mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-02 19:52:14 +08:00
Nicola Soranzo
7f89e0eab9
Found by running: ``` make pyupgrade ruff check --fix . ruff check --preview --unsafe-fixes --select=F401 --fix . make format make update-client-api-schema ``` The bulk of the changes are replacements of typing deprecated aliases such as `Dict` and `List` with the standard library classes. These aliases became redundant in Python 3.9 when the corresponding pre-existing classes were enhanced to support `[]`, see https://docs.python.org/3/library/typing.html#deprecated-aliases Also: - Update the `pyupgrade` Makefile target to use `--py38-plus` for the packages needed by Pulsar, including the new galaxy-tool-util-models package.
58 lines
1.5 KiB
Python
58 lines
1.5 KiB
Python
"""
|
|
Details of how the data model objects are mapped onto the relational database
|
|
are encapsulated here.
|
|
"""
|
|
|
|
import logging
|
|
from typing import (
|
|
Any,
|
|
Optional,
|
|
TYPE_CHECKING,
|
|
)
|
|
|
|
import tool_shed.webapp.model
|
|
import tool_shed.webapp.util.shed_statistics as shed_statistics
|
|
from galaxy.model.base import SharedModelMapping
|
|
from galaxy.model.orm.engine_factory import build_engine
|
|
from tool_shed.webapp.model import mapper_registry
|
|
from tool_shed.webapp.security import CommunityRBACAgent
|
|
|
|
if TYPE_CHECKING:
|
|
from tool_shed.webapp.model import User as ToolShedUser
|
|
|
|
log = logging.getLogger(__name__)
|
|
|
|
metadata = mapper_registry.metadata
|
|
|
|
|
|
class ToolShedModelMapping(SharedModelMapping):
|
|
User: type["ToolShedUser"]
|
|
security_agent: CommunityRBACAgent
|
|
shed_counter: shed_statistics.ShedCounter
|
|
create_tables: bool
|
|
|
|
|
|
def init(
|
|
url: str, engine_options: Optional[dict[str, Any]] = None, create_tables: bool = False
|
|
) -> ToolShedModelMapping:
|
|
"""Connect mappings to the database"""
|
|
engine_options = engine_options or {}
|
|
# Create the database engine
|
|
engine = build_engine(url, engine_options)
|
|
|
|
result = ToolShedModelMapping([tool_shed.webapp.model], engine=engine)
|
|
|
|
if create_tables:
|
|
metadata.create_all(bind=engine)
|
|
|
|
result.create_tables = create_tables
|
|
|
|
result.security_agent = CommunityRBACAgent(result)
|
|
result.shed_counter = shed_statistics.ShedCounter(result)
|
|
|
|
session = result.session()
|
|
with session.begin():
|
|
result.shed_counter.generate_statistics(session)
|
|
|
|
return result
|