send JSON object in body instead of uploading edited recipe

src/App.tsx

@@ -1,10 +1,8 @@
 import { useState } from "react";
-import { v4 as uuidv4 } from "uuid";
 import { Layout, Typography } from "antd";
-import { getJobStatus, addRecipe } from "./utils/firebase";
-import { getFirebaseRecipe, jsonToString } from "./utils/recipeLoader";
+import { getJobStatus, updateJobStatusTimestamp } from "./utils/firebase";
+import { getFirebaseRecipe, recipeToString } from "./utils/recipeLoader";
 import { getSubmitPackingUrl, JOB_STATUS } from "./constants/aws";
-import { FIRESTORE_FIELDS } from "./constants/firebase";
 import { SIMULARIUM_VIEWER_URL } from "./constants/urls";
 import {
     useCurrentRecipeData,
@@ -47,67 +45,41 @@ function App() {
         recipeString: string
     ): Promise<boolean> => {
         const originalRecipe = await getFirebaseRecipe(recipeId);
-        return !(jsonToString(originalRecipe) == recipeString);
-    };
-
-    const recipeToFirebase = (
-        recipe: string,
-        path: string,
-        id: string
-    ): object => {
-        const recipeJson = JSON.parse(recipe);
-        if (recipeJson.bounding_box) {
-            const flattened_array = Object.assign({}, recipeJson.bounding_box);
-            recipeJson.bounding_box = flattened_array;
-        }
-        recipeJson[FIRESTORE_FIELDS.RECIPE_PATH] = path;
-        recipeJson[FIRESTORE_FIELDS.NAME] = id;
-        return recipeJson;
+        return !(recipeToString(originalRecipe) == recipeString);
     };
 
     const submitRecipe = async (
         recipeId: string,
         configId: string,
         recipeString: string
     ) => {
-        let firebaseRecipe = "firebase:recipes/" + recipeId;
-        const firebaseConfig = configId
-            ? "firebase:configs/" + configId
-            : undefined;
         const recipeChanged: boolean = await recipeHasChanged(
             recipeId,
             recipeString
         );
-        if (recipeChanged) {
-            const recipeId = uuidv4();
-            firebaseRecipe = "firebase:recipes_edited/" + recipeId;
-            const recipeJson = recipeToFirebase(
-                recipeString,
-                firebaseRecipe,
-                recipeId
-            );
-            try {
-                await addRecipe(recipeId, recipeJson);
-            } catch (e) {
-                setJobStatus(JOB_STATUS.FAILED);
-                setJobLogs(String(e));
-                return;
-            }
-        }
+        const firebaseRecipe = recipeChanged
+            ? undefined
+            : "firebase:recipes/" + recipeId;
+        const firebaseConfig = configId
+            ? "firebase:configs/" + configId
+            : undefined;
+
         const url = getSubmitPackingUrl(firebaseRecipe, firebaseConfig);
-        const request: RequestInfo = new Request(url, { method: "POST" });
+        const requestBody = recipeChanged ? recipeString : undefined;
+        const request: RequestInfo = new Request(url, { method: "POST", body: requestBody });
         start = Date.now();
         const response = await fetch(request);
         setJobStatus(JOB_STATUS.SUBMITTED);
         setJobLogs("");
-        const data = await response.json();
         if (response.ok) {
+            const data = await response.json();
             setJobId(data.jobId);
             setJobStatus(JOB_STATUS.STARTING);
             return data.jobId;
         } else {
+            const errorText = await response.text();
             setJobStatus(JOB_STATUS.FAILED);
-            setJobLogs(JSON.stringify(data));
+            setJobLogs(errorText);
         }
     };
 
@@ -124,6 +96,9 @@ function App() {
     const checkStatus = async (jobIdFromSubmit: string) => {
         const id = jobIdFromSubmit || jobId;
         let localJobStatus = await getJobStatus(id);
+        if (localJobStatus) {
+            setJobStatus(localJobStatus.status);
+        }
         while (
             localJobStatus?.status !== JOB_STATUS.DONE &&
             localJobStatus?.status !== JOB_STATUS.FAILED
@@ -138,6 +113,11 @@ function App() {
                 setJobStatus(newJobStatus.status);
             }
         }
+
+        // Update the job status timestamp after reading the final status to
+        // ensure we have the most recent timestamp for retention policy
+        await updateJobStatusTimestamp(id);
+
         const range = (Date.now() - start) / 1000;
         if (localJobStatus.status == JOB_STATUS.DONE) {
             setPackingResults({

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/constants/aws.ts

@@ -5,12 +5,16 @@ const SUBMIT_PACKING_ECS = "https://bda21vau5c.execute-api.us-west-2.amazonaws.c
 const S3_BASE_URL = "https://s3.us-west-2.amazonaws.com";
 
 export const getSubmitPackingUrl = (
-    recipe: string,
+    recipe?: string,
     config?: string,
 ) => {
-    let url = `${SUBMIT_PACKING_ECS}?recipe=${recipe}`;
-    if (config) {
-        url += `&config=${config}`;
+    let url = SUBMIT_PACKING_ECS;
+    if (recipe && config) {
+        url += `?recipe=${recipe}&config=${config}`;
+    } else if (recipe) {
+        url += `?recipe=${recipe}`;
+    } else if (config) {
+        url += `?config=${config}`;
     }
     return url;
 };

src/constants/firebase.ts

@@ -42,7 +42,7 @@ export const FIRESTORE_FIELDS = {
 export const RETENTION_POLICY = {
     RETENTION_PERIODS: {
         RECIPES_EDITED: 24 * 60 * 60 * 1000, // 24 hours
-        JOB_STATUS: 24 * 60 * 60 * 1000, // 24 hours
+        JOB_STATUS: 30 * 24 * 60 * 60 * 1000, // 30 days
     },
 
     TIMESTAMP_FIELD: "timestamp",

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,
@@ -222,7 +222,7 @@ 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/firebase.ts

@@ -8,10 +8,10 @@ import {
     documentId,
     QuerySnapshot,
     DocumentData,
-    setDoc,
     doc,
     Timestamp,
     deleteDoc,
+    updateDoc
 } from "firebase/firestore";
 import { sortBy } from "lodash-es";
 import {
@@ -115,6 +115,13 @@ const getJobStatus = async (
     return docs[0] || undefined;
 };
 
+const updateJobStatusTimestamp = async (jobId: string) => {
+    const data = {
+        timestamp: Timestamp.now(),
+    };
+    await updateDoc(doc(db, FIRESTORE_COLLECTIONS.JOB_STATUS, jobId), data);
+};
+
 const getAllDocsFromCollection = async (collectionName: string) => {
     const querySnapshot = await queryAllDocuments(collectionName);
     return mapQuerySnapshotToDocs(querySnapshot);
@@ -211,14 +218,6 @@ const getDocsByIds = async (coll: string, ids: string[]) => {
     return docs;
 };
 
-const addRecipe = async (id: string, data: object) => {
-    const timestampedData = {
-        ...data,
-        [FIRESTORE_FIELDS.TIMESTAMP]: Timestamp.now(),
-    };
-    await setDoc(doc(db, FIRESTORE_COLLECTIONS.EDITED_RECIPES, id), timestampedData);
-};
-
 const docCleanup = async () => {
     const now = Date.now();
     const collectionsToClean = [
@@ -262,8 +261,8 @@ export {
     queryDocumentById,
     getDocsByIds,
     getJobStatus,
-    addRecipe,
     docCleanup,
     getRecipeManifestFromFirebase,
     getRecipeDataFromFirebase,
+    updateJobStatusTimestamp,
 };

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 in 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 };