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Merge pull request #51 from uclahs-cds/aholmes-add-alembic-support
Add Alembic migration support to database libraries
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| Original file line number | Diff line number | Diff line change |
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| # https://stackoverflow.com/a/932982 | ||
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| # Ignore everything in this directory | ||
| * | ||
| # Except this file | ||
| !.gitignore |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,13 +1,47 @@ | ||
| from typing import Any | ||
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| from BL_Python.programming.config import AbstractConfig | ||
| from pydantic import BaseModel | ||
| from pydantic.config import ConfigDict | ||
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| class DatabaseConnectArgsConfig(BaseModel): | ||
| # allow any values, as this type is not | ||
| # specifically the type to be used elsewhere | ||
| model_config = ConfigDict(extra="allow") | ||
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| class PostgreSQLDatabaseConnectArgsConfig(DatabaseConnectArgsConfig): | ||
| # ignore anything that DatabaseConnectArgsConfig | ||
| # allowed to be set, except for any other attributes | ||
| # of this class, which will end up assigned through | ||
| # the instatiation of the __init__ override of DatabaseConfig | ||
| model_config = ConfigDict(extra="ignore") | ||
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| sslmode: str = "" | ||
| options: str = "" | ||
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| class SQLiteDatabaseConnectArgsConfig(DatabaseConnectArgsConfig): | ||
| model_config = ConfigDict(extra="ignore") | ||
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| class DatabaseConfig(BaseModel, AbstractConfig): | ||
| def __init__(self, **data: Any): | ||
| super().__init__(**data) | ||
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| model_data = self.connect_args.model_dump() if self.connect_args else {} | ||
| if self.connection_string.startswith("sqlite://"): | ||
| self.connect_args = SQLiteDatabaseConnectArgsConfig(**model_data) | ||
| elif self.connection_string.startswith("postgresql://"): | ||
| self.connect_args = PostgreSQLDatabaseConnectArgsConfig(**model_data) | ||
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| connection_string: str = "sqlite:///:memory:" | ||
| sqlalchemy_echo: bool = False | ||
| # the static field allows Pydantic to store | ||
| # values from a dictionary | ||
| connect_args: DatabaseConnectArgsConfig | None = None | ||
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| class Config(BaseModel, AbstractConfig): | ||
| database: DatabaseConfig |
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| @@ -1,115 +0,0 @@ | ||
| from typing import TYPE_CHECKING, List, Optional, Protocol, cast, final | ||
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| from sqlalchemy.orm import DeclarativeMeta | ||
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| MetaBaseType = Type[DeclarativeMeta] | ||
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| if TYPE_CHECKING: | ||
| from typing import Dict, Protocol, Type, TypeVar, Union | ||
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| from sqlalchemy.engine import Dialect | ||
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| TBase = TypeVar("TBase") | ||
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| class TableNameCallback(Protocol): | ||
| def __call__( | ||
| self, | ||
| dialect_schema: "Union[str, None]", | ||
| full_table_name: str, | ||
| base_table: str, | ||
| meta_base: MetaBaseType, | ||
| ) -> None: ... | ||
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| class Connection(Protocol): | ||
| dialect: Dialect | ||
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| class Op(Protocol): | ||
| @staticmethod | ||
| def get_bind() -> Connection: ... | ||
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| @final | ||
| class DialectHelper: | ||
| """ | ||
| Utilities to get database schema and table names | ||
| for different SQL dialects and database engines. | ||
| For example, PostgreSQL supports schemas. This means: | ||
| * get_dialect_schema(meta) returns a schema name, if there is one, e.g. "cap" | ||
| * get_full_table_name(table_name, meta) returns the schema name, followed by the table name, e.g. " cap.assay_plate " | ||
| SQLite does not support schemas. This means: | ||
| * get_dialect_schema(meta) returns None | ||
| * get_full_table_name(table_name, meta) returns the table name, with the schema name prepended to it, e.g. " 'cap.assay_plate' " | ||
| The key difference is that there is no schema, and the table name comes from the SQLite | ||
| engine instantiation, which prepends the "schema" to the table name. | ||
| """ | ||
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| dialect: "Dialect" | ||
| dialect_supports_schemas: bool | ||
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| def __init__(self, dialect: "Dialect"): | ||
| self.dialect = dialect | ||
| # right now we only care about SQLite and PSQL, | ||
| # so if the dialect is PSQL, then we consider the | ||
| # dialect to support schemas, otherwise it does not. | ||
| self.dialect_supports_schemas = dialect.name == "postgresql" | ||
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| @staticmethod | ||
| def get_schema(meta: "MetaBaseType"): | ||
| table_args = cast( | ||
| Optional[dict[str, str]], getattr(meta, "__table_args__", None) | ||
| ) | ||
| if table_args is None: | ||
| return None | ||
| return table_args.get("schema") | ||
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| def get_dialect_schema(self, meta: "MetaBaseType"): | ||
| """Get the database schema as a string, or None if the dialect does not support schemas.""" | ||
| if not self.dialect_supports_schemas: | ||
| return None | ||
| return DialectHelper.get_schema(meta) | ||
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| def get_full_table_name(self, table_name: str, meta: "MetaBaseType"): | ||
| """ | ||
| If the dialect supports schemas, then the table name does not have the schema prepended. | ||
| In dialects that don't support schemas, e.g., SQLite, the table name has the schema prepended. | ||
| This is because, when schemas are supported, the dialect automatically handles which schema | ||
| to use, while non-schema dialects do not reference any schemas. | ||
| """ | ||
| if self.get_dialect_schema(meta): | ||
| return table_name | ||
| else: | ||
| return f"{DialectHelper.get_schema(meta)}.{table_name}" | ||
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| def get_timestamp_sql(self): | ||
| timestamp_default_sql = "now()" | ||
| if self.dialect.name == "sqlite": | ||
| timestamp_default_sql = "CURRENT_TIMESTAMP" | ||
| return timestamp_default_sql | ||
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| @staticmethod | ||
| def iterate_table_names( | ||
| op: "Op", | ||
| schema_tables: "Dict[MetaBaseType, List[str]]", | ||
| table_name_callback: "TableNameCallback", | ||
| ): | ||
| """ | ||
| Call `table_name_callback` once for every table in every Base. | ||
| op: The `op` object from Alembic. | ||
| schema_tables: A dictionary of the tables this call applies to for every Base. | ||
| table_name_callback: A callback executed for every table in `schema_tables`. | ||
| """ | ||
| dialect: Dialect = op.get_bind().dialect | ||
| schema = DialectHelper(dialect) | ||
| get_full_table_name = schema.get_full_table_name | ||
| get_dialect_schema = schema.get_dialect_schema | ||
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| for meta_base, schema_base_tables in schema_tables.items(): | ||
| dialect_schema = get_dialect_schema(meta_base) | ||
| for base_table in schema_base_tables: | ||
| full_table_name = get_full_table_name(base_table, meta_base) | ||
| table_name_callback( | ||
| dialect_schema, full_table_name, base_table, meta_base | ||
| ) | ||
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src/database/BL_Python/database/migrations/alembic/__main__.py
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| import logging | ||
| from os import environ | ||
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| # this is Alembic's main entry point | ||
| from .bl_alembic import BLAlembic | ||
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| def bl_alembic( | ||
| argv: list[str] | None = None, | ||
| log_level: int | str | None = None, | ||
| allow_overwrite: bool | None = None, | ||
| ) -> None: | ||
| """ | ||
| A method to support the `bl-alembic` command, which replaces `alembic. | ||
| :param list[str] | None argv: CLI arguments, defaults to None | ||
| :param int | str | None log_level: An integer log level to configure logging verbosity, defaults to None | ||
| """ | ||
| logging.basicConfig(level=logging.INFO) | ||
| if not log_level: | ||
| log_level = environ.get(BLAlembic.LOG_LEVEL_NAME) | ||
| log_level = int(log_level) if log_level else logging.INFO | ||
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| logger = logging.getLogger() | ||
| logger.setLevel(log_level) | ||
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| BLAlembic(argv, logger).run() | ||
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| if __name__ == "__main__": | ||
| bl_alembic() |
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