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Source code for tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns

"""
Migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns
tool_test_results, missing_test_components.
"""

import logging
import sys

from sqlalchemy import (
    Boolean,
    Column,
    MetaData,
    Table,
)
from sqlalchemy.exc import NoSuchTableError

# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import JSONType

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()


[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() # Initialize. if migrate_engine.name == "mysql" or migrate_engine.name == "sqlite": default_false = "0" elif migrate_engine.name in ["postgresql", "postgres"]: default_false = "false" try: RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True) except NoSuchTableError: RepositoryMetadata_table = None log.debug("Failed loading table repository_metadata.") if RepositoryMetadata_table is not None: # Drop the tool_test_errors column from the repository_metadata table as it is poorly named. It will be replaced with the new # tool_test_results column. try: col = RepositoryMetadata_table.c.tool_test_errors col.drop() except Exception: log.exception("Dropping column 'tool_test_errors' from repository_metadata table failed.") # Create the tool_test_results column to replace the ill-named tool_test_errors column just dropped above. c = Column("tool_test_results", JSONType, nullable=True) try: c.create(RepositoryMetadata_table) assert c is RepositoryMetadata_table.c.tool_test_results except Exception: log.exception("Adding tool_test_results column to the repository_metadata table failed.") # Create the missing_test_components column. c = Column("missing_test_components", Boolean, default=False, index=True) try: c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_mtc") assert c is RepositoryMetadata_table.c.missing_test_components migrate_engine.execute(f"UPDATE repository_metadata SET missing_test_components={default_false}") except Exception: log.exception("Adding missing_test_components column to the repository_metadata table failed.")
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # Drop missing_test_components and tool_test_results from the repository_metadata table and add tool_test_errors to the repository_metadata table. RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True) # Drop the missing_test_components column. try: RepositoryMetadata_table.c.missing_test_components.drop() except Exception: log.exception("Dropping column missing_test_components from the repository_metadata table failed.") # Drop the tool_test_results column. try: RepositoryMetadata_table.c.tool_test_results.drop() except Exception: log.exception("Dropping column tool_test_results from the repository_metadata table failed.") # Create the tool_test_errors column. c = Column("tool_test_errors", JSONType, nullable=True) try: c.create(RepositoryMetadata_table) assert c is RepositoryMetadata_table.c.tool_test_errors except Exception: log.exception("Adding tool_test_errors column to the repository_metadata table failed.")