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.")