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Source code for galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column

Migration script to add the installed_changeset_revision column to the tool_shed_repository table.

import logging

from sqlalchemy import (

from galaxy.model.custom_types import TrimmedString
from galaxy.model.migrate.versions.util import (

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 " \ + f"SET installed_changeset_revision = '{row.changeset_revision}' " \ + f"WHERE changeset_revision = '{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)