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galaxy.model.migrations package

class galaxy.model.migrations.DatabaseConfig(url, template, encoding)

Bases: tuple

url: str

Alias for field number 0

template: str

Alias for field number 1

encoding: str

Alias for field number 2

exception galaxy.model.migrations.InvalidModelIdError(model: str)

Bases: Exception

__init__(model: str) → None

class galaxy.model.migrations.AlembicManager(engine: Engine, config_dict: dict | None = None)

Bases: BaseAlembicManager

stamp_model_head(model: ModelId) → None

Partial proxy to alembic’s stamp command.

upgrade(model: ModelId) → None

Partial proxy to alembic’s upgrade command.

is_up_to_date(model: ModelId) → bool

True if the head revision for model in the script directory is stored in the database.

is_under_version_control(model: ModelId) → bool

True if the database version table contains a revision that corresponds to a revision in the script directory that has branch label model.

get_model_db_head(model: ModelId) → str | None

get_model_script_head(model: ModelId) → str | None

galaxy.model.migrations.verify_databases_via_script(gxy_config: DatabaseConfig, tsi_config: DatabaseConfig, is_auto_migrate: bool = False) → None

galaxy.model.migrations.verify_databases(gxy_engine: Engine, gxy_template: str | None, gxy_encoding: str | None, tsi_engine: Engine | None, tsi_template: str | None, tsi_encoding: str | None, is_auto_migrate: bool) → None

class galaxy.model.migrations.DatabaseStateVerifier(engine: Engine, model: ModelId, database_template: str | None, database_encoding: str | None, is_auto_migrate: bool, is_new_database: bool | None = False)

Bases: object

__init__(engine: Engine, model: ModelId, database_template: str | None, database_encoding: str | None, is_auto_migrate: bool, is_new_database: bool | None = False) → None

property is_auto_migrate: bool

property db_state: DatabaseStateCache

property alembic_manager: AlembicManager

run() → None

galaxy.model.migrations.get_last_sqlalchemymigrate_version(model: ModelId) → int

galaxy.model.migrations.get_alembic_manager(engine: Engine) → AlembicManager

galaxy.model.migrations.get_metadata(model: ModelId) → MetaData

galaxy.model.migrations.get_gxy_metadata() → MetaData

galaxy.model.migrations.get_tsi_metadata() → MetaData

Submodules

galaxy.model.migrations.scripts module

galaxy.model.migrations.scripts.verify_database_is_initialized(db_url: str) → None

Intended for use by scripts that run database migrations (manage_db.sh, run_alembic.sh). Those scripts are meant to run on a database that has been initialized with the appropriate metadata (e.g. galaxy or install model).

This function will raise an error if the database does not exist or has not been initialized*.

NOTE: this function cannot determine whether a database has been properly initialized; it can only tell when a database has *not been initialized.

galaxy.model.migrations.scripts.get_configuration(argv: List[str], cwd: str) → Tuple[DatabaseConfig, DatabaseConfig, bool]

Return a 3-item-tuple with configuration values used for managing databases.

galaxy.model.migrations.scripts.get_configuration_from_file(cwd: str, config_file: str | None = None) → Tuple[DatabaseConfig, DatabaseConfig, bool]

galaxy.model.migrations.scripts.add_db_urls_to_command_arguments(argv: List[str], gxy_url: str, tsi_url: str) → None

galaxy.model.migrations.scripts.invoke_alembic() → None

Invoke the Alembic command line runner.

Accept ‘heads’ as the target revision argument to enable upgrading both gxy and tsi in one command. This is consistent with Alembic’s CLI, which allows upgrade heads. However, this would not work for separate gxy and tsi databases: we can’t attach a database url to a revision after Alembic has been invoked with the ‘upgrade’ command and the ‘heads’ argument. So, instead we invoke Alembic for each head.

class galaxy.model.migrations.scripts.LegacyManageDb

Bases: object

LEGACY_CONFIG_FILE_ARG_NAMES = ['-c', '--config', '--config-file']

__init__()

get_gxy_version()

Get the head revision for the gxy branch from the Alembic script directory. (previously referred to as “max/repository version”)

get_gxy_db_version(gxy_db_url=None)

Get the head revision for the gxy branch from the galaxy database. If there is no alembic_version table, get the sqlalchemy migrate version. Raise error if that version is not the latest. (previously referred to as “database version”)

run_upgrade(gxy_db_url=None, tsi_db_url=None)

Alembic will upgrade both branches, gxy and tsi, to their head revisions.

rename_config_argument(argv: List[str]) → None

Rename the optional config argument: we can’t use ‘-c’ because that option is used by Alembic.

galaxy.model.migrations.scripts.get_alembic_cfg()

galaxy.model.migrations.scripts.get_alembic_manager(engine: Engine) → AlembicManager

galaxy.model.migrations.util module

class galaxy.model.migrations.util.DDLOperation

Bases: ABC

Base class for all DDL operations.

run() → Any | None

abstract execute() → Any | None

abstract pre_execute_check() → bool

abstract log_check_not_passed() → None

class galaxy.model.migrations.util.DDLAlterOperation(table_name: str)

Bases: DDLOperation

Base class for DDL operations that implement special handling of ALTER statements. Ref: - https://alembic.sqlalchemy.org/en/latest/ops.html#alembic.operations.Operations.batch_alter_table - https://alembic.sqlalchemy.org/en/latest/batch.html

__init__(table_name: str) → None

run() → Any | None

execute() → Any | None

abstract batch_execute(batch_op) → Any | None

abstract non_batch_execute() → Any | None

class galaxy.model.migrations.util.CreateTable(table_name: str, *columns: SchemaItem)

Bases: DDLOperation

Wraps alembic’s create_table directive.

__init__(table_name: str, *columns: SchemaItem) → None

execute() → Table | None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.DropTable(table_name: str)

Bases: DDLOperation

Wraps alembic’s drop_table directive.

__init__(table_name: str) → None

execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.CreateIndex(index_name: str, table_name: str, columns: Sequence, **kw: Any)

Bases: DDLOperation

Wraps alembic’s create_index directive.

__init__(index_name: str, table_name: str, columns: Sequence, **kw: Any) → None

execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.DropIndex(index_name: str, table_name: str)

Bases: DDLOperation

Wraps alembic’s drop_index directive.

__init__(index_name: str, table_name: str) → None

execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.AddColumn(table_name: str, column: Column)

Bases: DDLOperation

Wraps alembic’s add_column directive.

__init__(table_name: str, column: Column) → None

execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.DropColumn(table_name: str, column_name: str)

Bases: DDLAlterOperation

Wraps alembic’s drop_column directive.

__init__(table_name: str, column_name: str) → None

batch_execute(batch_op) → None

non_batch_execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.AlterColumn(table_name: str, column_name: str, **kw: Any)

Bases: DDLAlterOperation

Wraps alembic’s alter_column directive.

__init__(table_name: str, column_name: str, **kw: Any) → None

batch_execute(batch_op) → None

non_batch_execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.CreateForeignKey(foreign_key_name: str, table_name: str, referent_table: str, local_cols: List[str], remote_cols: List[str], **kw: Any)

Bases: DDLAlterOperation

Wraps alembic’s create_foreign_key directive.

__init__(foreign_key_name: str, table_name: str, referent_table: str, local_cols: List[str], remote_cols: List[str], **kw: Any) → None

batch_execute(batch_op) → None

non_batch_execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.CreateUniqueConstraint(constraint_name: str, table_name: str, columns: List[str])

Bases: DDLAlterOperation

Wraps alembic’s create_unique_constraint directive.

__init__(constraint_name: str, table_name: str, columns: List[str]) → None

batch_execute(batch_op) → None

non_batch_execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

class galaxy.model.migrations.util.DropConstraint(constraint_name: str, table_name: str)

Bases: DDLAlterOperation

Wraps alembic’s drop_constraint directive.

__init__(constraint_name: str, table_name: str) → None

batch_execute(batch_op) → None

non_batch_execute() → None

pre_execute_check() → bool

log_check_not_passed() → None

galaxy.model.migrations.util.create_table(table_name: str, *columns: SchemaItem) → Table | None

galaxy.model.migrations.util.drop_table(table_name: str) → None

galaxy.model.migrations.util.add_column(table_name: str, column: Column) → None

galaxy.model.migrations.util.drop_column(table_name, column_name) → None

galaxy.model.migrations.util.alter_column(table_name: str, column_name: str, **kw) → None

galaxy.model.migrations.util.create_index(index_name, table_name, columns, **kw) → None

galaxy.model.migrations.util.drop_index(index_name, table_name) → None

galaxy.model.migrations.util.create_foreign_key(foreign_key_name: str, table_name: str, referent_table: str, local_cols: List[str], remote_cols: List[str], **kw: Any) → None

galaxy.model.migrations.util.create_unique_constraint(constraint_name: str, table_name: str, columns: List[str]) → None

galaxy.model.migrations.util.drop_constraint(constraint_name: str, table_name: str) → None

galaxy.model.migrations.util.table_exists(table_name: str, default: bool) → bool

Check if table exists. If running in offline mode, return default.

galaxy.model.migrations.util.column_exists(table_name: str, column_name: str, default: bool) → bool

Check if column exists. If running in offline mode, return default.

galaxy.model.migrations.util.index_exists(index_name: str, table_name: str, default: bool) → bool

Check if index exists. If running in offline mode, return default.

galaxy.model.migrations.util.foreign_key_exists(constraint_name: str, table_name: str, default: bool) → bool

Check if unique constraint exists. If running in offline mode, return default.

galaxy.model.migrations.util.unique_constraint_exists(constraint_name: str, table_name: str, default: bool) → bool

Check if unique constraint exists. If running in offline mode, return default.

galaxy.model.migrations.util.legacy_alter_table()

Wrapper required for add/drop column statements. Prevents error when column belongs to a table referenced in a view. Relevant to sqlite only. Ref: https://github.com/sqlalchemy/alembic/issues/1207 Ref: https://sqlite.org/pragma.html#pragma_legacy_alter_table

galaxy.model.migrations.util.transaction()

Wraps multiple statements in upgrade/downgrade revision script functions in a database transaction, ensuring transactional control.

Used for SQLite only. Although SQLite supports transactional DDL, pysqlite does not. Ref: https://bugs.python.org/issue10740