Source code for galaxy.webapps.tool_shed.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns

"""
Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table.
"""
from __future__ import print_function

import logging
import sys

from sqlalchemy import Boolean, Column, DateTime, MetaData, Table

# 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()
    # 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)
    c = Column("tools_functionally_correct", Boolean, default=False, index=True)
    try:
        # Create tools_functionally_correct column
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tfc")
        assert c is RepositoryMetadata_table.c.tools_functionally_correct
        # Initialize.
        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
            default_false = "0"
        elif migrate_engine.name in ['postgresql', 'postgres']:
            default_false = "false"
        migrate_engine.execute("UPDATE repository_metadata SET tools_functionally_correct=%s" % default_false)
    except Exception:
        log.exception("Adding tools_functionally_correct column to the repository_metadata table failed.")
    c = Column("do_not_test", Boolean, default=False, index=True)
    try:
        # Create do_not_test column
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_dnt")
        assert c is RepositoryMetadata_table.c.do_not_test
        # Initialize.
        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
            default_false = "0"
        elif migrate_engine.name in ['postgresql', 'postgres']:
            default_false = "false"
        migrate_engine.execute("UPDATE repository_metadata SET do_not_test=%s" % default_false)
    except Exception:
        log.exception("Adding do_not_test column to the repository_metadata table failed.")
    c = Column("time_last_tested", DateTime, default=None, nullable=True)
    try:
        # Create time_last_tested column
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tlt")
        assert c is RepositoryMetadata_table.c.time_last_tested
    except Exception:
        log.exception("Adding time_last_tested column to the repository_metadata table failed.")
    c = Column("tool_test_errors", JSONType, nullable=True)
    try:
        # Create tool_test_errors column
        c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tte")
        assert c is RepositoryMetadata_table.c.tool_test_errors
    except Exception:
        log.exception("Adding tool_test_errors 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)
    try:
        RepositoryMetadata_table.c.tool_test_errors.drop()
    except Exception:
        log.exception("Dropping column tool_test_errors from the repository_metadata table failed.")
    try:
        RepositoryMetadata_table.c.time_last_tested.drop()
    except Exception:
        log.exception("Dropping column time_last_tested from the repository_metadata table failed.")
    try:
        RepositoryMetadata_table.c.do_not_test.drop()
    except Exception:
        log.exception("Dropping column do_not_test from the repository_metadata table failed.")
    try:
        RepositoryMetadata_table.c.tools_functionally_correct.drop()
    except Exception:
        log.exception("Dropping column tools_functionally_correct from the repository_metadata table failed.")