chore: UI Tweaks (#20)

* Units in parameter view * Units in form * Metabolite time series for Petri Dish fix
hicsail · Nov 26, 2024 · c7e011e · c7e011e
1 parent 69ad4a9
commit c7e011e
Show file tree

Hide file tree

Showing 6 changed files with 69 additions and 53 deletions.
diff --git a/packages/frontend/src/components/parameters/GlobalParamsView.tsx b/packages/frontend/src/components/parameters/GlobalParamsView.tsx
@@ -11,11 +11,11 @@ export const GlobalParamsView: React.FC<GlobalParamsViewProps> = ({ params }) =>
       <CardHeader title="Global Parameters" titleTypographyProps={{ variant: 'h3' }} />
       <CardContent>
         <List>
-          <ListItem>Time Step: {params.timeStep}</ListItem>
+          <ListItem>Time Step: {params.timeStep} (h/cycle)</ListItem>
           <ListItem>Log Frequency: {params.logFreq}</ListItem>
-          <ListItem>Nutrient Diffusivity: {params.defaultDiffConst} cm2/s</ListItem>
-          <ListItem>Default VMax: {params.defaultVMax}</ListItem>
-          <ListItem>Default KM: {params.defaultKm}</ListItem>
+          <ListItem>Nutrient Diffusivity: {params.defaultDiffConst} (cm^2/s)</ListItem>
+          <ListItem>Default VMax: {params.defaultVMax} (mmol/gh)</ListItem>
+          <ListItem>Default KM: {params.defaultKm} (M)</ListItem>
           <ListItem>Max Cycles: {params.maxCycles}</ListItem>
         </List>
       </CardContent>

diff --git a/packages/frontend/src/components/parameters/MetaboliteParamsView.tsx b/packages/frontend/src/components/parameters/MetaboliteParamsView.tsx
@@ -13,7 +13,7 @@ export const MetaboliteParamsView: React.FC<MetaboliteParamsViewProps> = ({ para
       <CardContent>
         <List>
           <ListItem>Type: {getMetaboliteName(params.type)}</ListItem>
-          <ListItem>Amount: {params.concentration} mmol/cm3</ListItem>
+          <ListItem>Amount: {params.concentration} (M)</ListItem>
         </List>
       </CardContent>
     </Card>

diff --git a/packages/frontend/src/components/parameters/ModelParamsView.tsx b/packages/frontend/src/components/parameters/ModelParamsView.tsx
@@ -29,8 +29,8 @@ const SingleModelParamsView: React.FC<{ params: ModelParametersInput }> = ({ par
         <ListItem>Neutral Drift: {params.neutralDrift ? 'True' : 'False'}</ListItem>
         <ListItem>Neutral Drift Amp: {params.neutralDriftAmp}</ListItem>
         <ListItem>Death Rate: {params.deathRate}</ListItem>
-        <ListItem>Linear Diffusivity: {params.linearDiffusivity}</ListItem>
-        <ListItem>Nonlinear Diffusivity: {params.nonlinearDiffusivity}</ListItem>
+        <ListItem>Linear Diffusivity: {params.linearDiffusivity} (cm^2/s)</ListItem>
+        <ListItem>Nonlinear Diffusivity: {params.nonlinearDiffusivity} (cm^2/sg)</ListItem>
       </List>
     </Paper>
   );

diff --git a/packages/frontend/src/pages/ExperimentForm.tsx b/packages/frontend/src/pages/ExperimentForm.tsx
@@ -1,6 +1,6 @@
 import { JsonForms } from '@jsonforms/react';
 import { materialRenderers, materialCells } from '@jsonforms/material-renderers';
-import { JsonSchema } from '@jsonforms/core';
+import { JsonSchema7 } from '@jsonforms/core';
 import { Box, Stack, Button } from '@mui/material';
 import { ErrorObject } from 'ajv';
 import { useState } from 'react';
@@ -29,7 +29,40 @@ const getSchema = (metaboliteType: MetaboliteType | null) => {
     ];
   }
 
-  const schema: JsonSchema = {
+  const metaboliteParams: JsonSchema7 = {
+    type: 'object',
+    title: 'Metabolite Parameters',
+    properties: {
+      type: {
+        type: 'string',
+        oneOf: [
+          {
+            const: MetaboliteType.Glucose,
+            title: getMetaboliteName(MetaboliteType.Glucose)
+          },
+          {
+            const: MetaboliteType.Acetate,
+            title: getMetaboliteName(MetaboliteType.Acetate)
+          },
+          {
+            const: MetaboliteType.Rich,
+            title: getMetaboliteName(MetaboliteType.Rich)
+          }
+        ]
+      }
+    },
+    required: ['type']
+  };
+
+  if (metaboliteType != MetaboliteType.Rich) {
+    metaboliteParams!.properties!['concentration'] = {
+      type: 'number',
+      title: 'Concentration (M)'
+    };
+    metaboliteParams.required!.push('concentration');
+  }
+
+  const schema: JsonSchema7 = {
     type: 'object',
     properties: {
       layoutParams: {
@@ -60,34 +93,7 @@ const getSchema = (metaboliteType: MetaboliteType | null) => {
         },
         required: ['type', 'volume']
       },
-      metaboliteParams: {
-        type: 'object',
-        title: 'Metabolite Parameters',
-        properties: {
-          type: {
-            type: 'string',
-            oneOf: [
-              {
-                const: MetaboliteType.Glucose,
-                title: getMetaboliteName(MetaboliteType.Glucose)
-              },
-              {
-                const: MetaboliteType.Acetate,
-                title: getMetaboliteName(MetaboliteType.Acetate)
-              },
-              {
-                const: MetaboliteType.Rich,
-                title: getMetaboliteName(MetaboliteType.Rich)
-              }
-            ]
-          },
-          concentration: {
-            type: 'number',
-            title: 'Concentration (mmol/cm3)'
-          }
-        },
-        required: ['type', 'concentration']
-      },
+      metaboliteParams: metaboliteParams,
       modelParams: {
         type: 'array',
         title: 'Model Parameters',
@@ -111,11 +117,13 @@ const getSchema = (metaboliteType: MetaboliteType | null) => {
             },
             linearDiffusivity: {
               type: 'number',
-              default: 0.001
+              default: 0.001,
+              title: 'Linear Diffusivity (cm^2/s)'
             },
             nonlinearDiffusivity: {
               type: 'number',
-              default: 0.6
+              default: 0.6,
+              title: 'Nonlinear Diffusivity (cm^2/sg)'
             }
           },
           required: ['name', 'neutralDriftAmp', 'deathRate', 'linearDiffusivity', 'nonlinearDiffusivity']
@@ -127,7 +135,8 @@ const getSchema = (metaboliteType: MetaboliteType | null) => {
         properties: {
           timeStep: {
             type: 'number',
-            default: 0.1
+            default: 0.1,
+            title: 'Timestep (Hours/Cycle)'
           },
           logFreq: {
             type: 'number',
@@ -136,15 +145,17 @@ const getSchema = (metaboliteType: MetaboliteType | null) => {
           defaultDiffConst: {
             type: 'number',
             default: 0.000006,
-            title: 'Nutrient Diffusivity (cm2/s)'
+            title: 'Nutrient Diffusivity (cm^2/s)'
           },
           defaultVMax: {
             type: 'number',
-            default: 10
+            default: 10,
+            title: 'Default VMax (mmol/gh)'
           },
           defaultKm: {
             type: 'number',
-            default: 0.00001
+            default: 0.00001,
+            title: 'Default KM (M)'
           },
           maxCycles: {
             type: 'number',

diff --git a/packages/frontend/src/pages/SummaryReview.tsx b/packages/frontend/src/pages/SummaryReview.tsx
@@ -58,6 +58,12 @@ const InformationSection: React.FC<InformationSectionProps> = ({ data }) => {
     for (const model of data['modelParams']) {
       model['neutralDrift'] = !!model['neutralDrift'];
     }
+
+    // If the concentration value is not present, provide a default
+    if (!data.metaboliteParams.concentration) {
+      data.metaboliteParams.concentration = 0.0;
+    }
+
     requestSimulation({
       variables: {
         request: {

diff --git a/packages/runner/runner/savers.py b/packages/runner/runner/savers.py
@@ -23,9 +23,9 @@ def upload_file(self, config: SaveConfig, key: str, filename: Path) -> None:
 
     @abstractmethod
     def save(self, experiment: c.comets, config: SaveConfig) -> dict:
-        """
+        '''
         Handles saving a component of the comets experiment
-        """
+        '''
 
 class BiomassSaver(Saver):
     def save(self, experiment: c.comets, config: SaveConfig) -> dict:
@@ -219,17 +219,16 @@ def save(self, experiment: c.comets, config: SaveConfig) -> dict:
         output_path = config.output_folder / filename
         bucket_location = f'{config.s3_folder}/{filename}'
 
-        media = experiment.media.copy()
-        media['time'] = media['cycle'] * experiment.parameters.get_param('timeStep')
-        media = media[media.conc_mmol<900]
+        # Get the time series media data and convert time to hours
+        media = experiment.get_metabolite_time_series(upper_threshold=900)
+        media['cycle'] = media['cycle'] * experiment.parameters.get_param('timeStep')
 
+        # Plot the media time series
         fig, ax = plt.subplots()
-        media.groupby('metabolite').plot(x='time', ax =ax, y='conc_mmol')
-        ax.legend(('acetate','CO2', 'formate', 'glucose'))
-        ax.set_ylabel("Concentration (mmol)")
-        ax.set_xlabel("Time (h)")
+        ax = media.plot(x='cycle', ax=ax)
+        ax.set_ylabel('Concentration (mmol)')
+        ax.set_xlabel('Time (h)')
 
-        # Save the file and upload
         plt.savefig(output_path, format='png', bbox_inches='tight')
         self.upload_file(config, bucket_location, output_path)