mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
John Davis
bd56131ebd
TODO: remove duplication between db.py and db_dev.py (split into multiple commits is intentional)
129 lines
3.5 KiB
Python
129 lines
3.5 KiB
Python
"""
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This script is intended to be invoked by the manage_db.sh script.
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"""
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import logging
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import os
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import sys
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from argparse import (
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ArgumentParser,
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Namespace,
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)
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import alembic
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
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from galaxy.model.migrations import verify_databases_via_script
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from galaxy.model.migrations.dbscript import DbScript
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from galaxy.model.migrations.scripts import get_configuration
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logging.basicConfig(level=logging.DEBUG)
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log = logging.getLogger(__name__)
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def exec_upgrade(args: Namespace) -> None:
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_exec_command("upgrade", args)
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def exec_downgrade(args: Namespace) -> None:
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_exec_command("downgrade", args)
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def exec_version(args: Namespace) -> None:
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_exec_command("version", args)
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def exec_dbversion(args: Namespace) -> None:
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_exec_command("dbversion", args)
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def exec_init(args: Namespace) -> None:
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gxy_config, tsi_config, is_auto_migrate = get_configuration(sys.argv, os.getcwd())
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verify_databases_via_script(gxy_config, tsi_config, is_auto_migrate)
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def _exec_command(command: str, args: Namespace) -> None:
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dbscript = DbScript(args.config)
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try:
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getattr(dbscript, command)(args)
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except alembic.util.exc.CommandError as e:
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if args.raiseerr:
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raise
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else:
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log.error(e)
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print(f"FAILED: {str(e)}")
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sys.exit(1)
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def main() -> None:
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def add_parser(command, func, help, aliases=None, parents=None):
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aliases = aliases or []
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parents = parents or []
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parser = subparsers.add_parser(command, aliases=aliases, help=help, parents=parents)
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parser.set_defaults(func=func)
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return parser
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verbose_arg_parser = ArgumentParser(add_help=False)
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verbose_arg_parser.add_argument("-v", "--verbose", action="store_true", help="Display more detailed output")
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sql_arg_parser = ArgumentParser(add_help=False)
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sql_arg_parser.add_argument(
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"--sql",
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action="store_true",
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help="Don't emit SQL to database - dump to standard output/file instead. See Alembic docs on offline mode.",
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)
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parser = ArgumentParser(
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prog="manage_db.sh",
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description="Common database schema migration operations",
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)
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parser.add_argument("-c", "--galaxy-config", help="Alternate Galaxy configuration file", dest="config")
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subparsers = parser.add_subparsers(required=True)
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upgrade_cmd_parser = add_parser(
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"upgrade",
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exec_upgrade,
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"Upgrade to a later version",
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parents=[sql_arg_parser],
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)
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upgrade_cmd_parser.add_argument("revision", help="Revision identifier", nargs="?")
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downgrade_cmd_parser = add_parser(
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"downgrade",
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exec_downgrade,
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"Revert to a previous version",
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parents=[sql_arg_parser],
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)
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downgrade_cmd_parser.add_argument("revision", help="Revision identifier")
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add_parser(
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"version",
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exec_version,
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"Show the head revision in the migrations script directory",
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aliases=["v"],
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parents=[verbose_arg_parser],
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)
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add_parser(
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"dbversion",
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exec_dbversion,
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"Show the current revision for Galaxy's database",
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aliases=["dv"],
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parents=[verbose_arg_parser],
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)
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add_parser(
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"init",
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exec_init,
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"Initialize empty database(s) for both branches (create database objects for gxy and tsi branch)",
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)
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args = parser.parse_args()
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args.func(args)
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if __name__ == "__main__":
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main()
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