mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 02:21:32 +08:00
John Davis
330d2043c1
1. Remove aliases from subcommands that change things (upgrade, downgrade, revision, init) to reduce risk of accidental usage. 2. Add aliases to readonly subcommands (history, show, version, dbversion) 3. Minor edits
158 lines
4.6 KiB
Python
158 lines
4.6 KiB
Python
"""
|
|
This script is intended to be invoked by the db.sh script.
|
|
"""
|
|
|
|
import logging
|
|
import os
|
|
import sys
|
|
from argparse import (
|
|
ArgumentParser,
|
|
Namespace,
|
|
)
|
|
|
|
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
|
|
|
|
from galaxy.model.migrations import verify_databases_via_script
|
|
from galaxy.model.migrations.dbscript import DbScript
|
|
from galaxy.model.migrations.scripts import get_configuration
|
|
|
|
logging.basicConfig(level=logging.DEBUG)
|
|
log = logging.getLogger(__name__)
|
|
|
|
|
|
def exec_upgrade(args: Namespace) -> None:
|
|
_exec_command("upgrade", args)
|
|
|
|
|
|
def exec_downgrade(args: Namespace) -> None:
|
|
_exec_command("downgrade", args)
|
|
|
|
|
|
def exec_revision(args: Namespace) -> None:
|
|
_exec_command("revision", args)
|
|
|
|
|
|
def exec_version(args: Namespace) -> None:
|
|
_exec_command("version", args)
|
|
|
|
|
|
def exec_dbversion(args: Namespace) -> None:
|
|
_exec_command("dbversion", args)
|
|
|
|
|
|
def exec_history(args: Namespace) -> None:
|
|
_exec_command("history", args)
|
|
|
|
|
|
def exec_show(args: Namespace) -> None:
|
|
_exec_command("show", args)
|
|
|
|
|
|
def exec_init(args: Namespace) -> None:
|
|
gxy_config, tsi_config, is_auto_migrate = get_configuration(sys.argv, os.getcwd())
|
|
verify_databases_via_script(gxy_config, tsi_config, is_auto_migrate)
|
|
|
|
|
|
def _exec_command(command, args):
|
|
dbscript = DbScript(args.config)
|
|
getattr(dbscript, command)(args)
|
|
|
|
|
|
def main() -> None:
|
|
def add_parser(command, func, help, aliases=None, parents=None):
|
|
aliases = aliases or []
|
|
parents = parents or []
|
|
parser = subparsers.add_parser(command, aliases=aliases, help=help, parents=parents)
|
|
parser.set_defaults(func=func)
|
|
return parser
|
|
|
|
config_arg_parser = ArgumentParser(add_help=False)
|
|
config_arg_parser.add_argument("-c", "--galaxy-config", help="Alternate Galaxy configuration file", dest="config")
|
|
|
|
verbose_arg_parser = ArgumentParser(add_help=False)
|
|
verbose_arg_parser.add_argument("-v", "--verbose", action="store_true", help="Display more detailed output")
|
|
|
|
sql_arg_parser = ArgumentParser(add_help=False)
|
|
sql_arg_parser.add_argument(
|
|
"--sql",
|
|
action="store_true",
|
|
help="Don't emit SQL to database - dump to standard output/file instead. See Alembic docs on offline mode.",
|
|
)
|
|
|
|
parser = ArgumentParser(
|
|
description="Common database schema migration operations",
|
|
epilog="Note: these operations are applied to the Galaxy model only (stored in the `gxy` branch)."
|
|
" For migrating the `tsi` branch, use the `run_alembic.sh` script.",
|
|
parents=[config_arg_parser],
|
|
)
|
|
|
|
subparsers = parser.add_subparsers(required=True)
|
|
|
|
upgrade_cmd_parser = add_parser(
|
|
"upgrade",
|
|
exec_upgrade,
|
|
"Upgrade to a later version",
|
|
parents=[sql_arg_parser],
|
|
)
|
|
upgrade_cmd_parser.add_argument("revision", help="Revision identifier", nargs="?")
|
|
|
|
downgrade_cmd_parser = add_parser(
|
|
"downgrade",
|
|
exec_downgrade,
|
|
"Revert to a previous version",
|
|
parents=[sql_arg_parser],
|
|
)
|
|
downgrade_cmd_parser.add_argument("revision", help="Revision identifier")
|
|
|
|
add_parser(
|
|
"version",
|
|
exec_version,
|
|
"Show the head revision in the migrations script directory",
|
|
aliases=["v"],
|
|
parents=[verbose_arg_parser],
|
|
)
|
|
|
|
add_parser(
|
|
"dbversion",
|
|
exec_dbversion,
|
|
"Show the current revision for Galaxy's database",
|
|
aliases=["dv"],
|
|
parents=[verbose_arg_parser],
|
|
)
|
|
|
|
history_cmd_parser = add_parser(
|
|
"history",
|
|
exec_history,
|
|
"List revision scripts in chronological order",
|
|
aliases=["h"],
|
|
parents=[verbose_arg_parser],
|
|
)
|
|
history_cmd_parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
|
|
|
|
show_cmd_parser = add_parser(
|
|
"show",
|
|
exec_show,
|
|
"Show the revision(s) denoted by the given symbol",
|
|
aliases=["s"],
|
|
)
|
|
show_cmd_parser.add_argument("revision", help="Revision identifier")
|
|
|
|
revision_cmd_parser = add_parser("revision", help="Create a new revision file", func=exec_revision)
|
|
revision_cmd_parser.add_argument("-m", "--message", help="Message string to use with 'revision'", required=True)
|
|
revision_cmd_parser.add_argument(
|
|
"--rev-id", help="Specify a revision id instead of generating one (This option is for testing purposes only)"
|
|
)
|
|
|
|
add_parser(
|
|
"init",
|
|
exec_init,
|
|
"Initialize empty database(s) for both branches (create database objects for gxy and tsi branch)",
|
|
)
|
|
|
|
args = parser.parse_args()
|
|
args.func(args)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|