mirror of
https://github.com/chanzuckerberg/cellxgene.git
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af3c6e1d8e
* split out config * add tests for base and app config, refactor client config out of app config * refactor default config retrieval * create config test class and helper functions * move default_config into server to fix import issue
72 lines
2.7 KiB
Python
72 lines
2.7 KiB
Python
import typing
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import uuid
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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, CellxGeneDataset, CellxGeneUser
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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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try:
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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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except IndexError:
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return None
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def get_or_create_dataset(self, dataset_name):
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try:
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dataset_id = self.query(table_args=[CellxGeneDataset], filter_args=[CellxGeneDataset.name == dataset_name])[
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0
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].id
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except IndexError:
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dataset_id = uuid.uuid4()
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dataset = CellxGeneDataset(id=dataset_id, name=dataset_name)
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self.session.add(dataset)
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self.session.commit()
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return str(dataset_id)
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def get_or_create_user(self, user_id):
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try:
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user_id = self.query(table_args=[CellxGeneUser], filter_args=[CellxGeneUser.id == user_id])[0].id
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except IndexError:
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user = CellxGeneUser(id=user_id)
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self.session.add(user)
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self.session.commit()
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return str(user_id)
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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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