mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 10:24:38 +08:00
Implement script handling for TS migrations; refactor core
This commit is contained in:
John Davis
@@ -0,0 +1,266 @@
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import abc
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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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from typing import (
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List,
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Optional,
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)
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import alembic
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from alembic import command
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from alembic.config import Config
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logging.basicConfig(level=logging.DEBUG)
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log = logging.getLogger(__name__)
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class BaseParserBuilder(abc.ABC):
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"""
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Assembler object that simplifies the construction of an argument parser for database migration scripts.
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"""
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@abc.abstractmethod
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def _get_command_object(self):
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...
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def __init__(self, parser, subcommand_required=True):
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self._cmd = self._get_command_object()
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self.parser = parser
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self.subparsers = parser.add_subparsers(required=subcommand_required)
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self._init_arg_parsers()
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def add_upgrade_command(self):
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parser = self._add_parser(
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"upgrade",
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self._cmd.upgrade,
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"Upgrade to a later version",
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parents=[self._sql_arg_parser],
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)
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parser.add_argument("revision", help="Revision identifier or release tag", nargs="?")
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def add_downgrade_command(self):
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parser = self._add_parser(
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"downgrade",
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self._cmd.downgrade,
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"Revert to a previous version",
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parents=[self._sql_arg_parser],
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)
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parser.add_argument("revision", help="Revision identifier or release tag")
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def add_version_command(self):
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self._add_parser(
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"version",
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self._cmd.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=[self._verbose_arg_parser],
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)
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def add_dbversion_command(self):
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self._add_parser(
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"dbversion",
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self._cmd.dbversion,
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"Show the current revision for the database",
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aliases=["dv"],
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parents=[self._verbose_arg_parser],
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)
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def add_init_command(self):
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self._add_parser(
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"init",
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self._cmd.init,
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"Initialize empty database(s)",
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)
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def add_revision_command(self):
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parser = self._add_parser("revision", help="Create a new revision file", func=self._cmd.revision)
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parser.add_argument("-m", "--message", help="Message string to use with 'revision'", required=True)
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parser.add_argument(
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"--rev-id",
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help="Specify a revision id instead of generating one (This option is for testing purposes only)",
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)
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def add_history_command(self):
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parser = self._add_parser(
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"history",
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self._cmd.history,
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"List revision scripts in chronological order",
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aliases=["h"],
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parents=[self._verbose_arg_parser],
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)
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parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
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def add_show_command(self):
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parser = self._add_parser(
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"show",
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self._cmd.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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parser.add_argument("revision", help="Revision identifier")
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def _init_arg_parsers(self):
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self._verbose_arg_parser = self._make_verbose_arg_parser()
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self._sql_arg_parser = self._make_sql_arg_parser()
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def _make_verbose_arg_parser(self):
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parser = ArgumentParser(add_help=False)
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parser.add_argument("-v", "--verbose", action="store_true", help="Display more detailed output")
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return parser
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def _make_sql_arg_parser(self):
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parser = ArgumentParser(add_help=False)
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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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return parser
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def _add_parser(self, 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 = self.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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class BaseDbScript(abc.ABC):
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"""
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Facade for common database schema migration operations on the gxy branch.
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When the gxy and tsi branches are persisted in the same database, some
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alembic commands will display output on the state on both branches (e.g.
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history, version, dbversion). The upgrade command is executed on both
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branches: gxy and tsi (the upgrade command ensures the branch has been
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initialized by stamping its version in the alembic_version table).
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"""
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@abc.abstractmethod
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def _set_dburl(self, config_file: Optional[str] = None) -> None:
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...
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@abc.abstractmethod
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def _upgrade_to_head(self, is_sql_mode: bool):
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...
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def __init__(self, config_file: Optional[str] = None) -> None:
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self.alembic_config = self._get_alembic_cfg()
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self._set_dburl(config_file)
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def revision(self, args: Namespace) -> None:
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head = self._add_branch_label("head")
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command.revision(self.alembic_config, message=args.message, rev_id=args.rev_id, head=head)
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def upgrade(self, args: Namespace) -> None:
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if args.revision:
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revision = self._parse_revision(args.revision)
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self._upgrade_to_revision(revision, args.sql)
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else:
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self._upgrade_to_head(args.sql)
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def downgrade(self, args: Namespace) -> None:
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revision = self._parse_revision(args.revision)
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command.downgrade(self.alembic_config, revision, args.sql)
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def version(self, args: Namespace) -> None:
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command.heads(self.alembic_config, verbose=args.verbose)
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def dbversion(self, args: Namespace) -> None:
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command.current(self.alembic_config, verbose=args.verbose)
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def history(self, args: Namespace) -> None:
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command.history(self.alembic_config, verbose=args.verbose, indicate_current=args.indicate_current)
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def show(self, args: Namespace) -> None:
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command.show(self.alembic_config, args.revision)
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def _get_alembic_cfg(self) -> Config:
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config_file = os.getenv("ALEMBIC_CONFIG")
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if not config_file:
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# We need to reference the runtime module because this is an abstract class,
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# so the path will be different for different concrete classes.
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module_file = sys.modules[self.__module__].__file__
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assert module_file
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config_file = os.path.join(os.path.dirname(module_file), "alembic.ini")
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# config_file = os.path.join(os.path.dirname(module.__file__), "alembic.ini")
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config_file = os.path.abspath(config_file)
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return Config(config_file)
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def _upgrade_to_revision(self, rev, is_sql_mode: bool):
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command.upgrade(self.alembic_config, rev, is_sql_mode)
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def _parse_revision(self, revision_id: str) -> str:
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# If branches are used, relative revision identifier requires a branch label.
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if revision_id.startswith("+") or revision_id.startswith("-"):
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return self._add_branch_label(revision_id)
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# Check if it's a tag, leave unchanged if not
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revision_id = self._revision_tags().get(revision_id, revision_id)
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return revision_id
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def _add_branch_label(self, revision_id: str) -> str:
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# Subclasses that need to add a branch label should overwrite this method.
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return revision_id
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def _revision_tags(self):
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# Subclasses that have revision tags should overwrite this method.
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return {}
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class BaseCommand(abc.ABC):
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@abc.abstractmethod
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def init(self, args: Namespace) -> None:
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...
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@abc.abstractmethod
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def _get_dbscript(self, config_file: str) -> BaseDbScript:
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...
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def upgrade(self, args: Namespace) -> None:
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self._exec_command("upgrade", args)
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def downgrade(self, args: Namespace) -> None:
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self._exec_command("downgrade", args)
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def version(self, args: Namespace) -> None:
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self._exec_command("version", args)
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def dbversion(self, args: Namespace) -> None:
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self._exec_command("dbversion", args)
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def revision(self, args: Namespace) -> None:
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self._exec_command("revision", args)
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def history(self, args: Namespace) -> None:
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self._exec_command("history", args)
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def show(self, args: Namespace) -> None:
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self._exec_command("show", args)
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def _exec_command(self, command: str, args: Namespace) -> None:
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dbscript = self._get_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 hasattr(args, "raiseerr") and 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 pop_arg_from_args(args: List[str], arg_name) -> Optional[str]:
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"""
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Pop and return argument name and value from args if arg_name is in args.
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"""
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if arg_name in args:
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pos = args.index(arg_name)
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args.pop(pos) # pop argument name
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return args.pop(pos) # pop and return argument value
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return None
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@@ -1,17 +1,15 @@
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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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from argparse import Namespace
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from typing import Optional
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import alembic
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from alembic import command
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from alembic.config import Config
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from galaxy.model.migrations import verify_databases_via_script
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from galaxy.model.migrations.base import (
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BaseCommand,
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BaseDbScript,
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BaseParserBuilder,
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)
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from galaxy.model.migrations.scripts import (
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get_configuration,
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get_configuration_from_file,
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@@ -39,229 +37,38 @@ REVISION_TAGS = {
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}
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class DbScript:
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"""
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Facade for common database schema migration operations on the gxy branch.
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When the gxy and tsi branches are persisted in the same database, some
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alembic commands will display output on the state on both branches (e.g.
|
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history, version, dbversion). The upgrade command is executed on both
|
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branches: gxy and tsi (the upgrade command ensures the branch has been
|
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initialized by stamping its version in the alembic_version table).
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"""
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class ParserBuilder(BaseParserBuilder):
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def _get_command_object(self):
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return Command()
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def __init__(self, config_file: Optional[str] = None) -> None:
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self.alembic_config = self._get_alembic_cfg()
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self._set_dburl(config_file)
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self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
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def upgrade(self, args: Namespace) -> None:
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def upgrade_to_revision(rev):
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command.upgrade(self.alembic_config, rev, args.sql)
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class Command(BaseCommand):
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def init(self, 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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if args.revision:
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revision = self._parse_revision(args.revision)
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upgrade_to_revision(revision)
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else:
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self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
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upgrade_to_revision("gxy@head")
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try:
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self.alembic_config.set_main_option("sqlalchemy.url", self.tsi_url)
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upgrade_to_revision("tsi@head")
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finally:
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self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
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def _get_dbscript(self, config_file: str) -> BaseDbScript:
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return DbScript(config_file)
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def downgrade(self, args: Namespace) -> None:
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revision = self._parse_revision(args.revision)
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command.downgrade(self.alembic_config, revision, args.sql)
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def revision(self, args: Namespace) -> None:
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"""Create revision script for the gxy branch only."""
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command.revision(self.alembic_config, message=args.message, rev_id=args.rev_id, head="gxy@head")
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class DbScript(BaseDbScript):
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def _add_branch_label(self, revision_id: str) -> str:
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return f"gxy@{revision_id}"
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def version(self, args: Namespace) -> None:
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command.heads(self.alembic_config, verbose=args.verbose)
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def dbversion(self, args: Namespace) -> None:
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command.current(self.alembic_config, verbose=args.verbose)
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def history(self, args: Namespace) -> None:
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command.history(self.alembic_config, verbose=args.verbose, indicate_current=args.indicate_current)
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def show(self, args: Namespace) -> None:
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command.show(self.alembic_config, args.revision)
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def _get_alembic_cfg(self) -> Config:
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config_file = os.getenv("ALEMBIC_CONFIG")
|
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if not config_file:
|
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config_file = os.path.join(os.path.dirname(__file__), "alembic.ini")
|
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config_file = os.path.abspath(config_file)
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return Config(config_file)
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def _revision_tags(self):
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return REVISION_TAGS
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def _set_dburl(self, config_file: Optional[str] = None) -> None:
|
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gxy_config, tsi_config, _ = get_configuration_from_file(os.getcwd(), config_file)
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self.gxy_url = gxy_config.url
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self.tsi_url = tsi_config.url
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self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
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def _parse_revision(self, rev: str) -> str:
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# Relative revision identifier requires a branch label
|
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if rev.startswith("+") or rev.startswith("-"):
|
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return f"gxy@{rev}"
|
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# Check if it's a tag, leave unchanged if not
|
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rev = REVISION_TAGS.get(rev, rev)
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return rev
|
||||
|
||||
|
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class ParserBuilder:
|
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"""
|
||||
Assembler object that simplifies the construction of an argument parser for db/db_dev migration scripts.
|
||||
"""
|
||||
|
||||
def __init__(self, parser, subcommand_required=True):
|
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self.parser = parser
|
||||
self.subparsers = parser.add_subparsers(required=subcommand_required)
|
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self._init_arg_parsers()
|
||||
|
||||
def add_upgrade_command(self):
|
||||
parser = self._add_parser(
|
||||
"upgrade",
|
||||
Command.upgrade,
|
||||
"Upgrade to a later version",
|
||||
parents=[self._sql_arg_parser],
|
||||
)
|
||||
parser.add_argument("revision", help="Revision identifier or release tag", nargs="?")
|
||||
|
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def add_downgrade_command(self):
|
||||
parser = self._add_parser(
|
||||
"downgrade",
|
||||
Command.downgrade,
|
||||
"Revert to a previous version",
|
||||
parents=[self._sql_arg_parser],
|
||||
)
|
||||
parser.add_argument("revision", help="Revision identifier or release tag")
|
||||
|
||||
def add_version_command(self):
|
||||
self._add_parser(
|
||||
"version",
|
||||
Command.version,
|
||||
"Show the head revision in the migrations script directory",
|
||||
aliases=["v"],
|
||||
parents=[self._verbose_arg_parser],
|
||||
)
|
||||
|
||||
def add_dbversion_command(self):
|
||||
self._add_parser(
|
||||
"dbversion",
|
||||
Command.dbversion,
|
||||
"Show the current revision for Galaxy's database",
|
||||
aliases=["dv"],
|
||||
parents=[self._verbose_arg_parser],
|
||||
)
|
||||
|
||||
def add_init_command(self):
|
||||
self._add_parser(
|
||||
"init",
|
||||
Command.init,
|
||||
"Initialize empty database(s)",
|
||||
)
|
||||
|
||||
def add_revision_command(self):
|
||||
parser = self._add_parser("revision", help="Create a new revision file", func=Command.revision)
|
||||
parser.add_argument("-m", "--message", help="Message string to use with 'revision'", required=True)
|
||||
parser.add_argument(
|
||||
"--rev-id",
|
||||
help="Specify a revision id instead of generating one (This option is for testing purposes only)",
|
||||
)
|
||||
|
||||
def add_history_command(self):
|
||||
parser = self._add_parser(
|
||||
"history",
|
||||
Command.history,
|
||||
"List revision scripts in chronological order",
|
||||
aliases=["h"],
|
||||
parents=[self._verbose_arg_parser],
|
||||
)
|
||||
parser.add_argument("-i", "--indicate-current", help="Indicate current revision", action="store_true")
|
||||
|
||||
def add_show_command(self):
|
||||
parser = self._add_parser(
|
||||
"show",
|
||||
Command.show,
|
||||
"Show the revision(s) denoted by the given symbol",
|
||||
aliases=["s"],
|
||||
)
|
||||
parser.add_argument("revision", help="Revision identifier")
|
||||
|
||||
def _init_arg_parsers(self):
|
||||
self._verbose_arg_parser = self._make_verbose_arg_parser()
|
||||
self._sql_arg_parser = self._make_sql_arg_parser()
|
||||
|
||||
def _make_verbose_arg_parser(self):
|
||||
parser = ArgumentParser(add_help=False)
|
||||
parser.add_argument("-v", "--verbose", action="store_true", help="Display more detailed output")
|
||||
return parser
|
||||
|
||||
def _make_sql_arg_parser(self):
|
||||
parser = ArgumentParser(add_help=False)
|
||||
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.",
|
||||
)
|
||||
return parser
|
||||
|
||||
def _add_parser(self, command, func, help, aliases=None, parents=None):
|
||||
aliases = aliases or []
|
||||
parents = parents or []
|
||||
parser = self.subparsers.add_parser(command, aliases=aliases, help=help, parents=parents)
|
||||
parser.set_defaults(func=func)
|
||||
return parser
|
||||
|
||||
|
||||
class Command:
|
||||
"""Execute commands."""
|
||||
|
||||
@staticmethod
|
||||
def upgrade(args: Namespace) -> None:
|
||||
Command._exec_command("upgrade", args)
|
||||
|
||||
@staticmethod
|
||||
def downgrade(args: Namespace) -> None:
|
||||
Command._exec_command("downgrade", args)
|
||||
|
||||
@staticmethod
|
||||
def version(args: Namespace) -> None:
|
||||
Command._exec_command("version", args)
|
||||
|
||||
@staticmethod
|
||||
def dbversion(args: Namespace) -> None:
|
||||
Command._exec_command("dbversion", args)
|
||||
|
||||
@staticmethod
|
||||
def 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)
|
||||
|
||||
@staticmethod
|
||||
def revision(args: Namespace) -> None:
|
||||
Command._exec_command("revision", args)
|
||||
|
||||
@staticmethod
|
||||
def history(args: Namespace) -> None:
|
||||
Command._exec_command("history", args)
|
||||
|
||||
@staticmethod
|
||||
def show(args: Namespace) -> None:
|
||||
Command._exec_command("show", args)
|
||||
|
||||
@staticmethod
|
||||
def _exec_command(command: str, args: Namespace) -> None:
|
||||
dbscript = DbScript(args.config)
|
||||
def _upgrade_to_head(self, is_sql_mode: bool):
|
||||
self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
|
||||
self._upgrade_to_revision("gxy@head", is_sql_mode)
|
||||
try:
|
||||
getattr(dbscript, command)(args)
|
||||
except alembic.util.exc.CommandError as e:
|
||||
if hasattr(args, "raiseerr") and args.raiseerr:
|
||||
raise
|
||||
else:
|
||||
log.error(e)
|
||||
print(f"FAILED: {str(e)}")
|
||||
sys.exit(1)
|
||||
self.alembic_config.set_main_option("sqlalchemy.url", self.tsi_url)
|
||||
self._upgrade_to_revision("tsi@head", is_sql_mode)
|
||||
finally:
|
||||
self.alembic_config.set_main_option("sqlalchemy.url", self.gxy_url)
|
||||
|
||||
@@ -24,6 +24,7 @@ from galaxy.model.migrations import (
|
||||
SQLALCHEMYMIGRATE_LAST_VERSION_GXY,
|
||||
TSI,
|
||||
)
|
||||
from galaxy.model.migrations.base import pop_arg_from_args
|
||||
from galaxy.util.properties import (
|
||||
find_config_file,
|
||||
get_data_dir,
|
||||
@@ -86,7 +87,7 @@ def get_configuration(argv: List[str], cwd: str) -> Tuple[DatabaseConfig, Databa
|
||||
"""
|
||||
Return a 3-item-tuple with configuration values used for managing databases.
|
||||
"""
|
||||
config_file = _pop_config_file(argv)
|
||||
config_file = pop_arg_from_args(argv, CONFIG_FILE_ARG)
|
||||
return get_configuration_from_file(cwd, config_file)
|
||||
|
||||
|
||||
@@ -117,14 +118,6 @@ def get_configuration_from_file(
|
||||
return (gxy_config, tsi_config, is_auto_migrate)
|
||||
|
||||
|
||||
def _pop_config_file(argv: List[str]) -> Optional[str]:
|
||||
if CONFIG_FILE_ARG in argv:
|
||||
pos = argv.index(CONFIG_FILE_ARG)
|
||||
argv.pop(pos) # pop argument name
|
||||
return argv.pop(pos) # pop and return argument value
|
||||
return None
|
||||
|
||||
|
||||
def add_db_urls_to_command_arguments(argv: List[str], gxy_url: str, tsi_url: str) -> None:
|
||||
_insert_x_argument(argv, f"{TSI}_url", tsi_url)
|
||||
_insert_x_argument(argv, f"{GXY}_url", gxy_url)
|
||||
|
||||
@@ -55,6 +55,7 @@ def verify_database(url, engine_options=None):
|
||||
engine = create_engine(url, **engine_options)
|
||||
verifier = DatabaseStateVerifier(engine)
|
||||
verifier.run()
|
||||
engine.dispose()
|
||||
|
||||
|
||||
class AlembicManager:
|
||||
|
||||
@@ -42,7 +42,7 @@ def _run_migrations_invoked_via_script(run_migrations: Callable[[str], None]) ->
|
||||
run_migrations(url)
|
||||
|
||||
|
||||
def _process_cmd_current(url: str) -> bool: # TODO check this!
|
||||
def _process_cmd_current(url: str) -> bool:
|
||||
if config.cmd_opts.cmd[0].__name__ == "current": # type: ignore[union-attr]
|
||||
# Run command for each url only if urls are different; otherwise run once.
|
||||
_configure_and_run_migrations_online(url)
|
||||
|
||||
@@ -0,0 +1,45 @@
|
||||
import logging
|
||||
import os
|
||||
import sys
|
||||
from argparse import Namespace
|
||||
from typing import Optional
|
||||
|
||||
from galaxy.model.migrations.base import (
|
||||
BaseCommand,
|
||||
BaseDbScript,
|
||||
BaseParserBuilder,
|
||||
)
|
||||
from tool_shed.webapp.model.migrations import verify_database
|
||||
from tool_shed.webapp.model.migrations.scripts import (
|
||||
get_dburl,
|
||||
get_dburl_from_file,
|
||||
)
|
||||
|
||||
logging.basicConfig(level=logging.DEBUG)
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
CONFIG_FILE_ARG = "--toolshed-config"
|
||||
|
||||
|
||||
class ParserBuilder(BaseParserBuilder):
|
||||
def _get_command_object(self):
|
||||
return Command()
|
||||
|
||||
|
||||
class Command(BaseCommand):
|
||||
def init(self, args: Namespace) -> None:
|
||||
url = get_dburl(sys.argv, os.getcwd())
|
||||
verify_database(url)
|
||||
|
||||
def _get_dbscript(self, config_file: str) -> BaseDbScript:
|
||||
return DbScript(config_file)
|
||||
|
||||
|
||||
class DbScript(BaseDbScript):
|
||||
def _set_dburl(self, config_file: Optional[str] = None) -> None:
|
||||
self.url = get_dburl_from_file(os.getcwd(), config_file)
|
||||
self.alembic_config.set_main_option("sqlalchemy.url", self.url)
|
||||
|
||||
def _upgrade_to_head(self, is_sql_mode: bool):
|
||||
self.alembic_config.set_main_option("sqlalchemy.url", self.url)
|
||||
self._upgrade_to_revision("head", is_sql_mode)
|
||||
@@ -0,0 +1,34 @@
|
||||
import os
|
||||
from typing import (
|
||||
List,
|
||||
Optional,
|
||||
)
|
||||
|
||||
from galaxy.model.migrations.base import pop_arg_from_args
|
||||
from galaxy.util.properties import (
|
||||
find_config_file,
|
||||
get_data_dir,
|
||||
load_app_properties,
|
||||
)
|
||||
|
||||
DEFAULT_CONFIG_NAMES = ["tool_shed", "tool_shed_wsgi"]
|
||||
CONFIG_FILE_ARG = "--toolshed-config"
|
||||
CONFIG_DIR_NAME = "config"
|
||||
TOOLSHED_CONFIG_PREFIX = "TOOL_SHED_CONFIG_"
|
||||
|
||||
|
||||
def get_dburl(argv: List[str], cwd: str) -> str:
|
||||
"""Return db url."""
|
||||
config_file = pop_arg_from_args(argv, CONFIG_FILE_ARG)
|
||||
return get_dburl_from_file(cwd, config_file)
|
||||
|
||||
|
||||
def get_dburl_from_file(cwd: str, config_file: Optional[str] = None) -> str:
|
||||
if config_file is None:
|
||||
cwds = [cwd, os.path.join(cwd, CONFIG_DIR_NAME)]
|
||||
config_file = find_config_file(DEFAULT_CONFIG_NAMES, dirs=cwds)
|
||||
|
||||
properties = load_app_properties(config_file=config_file, config_prefix=TOOLSHED_CONFIG_PREFIX)
|
||||
default_url = f"sqlite:///{os.path.join(get_data_dir(properties), 'community.sqlite')}?isolation_level=IMMEDIATE"
|
||||
url = properties.get("database_connection", default_url)
|
||||
return url
|
||||
Reference in New Issue
Block a user