Merge branch 'main' into fix-species-constraint-message

environments/environment-Linux.yml

@@ -17,7 +17,7 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@try_remove_packaing_bound#neuroconv[full]
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
       - dandi >= 0.60.0
       - pytest == 7.4.0
       - pytest-cov == 4.1.0

environments/environment-Windows.yml

@@ -17,7 +17,7 @@ dependencies:
       - flask == 2.3.2
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@try_remove_packaing_bound#neuroconv[full]
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
       - dandi >= 0.60.0
       - pytest == 7.2.2
       - pytest-cov == 4.1.0

src/renderer/src/stories/List.ts

@@ -6,7 +6,8 @@ type ListItemType = {
   key: string,
   content: string,
   value: any,
-  controls: HTMLElement[]
+  controls: HTMLElement[],
+  originalKey?: string
 }
 
 export interface ListProps {
@@ -140,11 +141,14 @@ export class List extends LitElement {
       return this.items.map(item => item.value)
     }
 
+    #previousItems = []
     #items: ListItemType[] = []
 
-    set items(value) {
-      const oldList = this.#items
+    set items(value: ListItemType[]) {
+
+      const oldList = this.#previousItems
       this.#items = value.map(item => this.transform ? this.transform(item) ?? item : item)
+      this.#previousItems = this.#items.map(item => ({...item})) // Clone items
       const oldObject = this.object
       this.#updateObject()
 
@@ -205,7 +209,7 @@ export class List extends LitElement {
       this.items.splice(draggedIdx, 1)
       this.items.splice(i, 0, movedItem)
 
-      this.items = [...this.items]
+      this.items = this.items
     }
 
 
@@ -225,7 +229,8 @@ export class List extends LitElement {
     }
 
     add = (item: ListItemType) => {
-      this.items = [...this.items, item]
+      this.items.push({ ...item }) // Update original
+      this.items = this.items
     }
 
     #removePlaceholder = () => {
@@ -235,6 +240,9 @@ export class List extends LitElement {
 
     #renderListItem = (item: ListItemType, i: number) => {
       const { key, value, content = value } = item;
+
+      if (!item.originalKey) item.originalKey = key
+
       const li = document.createElement("li");
       li.id = `item-${i}`;
 
@@ -283,7 +291,7 @@ export class List extends LitElement {
         let i = 0;
         while (resolvedKey in this.object) {
             i++;
-            resolvedKey = `${originalValue}_${i}`;
+            resolvedKey = `${originalValue} (${i})`;
         }
 
         const keyEl = editableElement
@@ -352,10 +360,13 @@ export class List extends LitElement {
                   delete this.object[oKey];
                   this.object[newKey] = value;
 
-                  if (!isUnordered) {
+                  if (isUnordered) {
+                    this.items[i].key = newKey
+                  } else {
                     this.items[i].value = newKey
-                    this.items = [...this.items]
                   }
+                  this.items = this.items
+
             }
         };
 
@@ -367,11 +378,13 @@ export class List extends LitElement {
 
     delete = (i: number) => {
       this.items.splice(i, 1)
-      this.items = [...this.items]
+      this.items = this.items
     }
 
     clear = () => {
-      this.items = []
+      // Remove items in original list
+      for (let i = this.items.length - 1; i >= 0; i--) this.items.splice(i, 1)
+      this.items = this.items
     }
 
     #updateObject = () => {
@@ -388,8 +401,8 @@ export class List extends LitElement {
           // Ensure no duplicate keys
           let kI = 0;
           while (resolvedKey in this.object) {
-              i++;
-              resolvedKey = `${key}_${kI}`;
+              kI++;
+              resolvedKey = `${key} (${kI})`;
           }
 
           this.object[resolvedKey] = value
@@ -403,6 +416,7 @@ export class List extends LitElement {
 
     render() {
 
+
       this.removeAttribute('unordered')
       if (this.unordered) this.setAttribute('unordered', '')
 

src/renderer/src/stories/Main.js

@@ -101,7 +101,7 @@ export class Main extends LitElement {
                     footer = Object.assign(
                         {
                             exit: false,
-                            next: "Complete Pipeline",
+                            next: "Exit Pipeline",
                             onNext: () => this.toRender.page.to("/"),
                         },
                         footer && typeof footer === "object" ? footer : {}

src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js

@@ -84,13 +84,20 @@ export class GuidedStructurePage extends Page {
     };
 
     beforeSave = async () => {
-        this.info.globalState.interfaces = { ...this.list.object };
+        const interfaces = (this.info.globalState.interfaces = { ...this.list.object });
 
-        // Remove extra interfaces from results
+        // Remove or reassign extra interfaces in results
         if (this.info.globalState.results) {
             this.mapSessions(({ info }) => {
-                Object.keys(info.source_data).forEach((key) => {
-                    if (!this.info.globalState.interfaces[key]) delete info.source_data[key];
+                const metadata = [info.source_data];
+                metadata.forEach((results) => {
+                    Object.keys(results).forEach((key) => {
+                        if (!interfaces[key]) {
+                            const renamed = this.list.items.find((item) => item.originalKey === key);
+                            if (renamed) results[renamed.key] = results[key];
+                            delete results[key];
+                        }
+                    });
                 });
             });
         }