feat: allow for multiple Myokit simulations

frontend-v2/src/app/backendApi.ts

@@ -1127,7 +1127,7 @@ export type CombinedModelSetVariablesFromInferenceUpdateApiArg = {
   combinedModel: CombinedModel;
 };
 export type CombinedModelSimulateCreateApiResponse =
-  /** status 200  */ SimulateResponse;
+  /** status 200  */ SimulateResponse[];
 export type CombinedModelSimulateCreateApiArg = {
   id: number;
   simulate: Simulate;
@@ -1350,7 +1350,7 @@ export type PharmacodynamicSetVariablesFromInferenceUpdateApiArg = {
   pharmacodynamic: Pharmacodynamic;
 };
 export type PharmacodynamicSimulateCreateApiResponse =
-  /** status 200  */ SimulateResponse;
+  /** status 200  */ SimulateResponse[];
 export type PharmacodynamicSimulateCreateApiArg = {
   id: number;
   simulate: Simulate;

frontend-v2/src/features/simulation/Simulations.tsx

@@ -180,7 +180,7 @@ const Simulations: FC = () => {
       ? (simulateErrorBase.data as ErrorObject)
       : { error: "Unknown error" }
     : undefined;
-  const [data, setData] = useState<SimulateResponse | null>(null);
+  const [data, setData] = useState<SimulateResponse[] | null>(null);
   const { data: compound, isLoading: isLoadingCompound } =
     useCompoundRetrieveQuery(
       { id: project?.compound || 0 },
@@ -303,7 +303,8 @@ const Simulations: FC = () => {
       }).then((response) => {
         setLoadingSimulate(false);
         if ("data" in response) {
-          const responseData = response.data as SimulateResponse;
+          const responseData = response.data as SimulateResponse[];
+          console.log({ responseData })
           setData(responseData);
         }
       });
@@ -342,10 +343,10 @@ const Simulations: FC = () => {
         ),
       }).then((response) => {
         if ("data" in response) {
-          const responseData = response.data as SimulateResponse;
+          const [ projectData ] = response.data;
           const nrows =
-            responseData.outputs[Object.keys(responseData.outputs)[0]].length;
-          const cols = Object.keys(responseData.outputs);
+            projectData.outputs[Object.keys(projectData.outputs)[0]].length;
+          const cols = Object.keys(projectData.outputs);
           const vars = cols.map((vid) =>
             variables.find((v) => v.id === parseInt(vid)),
           );
@@ -377,7 +378,7 @@ const Simulations: FC = () => {
           for (let i = 0; i < nrows; i++) {
             rows[rowi] = new Array(ncols);
             for (let j = 0; j < ncols; j++) {
-              rows[rowi][j] = responseData.outputs[cols[j]][i];
+              rows[rowi][j] = projectData.outputs[cols[j]][i];
             }
             rowi++;
           }
@@ -592,24 +593,26 @@ const Simulations: FC = () => {
         )}
         <Grid container spacing={1}>
           {plots.map((plot, index) => (
-            <Grid item xl={layout === "vertical" ? 12 : 6} md={layout === "vertical" ? 12 : 6} xs={layout === "vertical" ? 12 : 12} key={index}>
-              {data && model ? (
-                <SimulationPlotView
-                  index={index}
-                  plot={plot}
-                  data={data}
-                  variables={variables || []}
-                  control={control}
-                  setValue={setValue}
-                  remove={removePlot}
-                  units={units}
-                  compound={compound}
-                  model={model}
-                />
-              ) : (
-                <div>Loading...</div>
-              )}
-            </Grid>
+            data?.map(d => (
+              <Grid item xl={layout === "vertical" ? 12 : 6} md={layout === "vertical" ? 12 : 6} xs={layout === "vertical" ? 12 : 12} key={index}>
+                {d && model ? (
+                  <SimulationPlotView
+                    index={index}
+                    plot={plot}
+                    data={d}
+                    variables={variables || []}
+                    control={control}
+                    setValue={setValue}
+                    remove={removePlot}
+                    units={units}
+                    compound={compound}
+                    model={model}
+                  />
+                ) : (
+                  <div>Loading...</div>
+                )}
+              </Grid>
+            ))
           ))}
         </Grid>
         <Snackbar open={Boolean(simulateError)} autoHideDuration={6000}>

pkpdapp/pkpdapp/api/views/simulate.py

@@ -38,14 +38,18 @@ def to_representation(self, instance):
         }
 
 
+class SimulateResponseListSerializer(serializers.ListSerializer):
+    child = SimulateResponseSerializer()
+
+
 class ErrorResponseSerializer(serializers.Serializer):
     error = serializers.CharField()
 
 
 @extend_schema(
     request=SimulateSerializer,
     responses={
-        200: SimulateResponseSerializer,
+        200: SimulateResponseListSerializer,
         400: ErrorResponseSerializer,
         404: None,
     },
@@ -67,7 +71,7 @@ def post(self, request, pk, format=None):
             return Response(
                 serialized_result.data, status=status.HTTP_400_BAD_REQUEST
             )
-        serialized_result = SimulateResponseSerializer(result)
+        serialized_result = SimulateResponseSerializer(result, many=True)
         return Response(serialized_result.data)
 
 

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
@@ -440,6 +441,27 @@ def serialize_datalog(self, datalog, myokit_model):
     def get_time_max(self):
         return self.time_max
 
+    def simulate_model(
+            self, outputs=None, variables=None, time_max=None, dosing_protocols=None
+    ):
+        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)
+        # 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`
+        return self.serialize_datalog(sim.run(time_max, log=outputs), model)
+
     def simulate(self, outputs=None, variables=None, time_max=None):
         """
         Arguments
@@ -475,21 +497,32 @@ def simulate(self, outputs=None, variables=None, time_max=None):
                 **variables,
             }
 
-        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)
-        # create simulator
-        sim = self.create_myokit_simulator(
-            override_tlag=override_tlag, model=model, time_max=time_max
+        project_sim = self.simulate_model(
+            variables=variables, time_max=time_max, outputs=outputs
         )
-        # 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`
-        return self.serialize_datalog(sim.run(time_max, log=outputs), model)
+        project = self.get_project()
+        sims = [project_sim]
+        if project is not None:
+            for subjects in get_project_cohorts(project):
+                # find unique protocols for this subject cohort
+                dosing_protocols = {}
+                subject_protocols = [
+                    Protocol.objects.get(pk=p['protocol'])
+                    for p in subjects.values('protocol').distinct()
+                    if p['protocol'] is not None
+                ]
+                for protocol in subject_protocols:
+                    dosing_protocols[protocol.mapped_qname] = protocol
+                sim = self.simulate_model(
+                    outputs=outputs,
+                    variables=variables,
+                    time_max=time_max,
+                    dosing_protocols=dosing_protocols
+                )
+                sims.append(sim)
+
+        return sims
 
 
 def set_administration(model, drug_amount, direct=True):
@@ -689,3 +722,21 @@ def _get_dosing_events(
             elif abs(start + duration - time_max) < 1e-6:
                 dosing_events[i] = (level, start, time_max - start)
     return dosing_events
+
+
+def get_project_cohorts(project):
+    dataset = project.datasets.first()
+    cohorts = []
+    if dataset is not None:
+        # 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
+        ]
+        cohorts = [
+            dataset.subjects.filter(protocol=protocol)
+            for protocol in dataset_protocols
+        ]
+    return cohorts

pkpdapp/pkpdapp/tests/test_views/test_combined_model.py

@@ -135,11 +135,12 @@ def simulate_combined_model(self, id):
             format="json",
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
-        keys = [key for key in response.data["outputs"].keys()]
+        data = response.data[0]
+        keys = [key for key in data["outputs"].keys()]
         return (
-            response.data["outputs"][keys[0]],
-            response.data["outputs"][keys[1]],
-            response.data["outputs"][keys[2]],
+            data["outputs"][keys[0]],
+            data["outputs"][keys[1]],
+            data["outputs"][keys[2]],
         )
 
     def test_swap_mapped_pd_model(self):

pkpdapp/pkpdapp/tests/test_views/test_simulate.py

@@ -44,14 +44,15 @@ def test_simulate(self):
         response = self.client.post(url, data, format='json')
 
         self.assertEqual(response.status_code, status.HTTP_200_OK)
-        outputs = response.data.get('outputs')
-        self.assertCountEqual(
-            list(outputs.keys()),
-            [
-                Variable.objects.get(qname=qname, dosed_pk_model=m).id
-                for qname in data['outputs']
-            ]
-        )
+        for sim in response.data:
+            outputs = sim.get('outputs')
+            self.assertCountEqual(
+                list(outputs.keys()),
+                [
+                    Variable.objects.get(qname=qname, dosed_pk_model=m).id
+                    for qname in data['outputs']
+                ]
+            )
 
         url = reverse('simulate-combined-model', args=(123,))
         response = self.client.post(url, data, format='json')

pkpdapp/pkpdapp/tests/utils.py

@@ -30,7 +30,7 @@ def create_pd_inference(sampling=False):
     # generate some fake data
     output = model.variables.get(qname='PDCompartment.TS')
     time = model.variables.get(qname='environment.t')
-    data = model.simulate(outputs=[output.qname, time.qname])
+    data = model.simulate(outputs=[output.qname, time.qname])[0]
     print(data)
     TS = data[output.id]
     times = data[time.id]

pkpdapp/schema.yml

@@ -539,7 +539,9 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/SimulateResponse'
+                type: array
+                items:
+                  $ref: '#/components/schemas/SimulateResponse'
           description: ''
         '400':
           content:
@@ -1674,7 +1676,9 @@ paths:
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/SimulateResponse'
+                type: array
+                items:
+                  $ref: '#/components/schemas/SimulateResponse'
           description: ''
         '400':
           content: