Dunitz/db setup (#1619)

* initial database setup

server/db/db_utils.py

@@ -0,0 +1,43 @@
+import typing
+
+from sqlalchemy import create_engine
+from sqlalchemy.orm import sessionmaker
+
+from server.db.cellxgene_orm import Base
+
+
+class DbUtils:
+    def __init__(self, database_uri: str = "postgresql://postgres:test_pw@localhost:5432"):
+        self.session = DBSessionMaker(database_uri).session()
+        self.engine = self.session.get_bind()
+
+    def get(self, table: Base, entity_id: typing.Union[str, typing.Tuple[str]]) -> typing.Union[Base, None]:
+        """
+        Query a table row by its primary key
+        :param table: SQLAlchemy Table to query
+        :param entity_id: Primary key of desired row
+        :return: SQLAlchemy Table object, None if not found
+        """
+        return self.session.query(table).get(entity_id)
+
+    def query(self, table_args: typing.List[Base], filter_args: typing.List[bool] = None) -> typing.List[Base]:
+        """
+        Query the database using the current DB session
+        :param table_args: List of SQLAlchemy Tables to query/join
+        :param filter_args: List of SQLAlchemy filter conditions
+        :return: List of SQLAlchemy query response objects
+        """
+        return (
+            self.session.query(*table_args).filter(*filter_args).all()
+            if filter_args
+            else self.session.query(*table_args).all()
+        )
+
+
+class DBSessionMaker:
+    def __init__(self, database_uri):
+        self.engine = create_engine(database_uri, connect_args={"connect_timeout": 5})
+        self.session_maker = sessionmaker(bind=self.engine)
+
+    def session(self, **kwargs):
+        return self.session_maker(**kwargs)