refactor: add thresholds to variable model

Add `variable.lower_threshold` and `variable.upper_threshold` to the variable model, so that thresholds are savedin the app database.
pkpdapp-team · Nov 25, 2024 · b0395db · b0395db
1 parent 4f1692a
commit b0395db
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Showing 9 changed files with 88 additions and 69 deletions.
diff --git a/frontend-v2/src/App.tsx b/frontend-v2/src/App.tsx
@@ -17,27 +17,15 @@ import "react-toastify/dist/ReactToastify.css";
 import { SimulationContext } from "./contexts/SimulationContext";
 import { SimulateResponse } from "./app/backendApi";
 import { CollapsibleSidebarProvider } from "./shared/contexts/CollapsibleSidebarContext";
-import { useModelTimeIntervals } from "./hooks/useModelTimeIntervals";
-
-type Threshold = { lower: number; upper: number };
-export type Thresholds = { [key: string]: Threshold };
-
-const THRESHOLDS: Thresholds = {};
 
 function App() {
   const dispatch = useAppDispatch();
   const isAuth = useSelector(isAuthenticated);
   const error = useSelector((state: RootState) => state.login.error);
-  const [intervals, setIntervals] = useModelTimeIntervals();
   const [simulations, setSimulations] = useState<SimulateResponse[]>([]);
-  const [thresholds, setThresholds] = useState<Thresholds>(THRESHOLDS);
   const simulationContext = {
     simulations,
     setSimulations,
-    intervals,
-    setIntervals,
-    thresholds,
-    setThresholds,
   };
 
   const onLogin = (username: string, password: string) => {

diff --git a/frontend-v2/src/app/backendApi.ts b/frontend-v2/src/app/backendApi.ts
@@ -3507,6 +3507,10 @@ export type Variable = {
   upper_bound?: number | null;
   /** default value for this variable */
   default_value?: number;
+  /** lower threshold for this variable */
+  lower_threshold?: number | null;
+  /** upper threshold for this variable */
+  upper_threshold?: number | null;
   /** True if default_value is stored as the log of this value */
   is_log?: boolean;
   /** name of the variable */
@@ -3553,6 +3557,10 @@ export type VariableRead = {
   upper_bound?: number | null;
   /** default value for this variable */
   default_value?: number;
+  /** lower threshold for this variable */
+  lower_threshold?: number | null;
+  /** upper threshold for this variable */
+  upper_threshold?: number | null;
   /** True if default_value is stored as the log of this value */
   is_log?: boolean;
   /** name of the variable */
@@ -3598,6 +3606,10 @@ export type PatchedVariable = {
   upper_bound?: number | null;
   /** default value for this variable */
   default_value?: number;
+  /** lower threshold for this variable */
+  lower_threshold?: number | null;
+  /** upper threshold for this variable */
+  upper_threshold?: number | null;
   /** True if default_value is stored as the log of this value */
   is_log?: boolean;
   /** name of the variable */
@@ -3644,6 +3656,10 @@ export type PatchedVariableRead = {
   upper_bound?: number | null;
   /** default value for this variable */
   default_value?: number;
+  /** lower threshold for this variable */
+  lower_threshold?: number | null;
+  /** upper threshold for this variable */
+  upper_threshold?: number | null;
   /** True if default_value is stored as the log of this value */
   is_log?: boolean;
   /** name of the variable */

diff --git a/frontend-v2/src/contexts/SimulationContext.ts b/frontend-v2/src/contexts/SimulationContext.ts
@@ -1,10 +1,7 @@
 import { createContext } from "react";
-import { SimulateResponse, TimeIntervalRead } from "../app/backendApi";
-import { Thresholds } from "../App";
+import { SimulateResponse } from "../app/backendApi";
 
 export const SimulationContext = createContext({
   simulations: [] as SimulateResponse[],
   setSimulations: (simulations: SimulateResponse[]) => {},
-  thresholds: {} as Thresholds,
-  setThresholds: (thresholds: Thresholds) => {},
 });
diff --git a/frontend-v2/src/features/model/VariableRow.tsx b/frontend-v2/src/features/model/VariableRow.tsx
@@ -1,5 +1,5 @@
 // src/components/ProjectTable.tsx
-import { FC, useEffect, useContext } from "react";
+import { FC, useEffect } from "react";
 import { Control, useFieldArray, useForm } from "react-hook-form";
 import {
   TableCell,
@@ -25,7 +25,6 @@ import { useSelector } from "react-redux";
 import { RootState } from "../../app/store";
 import { selectIsProjectShared } from "../login/loginSlice";
 import useEditProtocol from "./useEditProtocol";
-import { SimulationContext } from "../../contexts/SimulationContext";
 
 interface Props {
   project: ProjectRead;
@@ -80,7 +79,6 @@ const VariableRow: FC<Props> = ({
     control,
     name: "model.derived_variables",
   });
-  const { thresholds, setThresholds } = useContext(SimulationContext);
 
   const {
     handleSubmit,
@@ -246,16 +244,6 @@ const VariableRow: FC<Props> = ({
       pkpd_model: model.id,
       type,
     });
-
-    if (type === "AUC") {
-      setThresholds({
-        ...thresholds,
-        [variable.name]: {
-          lower: 0,
-          upper: Infinity,
-        },
-      });
-    }
   };
 
   const removeDerived = (index: number | number[]) => {

diff --git a/frontend-v2/src/features/model/secondary/ThresholdsTable.tsx b/frontend-v2/src/features/model/secondary/ThresholdsTable.tsx
@@ -1,4 +1,4 @@
-import { ChangeEvent, FC, useContext, useState } from "react";
+import { ChangeEvent, FC, useState } from "react";
 import {
   MenuItem,
   Select,
@@ -21,9 +21,9 @@ import {
   useProjectRetrieveQuery,
   useUnitListQuery,
   useVariableListQuery,
+  useVariableUpdateMutation,
   VariableRead,
 } from "../../../app/backendApi";
-import { SimulationContext } from "../../../contexts/SimulationContext";
 
 function VariableRow({
   variable,
@@ -32,32 +32,30 @@ function VariableRow({
   variable: VariableRead;
   unit: UnitRead | undefined;
 }) {
-  const { thresholds, setThresholds } = useContext(SimulationContext);
+  const [updateVariable] = useVariableUpdateMutation();
   const [unitSymbol, setUnitSymbol] = useState<string | undefined>(
     unit?.symbol,
   );
   function onChangeLowerThreshold(event: ChangeEvent<HTMLInputElement>) {
     const newValue = parseFloat(event.target.value);
-    const oldThresholds = thresholds[variable.name];
     if (!isNaN(newValue)) {
-      setThresholds({
-        ...thresholds,
-        [variable.name]: {
-          ...oldThresholds,
-          lower: newValue,
+      updateVariable({
+        id: variable.id,
+        variable: {
+          ...variable,
+          lower_threshold: newValue,
         },
       });
     }
   }
   function onChangeUpperThreshold(event: ChangeEvent<HTMLInputElement>) {
     const newValue = parseFloat(event.target.value);
-    const oldThresholds = thresholds[variable.name];
     if (!isNaN(newValue)) {
-      setThresholds({
-        ...thresholds,
-        [variable.name]: {
-          ...oldThresholds,
-          upper: newValue,
+      updateVariable({
+        id: variable.id,
+        variable: {
+          ...variable,
+          upper_threshold: newValue,
         },
       });
     }
@@ -76,14 +74,14 @@ function VariableRow({
       <TableCell>
         <TextField
           type="number"
-          defaultValue={thresholds[variable.name]?.lower}
+          defaultValue={variable.lower_threshold || 0}
           onChange={onChangeLowerThreshold}
         />
       </TableCell>
       <TableCell>
         <TextField
           type="number"
-          defaultValue={thresholds[variable.name]?.upper}
+          defaultValue={variable.upper_threshold || Infinity}
           onChange={onChangeUpperThreshold}
         />
       </TableCell>

diff --git a/frontend-v2/src/features/results/useParameters.tsx b/frontend-v2/src/features/results/useParameters.tsx
@@ -1,5 +1,3 @@
-import { useContext } from "react";
-
 import {
   SimulateResponse,
   TimeIntervalRead,
@@ -11,9 +9,7 @@ import {
   timesPerInterval,
   valuesPerInterval,
 } from "./utils";
-import { SimulationContext } from "../../contexts/SimulationContext";
 import { useVariables } from "./useVariables";
-import { Thresholds } from "../../App";
 import { useModelTimeIntervals } from "../../hooks/useModelTimeIntervals";
 import { useUnits } from "./useUnits";
 
@@ -66,32 +62,21 @@ const timeOverLowerThresholdPerInterval = (
   intervalValues: number[],
   intervalTimes: number[],
   variable: VariableRead,
-  thresholds: Thresholds,
 ) => {
-  const threshold = variable && thresholds[variable.name];
-  return timeOverThreshold(
-    intervalTimes,
-    intervalValues,
-    threshold?.lower || 0,
-  );
+  const threshold = variable?.lower_threshold || 0;
+  return timeOverThreshold(intervalTimes, intervalValues, threshold);
 };
 
 const timeOverUpperThresholdPerInterval = (
   intervalValues: number[],
   intervalTimes: number[],
   variable: VariableRead,
-  thresholds: Thresholds,
 ) => {
-  const threshold = variable && thresholds[variable.name];
-  return timeOverThreshold(
-    intervalTimes,
-    intervalValues,
-    threshold?.upper || Infinity,
-  );
+  const threshold = variable?.upper_threshold || Infinity;
+  return timeOverThreshold(intervalTimes, intervalValues, threshold);
 };
 
 export function useParameters() {
-  const { thresholds } = useContext(SimulationContext);
   const [baseIntervals] = useModelTimeIntervals();
   const variables = useVariables();
   const intervals = useNormalisedIntervals(baseIntervals);
@@ -176,7 +161,6 @@ export function useParameters() {
                 intervalValues,
                 intervalTimes,
                 variable,
-                thresholds,
               ),
             )
           : 0;
@@ -205,7 +189,6 @@ export function useParameters() {
                 intervalValues,
                 intervalTimes,
                 variable,
-                thresholds,
               ),
             )
           : 0;
@@ -234,13 +217,11 @@ export function useParameters() {
                 intervalValues,
                 intervalTimes,
                 variable,
-                thresholds,
               ) -
                 timeOverUpperThresholdPerInterval(
                   intervalValues,
                   intervalTimes,
                   variable,
-                  thresholds,
                 ),
             )
           : 0;

diff --git a/pkpdapp/pkpdapp/migrations/0017_auto_20241125_1415.py b/pkpdapp/pkpdapp/migrations/0017_auto_20241125_1415.py
@@ -0,0 +1,23 @@
+# Generated by Django 3.2.25 on 2024-11-25 14:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('pkpdapp', '0016_auto_20241122_1523'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='variable',
+            name='lower_threshold',
+            field=models.FloatField(blank=True, help_text='lower threshold for this variable', null=True),
+        ),
+        migrations.AddField(
+            model_name='variable',
+            name='upper_threshold',
+            field=models.FloatField(blank=True, help_text='upper threshold for this variable', null=True),
+        ),
+    ]
diff --git a/pkpdapp/pkpdapp/models/variable.py b/pkpdapp/pkpdapp/models/variable.py
@@ -34,6 +34,12 @@ class Variable(StoredModel):
     default_value = models.FloatField(
         default=1, help_text="default value for this variable"
     )
+    lower_threshold = models.FloatField(
+        blank=True, null=True, help_text="lower threshold for this variable"
+    )
+    upper_threshold = models.FloatField(
+        blank=True, null=True, help_text="upper threshold for this variable"
+    )
 
     is_log = models.BooleanField(
         default=False,
@@ -411,4 +417,6 @@ def copy(self, variable, new_project):
         self.unit_symbol = variable.unit_symbol
         self.constant = variable.constant
         self.protocol = new_protocol
+        self.lower_threshold = variable.lower_threshold
+        self.upper_threshold = variable.upper_threshold
         self.save()
diff --git a/pkpdapp/schema.yml b/pkpdapp/schema.yml
@@ -4847,6 +4847,16 @@ components:
           type: number
           format: double
           description: default value for this variable
+        lower_threshold:
+          type: number
+          format: double
+          nullable: true
+          description: lower threshold for this variable
+        upper_threshold:
+          type: number
+          format: double
+          nullable: true
+          description: upper threshold for this variable
         is_log:
           type: boolean
           description: True if default_value is stored as the log of this value
@@ -5656,6 +5666,16 @@ components:
           type: number
           format: double
           description: default value for this variable
+        lower_threshold:
+          type: number
+          format: double
+          nullable: true
+          description: lower threshold for this variable
+        upper_threshold:
+          type: number
+          format: double
+          nullable: true
+          description: upper threshold for this variable
         is_log:
           type: boolean
           description: True if default_value is stored as the log of this value