feat: allow for multiple Myokit simulations

Refactor the Myokit model mixin to allow multiple simulations to be run.
Each simulation has its own dosing protocols and dosing events.

pkpdapp/pkpdapp/models/myokit_model_mixin.py

@@ -5,6 +5,7 @@
 #
 
 import pkpdapp
+from pkpdapp.models import Protocol
 import numpy as np
 from myokit.formats.mathml import MathMLExpressionWriter
 from myokit.formats.sbml import SBMLParser
@@ -118,6 +119,57 @@ def parse_mmt_string(mmt):
     def create_myokit_model(self):
         return self.parse_mmt_string(self.mmt)
 
+    def create_myokit_simulations_from_dataset(
+        self,
+        dataset=None,
+        variables=None,
+        time_max=None,
+        outputs=None
+    ):
+        override_tlag = self._get_override_tlag(variables),
+        if dataset is None:
+            subject_cohorts = []
+        else:
+            # TODO: create backend subject cohorts based on the frontend upload stepper
+            dataset_protocols = [
+                Protocol.objects.get(pk=p['protocol'])
+                for p in dataset.subjects.values('protocol').distinct()
+                if p['protocol'] is not None
+            ]
+            subject_cohorts = [
+                dataset.subjects.filter(protocol=protocol)
+                for protocol in dataset_protocols
+            ]
+        for cohort in subject_cohorts:
+            model = self.get_myokit_model()
+
+            # Convert units
+            variables = self._initialise_variables(model, variables)
+            time_max = self._convert_bound_unit("time", time_max, model)
+            # get tlag vars
+            override_tlag = self._get_override_tlag(variables)
+            # define a dosing protocol for each subject protocol
+            dosing_protocols = {}
+            subject_protocols = [
+                Protocol.objects.get(pk=p['protocol'])
+                for p in cohort.values('protocol').distinct()
+                if p['protocol'] is not None
+            ]
+            for protocol in subject_protocols:
+                dosing_protocols[protocol.mapped_qname] = protocol
+            # create simulator
+            sim = self.create_myokit_simulator(
+                override_tlag=override_tlag,
+                model=model,
+                time_max=time_max,
+                dosing_protocols=dosing_protocols
+            )
+            # TODO: take these from simulation model
+            sim.set_tolerance(abs_tol=1e-06, rel_tol=1e-08)
+            # Simulate, logging only state variables given by `outputs`
+            print('##########################################')
+            print(self.serialize_datalog(sim.run(time_max, log=outputs), model))
+
     def create_myokit_simulator(
             self, override_tlag=None, model=None, time_max=None, dosing_protocols=None
     ):
@@ -475,6 +527,16 @@ def simulate(self, outputs=None, variables=None, time_max=None):
                 **variables,
             }
 
+        project = self.get_project()
+        if project is not None:
+            dataset = project.datasets.first()
+            self.create_myokit_simulations_from_dataset(
+                dataset=dataset,
+                variables=variables,
+                time_max=time_max,
+                outputs=outputs
+            )
+
         model = self.get_myokit_model()
         # Convert units
         variables = self._initialise_variables(model, variables)