Source code for sbmlsim.examples.experiments.covid.experiments.cuadros2020

from pathlib import Path
from typing import Dict

from sbmlsim.experiment import SimulationExperiment
from sbmlsim.model import AbstractModel
from sbmlsim.plot import Axis, Figure
from sbmlsim.simulation import Timecourse, TimecourseSim
from sbmlsim.task import Task


class Cuadros2020(SimulationExperiment):
    def models(self) -> Dict[str, AbstractModel]:
        Q_ = self.Q_
        models = {
            "model": AbstractModel(
                source=Path(__file__).parent
                / ".."
                / "models"
                / "Cuadros2020"
                / "Cuadros2020.xml",
                language_type=AbstractModel.LanguageType.SBML,
                changes={},
            )
        }
        return models

    def simulations(self) -> Dict[str, TimecourseSim]:
        Q_ = self.Q_
        tcsims = {}
        tcsims["sim1"] = TimecourseSim(
            [
                Timecourse(
                    start=0,
                    end=75,
                    steps=74,
                    changes={},
                )
            ]
        )
        return tcsims

    def tasks(self) -> Dict[str, Task]:
        if self.simulations():
            return {
                f"task_{key}": Task(model="model", simulation=key)
                for key in self.simulations()
            }

    def figures(self) -> Dict[str, Figure]:
        unit_time = "time"
        unit_y = "substance"

        self.add_selections_data(["time", "Total_cumulative_cases", "Total_deaths"])

        fig_1 = Figure(self, sid="fig_plot_1", name=f"{self.sid} (plot_1)")
        plots = fig_1.create_plots(Axis("time", unit=unit_time), legend=True)
        plots[0].set_yaxis("Total_cumulative_cases", unit_y)

        # simulation
        plots[0].add_data(
            task="task_sim1",
            xid="time",
            yid="Total_cumulative_cases",
            label="Total_cumulative_cases",
            color="black",
            linewidth=2,
        )

        fig_3 = Figure(self, sid="fig_plot_3", name=f"{self.sid} (plot_3)")
        plots = fig_3.create_plots(Axis("time", unit=unit_time), legend=True)
        plots[0].set_yaxis("Total_deaths", unit_y)

        # simulation
        plots[0].add_data(
            task="task_sim1",
            xid="time",
            yid="Total_deaths",
            label="Total_deaths",
            color="black",
            linewidth=2,
        )

        return {"plot_1": fig_1, "plot_3": fig_3}