mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
Split script into admin and dev
TODO: remove duplication between db.py and db_dev.py (split into multiple commits is intentional)
This commit is contained in:
John Davis
@@ -30,10 +30,6 @@ def exec_downgrade(args: Namespace) -> None:
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_exec_command("downgrade", args)
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def exec_revision(args: Namespace) -> None:
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_exec_command("revision", args)
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def exec_version(args: Namespace) -> None:
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_exec_command("version", args)
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@@ -42,14 +38,6 @@ def exec_dbversion(args: Namespace) -> None:
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_exec_command("dbversion", args)
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def exec_history(args: Namespace) -> None:
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_exec_command("history", args)
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def exec_show(args: Namespace) -> None:
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_exec_command("show", 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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@@ -89,11 +77,8 @@ def main() -> None:
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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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epilog="Note: these operations are applied to the Galaxy model only (stored in the `gxy` branch)."
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" For migrating the `tsi` branch, use the `run_alembic.sh` script.",
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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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parser.add_argument("--raiseerr", help="Raise a full stack trace on error", action="store_true")
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subparsers = parser.add_subparsers(required=True)
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@@ -129,29 +114,6 @@ def main() -> None:
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parents=[verbose_arg_parser],
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)
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history_cmd_parser = add_parser(
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"history",
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exec_history,
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"List revision scripts in chronological order",
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aliases=["h"],
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parents=[verbose_arg_parser],
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)
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history_cmd_parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
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show_cmd_parser = add_parser(
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"show",
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exec_show,
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"Show the revision(s) denoted by the given symbol",
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aliases=["s"],
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)
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show_cmd_parser.add_argument("revision", help="Revision identifier")
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revision_cmd_parser = add_parser("revision", help="Create a new revision file", func=exec_revision)
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revision_cmd_parser.add_argument("-m", "--message", help="Message string to use with 'revision'", required=True)
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revision_cmd_parser.add_argument(
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"--rev-id", help="Specify a revision id instead of generating one (This option is for testing purposes only)"
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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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@@ -0,0 +1,166 @@
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"""
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This script is intended to be invoked by the scripts/db_dev.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_revision(args: Namespace) -> None:
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_exec_command("revision", 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_history(args: Namespace) -> None:
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_exec_command("history", args)
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def exec_show(args: Namespace) -> None:
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_exec_command("show", 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="db_dev.py",
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description="Common database schema migration operations",
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epilog="Note: these operations are applied to the Galaxy model only (stored in the `gxy` branch)."
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" For migrating the `tsi` branch, use the `run_alembic.sh` script.",
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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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parser.add_argument("--raiseerr", help="Raise a full stack trace on error", action="store_true")
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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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history_cmd_parser = add_parser(
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"history",
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exec_history,
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"List revision scripts in chronological order",
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aliases=["h"],
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parents=[verbose_arg_parser],
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)
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history_cmd_parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
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show_cmd_parser = add_parser(
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"show",
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exec_show,
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"Show the revision(s) denoted by the given symbol",
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aliases=["s"],
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)
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show_cmd_parser.add_argument("revision", help="Revision identifier")
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revision_cmd_parser = add_parser("revision", help="Create a new revision file", func=exec_revision)
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revision_cmd_parser.add_argument("-m", "--message", help="Message string to use with 'revision'", required=True)
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revision_cmd_parser.add_argument(
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"--rev-id", help="Specify a revision id instead of generating one (This option is for testing purposes only)"
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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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Executable
+17
@@ -0,0 +1,17 @@
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#!/bin/sh
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#######
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# Extended set of database schema migration operaions.
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# For help, run `sh db_dev.sh -h`.
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# For detailed help, see documentation at lib/galaxy/model/migrations/README.md.
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#######
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cd "$(dirname "$0")" || exit
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cd ..
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. ./scripts/common_startup_functions.sh
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setup_python
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python scripts/db_dev.py "$@"
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