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Source code for galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table

Migration script to add 'purged' column to the library_dataset table.

import logging

from sqlalchemy import Boolean, Column, MetaData

from galaxy.model.migrate.versions.util import add_column, drop_column, engine_false, engine_true

log = logging.getLogger(__name__)
metadata = MetaData()

[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() c = Column('purged', Boolean, index=True, default=False) add_column(c, 'library_dataset', metadata, index_name='ix_library_dataset_purged') # Update the purged flag to the default False cmd = f"UPDATE library_dataset SET purged = {engine_false(migrate_engine)};" try: migrate_engine.execute(cmd) except Exception: log.exception("Setting default data for library_dataset.purged column failed.") # Update the purged flag for those LibraryDatasets whose purged flag should be True. This happens # when the LibraryDataset has no active LibraryDatasetDatasetAssociations. cmd = f"SELECT * FROM library_dataset WHERE deleted = {engine_true(migrate_engine)};" deleted_lds = migrate_engine.execute(cmd).fetchall() for row in deleted_lds: cmd = "SELECT * FROM library_dataset_dataset_association WHERE library_dataset_id = %d AND library_dataset_dataset_association.deleted = %s;" % (int(row.id), engine_false(migrate_engine)) active_lddas = migrate_engine.execute(cmd).fetchall() if not active_lddas: print("Updating purged column to True for LibraryDataset id : ", int(row.id)) cmd = "UPDATE library_dataset SET purged = %s WHERE id = %d;" % (engine_true(migrate_engine), int(row.id)) migrate_engine.execute(cmd)
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite if migrate_engine.name != 'sqlite': drop_column('purged', 'library_dataset', metadata)