Source code for galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column

"""
Migration script to add the installed_changeset_revision column to the tool_shed_repository table.
"""
from __future__ import print_function

import logging

from sqlalchemy import (
    Column,
    MetaData
)

from galaxy.model.custom_types import TrimmedString
from galaxy.model.migrate.versions.util import (
    add_column,
    drop_column
)

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


[docs]def upgrade(migrate_engine):
    print(__doc__)
    metadata.bind = migrate_engine
    metadata.reflect()

    col = Column("installed_changeset_revision", TrimmedString(255))
    add_column(col, 'tool_shed_repository', metadata)
    # Update each row by setting the value of installed_changeset_revison to be the value of changeset_revision.
    # This will be problematic if the value of changeset_revision was updated to something other than the value
    # that it was when the repository was installed (because the install path determined in real time will attempt to
    # find the repository using the updated changeset_revison instead of the required installed_changeset_revision),
    # but at the time this script was written, this scenario is extremely unlikely.
    cmd = "SELECT id AS id, " \
        + "installed_changeset_revision AS installed_changeset_revision, " \
        + "changeset_revision AS changeset_revision " \
        + "FROM tool_shed_repository;"
    tool_shed_repositories = migrate_engine.execute(cmd).fetchall()
    update_count = 0
    for row in tool_shed_repositories:
        cmd = "UPDATE tool_shed_repository " \
            + "SET installed_changeset_revision = '%s' " % row.changeset_revision \
            + "WHERE changeset_revision = '%s';" % row.changeset_revision
        migrate_engine.execute(cmd)
        update_count += 1
    print("Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table.")


[docs]def downgrade(migrate_engine):
    metadata.bind = migrate_engine
    metadata.reflect()

    drop_column('installed_changeset_revision', 'tool_shed_repository', metadata)