Dunitz/db setup (#1619)

* initial database setup
This commit is contained in:
Madison Dunitz
2020-08-03 17:54:06 -05:00
committed by GitHub
parent 8bbc183647
commit f632a8db91
13 changed files with 278 additions and 5 deletions
+60
View File
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from datetime import datetime
from sqlalchemy import (
Column,
DateTime,
ForeignKey,
String,
)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship
Base = declarative_base()
class CellxGeneUser(Base):
"""
A registered CellxGene user.
Links a user to their annotations
"""
__tablename__ = "cxguser"
id = Column(String, primary_key=True)
created_at = Column(DateTime, nullable=False, default=datetime.utcnow)
updated_at = Column(DateTime, nullable=False, default=datetime.utcnow, onupdate=datetime.utcnow)
# Relationships
annotations = relationship("Annotation", back_populates="cxguser")
class Annotation(Base):
"""
An annotation is a link between a user, a dataset and tiledb dataframe. A user can have multiple annotations for a
dataset, the most recent annotation (based on created_at) will be the default returned when queried
"""
__tablename__ = "annotation"
id = Column(String, primary_key=True)
tiledb_uri = Column(String)
user_id = Column(String, ForeignKey("cxguser.id"), nullable=False)
dataset_id = Column(String, ForeignKey("cxgdataset.id"), nullable=False)
created_at = Column(DateTime, nullable=False, default=datetime.utcnow)
# Relationships
cxguser = relationship("CellxGeneUser", back_populates="annotations")
dataset = relationship("CellxGeneDataset", back_populates="annotations")
class CellxGeneDataset(Base):
"""
Datasets refer to cellxgene datasets stored in tiledb
"""
__tablename__ = "cxgdataset"
id = Column(String, primary_key=True)
name = Column(String)
created_at = Column(DateTime, nullable=False, default=datetime.utcnow)
annotations = relationship("Annotation", back_populates="dataset")