Source code for orm.experiment

import re
from typing import List

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

from app.model.orm.orm_base import OrmBase



[docs]
class Experiment(OrmBase):

[docs]
    __tablename__ = "Experiments"



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



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


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


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



[docs]
    bioreplicates: Mapped[List['Bioreplicate']] = relationship(
        order_by="Bioreplicate.id",
        back_populates='experiment',
        cascade="all, delete-orphan"
    )



[docs]
    communityId: Mapped[int] = mapped_column(sql.ForeignKey('Communities.id'))


[docs]
    community: Mapped['Community'] = relationship(back_populates='experiments')



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


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



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



[docs]
    experimentCompartments: Mapped[List['ExperimentCompartment']] = relationship(back_populates='experiment')


[docs]
    compartments: Mapped[List['Compartment']] = relationship(
        secondary='ExperimentCompartments',
        viewonly=True,
    )



[docs]
    perturbations: Mapped[List['Perturbation']] = relationship(back_populates='experiment')



[docs]
    measurementContexts: Mapped[List['MeasurementContext']] = relationship(
        secondary='Bioreplicates',
        viewonly=True,
    )


    @staticmethod

[docs]
    def generate_public_id(db_session):
        last_string_id = db_session.scalars(
            sql.select(Experiment.publicId)
            .order_by(Experiment.publicId.desc())
            .limit(1)
        ).one_or_none()

        if last_string_id:
            last_numeric_id = int(re.sub(r'EMGDB0*', '', last_string_id))
        else:
            last_numeric_id = 0

        return "EMGDB{:09d}".format(last_numeric_id + 1)