Source code for orm.bioreplicate

from typing import List

import sqlalchemy as sql
from sqlalchemy.orm import (
    Mapped,
    mapped_column,
    relationship,
)

from app.model.orm.orm_base import OrmBase




class Bioreplicate(OrmBase):


    __tablename__ = 'Bioreplicates'




    id:   Mapped[int] = mapped_column(primary_key=True)



    name: Mapped[str] = mapped_column(sql.String(100), nullable=False)




    position:     Mapped[str] = mapped_column(sql.String(100))



    biosampleUrl: Mapped[str] = mapped_column(sql.String)




    isControl: Mapped[bool] = mapped_column(sql.Boolean, nullable=False, default=False)



    isBlank:   Mapped[bool] = mapped_column(sql.Boolean, nullable=False, default=False)


    # Only set if the bioreplicate was generated and not uploaded


    calculationType: Mapped[str] = mapped_column(sql.String(50))




    studyId: Mapped[str] = mapped_column(sql.ForeignKey('Studies.studyId'), nullable=False)



    study: Mapped['Study'] = relationship(back_populates='bioreplicates')




    experimentId: Mapped[int] = mapped_column(sql.ForeignKey('Experiments.id'), nullable=False)



    experiment: Mapped['Experiment'] = relationship(back_populates='bioreplicates')




    measurementContexts: Mapped[List['MeasurementContext']] = relationship(
        back_populates='bioreplicate',
        cascade='all, delete-orphan'
    )



    measurements: Mapped[List['Measurement']] = relationship(
        order_by='Measurement.timeInSeconds',
        secondary='MeasurementContexts',
        viewonly=True,
    )


    @staticmethod


    def find_for_study(db_session, study_id, name):
        return db_session.scalars(
            sql.select(Bioreplicate.id)
            .where(
                Bioreplicate.studyId == study_id,
                Bioreplicate.name == name,
            )
        ).one()