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https://github.com/chanzuckerberg/cellxgene.git
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80f6137528
* add function to retrieve latest annotation from db, db updates * dont create directory in s3
47 lines
1.8 KiB
Python
47 lines
1.8 KiB
Python
import typing
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from sqlalchemy import create_engine
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from sqlalchemy.orm import sessionmaker
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from server.db.cellxgene_orm import Base
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class DbUtils:
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def __init__(self, database_uri: str = "postgresql://postgres:test_pw@localhost:5432"):
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self.session = DBSessionMaker(database_uri).session()
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self.engine = self.session.get_bind()
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def get(self, table: Base, entity_id: typing.Union[str, typing.Tuple[str]]) -> typing.Union[Base, None]:
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"""
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Query a table row by its primary key
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:param table: SQLAlchemy Table to query
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:param entity_id: Primary key of desired row
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:return: SQLAlchemy Table object, None if not found
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"""
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return self.session.query(table).get(entity_id)
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def query(self, table_args: typing.List[Base], filter_args: typing.List[bool] = None) -> typing.List[Base]:
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"""
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Query the database using the current DB session
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:param table_args: List of SQLAlchemy Tables to query/join
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:param filter_args: List of SQLAlchemy filter conditions
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:return: List of SQLAlchemy query response objects
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"""
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return (
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self.session.query(*table_args).filter(*filter_args).all()
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if filter_args
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else self.session.query(*table_args).all()
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)
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def query_for_most_recent(self, table: Base, filter_args: typing.List[bool] = None) -> Base:
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return self.session.query(table).filter(*filter_args).order_by(table.created_at.desc()).limit(1).all()[0]
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class DBSessionMaker:
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def __init__(self, database_uri):
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self.engine = create_engine(database_uri, connect_args={"connect_timeout": 5})
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self.session_maker = sessionmaker(bind=self.engine)
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def session(self, **kwargs):
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return self.session_maker(**kwargs)
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