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Source code for galaxy.model.migrate.versions.0006_change_qual_datatype
"""
This migration script changes certain values in the history_dataset_association.extension
column, specifically 'qual' is changed to be 'qual454'.
"""
import logging
from sqlalchemy import MetaData
log = logging.getLogger(__name__)
metadata = MetaData()
[docs]def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
# Set the default data in the galaxy_user table, but only for null values
cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'"
try:
migrate_engine.execute(cmd)
except Exception:
log.exception("Resetting extension qual to qual454 in history_dataset_association failed.")
cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'"
try:
migrate_engine.execute(cmd)
except Exception:
log.exception("Resetting extension qual to qualsolexa in history_dataset_association failed.")