feat(frontend): units for variable thresholds (#588)

- Store display units for variable thresholds separately from variable units. - Normalise threshold units to `pmol/L` in the Results tables.
pkpdapp-team · Nov 25, 2024 · 3faa1ec · 3faa1ec
1 parent ced28aa
commit 3faa1ec
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Showing 6 changed files with 155 additions and 52 deletions.
diff --git a/frontend-v2/src/app/backendApi.ts b/frontend-v2/src/app/backendApi.ts
@@ -3533,6 +3533,8 @@ export type Variable = {
   display?: boolean;
   /** False/True if biomarker type displayed on LHS/RHS axis */
   axis?: boolean;
+  /** unit for the threshold values */
+  threshold_unit?: number | null;
   /** variable values are in this unit (note this might be different from the unit in the stored sbml) */
   unit?: number | null;
   /** pharmacodynamic model */
@@ -3583,6 +3585,8 @@ export type VariableRead = {
   display?: boolean;
   /** False/True if biomarker type displayed on LHS/RHS axis */
   axis?: boolean;
+  /** unit for the threshold values */
+  threshold_unit?: number | null;
   /** variable values are in this unit (note this might be different from the unit in the stored sbml) */
   unit?: number | null;
   /** pharmacodynamic model */
@@ -3632,6 +3636,8 @@ export type PatchedVariable = {
   display?: boolean;
   /** False/True if biomarker type displayed on LHS/RHS axis */
   axis?: boolean;
+  /** unit for the threshold values */
+  threshold_unit?: number | null;
   /** variable values are in this unit (note this might be different from the unit in the stored sbml) */
   unit?: number | null;
   /** pharmacodynamic model */
@@ -3682,6 +3688,8 @@ export type PatchedVariableRead = {
   display?: boolean;
   /** False/True if biomarker type displayed on LHS/RHS axis */
   axis?: boolean;
+  /** unit for the threshold values */
+  threshold_unit?: number | null;
   /** variable values are in this unit (note this might be different from the unit in the stored sbml) */
   unit?: number | null;
   /** pharmacodynamic model */

diff --git a/frontend-v2/src/features/model/secondary/ThresholdsTable.tsx b/frontend-v2/src/features/model/secondary/ThresholdsTable.tsx
@@ -69,6 +69,7 @@ function VariableRow({
   variable: VariableRead;
   unit: UnitRead | undefined;
 }) {
+  const units = useUnits();
   const [updateVariable] = useVariableUpdateMutation();
   const [unitSymbol, setUnitSymbol] = useState<string | undefined>(
     unit?.symbol,
@@ -99,6 +100,16 @@ function VariableRow({
   }
   function onChangeUnit(event: SelectChangeEvent) {
     setUnitSymbol(event.target.value as string);
+    const unit = units?.find((unit) => unit.symbol === event.target.value);
+    if (unit) {
+      updateVariable({
+        id: variable.id,
+        variable: {
+          ...variable,
+          threshold_unit: unit.id,
+        },
+      });
+    }
   }
 
   return (
@@ -158,7 +169,9 @@ const ThresholdsTable: FC<TableProps> = (props) => {
           <VariableRow
             key={variable.id}
             variable={variable}
-            unit={units?.find((unit) => unit.id === variable.unit)}
+            unit={units?.find(
+              (unit) => unit.id === (variable.threshold_unit || variable.unit),
+            )}
           />
         ))}
       </TableBody>

diff --git a/frontend-v2/src/features/results/useParameters.tsx b/frontend-v2/src/features/results/useParameters.tsx
@@ -1,6 +1,7 @@
 import {
   SimulateResponse,
   TimeIntervalRead,
+  VariableListApiResponse,
   VariableRead,
 } from "../../app/backendApi";
 import {
@@ -41,6 +42,30 @@ function useNormalisedIntervals(intervals: TimeIntervalRead[]) {
   });
 }
 
+function useNormalisedVariables(variables: VariableListApiResponse) {
+  const units = useUnits();
+  return variables.map((variable) => {
+    const variableUnit = units?.find(
+      (unit) => unit.id === variable.threshold_unit,
+    );
+    const defaultUnit = variableUnit?.compatible_units.find(
+      (u) => u.symbol === "pmol/L",
+    );
+    const conversionFactor = parseFloat(defaultUnit?.conversion_factor || "1");
+    const lower_threshold = variable.lower_threshold
+      ? variable.lower_threshold * conversionFactor
+      : null;
+    const upper_threshold = variable.upper_threshold
+      ? variable.upper_threshold * conversionFactor
+      : null;
+    return {
+      ...variable,
+      lower_threshold,
+      upper_threshold,
+    };
+  });
+}
+
 const variablePerInterval = (
   intervals: TimeIntervalRead[],
   variable: VariableRead,
@@ -78,8 +103,9 @@ const timeOverUpperThresholdPerInterval = (
 
 export function useParameters() {
   const [baseIntervals] = useModelTimeIntervals();
-  const variables = useVariables();
+  const baseVariables = useVariables();
   const intervals = useNormalisedIntervals(baseIntervals);
+  const variables = useNormalisedVariables(baseVariables || []);
   return [
     {
       name: "Min",
@@ -147,23 +173,26 @@ export function useParameters() {
       value(
         intervalIndex: number,
         simulation: SimulateResponse,
-        variable: VariableRead,
+        baseVariable: VariableRead,
       ) {
-        const [intervalValues, intervalTimes] = variablePerInterval(
-          intervals,
-          variable,
-          simulation,
-          intervalIndex,
-        );
-        return intervalValues
-          ? formattedNumber(
-              timeOverLowerThresholdPerInterval(
-                intervalValues,
-                intervalTimes,
-                variable,
-              ),
-            )
-          : 0;
+        const variable = variables.find((v) => v.id === baseVariable.id);
+        if (variable) {
+          const [intervalValues, intervalTimes] = variablePerInterval(
+            intervals,
+            variable,
+            simulation,
+            intervalIndex,
+          );
+          return intervalValues
+            ? formattedNumber(
+                timeOverLowerThresholdPerInterval(
+                  intervalValues,
+                  intervalTimes,
+                  variable,
+                ),
+              )
+            : 0;
+        }
       },
     },
     {
@@ -175,23 +204,26 @@ export function useParameters() {
       value(
         intervalIndex: number,
         simulation: SimulateResponse,
-        variable: VariableRead,
+        baseVariable: VariableRead,
       ) {
-        const [intervalValues, intervalTimes] = variablePerInterval(
-          intervals,
-          variable,
-          simulation,
-          intervalIndex,
-        );
-        return intervalValues
-          ? formattedNumber(
-              timeOverUpperThresholdPerInterval(
-                intervalValues,
-                intervalTimes,
-                variable,
-              ),
-            )
-          : 0;
+        const variable = variables.find((v) => v.id === baseVariable.id);
+        if (variable) {
+          const [intervalValues, intervalTimes] = variablePerInterval(
+            intervals,
+            variable,
+            simulation,
+            intervalIndex,
+          );
+          return intervalValues
+            ? formattedNumber(
+                timeOverUpperThresholdPerInterval(
+                  intervalValues,
+                  intervalTimes,
+                  variable,
+                ),
+              )
+            : 0;
+        }
       },
     },
     {
@@ -203,28 +235,31 @@ export function useParameters() {
       value(
         intervalIndex: number,
         simulation: SimulateResponse,
-        variable: VariableRead,
+        baseVariable: VariableRead,
       ) {
-        const [intervalValues, intervalTimes] = variablePerInterval(
-          intervals,
-          variable,
-          simulation,
-          intervalIndex,
-        );
-        return intervalValues
-          ? formattedNumber(
-              timeOverLowerThresholdPerInterval(
-                intervalValues,
-                intervalTimes,
-                variable,
-              ) -
-                timeOverUpperThresholdPerInterval(
+        const variable = variables.find((v) => v.id === baseVariable.id);
+        if (variable) {
+          const [intervalValues, intervalTimes] = variablePerInterval(
+            intervals,
+            variable,
+            simulation,
+            intervalIndex,
+          );
+          return intervalValues
+            ? formattedNumber(
+                timeOverLowerThresholdPerInterval(
                   intervalValues,
                   intervalTimes,
                   variable,
-                ),
-            )
-          : 0;
+                ) -
+                  timeOverUpperThresholdPerInterval(
+                    intervalValues,
+                    intervalTimes,
+                    variable,
+                  ),
+              )
+            : 0;
+        }
       },
     },
   ] as Parameter[];

diff --git a/pkpdapp/pkpdapp/migrations/0018_variable_threshold_unit.py b/pkpdapp/pkpdapp/migrations/0018_variable_threshold_unit.py
@@ -0,0 +1,31 @@
+#
+# This file is part of PKPDApp (https://github.com/pkpdapp-team/pkpdapp) which
+# is released under the BSD 3-clause license. See accompanying LICENSE.md for
+# copyright notice and full license details.
+#
+# Generated by Django 3.2.25 on 2024-11-25 16:37
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('pkpdapp', '0017_auto_20241125_1415'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='variable',
+            name='threshold_unit',
+            field=models.ForeignKey(
+                blank=True,
+                help_text='unit for the threshold values',
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name='thresholds',
+                to='pkpdapp.unit'
+            ),
+        ),
+    ]
diff --git a/pkpdapp/pkpdapp/models/variable.py b/pkpdapp/pkpdapp/models/variable.py
@@ -40,6 +40,14 @@ class Variable(StoredModel):
     upper_threshold = models.FloatField(
         blank=True, null=True, help_text="upper threshold for this variable"
     )
+    threshold_unit = models.ForeignKey(
+        Unit,
+        on_delete=models.PROTECT,
+        blank=True,
+        null=True,
+        related_name="thresholds",
+        help_text="unit for the threshold values",
+    )
 
     is_log = models.BooleanField(
         default=False,

diff --git a/pkpdapp/schema.yml b/pkpdapp/schema.yml
@@ -4902,6 +4902,10 @@ components:
         axis:
           type: boolean
           description: False/True if biomarker type displayed on LHS/RHS axis
+        threshold_unit:
+          type: integer
+          nullable: true
+          description: unit for the threshold values
         unit:
           type: integer
           nullable: true
@@ -5721,6 +5725,10 @@ components:
         axis:
           type: boolean
           description: False/True if biomarker type displayed on LHS/RHS axis
+        threshold_unit:
+          type: integer
+          nullable: true
+          description: unit for the threshold values
         unit:
           type: integer
           nullable: true