Fix/recipe json cleanup (#181)

* remove irrelevant gradient data from final recipe string

* round radius to 2 decimal points

* update test file to remove unnecessary gradients

* copilot suggestions

Author: ascibisz

src/App.tsx

@@ -1,7 +1,7 @@
 import { useState } from "react";
 import { Layout, Typography } from "antd";
 import { getJobStatus, updateJobStatusTimestamp } from "./utils/firebase";
-import { getFirebaseRecipe, jsonToString } from "./utils/recipeLoader";
+import { getFirebaseRecipe, recipeToString } from "./utils/recipeLoader";
 import { getSubmitPackingUrl, JOB_STATUS } from "./constants/aws";
 import {
     useJobId,
@@ -43,7 +43,7 @@ function App() {
         recipeString: string
     ): Promise<boolean> => {
         const originalRecipe = await getFirebaseRecipe(recipeId);
-        return !(jsonToString(originalRecipe) == recipeString);
+        return !(recipeToString(originalRecipe) == recipeString);
     };
 
     const submitRecipe = async (

src/components/InputSwitch/index.tsx

@@ -49,7 +49,7 @@ const InputSwitch = (props: InputSwitchProps): JSX.Element => {
         }
         if (typeof value == "number") {
             value = value * conversion;
-            value = Number(value.toFixed(4));
+            value = Number(value.toFixed(2));
         }
         return value;
     }, [getCurrentValue, id, min, conversion, dataType]);

src/state/store.ts

@@ -2,7 +2,7 @@ import { create } from "zustand";
 import { subscribeWithSelector } from "zustand/middleware";
 import { isEmpty, isEqual, get as lodashGet } from "lodash-es";
 import { PackingResult, RecipeData, RecipeManifest } from "../types";
-import { jsonToString } from "../utils/recipeLoader";
+import { recipeToString } from "../utils/recipeLoader";
 import {
     getRecipeDataFromFirebase,
     getRecipeManifestFromFirebase,
@@ -236,7 +236,7 @@ export const useRecipeStore = create<RecipeStore>()(
                 edits
             );
             if (!recipeObject) return;
-            const recipeString = jsonToString(recipeObject);
+            const recipeString = recipeToString(recipeObject);
             set({ isPacking: true });
             try {
                 await callback(s.selectedRecipeId, configId, recipeString);

src/test/recipeLoader.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 import fs from 'fs';
-import { isFirebaseRef, getFirebaseRecipe, jsonToString } from '../utils/recipeLoader';
+import { isFirebaseRef, getFirebaseRecipe, recipeToString } from '../utils/recipeLoader';
 
 test('isFirebaseRef detects Firebase references correctly', () => {
     expect(isFirebaseRef('firebase:recipes/some_id')).toBe(true);
@@ -14,7 +14,7 @@ test('isFirebaseRef detects Firebase references correctly', () => {
 test('getFirebaseRecipe works as expected for ER_peroxisome_v_struct_gradient_370574', async () => {
     const recipeId = 'ER_peroxisome_v_struct_gradient_370574';
     const recipeJson = await getFirebaseRecipe(recipeId);
-    const recipeString = jsonToString(recipeJson);
+    const recipeString = recipeToString(recipeJson);
 
     expect(recipeString).toBeDefined();
     expect(typeof recipeString).toBe('string');
@@ -30,7 +30,7 @@ test('getFirebaseRecipe works as expected for ER_peroxisome_v_struct_gradient_37
 test('getFirebaseRecipe works as expected for one_sphere', async () => {
     const recipeId = 'one_sphere_v_1.0.0';
     const recipeJson = await getFirebaseRecipe(recipeId);
-    const recipeString = jsonToString(recipeJson);
+    const recipeString = recipeToString(recipeJson);
 
     expect(recipeString).toBeDefined();
     expect(typeof recipeString).toBe('string');

src/test/test-files/ER_peroxisome.json

@@ -132,54 +132,6 @@
         }
     },
     "gradients": {
-        "apical_gradient": {
-            "description": "gradient based on distance from a plane",
-            "invert": null,
-            "mode": "vector",
-            "mode_settings": {
-                "center": [0, 0, 106.875],
-                "direction": [0, 0, 1]
-            },
-            "name": "apical_gradient",
-            "pick_mode": "linear",
-            "reversed": false,
-            "weight_mode": "exponential",
-            "weight_mode_settings": {
-                "decay_length": 0.1
-            }
-        },
-        "membrane_gradient": {
-            "description": "gradient based on distance from the surface of the membrane mesh",
-            "invert": null,
-            "mode": "surface",
-            "mode_settings": {
-                "object": "membrane",
-                "scale_to_next_surface": false
-            },
-            "name": "membrane_gradient",
-            "pick_mode": "linear",
-            "reversed": false,
-            "weight_mode": "exponential",
-            "weight_mode_settings": {
-                "decay_length": 0.01
-            }
-        },
-        "nucleus_gradient": {
-            "description": "gradient based on distance from the surface of the nucleus mesh",
-            "invert": null,
-            "mode": "surface",
-            "mode_settings": {
-                "object": "nucleus",
-                "scale_to_next_surface": false
-            },
-            "name": "nucleus_gradient",
-            "pick_mode": "linear",
-            "reversed": false,
-            "weight_mode": "exponential",
-            "weight_mode_settings": {
-                "decay_length": 0.1
-            }
-        },
         "struct_gradient": {
             "name": "struct_gradient",
             "invert": null,

src/utils/recipeLoader.ts

@@ -328,9 +328,34 @@ const getFirebaseRecipe = async (name: string): Promise<ViewableRecipe> => {
     return unpackedRecipe;
 }
 
-const jsonToString = (json: ViewableRecipe): string => {
-    return JSON.stringify(json, null, 2);
+const recipeToString = (rec: ViewableRecipe): string => {
+    // Deep copy recipe to avoid mutating original object
+    const recipe: ViewableRecipe = structuredClone(rec);
+
+    // Collect a list of gradients that are referenced by objects the recipe
+    const referencedGradients: Set<string> = new Set();
+    if (recipe.objects) {
+        for (const obj of Object.values(recipe.objects)) {
+            if (obj.packing_mode === "gradient" && obj.gradient) {
+                referencedGradients.add(obj.gradient);
+            } else if (obj.packing_mode === "random" && obj.gradient) {
+                // If packing mode is random, gradient field is irrelevant
+                // and should be cleared
+                delete obj.gradient;
+            }
+        }
+    }
+
+    // If the recipe has gradients that aren't referenced in any objects, delete them
+    if (recipe.gradients) {
+        for (const gradientName of Object.keys(recipe.gradients)) {
+            if (!referencedGradients.has(gradientName)) {
+                delete recipe.gradients[gradientName];
+            }
+        }
+    }
+    return JSON.stringify(recipe, null, 2);
 }
 
 
-export { getFirebaseRecipe, isFirebaseRef, jsonToString };
+export { getFirebaseRecipe, isFirebaseRef, recipeToString };