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Change parsing of --galaxy-config option

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Rationale: alternate config file applies to all subcommands, so, I
think, it is more correct to run this:

> ./db.sh -c mygalaxy.yml upgrade some-revision-id

than this:

> ./db.sh upgrade some-revision-id -c mygalaxy.yml

That's also consistent with how alembic handles this option.
This commit is contained in:
John Davis
2022-09-28 15:24:49 -04:00
parent bf83b4347a
commit 889a8445bd
1 changed files with 8 additions and 12 deletions
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scripts/db.py
+8 -12
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@@ -67,8 +67,7 @@ def main() -> None:
return parser
config_arg_parser = ArgumentParser(add_help=False)
# TODO: after refactoring legacy scripts, this can be changed to "-c, --config"
config_arg_parser.add_argument("--galaxy-config", help="Alternate Galaxy configuration file", dest="config")
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")
@@ -84,6 +83,7 @@ def main() -> None:
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)
@@ -93,7 +93,7 @@ def main() -> None:
exec_upgrade,
"Upgrade to a later version",
aliases=["u"],
parents=[config_arg_parser, sql_arg_parser],
parents=[sql_arg_parser],
)
upgrade_cmd_parser.add_argument("revision", help="Revision identifier", nargs="?")
@@ -102,7 +102,7 @@ def main() -> None:
exec_downgrade,
"Revert to a previous version",
aliases=["d"],
parents=[config_arg_parser, sql_arg_parser],
parents=[sql_arg_parser],
)
downgrade_cmd_parser.add_argument("revision", help="Revision identifier")
@@ -111,7 +111,7 @@ def main() -> None:
exec_version,
"Show the head revision in the migrations script directory",
aliases=["v"],
parents=[config_arg_parser, verbose_arg_parser],
parents=[verbose_arg_parser],
)
add_parser(
@@ -119,14 +119,14 @@ def main() -> None:
exec_dbversion,
"Show the current revision for Galaxy's database",
aliases=["dbv"],
parents=[config_arg_parser, verbose_arg_parser],
parents=[verbose_arg_parser],
)
history_cmd_parser = add_parser(
"history",
exec_history,
"List revision scripts in chronological order",
parents=[config_arg_parser, verbose_arg_parser],
parents=[verbose_arg_parser],
)
history_cmd_parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
@@ -134,13 +134,10 @@ def main() -> None:
"show",
exec_show,
"Show the revision(s) denoted by the given symbol",
parents=[config_arg_parser],
)
show_cmd_parser.add_argument("revision", help="Revision identifier")
revision_cmd_parser = add_parser(
"revision", aliases=["r"], help="Create a new revision file", parents=[config_arg_parser], func=exec_revision
)
revision_cmd_parser = add_parser("revision", aliases=["r"], 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")
@@ -148,7 +145,6 @@ def main() -> None:
"init",
exec_init,
"Initialize empty database(s) for both branches (create database objects for gxy and tsi branch)",
parents=[config_arg_parser],
)
args = parser.parse_args()