Source code for tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table

"""
Migration script to add the includes_datatypes, has_repository_dependencies, includes_tools, includes_tool_dependencies and includes_workflows
columns to the repository_metadata table.
"""

import logging
import sys

from sqlalchemy import (
    Boolean,
    Column,
    MetaData,
    Table,
)

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 ["postgres", "postgresql"]:
        default_false = "false"
    # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table.
    RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)

    # Create tools_functionally_correct column
    c = Column("includes_datatypes", Boolean, default=False, index=True)
    try:
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_datatypes")
        assert c is RepositoryMetadata_table.c.includes_datatypes
        migrate_engine.execute(f"UPDATE repository_metadata SET includes_datatypes={default_false}")
    except Exception:
        log.exception("Adding includes_datatypes column to the repository_metadata table failed.")

    # Create includes_datatypes column
    c = Column("has_repository_dependencies", Boolean, default=False, index=True)
    try:
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_has_repo_deps")
        assert c is RepositoryMetadata_table.c.has_repository_dependencies
        migrate_engine.execute(f"UPDATE repository_metadata SET has_repository_dependencies={default_false}")
    except Exception:
        log.exception("Adding has_repository_dependencies column to the repository_metadata table failed.")

    # Create includes_tools column
    c = Column("includes_tools", Boolean, default=False, index=True)
    try:
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_tools")
        assert c is RepositoryMetadata_table.c.includes_tools
        migrate_engine.execute(f"UPDATE repository_metadata SET includes_tools={default_false}")
    except Exception:
        log.exception("Adding includes_tools column to the repository_metadata table failed.")

    # Create includes_tool_dependencies column
    c = Column("includes_tool_dependencies", Boolean, default=False, index=True)
    try:
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_tool_deps")
        assert c is RepositoryMetadata_table.c.includes_tool_dependencies
        migrate_engine.execute(f"UPDATE repository_metadata SET includes_tool_dependencies={default_false}")
    except Exception:
        log.exception("Adding includes_tool_dependencies column to the repository_metadata table failed.")

    # Create includes_workflows column
    c = Column("includes_workflows", Boolean, default=False, index=True)
    try:
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_workflows")
        assert c is RepositoryMetadata_table.c.includes_workflows
        migrate_engine.execute(f"UPDATE repository_metadata SET includes_workflows={default_false}")
    except Exception:
        log.exception("Adding includes_workflows column to the repository_metadata table failed.")


[docs]def downgrade(migrate_engine):
    metadata.bind = migrate_engine
    metadata.reflect()
    # Drop tool_test_errors, time_last_tested, do_not_test, and tools_functionally_correct columns from repository_metadata table.
    RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)

    # Drop the includes_workflows column.
    try:
        RepositoryMetadata_table.c.includes_workflows.drop()
    except Exception:
        log.exception("Dropping column includes_workflows from the repository_metadata table failed.")

    # Drop the includes_tool_dependencies column.
    try:
        RepositoryMetadata_table.c.includes_tool_dependencies.drop()
    except Exception:
        log.exception("Dropping column includes_tool_dependencies from the repository_metadata table failed.")

    # Drop the includes_tools column.
    try:
        RepositoryMetadata_table.c.includes_tools.drop()
    except Exception:
        log.exception("Dropping column includes_tools from the repository_metadata table failed.")

    # Drop the has_repository_dependencies column.
    try:
        RepositoryMetadata_table.c.has_repository_dependencies.drop()
    except Exception:
        log.exception("Dropping column has_repository_dependencies from the repository_metadata table failed.")

    # Drop the includes_datatypes column.
    try:
        RepositoryMetadata_table.c.includes_datatypes.drop()
    except Exception:
        log.exception("Dropping column includes_datatypes from the repository_metadata table failed.")