLevel(logging.DEBUG) |
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| 12 | handler = logging.StreamHandler( sys.stdout ) |
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| 13 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 14 | formatter = logging.Formatter( format ) |
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| 15 | handler.setFormatter( formatter ) |
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| 16 | log.addHandler( handler ) |
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| 17 | |
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| 18 | metadata = MetaData( migrate_engine ) |
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| 19 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 20 | |
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| 21 | def display_migration_details(): |
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| 22 | print "========================================" |
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| 23 | print "This migration script changes certain values in the history_dataset_association.extension" |
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| 24 | print "column, specifically 'qual' is chaged to be 'qual454'." |
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| 25 | print "========================================" |
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| 26 | |
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| 27 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) |
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| 28 | |
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| 29 | def upgrade(): |
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| 30 | display_migration_details() |
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| 31 | # Load existing tables |
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| 32 | metadata.reflect() |
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| 33 | # Add 2 indexes to the galaxy_user table |
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| 34 | i = Index( 'ix_hda_extension', HistoryDatasetAssociation_table.c.extension ) |
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| 35 | try: |
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| 36 | i.create() |
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| 37 | except Exception, e: |
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| 38 | log.debug( "Adding index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) ) |
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| 39 | |
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| 40 | # Set the default data in the galaxy_user table, but only for null values |
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| 41 | cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'" |
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| 42 | try: |
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| 43 | db_session.execute( cmd ) |
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| 44 | except Exception, e: |
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| 45 | log.debug( "Resetting extension qual to qual454 in history_dataset_association failed: %s" % ( str( e ) ) ) |
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| 46 | cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'" |
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| 47 | try: |
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| 48 | db_session.execute( cmd ) |
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| 49 | except Exception, e: |
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| 50 | log.debug( "Resetting extension qual to qualsolexa in history_dataset_association failed: %s" % ( str( e ) ) ) |
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| 51 | # Add 1 index to the history_dataset_association table |
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| 52 | try: |
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| 53 | i.drop() |
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| 54 | except Exception, e: |
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| 55 | log.debug( "Dropping index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) ) |
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| 56 | |
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| 57 | def downgrade(): |
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| 58 | pass |
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