From 336f146b579bf7378e3f1531c043e93119697786 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 5 Sep 2023 13:05:41 -0700
Subject: [PATCH 01/60] Update file handling to support and block multiple file
 uploads

---
 .../src/stories/FileSystemSelector.js         | 86 +++++++++++++++----
 src/renderer/src/stories/JSONSchemaInput.js   | 47 ++++++----
 2 files changed, 96 insertions(+), 37 deletions(-)

diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index 06d397672..c154c5755 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -55,6 +55,8 @@ export class FilesystemSelector extends LitElement {
         super();
         if (props.onSelect) this.onSelect = props.onSelect;
         if (props.onChange) this.onChange = props.onChange;
+        if (props.onThrow) this.onThrow = props.onThrow
+        this.multiple = props.multiple
         this.type = props.type ?? "file";
         this.value = props.value ?? "";
         this.dialogOptions = props.dialogOptions ?? {};
@@ -66,6 +68,11 @@ export class FilesystemSelector extends LitElement {
 
     onSelect = () => {};
     onChange = () => {};
+    #onThrow = (title, message) => {
+        message = message ? `<h5 style="margin-bottom: 0;">${title}</h5> <small>${message}</small>` : title
+        if (this.onThrow) this.onThrow(message)
+        throw new Error(message);
+    }
 
     display = document.createElement("small");
 
@@ -76,41 +83,85 @@ export class FilesystemSelector extends LitElement {
             "noResolveAliases",
             ...(options.properties ?? []),
         ];
+
+        if (this.multiple && !options.properties.includes('multiSelections')) options.properties.push('multiSelections')
+        
         this.classList.add("active");
         const result = await dialog[this.dialogType](options);
+
         this.classList.remove("active");
-        if (result.canceled) throw new Error("No file selected");
+        if (result.canceled) this.#onCancel();
         return result;
     };
 
-    #handleFile = async (path) => {
-        if (!path) throw new Error("Unable to parse file path");
-        this.value = path;
+    #onCancel = () => {
+        this.#onThrow(`No ${this.type} selected`, "The request was cancelled by the user");
+    }
+
+    #checkType = (value) => {
+        const isLikelyFile = value.split('.').length !== 1
+        if ((this.type === 'directory' && isLikelyFile) || (this.type === 'file' && !isLikelyFile)) this.#onThrow("Incorrect filesystem object", `Please provide a <b>${this.type}</b> instead.`)
+    }
+
+    #handleFiles = async (pathOrPaths) => {
+        if (!pathOrPaths) this.#onThrow("No paths detected", `Unable to parse ${this.type} path${this.multiple ? 's' : ''}`);
+
+        if (Array.isArray(pathOrPaths)) pathOrPaths.forEach(this.#checkType)
+        else this.#checkType(pathOrPaths)
+
+        let resolvedValue = pathOrPaths
+        if (Array.isArray(resolvedValue) && !this.multiple) {
+            if (resolvedValue.length > 1) this.#onThrow(`Too many ${this.type === 'directory' ? 'directories' : 'files'} detected`, `This selector will only accept one.`);
+            resolvedValue = resolvedValue[0]
+        }
+
+
+        if (this.multiple && !Array.isArray(resolvedValue)) resolvedValue = []
+
+        this.value = resolvedValue;
         this.onSelect(this.value);
         const event = new Event("change"); // Create a new change event
         this.dispatchEvent(event);
     };
 
     render() {
-        const preprocessed = this.value.replaceAll("\\", "/");
-        if (preprocessed !== this.value) {
-            this.value = preprocessed;
-            this.#handleFile(this.value); // Notify of the change to the separators
+
+        let resolved, isUpdated;
+
+        const isArray = Array.isArray(this.value)
+        const len = isArray ? this.value.length : 0
+
+        if (isArray) {
+            resolved = this.value.map(str => str.replaceAll("\\", "/"));
+            isUpdated = JSON.stringify(resolved) !== JSON.stringify(this.value)
+        } else {
+            resolved = this.value.replaceAll("\\", "/");
+            isUpdated = resolved !== this.value
+        }
+
+        if (isUpdated) {
+            this.value = resolved;
+            this.#handleFiles(this.value); // Notify of the change to the separators
+            return
         }
 
         return html`
             <button
+            title=${isArray ? this.value.map((v, i) => `${i+1}. ${v}`).join('\n') : this.value}
                 @click=${async () => {
                     if (dialog) {
                         const file = await this.#useElectronDialog(this.type);
                         const path = file.filePath ?? file.filePaths?.[0];
-                        this.#handleFile(path);
+                        this.#handleFiles(path);
                     } else {
                         let handles =
-                            this.type === "directory"
-                                ? await window.showDirectoryPicker()
-                                : await window.showOpenFilePicker();
-                        this.#handleFile((handles[0] ?? handles).name);
+                            await (this.type === "directory"
+                                ? window.showDirectoryPicker
+                                : window.showOpenFilePicker)({ multiple: this.multiple }).catch(e => this.#onCancel()); // Call using the same options
+                        
+                        
+                        const result = Array.isArray(handles) ? handles.map(o => o.name) : handles.name
+                        this.#handleFiles(result);
                     }
                 }}
                 @dragenter=${() => {
@@ -125,13 +176,12 @@ export class FilesystemSelector extends LitElement {
                     this.classList.remove("active");
 
                     let pathArr = [];
-                    for (const f of event.dataTransfer.files) pathArr.push(f.path);
-                    if (pathArr.length > 1) console.error("Only one file can be registered at a time");
-                    this.#handleFile(pathArr[0]);
+                    for (const f of event.dataTransfer.files) pathArr.push(f.path ?? f.name);
+                    this.#handleFiles(pathArr);
                 }}
             >
-                ${this.value || `Drop a ${this.type} here, or click to choose a ${this.type}`}
-                ${dialog ? "" : html`<br /><small>Cannot get full ${this.type} path on web distribution</small>`}
+                ${(isArray ? (len > 1 ? `${this.value[0]} and ${len - 1} other${len > 2 ? 's' : ''}` : this.value[0] ) : this.value) || `Drop a ${this.type} here, or click to choose a ${this.type}`}
+                ${dialog ? "" : html`<br /><small>Cannot get full ${this.type} path${this.multiple ? 's' : ''} on web distribution</small>`}
             </button>
         `;
     }
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 84b4fcf08..78894c9a2 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -8,7 +8,11 @@ import { Button } from "./Button";
 import { List } from "./List";
 import { Modal } from "./Modal";
 
-const filesystemQueries = ["file", "directory"];
+const isFilesystemSelector = (format) => {
+    const matched = name.match(/(.+_)?(.+)_paths?/);
+    if (!format && matched) format = matched[2] === "folder" ? "directory" : matched[2];
+    return ["file", "directory"].includes(format) ? format : null; // Handle file and directory formats
+}
 
 export class JSONSchemaInput extends LitElement {
     static get styles() {
@@ -127,6 +131,22 @@ export class JSONSchemaInput extends LitElement {
 
         const hasItemsRef = "items" in info && "$ref" in info.items;
         if (!("items" in info) || (!("type" in info.items) && !hasItemsRef)) info.items = { type: "string" };
+        
+        // Handle file and directory formats
+        const createFilesystemSelector = (format) => {
+            const el = new FilesystemSelector({
+                type: format,
+                value: this.value,
+                onSelect: (filePath) => this.#updateData(fullPath, filePath),
+                onChange: (filePath) => validateOnChange && this.#triggerValidation(name, el, path),
+                onThrow: (...args) => this.form.onThrow(...args),
+                dialogOptions: this.form.dialogOptions,
+                dialogType: this.form.dialogType,
+                multiple: isArray
+            });
+            el.classList.add("schema-input");
+            return el;
+        }
 
         if (isArray) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
@@ -134,7 +154,10 @@ export class JSONSchemaInput extends LitElement {
             // Catch tables
             const itemSchema = this.form.getSchema("items", info);
             const isTable = itemSchema.type === "object";
-            if (isTable) {
+
+            const fileSystemFormat = isFilesystemSelector(itemSchema.format)
+            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat)
+            else if (isTable) {
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
@@ -242,23 +265,9 @@ export class JSONSchemaInput extends LitElement {
                 @change=${(ev) => validateOnChange && this.#triggerValidation(name, ev.target, path)}
             />`;
         } else if (info.type === "string" || info.type === "number") {
-            let format = info.format;
-            const matched = name.match(/(.+_)?(.+)_path/);
-            if (!format && matched) format = matched[2] === "folder" ? "directory" : matched[2];
-
-            // Handle file and directory formats
-            if (filesystemQueries.includes(format)) {
-                const el = new FilesystemSelector({
-                    type: format,
-                    value: this.value,
-                    onSelect: (filePath) => this.#updateData(fullPath, filePath),
-                    onChange: (filePath) => validateOnChange && this.#triggerValidation(name, el, path),
-                    dialogOptions: this.form.dialogOptions,
-                    dialogType: this.form.dialogType,
-                });
-                el.classList.add("schema-input");
-                return el;
-            }
+
+            const fileSystemFormat = isFilesystemSelector(info.format)
+            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat)
 
             // Handle long string formats
             else if (info.format === "long" || isArray)

From 410d6f906641944ffb7ab5cf1c273476f56377d7 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 5 Sep 2023 20:09:16 +0000
Subject: [PATCH 02/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/FileSystemSelector.js         | 83 +++++++++++--------
 src/renderer/src/stories/JSONSchemaInput.js   | 18 ++--
 2 files changed, 55 insertions(+), 46 deletions(-)

diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index c154c5755..fe3262220 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -55,8 +55,8 @@ export class FilesystemSelector extends LitElement {
         super();
         if (props.onSelect) this.onSelect = props.onSelect;
         if (props.onChange) this.onChange = props.onChange;
-        if (props.onThrow) this.onThrow = props.onThrow
-        this.multiple = props.multiple
+        if (props.onThrow) this.onThrow = props.onThrow;
+        this.multiple = props.multiple;
         this.type = props.type ?? "file";
         this.value = props.value ?? "";
         this.dialogOptions = props.dialogOptions ?? {};
@@ -69,10 +69,10 @@ export class FilesystemSelector extends LitElement {
     onSelect = () => {};
     onChange = () => {};
     #onThrow = (title, message) => {
-        message = message ? `<h5 style="margin-bottom: 0;">${title}</h5> <small>${message}</small>` : title
-        if (this.onThrow) this.onThrow(message)
+        message = message ? `<h5 style="margin-bottom: 0;">${title}</h5> <small>${message}</small>` : title;
+        if (this.onThrow) this.onThrow(message);
         throw new Error(message);
-    }
+    };
 
     display = document.createElement("small");
 
@@ -84,8 +84,9 @@ export class FilesystemSelector extends LitElement {
             ...(options.properties ?? []),
         ];
 
-        if (this.multiple && !options.properties.includes('multiSelections')) options.properties.push('multiSelections')
-        
+        if (this.multiple && !options.properties.includes("multiSelections"))
+            options.properties.push("multiSelections");
+
         this.classList.add("active");
         const result = await dialog[this.dialogType](options);
 
@@ -96,27 +97,32 @@ export class FilesystemSelector extends LitElement {
 
     #onCancel = () => {
         this.#onThrow(`No ${this.type} selected`, "The request was cancelled by the user");
-    }
+    };
 
     #checkType = (value) => {
-        const isLikelyFile = value.split('.').length !== 1
-        if ((this.type === 'directory' && isLikelyFile) || (this.type === 'file' && !isLikelyFile)) this.#onThrow("Incorrect filesystem object", `Please provide a <b>${this.type}</b> instead.`)
-    }
+        const isLikelyFile = value.split(".").length !== 1;
+        if ((this.type === "directory" && isLikelyFile) || (this.type === "file" && !isLikelyFile))
+            this.#onThrow("Incorrect filesystem object", `Please provide a <b>${this.type}</b> instead.`);
+    };
 
     #handleFiles = async (pathOrPaths) => {
-        if (!pathOrPaths) this.#onThrow("No paths detected", `Unable to parse ${this.type} path${this.multiple ? 's' : ''}`);
+        if (!pathOrPaths)
+            this.#onThrow("No paths detected", `Unable to parse ${this.type} path${this.multiple ? "s" : ""}`);
 
-        if (Array.isArray(pathOrPaths)) pathOrPaths.forEach(this.#checkType)
-        else this.#checkType(pathOrPaths)
+        if (Array.isArray(pathOrPaths)) pathOrPaths.forEach(this.#checkType);
+        else this.#checkType(pathOrPaths);
 
-        let resolvedValue = pathOrPaths
+        let resolvedValue = pathOrPaths;
         if (Array.isArray(resolvedValue) && !this.multiple) {
-            if (resolvedValue.length > 1) this.#onThrow(`Too many ${this.type === 'directory' ? 'directories' : 'files'} detected`, `This selector will only accept one.`);
-            resolvedValue = resolvedValue[0]
+            if (resolvedValue.length > 1)
+                this.#onThrow(
+                    `Too many ${this.type === "directory" ? "directories" : "files"} detected`,
+                    `This selector will only accept one.`
+                );
+            resolvedValue = resolvedValue[0];
         }
 
-
-        if (this.multiple && !Array.isArray(resolvedValue)) resolvedValue = []
+        if (this.multiple && !Array.isArray(resolvedValue)) resolvedValue = [];
 
         this.value = resolvedValue;
         this.onSelect(this.value);
@@ -125,42 +131,39 @@ export class FilesystemSelector extends LitElement {
     };
 
     render() {
-
         let resolved, isUpdated;
 
-        const isArray = Array.isArray(this.value)
-        const len = isArray ? this.value.length : 0
+        const isArray = Array.isArray(this.value);
+        const len = isArray ? this.value.length : 0;
 
         if (isArray) {
-            resolved = this.value.map(str => str.replaceAll("\\", "/"));
-            isUpdated = JSON.stringify(resolved) !== JSON.stringify(this.value)
+            resolved = this.value.map((str) => str.replaceAll("\\", "/"));
+            isUpdated = JSON.stringify(resolved) !== JSON.stringify(this.value);
         } else {
             resolved = this.value.replaceAll("\\", "/");
-            isUpdated = resolved !== this.value
+            isUpdated = resolved !== this.value;
         }
 
         if (isUpdated) {
             this.value = resolved;
             this.#handleFiles(this.value); // Notify of the change to the separators
-            return
+            return;
         }
 
         return html`
             <button
-            title=${isArray ? this.value.map((v, i) => `${i+1}. ${v}`).join('\n') : this.value}
+                title=${isArray ? this.value.map((v, i) => `${i + 1}. ${v}`).join("\n") : this.value}
                 @click=${async () => {
                     if (dialog) {
                         const file = await this.#useElectronDialog(this.type);
                         const path = file.filePath ?? file.filePaths?.[0];
                         this.#handleFiles(path);
                     } else {
-                        let handles =
-                            await (this.type === "directory"
-                                ? window.showDirectoryPicker
-                                : window.showOpenFilePicker)({ multiple: this.multiple }).catch(e => this.#onCancel()); // Call using the same options
-                        
-                        
-                        const result = Array.isArray(handles) ? handles.map(o => o.name) : handles.name
+                        let handles = await (this.type === "directory"
+                            ? window.showDirectoryPicker
+                            : window.showOpenFilePicker)({ multiple: this.multiple }).catch((e) => this.#onCancel()); // Call using the same options
+
+                        const result = Array.isArray(handles) ? handles.map((o) => o.name) : handles.name;
                         this.#handleFiles(result);
                     }
                 }}
@@ -180,8 +183,16 @@ export class FilesystemSelector extends LitElement {
                     this.#handleFiles(pathArr);
                 }}
             >
-                ${(isArray ? (len > 1 ? `${this.value[0]} and ${len - 1} other${len > 2 ? 's' : ''}` : this.value[0] ) : this.value) || `Drop a ${this.type} here, or click to choose a ${this.type}`}
-                ${dialog ? "" : html`<br /><small>Cannot get full ${this.type} path${this.multiple ? 's' : ''} on web distribution</small>`}
+                ${(isArray
+                    ? len > 1
+                        ? `${this.value[0]} and ${len - 1} other${len > 2 ? "s" : ""}`
+                        : this.value[0]
+                    : this.value) || `Drop a ${this.type} here, or click to choose a ${this.type}`}
+                ${dialog
+                    ? ""
+                    : html`<br /><small
+                              >Cannot get full ${this.type} path${this.multiple ? "s" : ""} on web distribution</small
+                          >`}
             </button>
         `;
     }
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 78894c9a2..f87a96b94 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -12,7 +12,7 @@ const isFilesystemSelector = (format) => {
     const matched = name.match(/(.+_)?(.+)_paths?/);
     if (!format && matched) format = matched[2] === "folder" ? "directory" : matched[2];
     return ["file", "directory"].includes(format) ? format : null; // Handle file and directory formats
-}
+};
 
 export class JSONSchemaInput extends LitElement {
     static get styles() {
@@ -131,7 +131,7 @@ export class JSONSchemaInput extends LitElement {
 
         const hasItemsRef = "items" in info && "$ref" in info.items;
         if (!("items" in info) || (!("type" in info.items) && !hasItemsRef)) info.items = { type: "string" };
-        
+
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
             const el = new FilesystemSelector({
@@ -142,11 +142,11 @@ export class JSONSchemaInput extends LitElement {
                 onThrow: (...args) => this.form.onThrow(...args),
                 dialogOptions: this.form.dialogOptions,
                 dialogType: this.form.dialogType,
-                multiple: isArray
+                multiple: isArray,
             });
             el.classList.add("schema-input");
             return el;
-        }
+        };
 
         if (isArray) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
@@ -155,8 +155,8 @@ export class JSONSchemaInput extends LitElement {
             const itemSchema = this.form.getSchema("items", info);
             const isTable = itemSchema.type === "object";
 
-            const fileSystemFormat = isFilesystemSelector(itemSchema.format)
-            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat)
+            const fileSystemFormat = isFilesystemSelector(itemSchema.format);
+            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             else if (isTable) {
                 const tableMetadata = {
                     schema: itemSchema,
@@ -265,10 +265,8 @@ export class JSONSchemaInput extends LitElement {
                 @change=${(ev) => validateOnChange && this.#triggerValidation(name, ev.target, path)}
             />`;
         } else if (info.type === "string" || info.type === "number") {
-
-            const fileSystemFormat = isFilesystemSelector(info.format)
-            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat)
-
+            const fileSystemFormat = isFilesystemSelector(info.format);
+            if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Handle long string formats
             else if (info.format === "long" || isArray)
                 return html`<textarea

From 867279b9cc86f19c67d1751db756144f1a1bee8e Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 5 Sep 2023 16:01:00 -0700
Subject: [PATCH 03/60] Create draft of standalone preview page

---
 pyflask/app.py                                | 27 ++++++++-
 src/renderer/src/pages.js                     | 15 +++--
 src/renderer/src/stories/assets/inspect.svg   |  2 +-
 src/renderer/src/stories/assets/preview.svg   |  7 +++
 .../pages/guided-mode/options/utils.js        |  4 +-
 .../src/stories/pages/preview/PreviewPage.js  | 55 +++++++++++++++++++
 src/renderer/src/stories/preview/Neurosift.js | 14 +++--
 7 files changed, 113 insertions(+), 11 deletions(-)
 create mode 100644 src/renderer/src/stories/assets/preview.svg
 create mode 100644 src/renderer/src/stories/pages/preview/PreviewPage.js

diff --git a/pyflask/app.py b/pyflask/app.py
index a87618798..da0205fdf 100644
--- a/pyflask/app.py
+++ b/pyflask/app.py
@@ -2,15 +2,18 @@
 import sys
 import json
 import multiprocessing
+from os.path import sep
 from logging import Formatter, DEBUG
 from logging.handlers import RotatingFileHandler
 from pathlib import Path
+from urllib.parse import unquote
+
 
 # https://stackoverflow.com/questions/32672596/pyinstaller-loads-script-multiple-times#comment103216434_32677108
 multiprocessing.freeze_support()
 
 
-from flask import Flask, request, send_from_directory
+from flask import Flask, request, send_from_directory, send_file
 from flask_cors import CORS
 from flask_restx import Api, Resource
 
@@ -52,6 +55,28 @@
 api.add_namespace(neuroconv_api)
 api.init_app(app)
 
+registered = {}
+
+@app.route("/files")
+def get_all_files():
+    return list(registered.keys())
+
+@app.route("/files/<path:path>", methods=["GET", "POST"])
+def handle_file_request(path):
+    
+
+    if request.method == 'GET':
+        if registered[path]:
+            return send_file(f"{sep}{unquote(path)}")
+        else:
+            app.abort(404, 'Resource is not accessible.')
+
+    else:
+        if ('.nwb' in path):
+            registered[path] = True
+            return request.base_url
+        else:
+            app.abort(400, str('Path does not point to an NWB file.'))
 
 @app.route("/conversions/<path:path>")
 def send_conversions(path):
diff --git a/src/renderer/src/pages.js b/src/renderer/src/pages.js
index 09ba41811..d53784f4d 100644
--- a/src/renderer/src/pages.js
+++ b/src/renderer/src/pages.js
@@ -22,11 +22,14 @@ import { TutorialPage } from "./stories/pages/tutorial/Tutorial";
 import tutorialIcon from "./stories/assets/exploration.svg?raw";
 import uploadIcon from "./stories/assets/dandi.svg?raw";
 import inspectIcon from "./stories/assets/inspect.svg?raw";
+import previewIcon from "./stories/assets/preview.svg?raw";
+
 import settingsIcon from "./stories/assets/settings.svg?raw";
 
 import { UploadsPage } from "./stories/pages/uploads/UploadsPage";
 import { SettingsPage } from "./stories/pages/settings/SettingsPage";
 import { InspectPage } from "./stories/pages/inspect/InspectPage";
+import { PreviewPage } from "./stories/pages/preview/PreviewPage";
 
 let dashboard = document.querySelector("nwb-dashboard");
 if (!dashboard) dashboard = new Dashboard();
@@ -165,14 +168,18 @@ const pages = {
             }),
         },
     }),
-    uploads: new UploadsPage({
-        label: "Uploads",
-        icon: uploadIcon,
-    }),
     inspect: new InspectPage({
         label: "Inspect",
         icon: inspectIcon,
     }),
+    preview: new PreviewPage({
+        label: "Preview",
+        icon: previewIcon,
+    }),
+    uploads: new UploadsPage({
+        label: "Uploads",
+        icon: uploadIcon,
+    }),
     tutorial: new TutorialPage({
         label: "Tutorial",
         icon: tutorialIcon,
diff --git a/src/renderer/src/stories/assets/inspect.svg b/src/renderer/src/stories/assets/inspect.svg
index dbbbd8f77..a94da7c42 100644
--- a/src/renderer/src/stories/assets/inspect.svg
+++ b/src/renderer/src/stories/assets/inspect.svg
@@ -4,4 +4,4 @@ height="25"
 viewBox="0 -960 960 960" 
 width="25"
 style="margin-right: 30px; margin-bottom: -5px"
-><path d="M838-120 627-331q-40 32-91.5 51.5T430-260q-81 0-149-38.5T171-400h76q35 37 82 58.5T430-320q104 0 177-73.5T680-570q0-104-73-177t-177-73q-101 0-173.5 70T180-580h-60q4-125 93.5-212.5T430-880q129 0 219.5 90.5T740-570q0 54-19.5 105.5T669-373l211 211-42 42ZM397-400l-63-208-52 148H80v-60h160l66-190h60l61 204 43-134h60l60 120h30v60h-67l-47-94-50 154h-59Z"/></svg>
\ No newline at end of file
+><path d="M80-200v-60h400v60H80Zm0-210v-60h200v60H80Zm0-210v-60h200v60H80Zm758 420L678-360q-26 20-56 30t-62 10q-83 0-141.5-58.5T360-520q0-83 58.5-141.5T560-720q83 0 141.5 58.5T760-520q0 32-10 62t-30 56l160 160-42 42ZM559.765-380Q618-380 659-420.765q41-40.764 41-99Q700-578 659.235-619q-40.764-41-99-41Q502-660 461-619.235q-41 40.764-41 99Q420-462 460.765-421q40.764 41 99 41Z"/></svg>
\ No newline at end of file
diff --git a/src/renderer/src/stories/assets/preview.svg b/src/renderer/src/stories/assets/preview.svg
new file mode 100644
index 000000000..dbbbd8f77
--- /dev/null
+++ b/src/renderer/src/stories/assets/preview.svg
@@ -0,0 +1,7 @@
+<svg 
+xmlns="http://www.w3.org/2000/svg" 
+height="25" 
+viewBox="0 -960 960 960" 
+width="25"
+style="margin-right: 30px; margin-bottom: -5px"
+><path d="M838-120 627-331q-40 32-91.5 51.5T430-260q-81 0-149-38.5T171-400h76q35 37 82 58.5T430-320q104 0 177-73.5T680-570q0-104-73-177t-177-73q-101 0-173.5 70T180-580h-60q4-125 93.5-212.5T430-880q129 0 219.5 90.5T740-570q0 54-19.5 105.5T669-373l211 211-42 42ZM397-400l-63-208-52 148H80v-60h160l66-190h60l61 204 43-134h60l60 120h30v60h-67l-47-94-50 154h-59Z"/></svg>
\ No newline at end of file
diff --git a/src/renderer/src/stories/pages/guided-mode/options/utils.js b/src/renderer/src/stories/pages/guided-mode/options/utils.js
index 6d1d0020e..20785b4f2 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/utils.js
@@ -24,7 +24,9 @@ export const run = async (url, payload, options = {}) => {
     const needsSwal = !options.swal && options.swal !== false;
     if (needsSwal) openProgressSwal(options).then((swal) => (options.onOpen ? options.onOpen(swal) : undefined));
 
-    const results = await fetch(`${baseUrl}/neuroconv/${url}`, {
+    if (!('base' in options)) options.base = '/neuroconv'
+
+    const results = await fetch(`${baseUrl}${options.base || ''}/${url}`, {
         method: "POST",
         headers: { "Content-Type": "application/json" },
         body: JSON.stringify(payload),
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
new file mode 100644
index 000000000..5f2b276c5
--- /dev/null
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -0,0 +1,55 @@
+import { html } from "lit";
+import { Page } from "../Page.js";
+import { onThrow } from "../../../errors";
+import { Button } from "../../Button.js";
+
+import { run } from "../guided-mode/options/utils.js";
+import { JSONSchemaInput } from "../../JSONSchemaInput.js";
+import { Modal } from "../../Modal";
+import { truncateFilePaths } from "../../preview/NWBFilePreview.js";
+import { InspectorList } from "../../preview/inspector/InspectorList.js";
+import { Neurosift } from "../../preview/Neurosift.js";
+import { baseUrl } from "../../../globals.js";
+
+
+export class PreviewPage extends Page {
+    constructor(...args) {
+        super(...args);
+    }
+
+    render() {
+
+        const neurosift = new Neurosift()
+
+        this.input = new JSONSchemaInput({
+            path: ['file_path'],
+            info: {
+                type: 'string',
+                format: 'file'
+            },
+            onUpdate: async (path) => {
+
+                const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
+            
+                if (result) neurosift.url = result
+            },
+            onThrow,
+        });
+
+        return html`
+            <div style="display: grid; height: 100%; grid-template-rows: min-content min-content 1fr; gap: 10px;">
+                <div>
+                    <div style="display: flex; align-items: end; justify-content: space-between;">
+                        <h1 style="margin: 0;">NWB File Preview</h1>
+                    </div>
+                    <p>Use Neurosift to preview of your NWB file.</p>
+                    <hr />
+                </div>
+                ${this.input}
+                ${neurosift}
+            </div>
+        `;
+    }
+}
+
+customElements.get("nwbguide-preview-page") || customElements.define("nwbguide-preview-page", PreviewPage);
diff --git a/src/renderer/src/stories/preview/Neurosift.js b/src/renderer/src/stories/preview/Neurosift.js
index 5c8b81d8a..eee813c05 100644
--- a/src/renderer/src/stories/preview/Neurosift.js
+++ b/src/renderer/src/stories/preview/Neurosift.js
@@ -26,7 +26,7 @@ export class Neurosift extends LitElement {
                 height: 100%;
             }
 
-            div {
+            .loader-container {
                 display: flex;
                 align-items: center;
                 justify-content: center;
@@ -49,20 +49,26 @@ export class Neurosift extends LitElement {
         `;
     }
 
-    constructor({ url }) {
+    static get properties() {
+        return { 
+            url: {type: String, reflect: true}
+        }
+    }
+
+    constructor({ url } = {}) {
         super();
         this.url = url;
     }
 
     render() {
-        return html` <div>${new Loader({ message: "Loading Neurosift view..." })}</div>
+        return this.url ? html` <div class="loader-container">${new Loader({ message: "Loading Neurosift view..." })}</div>
             <iframe
                 class="iframe-placeholder"
                 src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"
                 @load=${function (ev) {
                     ev.target.previousElementSibling.remove();
                 }}
-            ></iframe>`;
+            ></iframe>` : ``;
     }
 }
 

From b0163228435e3220e648f401334d551627b19585 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 5 Sep 2023 18:25:55 -0700
Subject: [PATCH 04/60] Support previewing NWB files when selected in native
 file explorer

---
 package.json                                  |  2 +-
 src/renderer/src/electron/index.js            |  9 ++-
 src/renderer/src/globals.js                   | 14 ++++
 src/renderer/src/progress/index.js            |  4 +-
 src/renderer/src/progress/update.js           | 17 +----
 src/renderer/src/stories/Dashboard.js         |  4 ++
 .../src/stories/pages/inspect/InspectPage.js  | 72 ++++++++++---------
 .../src/stories/pages/preview/PreviewPage.js  | 45 ++++++------
 8 files changed, 92 insertions(+), 75 deletions(-)

diff --git a/package.json b/package.json
index bad2cfe3e..59c58571f 100644
--- a/package.json
+++ b/package.json
@@ -56,7 +56,7 @@
       {
         "ext": "nwb",
         "name": "NWB File",
-        "role": "Editor"
+        "role": "Viewer"
       }
     ],
     "files": [
diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 4f9b30865..537ee2dd3 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -1,3 +1,4 @@
+import { updateURLParams } from "../globals.js";
 import isElectron from "./check.js";
 
 export { isElectron };
@@ -21,8 +22,12 @@ if (isElectron) {
         remote = require("@electron/remote");
         app = remote.app;
 
-        electron.ipcRenderer.on("fileOpened", (info, ...args) => {
-            console.log("File opened!", ...args);
+        electron.ipcRenderer.on("fileOpened", (info, filepath) => {
+            updateURLParams({ file: filepath })
+            const dashboard = document.querySelector("nwb-dashboard");
+            const activePage = dashboard.getAttribute('activePage')
+            if (activePage === 'preview') dashboard.requestUpdate()
+            else dashboard.setAttribute("activePage", 'preview')
         });
 
         ["log", "warn", "error"].forEach((method) =>
diff --git a/src/renderer/src/globals.js b/src/renderer/src/globals.js
index b235577dd..1cb3ad5bf 100644
--- a/src/renderer/src/globals.js
+++ b/src/renderer/src/globals.js
@@ -13,3 +13,17 @@ export let runOnLoad = (fn) => {
 export const baseUrl = `http://127.0.0.1:${port}`;
 
 export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;
+
+export function updateURLParams(paramsToUpdate) {
+    const params = new URLSearchParams(location.search);
+    for (let key in paramsToUpdate) {
+        const value = paramsToUpdate[key];
+        if (value == undefined) params.delete(key);
+        else params.set(key, value);
+    }
+
+    // Update browser history state
+    const value = `${location.pathname}?${params}`;
+    if (history.state) Object.assign(history.state, paramsToUpdate);
+    window.history.pushState(history.state, null, value);
+}
diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index b5c7c2121..a2aa06dfe 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -2,9 +2,9 @@ import Swal from "sweetalert2";
 
 import { guidedProgressFilePath, reloadPageToHome, isStorybook, appDirectory } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
-import { joinPath, runOnLoad } from "../globals.js";
+import { joinPath, runOnLoad, updateURLParams } from "../globals.js";
 import { merge } from "../stories/pages/utils.js";
-import { updateAppProgress, updateFile, updateURLParams } from "./update.js";
+import { updateAppProgress, updateFile } from "./update.js";
 
 export * from "./update";
 
diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 06b422639..5c4f72aea 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -1,6 +1,6 @@
 import { guidedProgressFilePath } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
-import { joinPath } from "../globals.js";
+import { joinPath, updateURLParams } from "../globals.js";
 import { get } from "./index.js";
 
 export const update = (newDatasetName, previousDatasetName) => {
@@ -23,21 +23,6 @@ export const update = (newDatasetName, previousDatasetName) => {
         return "Dataset name updated";
     } else throw new Error("No previous dataset name provided");
 };
-
-export function updateURLParams(paramsToUpdate) {
-    const params = new URLSearchParams(location.search);
-    for (let key in paramsToUpdate) {
-        const value = paramsToUpdate[key];
-        if (value == undefined) params.delete(key);
-        else params.set(key, value);
-    }
-
-    // Update browser history state
-    const value = `${location.pathname}?${params}`;
-    if (history.state) Object.assign(history.state, paramsToUpdate);
-    window.history.pushState(history.state, null, value);
-}
-
 export const updateAppProgress = (
     pageId,
     dataOrProjectName = {},
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 3d3240331..1c6971117 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -133,6 +133,10 @@ export class Dashboard extends LitElement {
         this.#updated();
     }
 
+    requestPageUpdate() {
+        if (this.#active) this.#active.requestUpdate()
+    }
+
     createRenderRoot() {
         return this;
     }
diff --git a/src/renderer/src/stories/pages/inspect/InspectPage.js b/src/renderer/src/stories/pages/inspect/InspectPage.js
index 5645f77f5..aeceb80fc 100644
--- a/src/renderer/src/stories/pages/inspect/InspectPage.js
+++ b/src/renderer/src/stories/pages/inspect/InspectPage.js
@@ -15,44 +15,52 @@ export class InspectPage extends Page {
         super(...args);
     }
 
+    showReport = async (value) => {
+        if (!value) {
+            const message = "Please provide a folder to inspect."
+            onThrow(message)
+            throw new Error(message)
+        }
+
+        const items = truncateFilePaths(await run("inspect_folder", { path: value }, { title: "Inspecting your files" }).catch((e) => {
+            this.notify(e.message, "error");
+            throw e;
+        }), value);
+
+        const list = new InspectorList({ items });
+        list.style.padding = "25px";
+
+        const modal = new Modal({
+            header: value
+        })
+        modal.append(list)
+        document.body.append(modal)
+
+        modal.toggle(true)
+    }
+
+    input = new JSONSchemaInput({
+        path: ['folder_path'],
+        info: {
+            type: 'string',
+            format: 'directory'
+        },
+        onThrow,
+    });
+
     render() {
 
         const button = new Button({
             label: "Inspect Files",
-            onClick: async () => {
-                const { value } = this.input
-                if (!value) {
-                    const message = "Please provide a folder to inspect."
-                    onThrow(message)
-                    throw new Error(message)
-                }
-
-                const items = truncateFilePaths(await run("inspect_folder", { path: value }, { title: "Inspecting your files" }).catch((e) => {
-                    this.notify(e.message, "error");
-                    throw e;
-                }), value);
-
-                const list = new InspectorList({ items });
-                list.style.padding = "25px";
-
-                const modal = new Modal({
-                    header: value
-                })
-                modal.append(list)
-                document.body.append(modal)
-
-                modal.toggle(true)
-            },
+            onClick: async () => this.showReport(this.input.value),
         });
 
-        this.input = new JSONSchemaInput({
-            path: ['folder_path'],
-            info: {
-                type: 'string',
-                format: 'directory'
-            },
-            onThrow,
-        });
+        const urlFilePath = new URL(document.location).searchParams.get('file')
+
+        if (urlFilePath) {
+            this.showReport(urlFilePath)
+            this.input.value = urlFilePath
+        }
 
         return html`
             <div style="display: flex; align-items: end; justify-content: space-between; margin-bottom: 10px;">
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index 5f2b276c5..5f9d07214 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -1,13 +1,7 @@
 import { html } from "lit";
 import { Page } from "../Page.js";
 import { onThrow } from "../../../errors";
-import { Button } from "../../Button.js";
-
-import { run } from "../guided-mode/options/utils.js";
 import { JSONSchemaInput } from "../../JSONSchemaInput.js";
-import { Modal } from "../../Modal";
-import { truncateFilePaths } from "../../preview/NWBFilePreview.js";
-import { InspectorList } from "../../preview/inspector/InspectorList.js";
 import { Neurosift } from "../../preview/Neurosift.js";
 import { baseUrl } from "../../../globals.js";
 
@@ -17,24 +11,31 @@ export class PreviewPage extends Page {
         super(...args);
     }
 
-    render() {
+    updatePath = async (path) => {
+        const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
+        if (result) this.neurosift.url = result
+    }
 
-        const neurosift = new Neurosift()
+    neurosift = new Neurosift()
+
+    input = new JSONSchemaInput({
+        path: ['file_path'],
+        info: {
+            type: 'string',
+            format: 'file'
+        },
+        onUpdate: this.updatePath,
+        onThrow,
+    });
+
+    render() {
 
-        this.input = new JSONSchemaInput({
-            path: ['file_path'],
-            info: {
-                type: 'string',
-                format: 'file'
-            },
-            onUpdate: async (path) => {
+        const urlFilePath = new URL(document.location).searchParams.get('file')
 
-                const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
-            
-                if (result) neurosift.url = result
-            },
-            onThrow,
-        });
+        if (urlFilePath) {
+            this.updatePath(urlFilePath)
+            this.input.value = urlFilePath
+        }
 
         return html`
             <div style="display: grid; height: 100%; grid-template-rows: min-content min-content 1fr; gap: 10px;">
@@ -46,7 +47,7 @@ export class PreviewPage extends Page {
                     <hr />
                 </div>
                 ${this.input}
-                ${neurosift}
+                ${this.neurosift}
             </div>
         `;
     }

From b9129faab99b8402d00836e01edbf44a2ec63f2c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 6 Sep 2023 01:26:46 +0000
Subject: [PATCH 05/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/app.py                                | 13 +++---
 src/renderer/src/electron/index.js            |  8 ++--
 src/renderer/src/stories/Dashboard.js         |  2 +-
 src/renderer/src/stories/assets/inspect.svg   | 10 ++---
 src/renderer/src/stories/assets/preview.svg   | 10 ++---
 .../pages/guided-mode/options/utils.js        |  4 +-
 .../src/stories/pages/inspect/InspectPage.js  | 43 ++++++++++---------
 .../src/stories/pages/preview/PreviewPage.js  | 23 +++++-----
 src/renderer/src/stories/preview/Neurosift.js | 24 ++++++-----
 .../preview/inspector/InspectorList.js        | 10 ++---
 10 files changed, 74 insertions(+), 73 deletions(-)

diff --git a/pyflask/app.py b/pyflask/app.py
index da0205fdf..8a978e0d0 100644
--- a/pyflask/app.py
+++ b/pyflask/app.py
@@ -57,26 +57,27 @@
 
 registered = {}
 
+
 @app.route("/files")
 def get_all_files():
     return list(registered.keys())
 
+
 @app.route("/files/<path:path>", methods=["GET", "POST"])
 def handle_file_request(path):
-    
-
-    if request.method == 'GET':
+    if request.method == "GET":
         if registered[path]:
             return send_file(f"{sep}{unquote(path)}")
         else:
-            app.abort(404, 'Resource is not accessible.')
+            app.abort(404, "Resource is not accessible.")
 
     else:
-        if ('.nwb' in path):
+        if ".nwb" in path:
             registered[path] = True
             return request.base_url
         else:
-            app.abort(400, str('Path does not point to an NWB file.'))
+            app.abort(400, str("Path does not point to an NWB file."))
+
 
 @app.route("/conversions/<path:path>")
 def send_conversions(path):
diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 537ee2dd3..49545692f 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -23,11 +23,11 @@ if (isElectron) {
         app = remote.app;
 
         electron.ipcRenderer.on("fileOpened", (info, filepath) => {
-            updateURLParams({ file: filepath })
+            updateURLParams({ file: filepath });
             const dashboard = document.querySelector("nwb-dashboard");
-            const activePage = dashboard.getAttribute('activePage')
-            if (activePage === 'preview') dashboard.requestUpdate()
-            else dashboard.setAttribute("activePage", 'preview')
+            const activePage = dashboard.getAttribute("activePage");
+            if (activePage === "preview") dashboard.requestUpdate();
+            else dashboard.setAttribute("activePage", "preview");
         });
 
         ["log", "warn", "error"].forEach((method) =>
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 1c6971117..121391965 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -134,7 +134,7 @@ export class Dashboard extends LitElement {
     }
 
     requestPageUpdate() {
-        if (this.#active) this.#active.requestUpdate()
+        if (this.#active) this.#active.requestUpdate();
     }
 
     createRenderRoot() {
diff --git a/src/renderer/src/stories/assets/inspect.svg b/src/renderer/src/stories/assets/inspect.svg
index a94da7c42..8b59b651e 100644
--- a/src/renderer/src/stories/assets/inspect.svg
+++ b/src/renderer/src/stories/assets/inspect.svg
@@ -1,7 +1,7 @@
-<svg 
-xmlns="http://www.w3.org/2000/svg" 
-height="25" 
-viewBox="0 -960 960 960" 
+<svg
+xmlns="http://www.w3.org/2000/svg"
+height="25"
+viewBox="0 -960 960 960"
 width="25"
 style="margin-right: 30px; margin-bottom: -5px"
-><path d="M80-200v-60h400v60H80Zm0-210v-60h200v60H80Zm0-210v-60h200v60H80Zm758 420L678-360q-26 20-56 30t-62 10q-83 0-141.5-58.5T360-520q0-83 58.5-141.5T560-720q83 0 141.5 58.5T760-520q0 32-10 62t-30 56l160 160-42 42ZM559.765-380Q618-380 659-420.765q41-40.764 41-99Q700-578 659.235-619q-40.764-41-99-41Q502-660 461-619.235q-41 40.764-41 99Q420-462 460.765-421q40.764 41 99 41Z"/></svg>
\ No newline at end of file
+><path d="M80-200v-60h400v60H80Zm0-210v-60h200v60H80Zm0-210v-60h200v60H80Zm758 420L678-360q-26 20-56 30t-62 10q-83 0-141.5-58.5T360-520q0-83 58.5-141.5T560-720q83 0 141.5 58.5T760-520q0 32-10 62t-30 56l160 160-42 42ZM559.765-380Q618-380 659-420.765q41-40.764 41-99Q700-578 659.235-619q-40.764-41-99-41Q502-660 461-619.235q-41 40.764-41 99Q420-462 460.765-421q40.764 41 99 41Z"/></svg>
diff --git a/src/renderer/src/stories/assets/preview.svg b/src/renderer/src/stories/assets/preview.svg
index dbbbd8f77..467b1d186 100644
--- a/src/renderer/src/stories/assets/preview.svg
+++ b/src/renderer/src/stories/assets/preview.svg
@@ -1,7 +1,7 @@
-<svg 
-xmlns="http://www.w3.org/2000/svg" 
-height="25" 
-viewBox="0 -960 960 960" 
+<svg
+xmlns="http://www.w3.org/2000/svg"
+height="25"
+viewBox="0 -960 960 960"
 width="25"
 style="margin-right: 30px; margin-bottom: -5px"
-><path d="M838-120 627-331q-40 32-91.5 51.5T430-260q-81 0-149-38.5T171-400h76q35 37 82 58.5T430-320q104 0 177-73.5T680-570q0-104-73-177t-177-73q-101 0-173.5 70T180-580h-60q4-125 93.5-212.5T430-880q129 0 219.5 90.5T740-570q0 54-19.5 105.5T669-373l211 211-42 42ZM397-400l-63-208-52 148H80v-60h160l66-190h60l61 204 43-134h60l60 120h30v60h-67l-47-94-50 154h-59Z"/></svg>
\ No newline at end of file
+><path d="M838-120 627-331q-40 32-91.5 51.5T430-260q-81 0-149-38.5T171-400h76q35 37 82 58.5T430-320q104 0 177-73.5T680-570q0-104-73-177t-177-73q-101 0-173.5 70T180-580h-60q4-125 93.5-212.5T430-880q129 0 219.5 90.5T740-570q0 54-19.5 105.5T669-373l211 211-42 42ZM397-400l-63-208-52 148H80v-60h160l66-190h60l61 204 43-134h60l60 120h30v60h-67l-47-94-50 154h-59Z"/></svg>
diff --git a/src/renderer/src/stories/pages/guided-mode/options/utils.js b/src/renderer/src/stories/pages/guided-mode/options/utils.js
index 20785b4f2..48031dd06 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/utils.js
@@ -24,9 +24,9 @@ export const run = async (url, payload, options = {}) => {
     const needsSwal = !options.swal && options.swal !== false;
     if (needsSwal) openProgressSwal(options).then((swal) => (options.onOpen ? options.onOpen(swal) : undefined));
 
-    if (!('base' in options)) options.base = '/neuroconv'
+    if (!("base" in options)) options.base = "/neuroconv";
 
-    const results = await fetch(`${baseUrl}${options.base || ''}/${url}`, {
+    const results = await fetch(`${baseUrl}${options.base || ""}/${url}`, {
         method: "POST",
         headers: { "Content-Type": "application/json" },
         body: JSON.stringify(payload),
diff --git a/src/renderer/src/stories/pages/inspect/InspectPage.js b/src/renderer/src/stories/pages/inspect/InspectPage.js
index aeceb80fc..5b5164a2c 100644
--- a/src/renderer/src/stories/pages/inspect/InspectPage.js
+++ b/src/renderer/src/stories/pages/inspect/InspectPage.js
@@ -9,7 +9,6 @@ import { Modal } from "../../Modal";
 import { truncateFilePaths } from "../../preview/NWBFilePreview.js";
 import { InspectorList } from "../../preview/inspector/InspectorList.js";
 
-
 export class InspectPage extends Page {
     constructor(...args) {
         super(...args);
@@ -17,49 +16,51 @@ export class InspectPage extends Page {
 
     showReport = async (value) => {
         if (!value) {
-            const message = "Please provide a folder to inspect."
-            onThrow(message)
-            throw new Error(message)
+            const message = "Please provide a folder to inspect.";
+            onThrow(message);
+            throw new Error(message);
         }
 
-        const items = truncateFilePaths(await run("inspect_folder", { path: value }, { title: "Inspecting your files" }).catch((e) => {
-            this.notify(e.message, "error");
-            throw e;
-        }), value);
+        const items = truncateFilePaths(
+            await run("inspect_folder", { path: value }, { title: "Inspecting your files" }).catch((e) => {
+                this.notify(e.message, "error");
+                throw e;
+            }),
+            value
+        );
 
         const list = new InspectorList({ items });
         list.style.padding = "25px";
 
         const modal = new Modal({
-            header: value
-        })
-        modal.append(list)
-        document.body.append(modal)
+            header: value,
+        });
+        modal.append(list);
+        document.body.append(modal);
 
-        modal.toggle(true)
-    }
+        modal.toggle(true);
+    };
 
     input = new JSONSchemaInput({
-        path: ['folder_path'],
+        path: ["folder_path"],
         info: {
-            type: 'string',
-            format: 'directory'
+            type: "string",
+            format: "directory",
         },
         onThrow,
     });
 
     render() {
-
         const button = new Button({
             label: "Inspect Files",
             onClick: async () => this.showReport(this.input.value),
         });
 
-        const urlFilePath = new URL(document.location).searchParams.get('file')
+        const urlFilePath = new URL(document.location).searchParams.get("file");
 
         if (urlFilePath) {
-            this.showReport(urlFilePath)
-            this.input.value = urlFilePath
+            this.showReport(urlFilePath);
+            this.input.value = urlFilePath;
         }
 
         return html`
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index 5f9d07214..92acdf666 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -5,7 +5,6 @@ import { JSONSchemaInput } from "../../JSONSchemaInput.js";
 import { Neurosift } from "../../preview/Neurosift.js";
 import { baseUrl } from "../../../globals.js";
 
-
 export class PreviewPage extends Page {
     constructor(...args) {
         super(...args);
@@ -13,28 +12,27 @@ export class PreviewPage extends Page {
 
     updatePath = async (path) => {
         const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
-        if (result) this.neurosift.url = result
-    }
+        if (result) this.neurosift.url = result;
+    };
 
-    neurosift = new Neurosift()
+    neurosift = new Neurosift();
 
     input = new JSONSchemaInput({
-        path: ['file_path'],
+        path: ["file_path"],
         info: {
-            type: 'string',
-            format: 'file'
+            type: "string",
+            format: "file",
         },
         onUpdate: this.updatePath,
         onThrow,
     });
 
     render() {
-
-        const urlFilePath = new URL(document.location).searchParams.get('file')
+        const urlFilePath = new URL(document.location).searchParams.get("file");
 
         if (urlFilePath) {
-            this.updatePath(urlFilePath)
-            this.input.value = urlFilePath
+            this.updatePath(urlFilePath);
+            this.input.value = urlFilePath;
         }
 
         return html`
@@ -46,8 +44,7 @@ export class PreviewPage extends Page {
                     <p>Use Neurosift to preview of your NWB file.</p>
                     <hr />
                 </div>
-                ${this.input}
-                ${this.neurosift}
+                ${this.input} ${this.neurosift}
             </div>
         `;
     }
diff --git a/src/renderer/src/stories/preview/Neurosift.js b/src/renderer/src/stories/preview/Neurosift.js
index eee813c05..41cbff439 100644
--- a/src/renderer/src/stories/preview/Neurosift.js
+++ b/src/renderer/src/stories/preview/Neurosift.js
@@ -50,9 +50,9 @@ export class Neurosift extends LitElement {
     }
 
     static get properties() {
-        return { 
-            url: {type: String, reflect: true}
-        }
+        return {
+            url: { type: String, reflect: true },
+        };
     }
 
     constructor({ url } = {}) {
@@ -61,14 +61,16 @@ export class Neurosift extends LitElement {
     }
 
     render() {
-        return this.url ? html` <div class="loader-container">${new Loader({ message: "Loading Neurosift view..." })}</div>
-            <iframe
-                class="iframe-placeholder"
-                src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"
-                @load=${function (ev) {
-                    ev.target.previousElementSibling.remove();
-                }}
-            ></iframe>` : ``;
+        return this.url
+            ? html` <div class="loader-container">${new Loader({ message: "Loading Neurosift view..." })}</div>
+                  <iframe
+                      class="iframe-placeholder"
+                      src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"
+                      @load=${function (ev) {
+                          ev.target.previousElementSibling.remove();
+                      }}
+                  ></iframe>`
+            : ``;
     }
 }
 
diff --git a/src/renderer/src/stories/preview/inspector/InspectorList.js b/src/renderer/src/stories/preview/inspector/InspectorList.js
index ec5bb3bc0..b4fedb670 100644
--- a/src/renderer/src/stories/preview/inspector/InspectorList.js
+++ b/src/renderer/src/stories/preview/inspector/InspectorList.js
@@ -29,14 +29,15 @@ const aggregateMessages = (items) => {
 };
 
 export class InspectorList extends List {
-
     static get styles() {
-
-        return [super.styles, css`
+        return [
+            super.styles,
+            css`
             :host {
                 display: block;
             }
-        }`]
+        }`,
+        ];
     }
 
     constructor({ items, listStyles }) {
@@ -64,7 +65,6 @@ customElements.get("inspector-list") || customElements.define("inspector-list",
 export class InspectorListItem extends LitElement {
     static get styles() {
         return css`
-        
             :host {
                 display: block;
                 background: gainsboro;

From a1675558085bee67ac37f095638af45e6aaa5b49 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 6 Sep 2023 14:50:39 -0700
Subject: [PATCH 06/60] Add comprehensive stories and fix multi-directory
 selection

---
 .../src/stories/FileSystemSelector.js         | 23 +++++++++++--------
 .../src/stories/FileSystemSelector.stories.js |  9 ++++++++
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index fe3262220..2d07756e0 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -150,6 +150,15 @@ export class FilesystemSelector extends LitElement {
             return;
         }
 
+        const resolvedValueDisplay = (isArray
+            ? len > 1
+                ? `${this.value[0]} and ${len - 1} other${len > 2 ? "s" : ""}`
+                : this.value[0]
+            : this.value)
+
+
+        const objectTypeReference = this.multiple ? this.type === 'directory' ? 'directories' : 'files' : `a ${this.type}`
+
         return html`
             <button
                 title=${isArray ? this.value.map((v, i) => `${i + 1}. ${v}`).join("\n") : this.value}
@@ -183,16 +192,10 @@ export class FilesystemSelector extends LitElement {
                     this.#handleFiles(pathArr);
                 }}
             >
-                ${(isArray
-                    ? len > 1
-                        ? `${this.value[0]} and ${len - 1} other${len > 2 ? "s" : ""}`
-                        : this.value[0]
-                    : this.value) || `Drop a ${this.type} here, or click to choose a ${this.type}`}
-                ${dialog
-                    ? ""
-                    : html`<br /><small
-                              >Cannot get full ${this.type} path${this.multiple ? "s" : ""} on web distribution</small
-                          >`}
+                ${resolvedValueDisplay ? html`
+                    ${resolvedValueDisplay}
+                    ${dialog ? "" : html`<br /><small>Cannot get full ${this.type} path${this.multiple ? "s" : ""} on web distribution</small>`}
+                ` :  html`<span>Drop ${objectTypeReference} here, or click to choose ${objectTypeReference}</span>${this.multiple && this.type === 'directory' ? html`<br /><small>Multiple directory support only available using drag-and-drop.</small>` : ''}`}
             </button>
         `;
     }
diff --git a/src/renderer/src/stories/FileSystemSelector.stories.js b/src/renderer/src/stories/FileSystemSelector.stories.js
index 6656407c0..68fdc3d66 100644
--- a/src/renderer/src/stories/FileSystemSelector.stories.js
+++ b/src/renderer/src/stories/FileSystemSelector.stories.js
@@ -11,3 +11,12 @@ export const Folder = Template.bind({});
 Folder.args = {
     type: "directory",
 };
+
+export const FileMultiple = Template.bind({});
+FileMultiple.args = { multiple: true }
+
+export const FolderMultiple = Template.bind({});
+FolderMultiple.args = {
+    type: "directory",
+    multiple: true
+};

From 957c0fadea2a8f4651a9e98a07361b1751d670e0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 6 Sep 2023 21:51:42 +0000
Subject: [PATCH 07/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/FileSystemSelector.js         | 31 ++++++++++++++-----
 .../src/stories/FileSystemSelector.stories.js |  4 +--
 src/renderer/src/stories/JSONSchemaInput.js   |  1 -
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index 2d07756e0..81967a6ad 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -150,14 +150,17 @@ export class FilesystemSelector extends LitElement {
             return;
         }
 
-        const resolvedValueDisplay = (isArray
+        const resolvedValueDisplay = isArray
             ? len > 1
                 ? `${this.value[0]} and ${len - 1} other${len > 2 ? "s" : ""}`
                 : this.value[0]
-            : this.value)
+            : this.value;
 
-
-        const objectTypeReference = this.multiple ? this.type === 'directory' ? 'directories' : 'files' : `a ${this.type}`
+        const objectTypeReference = this.multiple
+            ? this.type === "directory"
+                ? "directories"
+                : "files"
+            : `a ${this.type}`;
 
         return html`
             <button
@@ -192,10 +195,22 @@ export class FilesystemSelector extends LitElement {
                     this.#handleFiles(pathArr);
                 }}
             >
-                ${resolvedValueDisplay ? html`
-                    ${resolvedValueDisplay}
-                    ${dialog ? "" : html`<br /><small>Cannot get full ${this.type} path${this.multiple ? "s" : ""} on web distribution</small>`}
-                ` :  html`<span>Drop ${objectTypeReference} here, or click to choose ${objectTypeReference}</span>${this.multiple && this.type === 'directory' ? html`<br /><small>Multiple directory support only available using drag-and-drop.</small>` : ''}`}
+                ${resolvedValueDisplay
+                    ? html`
+                          ${resolvedValueDisplay}
+                          ${dialog
+                              ? ""
+                              : html`<br /><small
+                                        >Cannot get full ${this.type} path${this.multiple ? "s" : ""} on web
+                                        distribution</small
+                                    >`}
+                      `
+                    : html`<span>Drop ${objectTypeReference} here, or click to choose ${objectTypeReference}</span
+                          >${this.multiple && this.type === "directory"
+                              ? html`<br /><small
+                                        >Multiple directory support only available using drag-and-drop.</small
+                                    >`
+                              : ""}`}
             </button>
         `;
     }
diff --git a/src/renderer/src/stories/FileSystemSelector.stories.js b/src/renderer/src/stories/FileSystemSelector.stories.js
index 68fdc3d66..035d61938 100644
--- a/src/renderer/src/stories/FileSystemSelector.stories.js
+++ b/src/renderer/src/stories/FileSystemSelector.stories.js
@@ -13,10 +13,10 @@ Folder.args = {
 };
 
 export const FileMultiple = Template.bind({});
-FileMultiple.args = { multiple: true }
+FileMultiple.args = { multiple: true };
 
 export const FolderMultiple = Template.bind({});
 FolderMultiple.args = {
     type: "directory",
-    multiple: true
+    multiple: true,
 };
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 536ff8654..f87a96b94 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -267,7 +267,6 @@ export class JSONSchemaInput extends LitElement {
         } else if (info.type === "string" || info.type === "number") {
             const fileSystemFormat = isFilesystemSelector(info.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
-            
             // Handle long string formats
             else if (info.format === "long" || isArray)
                 return html`<textarea

From 753ccce30e61419455b5259b7a5ddadab76efe79 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 7 Sep 2023 11:04:08 -0700
Subject: [PATCH 08/60] Create new standalone results page for DANDI uploads

---
 src/renderer/assets/css/global.css            |  10 ++
 src/renderer/src/stories/DandiResults.js      | 109 ++++++++++++++++++
 .../guided-mode/results/GuidedResults.js      |  93 +--------------
 .../src/stories/pages/uploads/UploadsPage.js  |  31 +++--
 4 files changed, 148 insertions(+), 95 deletions(-)
 create mode 100644 src/renderer/src/stories/DandiResults.js

diff --git a/src/renderer/assets/css/global.css b/src/renderer/assets/css/global.css
index 69b046c46..d35cd901c 100755
--- a/src/renderer/assets/css/global.css
+++ b/src/renderer/assets/css/global.css
@@ -8,6 +8,16 @@
     /* src: local('Source Code Pro'), local('SourceCodePro'), url(fonts/SourceCodePro-Regular.ttf) format('truetype'); */
 }
 
+/*  Notfy */
+.notyf__toast {
+    max-width: clamp(300px, 40vw, 500px) !important;
+}
+
+.notyf__message {
+    word-wrap: break-word;
+}
+
+
 /* Global ---------------------------- */
 
 * {
diff --git a/src/renderer/src/stories/DandiResults.js b/src/renderer/src/stories/DandiResults.js
new file mode 100644
index 000000000..51f2fa682
--- /dev/null
+++ b/src/renderer/src/stories/DandiResults.js
@@ -0,0 +1,109 @@
+import { LitElement, css, html } from "lit";
+
+import { get } from "dandi";
+import { isStaging } from "./pages/uploads/UploadsPage.js";
+
+export class DandiResults extends LitElement {
+
+    static get styles () {
+        return css`
+            :host {
+                display:block;
+            }
+        `
+    }
+
+    constructor(props) {
+        super();
+        Object.assign(this, props)
+    }
+
+    async updated() {
+        const handleId = (str, info) => {
+            let value = info[str];
+            if (str === "modified") value = new Date(value).toString();
+
+            const el = this.shadowRoot.querySelector(`#${str}`);
+            el.innerText = value;
+
+            if (el.tagName === "A") {
+                if (str === "doi") value = `http://doi.org/${value}`;
+                el.href = value;
+                el.target = "_blank";
+            }
+        };
+
+        const elIds = ["name", "modified"];
+
+        const otherElIds = ["embargo_status"];
+
+        const liveId = this.id; // '000552' // From Huszar
+        const dandiset = await get(liveId, isStaging(this.id) ? "staging" : undefined);
+
+        otherElIds.forEach((str) => handleId(str, dandiset));
+        elIds.forEach((str) => handleId(str, dandiset.draft_version));
+
+        const info = await dandiset.getInfo({ version: dandiset.draft_version.version });
+
+        const secondElIds = ["description", "url"];
+        secondElIds.forEach((str) => handleId(str, info));
+
+        const publicationEl = this.shadowRoot.querySelector(`#publication`);;
+        publicationEl.innerHTML = "";
+        const publications = (info.relatedResource ?? []).filter((o) => o.relation === "dcite:IsDescribedBy");
+
+        if (publications.length)
+            publicationEl.append(
+                ...(await Promise.all(
+                    publications.map(async (o) => {
+                        const li = document.createElement("li");
+                        const { message } = await fetch(
+                            `http://api.crossref.org/works${new URL(o.identifier).pathname}`
+                        ).then((res) => res.json());
+                        li.innerHTML = `${message.author.map((o) => `${o.family}, ${o.given[0]}.`).join(", ")} (${
+                            message.created["date-parts"][0][0]
+                        }). ${message.title[0]}. <i>${message["container-title"]}</i>, <i>${message.volume}</i>(${
+                            message.issue
+                        }), ${message.page}. doi:${message.DOI}`;
+                        return li;
+                    })
+                ))
+            );
+        else publicationEl.innerText = "N/A";
+    }
+
+    render() {
+
+        return html`
+            <div style="text-align: center;">
+                <div style="display: inline-block; width: 100%; text-align: left;">
+                    <h2 style="margin: 0; margin-bottom: 10px;"><span id="name"></span></h2>
+                    <p><span id="description"></span></p>
+
+                    <p><b>Identifier:</b> ${this.id}</p>
+                    <p><b>Upload Time:</b> <span id="modified"></span></p>
+                    <p><b>Embargo Status:</b> <span id="embargo_status"></span></p>
+
+                    <small><b>URL:</b> <a id="url"></a></small><br />
+
+                    <h3 style="padding: 0;">Related Publications</h3>
+                    <hr />
+                    <ol id="publication"></ol>
+
+                    ${this.files ? html`
+                        <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
+                        <hr />
+                        <ol>
+                            ${Object.values(this.files)
+                                .map((v) => Object.values(v))
+                                .flat()
+                                .map((o) => html`<li>${o.file}</li>`)}
+                        </ol>` : ''}
+                </div>
+            </div>
+        `;
+    }
+}
+
+customElements.get("dandi-results") ||
+    customElements.define("dandi-results", DandiResults);
diff --git a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
index fc3d64df2..b25ae1ceb 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -1,105 +1,22 @@
-import { css, html } from "lit";
+import { html } from "lit";
 import { Page } from "../../Page.js";
 
-import { get } from "dandi";
+import { DandiResults } from "../../../DandiResults.js";
 
 export class GuidedResultsPage extends Page {
     constructor(...args) {
         super(...args);
     }
 
-    async updated() {
-        const handleId = (str, info) => {
-            let value = info[str];
-            if (str === "modified") value = new Date(value).toString();
-
-            const el = this.query(`#${str}`);
-            el.innerText = value;
-
-            if (el.tagName === "A") {
-                if (str === "doi") value = `http://doi.org/${value}`;
-                el.href = value;
-                el.target = "_blank";
-            }
-        };
-
-        const { dandiset_id, staging } = this.info.globalState.upload?.info ?? {};
-
-        const elIds = ["name", "modified"];
-
-        const otherElIds = ["embargo_status"];
-
-        const liveId = dandiset_id; // '000552' // From Huszar
-        const isStaging = staging; //false
-        const dandiset = await get(liveId, isStaging ? "staging" : undefined);
-
-        otherElIds.forEach((str) => handleId(str, dandiset));
-        elIds.forEach((str) => handleId(str, dandiset.draft_version));
-
-        const info = await dandiset.getInfo({ version: dandiset.draft_version.version });
-
-        const secondElIds = ["description", "url"];
-        secondElIds.forEach((str) => handleId(str, info));
-
-        const publicationEl = document.getElementById("publication");
-        publicationEl.innerHTML = "";
-        const publications = (info.relatedResource ?? []).filter((o) => o.relation === "dcite:IsDescribedBy");
-
-        if (publications.length)
-            publicationEl.append(
-                ...(await Promise.all(
-                    publications.map(async (o) => {
-                        const li = document.createElement("li");
-                        const { message } = await fetch(
-                            `http://api.crossref.org/works${new URL(o.identifier).pathname}`
-                        ).then((res) => res.json());
-                        li.innerHTML = `${message.author.map((o) => `${o.family}, ${o.given[0]}.`).join(", ")} (${
-                            message.created["date-parts"][0][0]
-                        }). ${message.title[0]}. <i>${message["container-title"]}</i>, <i>${message.volume}</i>(${
-                            message.issue
-                        }), ${message.page}. doi:${message.DOI}`;
-                        return li;
-                    })
-                ))
-            );
-        else publicationEl.innerText = "N/A";
-    }
-
     render() {
-        const results = this.info.globalState.conversion;
+        const { conversion } = this.info.globalState.conversion;
 
-        if (!results)
+        if (!conversion)
             return html`<div style="text-align: center;"><p>Your conversion failed. Please try again.</p></div>`;
 
         const { dandiset_id } = this.info.globalState.upload?.info ?? {};
 
-        return html`
-            <div style="text-align: center;">
-                <div style="display: inline-block; width: 100%; text-align: left;">
-                    <h2 style="margin: 0; margin-bottom: 10px;"><span id="name"></span></h2>
-                    <p><span id="description"></span></p>
-
-                    <p><b>Identifier:</b> ${dandiset_id}</p>
-                    <p><b>Upload Time:</b> <span id="modified"></span></p>
-                    <p><b>Embargo Status:</b> <span id="embargo_status"></span></p>
-
-                    <small><b>URL:</b> <a id="url"></a></small><br />
-
-                    <h3 style="padding: 0;">Related Publications</h3>
-                    <hr />
-                    <ol id="publication"></ol>
-
-                    <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
-                    <hr />
-                    <ol>
-                        ${Object.values(results)
-                            .map((v) => Object.values(v))
-                            .flat()
-                            .map((o) => html`<li>${o.file}</li>`)}
-                    </ol>
-                </div>
-            </div>
-        `;
+        return DandiResults({ id: dandiset_id, files: conversion })
     }
 }
 
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index a21742392..573eab0dc 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -13,9 +13,15 @@ import { merge } from "../utils.js";
 import { run } from "../guided-mode/options/utils.js";
 import { notyf } from "../../../dependencies/globals.js";
 import Swal from "sweetalert2";
+import { Modal } from "../../Modal";
+import { DandiResults } from "../../DandiResults.js";
+
+export const isStaging = (id) => parseInt(id) >= 100000
 
 export async function uploadToDandi(info) {
-    if (!global.data.DANDI?.api_key) {
+
+    const api_key = global.data.DANDI?.api_key
+    if (!api_key) {
         await Swal.fire({
             title: "Your DANDI API key is not configured.",
             html: "Edit your settings to include this value.",
@@ -26,10 +32,11 @@ export async function uploadToDandi(info) {
         return this.to("settings");
     }
 
-    info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs
-    info.api_key = global.data.DANDI.api_key;
-
-    return await run("upload/folder", info, { title: "Uploading to DANDI" }).catch((e) => {
+    return await run("upload/folder", {
+        ...info, 
+        staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
+        api_key
+    }, { title: "Uploading to DANDI" }).catch((e) => {
         this.notify(e.message, "error");
         throw e;
     });
@@ -48,15 +55,25 @@ export class UploadsPage extends Page {
             label: defaultButtonMessage,
             onClick: async () => {
                 await this.form.validate(); // Will throw an error in the callback
-                const results = await uploadToDandi.call(this, { ...global.data.uploads });
+                const results = await uploadToDandi.call(this, { ...globalState });
+
                 if (results)
                     notyf.open({
                         type: "success",
-                        message: `${global.data.uploads.nwb_folder_path} successfully uploaded to Dandiset ${global.data.uploads.dandiset_id}`,
+                        message: `${globalState.nwb_folder_path} successfully uploaded to Dandiset ${globalState.dandiset_id}`,
                     });
 
                 global.data.uploads = {};
                 global.save();
+
+                const modal = new Modal({ open: true })
+                modal.header = "DANDI Upload Summary"
+                const summary = new DandiResults({ id: globalState.dandiset_id })
+                summary.style.padding = '25px'
+                modal.append(summary)
+            
+                document.body.append(modal)
+
                 this.requestUpdate();
             },
         });

From 4c7a253fce9cd21b4531b4b5abc4f1334d559784 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Sep 2023 18:05:32 +0000
Subject: [PATCH 09/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/assets/css/global.css            |  1 -
 src/renderer/src/stories/DandiResults.js      | 34 +++++++++----------
 .../guided-mode/results/GuidedResults.js      |  2 +-
 .../src/stories/pages/uploads/UploadsPage.js  | 33 ++++++++++--------
 4 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/src/renderer/assets/css/global.css b/src/renderer/assets/css/global.css
index d35cd901c..252a2e657 100755
--- a/src/renderer/assets/css/global.css
+++ b/src/renderer/assets/css/global.css
@@ -17,7 +17,6 @@
     word-wrap: break-word;
 }
 
-
 /* Global ---------------------------- */
 
 * {
diff --git a/src/renderer/src/stories/DandiResults.js b/src/renderer/src/stories/DandiResults.js
index 51f2fa682..86cb1e29b 100644
--- a/src/renderer/src/stories/DandiResults.js
+++ b/src/renderer/src/stories/DandiResults.js
@@ -4,18 +4,17 @@ import { get } from "dandi";
 import { isStaging } from "./pages/uploads/UploadsPage.js";
 
 export class DandiResults extends LitElement {
-
-    static get styles () {
+    static get styles() {
         return css`
             :host {
-                display:block;
+                display: block;
             }
-        `
+        `;
     }
 
     constructor(props) {
         super();
-        Object.assign(this, props)
+        Object.assign(this, props);
     }
 
     async updated() {
@@ -48,7 +47,7 @@ export class DandiResults extends LitElement {
         const secondElIds = ["description", "url"];
         secondElIds.forEach((str) => handleId(str, info));
 
-        const publicationEl = this.shadowRoot.querySelector(`#publication`);;
+        const publicationEl = this.shadowRoot.querySelector(`#publication`);
         publicationEl.innerHTML = "";
         const publications = (info.relatedResource ?? []).filter((o) => o.relation === "dcite:IsDescribedBy");
 
@@ -73,7 +72,6 @@ export class DandiResults extends LitElement {
     }
 
     render() {
-
         return html`
             <div style="text-align: center;">
                 <div style="display: inline-block; width: 100%; text-align: left;">
@@ -90,20 +88,20 @@ export class DandiResults extends LitElement {
                     <hr />
                     <ol id="publication"></ol>
 
-                    ${this.files ? html`
-                        <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
-                        <hr />
-                        <ol>
-                            ${Object.values(this.files)
-                                .map((v) => Object.values(v))
-                                .flat()
-                                .map((o) => html`<li>${o.file}</li>`)}
-                        </ol>` : ''}
+                    ${this.files
+                        ? html` <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
+                              <hr />
+                              <ol>
+                                  ${Object.values(this.files)
+                                      .map((v) => Object.values(v))
+                                      .flat()
+                                      .map((o) => html`<li>${o.file}</li>`)}
+                              </ol>`
+                        : ""}
                 </div>
             </div>
         `;
     }
 }
 
-customElements.get("dandi-results") ||
-    customElements.define("dandi-results", DandiResults);
+customElements.get("dandi-results") || customElements.define("dandi-results", DandiResults);
diff --git a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
index b25ae1ceb..43e5ad642 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -16,7 +16,7 @@ export class GuidedResultsPage extends Page {
 
         const { dandiset_id } = this.info.globalState.upload?.info ?? {};
 
-        return DandiResults({ id: dandiset_id, files: conversion })
+        return DandiResults({ id: dandiset_id, files: conversion });
     }
 }
 
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 573eab0dc..7d366467d 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -16,11 +16,10 @@ import Swal from "sweetalert2";
 import { Modal } from "../../Modal";
 import { DandiResults } from "../../DandiResults.js";
 
-export const isStaging = (id) => parseInt(id) >= 100000
+export const isStaging = (id) => parseInt(id) >= 100000;
 
 export async function uploadToDandi(info) {
-
-    const api_key = global.data.DANDI?.api_key
+    const api_key = global.data.DANDI?.api_key;
     if (!api_key) {
         await Swal.fire({
             title: "Your DANDI API key is not configured.",
@@ -32,11 +31,15 @@ export async function uploadToDandi(info) {
         return this.to("settings");
     }
 
-    return await run("upload/folder", {
-        ...info, 
-        staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
-        api_key
-    }, { title: "Uploading to DANDI" }).catch((e) => {
+    return await run(
+        "upload/folder",
+        {
+            ...info,
+            staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
+            api_key,
+        },
+        { title: "Uploading to DANDI" }
+    ).catch((e) => {
         this.notify(e.message, "error");
         throw e;
     });
@@ -66,13 +69,13 @@ export class UploadsPage extends Page {
                 global.data.uploads = {};
                 global.save();
 
-                const modal = new Modal({ open: true })
-                modal.header = "DANDI Upload Summary"
-                const summary = new DandiResults({ id: globalState.dandiset_id })
-                summary.style.padding = '25px'
-                modal.append(summary)
-            
-                document.body.append(modal)
+                const modal = new Modal({ open: true });
+                modal.header = "DANDI Upload Summary";
+                const summary = new DandiResults({ id: globalState.dandiset_id });
+                summary.style.padding = "25px";
+                modal.append(summary);
+
+                document.body.append(modal);
 
                 this.requestUpdate();
             },

From fc84ec33bf35893b2df248ceb7f8645e8987413a Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 7 Sep 2023 11:24:17 -0700
Subject: [PATCH 10/60] Ensure pages always save once

---
 src/renderer/src/stories/Dashboard.js                         | 3 +++
 src/renderer/src/stories/pages/Page.js                        | 4 +++-
 .../src/stories/pages/guided-mode/data/GuidedStructure.js     | 2 ++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 3d3240331..68a3c01a3 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -229,10 +229,13 @@ export class Dashboard extends LitElement {
                     pageState = state.pages[id] = {
                         visited: false,
                         active: false,
+                        saved: false,
                         pageLabel: page.info.label,
                         pageTitle: page.info.title,
                     };
 
+                info.states =pageState
+
                 state.active = false;
                 pageState.active = false;
 
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index bbcc0d0a6..3eb6b1e45 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -63,8 +63,9 @@ export class Page extends LitElement {
     to = async (transition) => {
         this.beforeTransition();
 
+
         // Otherwise note unsaved updates if present
-        if (this.unsavedUpdates) {
+        if (this.unsavedUpdates || this.info.states?.saved) {
             if (transition === 1) await this.save(); // Save before a single forward transition
             else {
                 Swal.fire({
@@ -95,6 +96,7 @@ export class Page extends LitElement {
     save = async (overrides, runBeforeSave = true) => {
         if (runBeforeSave) await this.beforeSave();
         save(this, overrides);
+        this.info.states.saved = true
         this.unsavedUpdates = false;
     };
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 93938a8ca..5b32d2821 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -75,6 +75,8 @@ export class GuidedStructurePage extends Page {
     };
 
     async updated() {
+
+        console.log(this.info)
         const selected = this.info.globalState.interfaces;
 
         if (Object.keys(selected).length > 0) this.list.emptyMessage = "Loading valid interfaces...";

From 75c85e7a96601fc60387da5cb20a675189b210cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Sep 2023 18:29:24 +0000
Subject: [PATCH 11/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/Dashboard.js                          | 2 +-
 src/renderer/src/stories/pages/Page.js                         | 3 +--
 .../src/stories/pages/guided-mode/data/GuidedStructure.js      | 3 +--
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 68a3c01a3..a75846ca6 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -234,7 +234,7 @@ export class Dashboard extends LitElement {
                         pageTitle: page.info.title,
                     };
 
-                info.states =pageState
+                info.states = pageState;
 
                 state.active = false;
                 pageState.active = false;
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 3eb6b1e45..c4a52659b 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -63,7 +63,6 @@ export class Page extends LitElement {
     to = async (transition) => {
         this.beforeTransition();
 
-
         // Otherwise note unsaved updates if present
         if (this.unsavedUpdates || this.info.states?.saved) {
             if (transition === 1) await this.save(); // Save before a single forward transition
@@ -96,7 +95,7 @@ export class Page extends LitElement {
     save = async (overrides, runBeforeSave = true) => {
         if (runBeforeSave) await this.beforeSave();
         save(this, overrides);
-        this.info.states.saved = true
+        this.info.states.saved = true;
         this.unsavedUpdates = false;
     };
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 5b32d2821..d5f82e0a7 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -75,8 +75,7 @@ export class GuidedStructurePage extends Page {
     };
 
     async updated() {
-
-        console.log(this.info)
+        console.log(this.info);
         const selected = this.info.globalState.interfaces;
 
         if (Object.keys(selected).length > 0) this.list.emptyMessage = "Loading valid interfaces...";

From ad6f4fc0d81302d62ca7125e2ad93c25035527ef Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 7 Sep 2023 16:08:51 -0700
Subject: [PATCH 12/60] Add instructions to DANDI api_key input

---
 schemas/json/dandi/global.json             | 3 ++-
 src/renderer/src/stories/JSONSchemaForm.js | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
index 15ad771c0..c58151ee7 100644
--- a/schemas/json/dandi/global.json
+++ b/schemas/json/dandi/global.json
@@ -2,7 +2,8 @@
     "properties": {
         "api_key": {
             "type": "string",
-            "format": "password"
+            "format": "password",
+            "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>Production</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>staging</a> servers have different API keys and different logins</small>"
         }
     },
     "required": ["api_key"]
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f16987160..0ffdd0fbe 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1,4 +1,6 @@
 import { LitElement, css, html } from "lit";
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
+
 import { Accordion } from "./Accordion";
 
 import { checkStatus } from "../validation";
@@ -424,7 +426,7 @@ export class JSONSchemaForm extends LitElement {
                 ${interactiveInput}
                 ${info.description
                     ? html`<p class="guided--text-input-instructions">
-                          ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
+                          ${unsafeHTML(capitalize(info.description))}${info.description.slice(-1)[0] === "." ? "" : "."}
                       </p>`
                     : ""}
                 <div class="errors"></div>

From 39bc950db2e2b7354d1b9285c6e91edcfa3aaf7d Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 12 Sep 2023 16:15:05 -0700
Subject: [PATCH 13/60] Update GuidedUpload.js

---
 .../src/stories/pages/guided-mode/options/GuidedUpload.js       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
index d05b9bcd9..13987af4b 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -17,7 +17,7 @@ export class GuidedUploadPage extends Page {
 
     beforeSave = () => {
         const globalState = this.info.globalState;
-        const isNewDandiset = globalState.upload.dandiset_id !== this.localState.dandiset_id;
+        const isNewDandiset = globalState.upload?.dandiset_id !== this.localState.dandiset_id;
         merge({ upload: this.localState }, globalState); // Merge the local and global states
         if (isNewDandiset) delete globalState.upload.results; // Clear the preview results entirely if a new dandiset
     };

From 00cf557b0374dbba5ddeb037e535ba590aab3aec Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 12 Sep 2023 17:25:43 -0700
Subject: [PATCH 14/60] Initialize without activate call

---
 src/main/main.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index d00c1219b..da68ea02b 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -383,7 +383,7 @@ function makeSingleInstance() {
   else app.on("second-instance", () => restoreWindow());
 }
 
-if (process.platform === 'darwin') initialize();
+initialize();
 
 app.on('activate', () => {
   if (BrowserWindow.getAllWindows().length === 0) initialize()

From ee41639327cbb772941c355c9dd54eb0af01e729 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 07:58:39 -0700
Subject: [PATCH 15/60] Update logo, name, and backend path usage for Windows

---
 pyflask/app.py                                |  2 +-
 src/renderer/src/pages.js                     |  6 ++--
 .../src/stories/assets/neurosift-logo.svg     | 34 +++++++++++++++++++
 .../src/stories/pages/preview/PreviewPage.js  |  4 +--
 4 files changed, 40 insertions(+), 6 deletions(-)
 create mode 100644 src/renderer/src/stories/assets/neurosift-logo.svg

diff --git a/pyflask/app.py b/pyflask/app.py
index 8a978e0d0..890d9bede 100644
--- a/pyflask/app.py
+++ b/pyflask/app.py
@@ -67,7 +67,7 @@ def get_all_files():
 def handle_file_request(path):
     if request.method == "GET":
         if registered[path]:
-            return send_file(f"{sep}{unquote(path)}")
+            return send_file(unquote(path))
         else:
             app.abort(404, "Resource is not accessible.")
 
diff --git a/src/renderer/src/pages.js b/src/renderer/src/pages.js
index d53784f4d..a02bed0c8 100644
--- a/src/renderer/src/pages.js
+++ b/src/renderer/src/pages.js
@@ -22,7 +22,7 @@ import { TutorialPage } from "./stories/pages/tutorial/Tutorial";
 import tutorialIcon from "./stories/assets/exploration.svg?raw";
 import uploadIcon from "./stories/assets/dandi.svg?raw";
 import inspectIcon from "./stories/assets/inspect.svg?raw";
-import previewIcon from "./stories/assets/preview.svg?raw";
+import neurosiftIcon from "./stories/assets/neurosift-logo.svg?raw";
 
 import settingsIcon from "./stories/assets/settings.svg?raw";
 
@@ -173,8 +173,8 @@ const pages = {
         icon: inspectIcon,
     }),
     preview: new PreviewPage({
-        label: "Preview",
-        icon: previewIcon,
+        label: "Neurosift",
+        icon: neurosiftIcon,
     }),
     uploads: new UploadsPage({
         label: "Uploads",
diff --git a/src/renderer/src/stories/assets/neurosift-logo.svg b/src/renderer/src/stories/assets/neurosift-logo.svg
new file mode 100644
index 000000000..94a564956
--- /dev/null
+++ b/src/renderer/src/stories/assets/neurosift-logo.svg
@@ -0,0 +1,34 @@
+<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN"
+ "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
+<svg 
+    version="1.0" 
+    xmlns="http://www.w3.org/2000/svg"
+    height="22"
+    width="22"
+    style="margin-right: 30px; margin-bottom: -5px"
+    viewBox="0 0 192.000000 192.000000"
+    preserveAspectRatio="xMidYMid meet"
+ >
+<metadata>
+Created by potrace 1.16, written by Peter Selinger 2001-2019
+</metadata>
+<g transform="translate(0.000000,192.000000) scale(0.100000,-0.100000)"
+fill="#000000" stroke="none">
+<path d="M835 1905 c-64 -21 -98 -38 -142 -70 -46 -33 -112 -118 -130 -168 -8
+-22 -12 -135 -12 -357 -1 -320 0 -326 23 -375 45 -97 145 -179 265 -215 150
+-47 261 -11 261 84 -1 66 -41 99 -133 109 -72 7 -144 54 -163 107 -15 42 -19
+545 -5 583 13 33 58 75 100 93 83 35 192 3 243 -71 27 -39 27 -44 28 -187 0
+-91 4 -148 10 -149 19 -3 25 -5 65 -26 22 -12 68 -44 103 -72 l62 -51 0 243
+c0 166 -4 253 -13 277 -32 92 -107 170 -213 222 -65 31 -75 33 -189 35 -80 1
+-133 -3 -160 -12z"/>
+<path d="M1024 1164 c-36 -37 -42 -69 -22 -107 15 -29 52 -63 88 -82 16 -8 39
+-29 52 -47 22 -32 23 -39 26 -294 2 -170 0 -276 -8 -303 -20 -77 -84 -121
+-175 -121 -67 0 -109 18 -156 66 -33 34 -34 36 -37 139 -3 58 -8 105 -13 105
+-26 0 -156 46 -196 70 l-33 19 1 -162 c1 -180 5 -201 63 -279 84 -116 202
+-169 370 -167 107 2 166 15 232 54 91 53 93 58 140 258 33 139 43 201 43 262
+l-1 80 -18 -70 c-9 -38 -38 -162 -65 -275 -42 -184 -60 -239 -72 -227 -2 2 10
+62 27 133 17 71 39 165 50 209 10 44 35 149 55 233 44 183 44 259 1 339 -34
+60 -50 79 -106 124 -58 47 -129 79 -176 79 -29 0 -44 -7 -70 -36z"/>
+</g>
+</svg>
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index 92acdf666..e889c48e9 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -39,9 +39,9 @@ export class PreviewPage extends Page {
             <div style="display: grid; height: 100%; grid-template-rows: min-content min-content 1fr; gap: 10px;">
                 <div>
                     <div style="display: flex; align-items: end; justify-content: space-between;">
-                        <h1 style="margin: 0;">NWB File Preview</h1>
+                        <h1 style="margin: 0;">Neurosift File Visualization</h1>
                     </div>
-                    <p>Use Neurosift to preview of your NWB file.</p>
+                    <p>Explore your NWB file using Neurosift</p>
                     <hr />
                 </div>
                 ${this.input} ${this.neurosift}

From eb795ac7cd07ba9f250205563ae7edf7d70e5f21 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 15:00:48 +0000
Subject: [PATCH 16/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/assets/neurosift-logo.svg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/assets/neurosift-logo.svg b/src/renderer/src/stories/assets/neurosift-logo.svg
index 94a564956..460120d59 100644
--- a/src/renderer/src/stories/assets/neurosift-logo.svg
+++ b/src/renderer/src/stories/assets/neurosift-logo.svg
@@ -1,8 +1,8 @@
 <?xml version="1.0" standalone="no"?>
 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN"
  "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
-<svg 
-    version="1.0" 
+<svg
+    version="1.0"
     xmlns="http://www.w3.org/2000/svg"
     height="22"
     width="22"

From efd6657d0ba903891502311f94dbf8c03d28e066 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <46533749+GarrettMFlynn@users.noreply.github.com>
Date: Wed, 13 Sep 2023 08:09:27 -0700
Subject: [PATCH 17/60] Catch windows file-open bug

---
 src/renderer/src/electron/index.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 49545692f..ece0741c1 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -23,6 +23,7 @@ if (isElectron) {
         app = remote.app;
 
         electron.ipcRenderer.on("fileOpened", (info, filepath) => {
+            if (filepath === '.') return // BUG: Windows throws . when the application is opened (at least dev mode)...
             updateURLParams({ file: filepath });
             const dashboard = document.querySelector("nwb-dashboard");
             const activePage = dashboard.getAttribute("activePage");

From 33b5cd6d8d807527568c581478e025b2242bad75 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 15:10:26 +0000
Subject: [PATCH 18/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/electron/index.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index ece0741c1..53f07f615 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -23,7 +23,7 @@ if (isElectron) {
         app = remote.app;
 
         electron.ipcRenderer.on("fileOpened", (info, filepath) => {
-            if (filepath === '.') return // BUG: Windows throws . when the application is opened (at least dev mode)...
+            if (filepath === ".") return; // BUG: Windows throws . when the application is opened (at least dev mode)...
             updateURLParams({ file: filepath });
             const dashboard = document.querySelector("nwb-dashboard");
             const activePage = dashboard.getAttribute("activePage");

From ad0554bb024efb84f4dffb88dd43d27cfdf3b484 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <46533749+GarrettMFlynn@users.noreply.github.com>
Date: Wed, 13 Sep 2023 08:16:48 -0700
Subject: [PATCH 19/60] Fix backend cause of windows issue

---
 src/main/main.ts                   | 10 +++++++---
 src/renderer/src/electron/index.js |  1 -
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index da68ea02b..39001a2e4 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -355,14 +355,18 @@ function initialize() {
   else app.on("ready", onAppReady)
 }
 
-function onFileOpened(_, path: string) {
+function isValidFile(filepath: string) {
+  return !fs.existsSync(filepath) && path.extname(filepath) === '.nwb'
+}
+
+function onFileOpened(_, filepath: string) {
     restoreWindow() || initialize(); // Ensure the application is properly visible
-    onWindowReady((win) => win.webContents.send('fileOpened', path))
+    onWindowReady((win) => win.webContents.send('fileOpened', filepath))
 }
 
 if (isWindows && process.argv.length >= 2) {
   const openFilePath = process.argv[1];
-  if (openFilePath !== "") onFileOpened(null, openFilePath)
+  if (isValidFile(openFilePath)) onFileOpened(null, openFilePath)
 }
 
 // Make this app a single instance app.
diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index ece0741c1..49545692f 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -23,7 +23,6 @@ if (isElectron) {
         app = remote.app;
 
         electron.ipcRenderer.on("fileOpened", (info, filepath) => {
-            if (filepath === '.') return // BUG: Windows throws . when the application is opened (at least dev mode)...
             updateURLParams({ file: filepath });
             const dashboard = document.querySelector("nwb-dashboard");
             const activePage = dashboard.getAttribute("activePage");

From b6993325ea4035167dc721a52723beee4ffa87c6 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 08:25:34 -0700
Subject: [PATCH 20/60] Add description to neurosift loader

---
 src/renderer/src/stories/JSONSchemaForm.js    | 15 +-----------
 src/renderer/src/stories/JSONSchemaInput.js   | 24 +++++++++++++++++++
 src/renderer/src/stories/Loader.ts            |  3 ++-
 .../src/stories/pages/preview/PreviewPage.js  |  1 +
 src/renderer/src/stories/preview/Neurosift.js |  2 +-
 5 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f16987160..3fc1d1219 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -2,7 +2,7 @@ import { LitElement, css, html } from "lit";
 import { Accordion } from "./Accordion";
 
 import { checkStatus } from "../validation";
-import { capitalize, header } from "./forms/utils";
+import { header } from "./forms/utils";
 import { resolve } from "../promises";
 import { merge } from "./pages/utils";
 import { resolveProperties } from "./pages/guided-mode/data/utils";
@@ -112,14 +112,6 @@ pre {
   .required.conditional label:after {
     color: transparent;
   }
-
-
-  .guided--text-input-instructions {
-    font-size: 13px;
-    width: 100%;
-    padding-top: 4px;
-    color: dimgray !important;
-  }
 `;
 
 document.addEventListener("dragover", (e) => {
@@ -422,11 +414,6 @@ export class JSONSchemaForm extends LitElement {
             >
                 <label class="guided--form-label">${header(name)}</label>
                 ${interactiveInput}
-                ${info.description
-                    ? html`<p class="guided--text-input-instructions">
-                          ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
-                      </p>`
-                    : ""}
                 <div class="errors"></div>
                 <div class="warnings"></div>
             </div>
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 5d13ea390..fe231617c 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -8,6 +8,8 @@ import { Button } from "./Button";
 import { List } from "./List";
 import { Modal } from "./Modal";
 
+import { capitalize } from "./forms/utils";
+
 const filesystemQueries = ["file", "directory"];
 
 export class JSONSchemaInput extends LitElement {
@@ -69,6 +71,13 @@ export class JSONSchemaInput extends LitElement {
             input[type="number"].hideStep {
                 -moz-appearance: textfield;
             }
+
+            .guided--text-input-instructions {
+                font-size: 13px;
+                width: 100%;
+                padding-top: 4px;
+                color: dimgray !important;
+              }
         `;
     }
 
@@ -118,6 +127,21 @@ export class JSONSchemaInput extends LitElement {
     }
 
     render() {
+
+        const { info } = this;
+
+        const input = this.#render()
+        return html`
+            ${input}
+            ${info.description
+                ? html`<p class="guided--text-input-instructions">
+                      ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
+                  </p>`
+                : ""}
+        `
+    }
+
+    #render() {
         const { validateOnChange, info, path: fullPath } = this;
 
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
diff --git a/src/renderer/src/stories/Loader.ts b/src/renderer/src/stories/Loader.ts
index 97e3febf9..ef52cfe30 100644
--- a/src/renderer/src/stories/Loader.ts
+++ b/src/renderer/src/stories/Loader.ts
@@ -1,4 +1,5 @@
 import { LitElement, css, html } from "lit";
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
 
 // From https://loading.io/css/
 
@@ -120,7 +121,7 @@ export class Loader extends LitElement {
         return html`
           <div>
           <div class="lds-default"><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div></div>
-          ${this.message ? html`<span>${this.message}</span>` : ''}
+          ${this.message ? html`<span>${unsafeHTML(this.message)}</span>` : ''}
           </div>
       `
     }
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index e889c48e9..c07d0c01d 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -22,6 +22,7 @@ export class PreviewPage extends Page {
         info: {
             type: "string",
             format: "file",
+            description: "Please provide a file path that you'd like to visualize using Neurosift. The NWB GUIDE will serve this file and access the appropriate URL automatically."
         },
         onUpdate: this.updatePath,
         onThrow,
diff --git a/src/renderer/src/stories/preview/Neurosift.js b/src/renderer/src/stories/preview/Neurosift.js
index 41cbff439..14dd499ec 100644
--- a/src/renderer/src/stories/preview/Neurosift.js
+++ b/src/renderer/src/stories/preview/Neurosift.js
@@ -62,7 +62,7 @@ export class Neurosift extends LitElement {
 
     render() {
         return this.url
-            ? html` <div class="loader-container">${new Loader({ message: "Loading Neurosift view..." })}</div>
+            ? html` <div class="loader-container">${new Loader({ message: `Loading Neurosift view...<br/><small>${this.url}</small>` })}</div>
                   <iframe
                       class="iframe-placeholder"
                       src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"

From b79980a97334877d2127a6bf91462d03186d95cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 15:26:57 +0000
Subject: [PATCH 21/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js           | 7 +++----
 src/renderer/src/stories/pages/preview/PreviewPage.js | 3 ++-
 src/renderer/src/stories/preview/Neurosift.js         | 4 +++-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index fe231617c..b6bfd37cd 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -77,7 +77,7 @@ export class JSONSchemaInput extends LitElement {
                 width: 100%;
                 padding-top: 4px;
                 color: dimgray !important;
-              }
+            }
         `;
     }
 
@@ -127,10 +127,9 @@ export class JSONSchemaInput extends LitElement {
     }
 
     render() {
-
         const { info } = this;
 
-        const input = this.#render()
+        const input = this.#render();
         return html`
             ${input}
             ${info.description
@@ -138,7 +137,7 @@ export class JSONSchemaInput extends LitElement {
                       ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
                   </p>`
                 : ""}
-        `
+        `;
     }
 
     #render() {
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index c07d0c01d..13fea6714 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -22,7 +22,8 @@ export class PreviewPage extends Page {
         info: {
             type: "string",
             format: "file",
-            description: "Please provide a file path that you'd like to visualize using Neurosift. The NWB GUIDE will serve this file and access the appropriate URL automatically."
+            description:
+                "Please provide a file path that you'd like to visualize using Neurosift. The NWB GUIDE will serve this file and access the appropriate URL automatically.",
         },
         onUpdate: this.updatePath,
         onThrow,
diff --git a/src/renderer/src/stories/preview/Neurosift.js b/src/renderer/src/stories/preview/Neurosift.js
index 14dd499ec..cc5374af3 100644
--- a/src/renderer/src/stories/preview/Neurosift.js
+++ b/src/renderer/src/stories/preview/Neurosift.js
@@ -62,7 +62,9 @@ export class Neurosift extends LitElement {
 
     render() {
         return this.url
-            ? html` <div class="loader-container">${new Loader({ message: `Loading Neurosift view...<br/><small>${this.url}</small>` })}</div>
+            ? html` <div class="loader-container">
+                      ${new Loader({ message: `Loading Neurosift view...<br/><small>${this.url}</small>` })}
+                  </div>
                   <iframe
                       class="iframe-placeholder"
                       src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"

From e4cd9a47795f6dd4219fd9d39f898022e79404e0 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 13 Sep 2023 08:27:44 -0700
Subject: [PATCH 22/60] Update schemas/json/dandi/global.json

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 schemas/json/dandi/global.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
index c58151ee7..c841a1cf8 100644
--- a/schemas/json/dandi/global.json
+++ b/schemas/json/dandi/global.json
@@ -3,7 +3,7 @@
         "api_key": {
             "type": "string",
             "format": "password",
-            "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>Production</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>staging</a> servers have different API keys and different logins</small>"
+            "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>The main archive</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>the staging (testing) server</a> have different API keys.</small>"
         }
     },
     "required": ["api_key"]

From e371eb8f13a27de60285b3b8ab015ad9ee8d0716 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:22:13 -0700
Subject: [PATCH 23/60] Fix this.form references

---
 src/renderer/src/stories/JSONSchemaInput.js | 27 ++++++++++++---------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f87a96b94..cb70aa700 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -139,9 +139,9 @@ export class JSONSchemaInput extends LitElement {
                 value: this.value,
                 onSelect: (filePath) => this.#updateData(fullPath, filePath),
                 onChange: (filePath) => validateOnChange && this.#triggerValidation(name, el, path),
-                onThrow: (...args) => this.form.onThrow(...args),
-                dialogOptions: this.form.dialogOptions,
-                dialogType: this.form.dialogType,
+                onThrow: (...args) => this.form?.onThrow(...args),
+                dialogOptions:  this.form?.dialogOptions,
+                dialogType: this.form?.dialogType,
                 multiple: isArray,
             });
             el.classList.add("schema-input");
@@ -152,7 +152,7 @@ export class JSONSchemaInput extends LitElement {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
             // Catch tables
-            const itemSchema = this.form.getSchema("items", info);
+            const itemSchema = this.form ? this.form.getSchema("items", info) : info['items'];
             const isTable = itemSchema.type === "object";
 
             const fileSystemFormat = isFilesystemSelector(itemSchema.format);
@@ -161,17 +161,22 @@ export class JSONSchemaInput extends LitElement {
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
+
+                    // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && this.form.validateOnChange(key, parent, fullPath, v);
+                        return validateOnChange && this.#triggerValidation(key, this.form.tables[name], path) // this.form.validateOnChange(key, parent, fullPath, v);
                     },
-                    onStatusChange: () => this.form.checkStatus(), // Check status on all elements
-                    validateEmptyCells: this.form.validateEmptyValues,
-                    deferLoading: this.form.deferLoading,
+
+                    onStatusChange: () => this.form?.checkStatus(), // Check status on all elements
+                    validateEmptyCells: this.form?.validateEmptyValues,
+                    deferLoading: this.form?.deferLoading,
                     onLoaded: () => {
-                        this.form.nLoaded++;
-                        this.form.checkAllLoaded();
+                        if (this.form) {
+                            this.form.nLoaded++;
+                            this.form.checkAllLoaded();
+                        }
                     },
-                    onThrow: (...args) => this.form.onThrow(...args),
+                    onThrow: (...args) => this.form?.onThrow(...args),
                 };
 
                 return (this.form.tables[name] =

From 56e97a8a9cb6e527d46684ada8b213dea4fd8cef Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 17:22:35 +0000
Subject: [PATCH 24/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index cb70aa700..b5db2fd89 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -140,7 +140,7 @@ export class JSONSchemaInput extends LitElement {
                 onSelect: (filePath) => this.#updateData(fullPath, filePath),
                 onChange: (filePath) => validateOnChange && this.#triggerValidation(name, el, path),
                 onThrow: (...args) => this.form?.onThrow(...args),
-                dialogOptions:  this.form?.dialogOptions,
+                dialogOptions: this.form?.dialogOptions,
                 dialogType: this.form?.dialogType,
                 multiple: isArray,
             });
@@ -152,7 +152,7 @@ export class JSONSchemaInput extends LitElement {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
             // Catch tables
-            const itemSchema = this.form ? this.form.getSchema("items", info) : info['items'];
+            const itemSchema = this.form ? this.form.getSchema("items", info) : info["items"];
             const isTable = itemSchema.type === "object";
 
             const fileSystemFormat = isFilesystemSelector(itemSchema.format);
@@ -164,7 +164,7 @@ export class JSONSchemaInput extends LitElement {
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && this.#triggerValidation(key, this.form.tables[name], path) // this.form.validateOnChange(key, parent, fullPath, v);
+                        return validateOnChange && this.#triggerValidation(key, this.form.tables[name], path); // this.form.validateOnChange(key, parent, fullPath, v);
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements

From f7ce052d7f1517ce4eb9c75c04cf84bc50002de5 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:28:18 -0700
Subject: [PATCH 25/60] Fix interface saving and empty message

---
 .../stories/pages/guided-mode/data/GuidedStructure.js    | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index b4c24266d..410d7c9fb 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -8,6 +8,8 @@ import { Search } from "../../../Search.js";
 import { Modal } from "../../../Modal";
 import { List } from "../../../List";
 
+const defaultEmptyMessage = "No interfaces selected"
+
 export class GuidedStructurePage extends Page {
     constructor(...args) {
         super(...args);
@@ -32,7 +34,8 @@ export class GuidedStructurePage extends Page {
     });
 
     list = new List({
-        emptyMessage: "No interfaces selected",
+        emptyMessage: defaultEmptyMessage,
+        onChange: () => this.unsavedUpdates = true
     });
 
     addButton = new Button();
@@ -77,7 +80,7 @@ export class GuidedStructurePage extends Page {
     async updated() {
         const { interfaces = {} } = this.info.globalState;
 
-        if (Object.keys(interfaces).length > 0) this.list.emptyMessage = "Loading valid interfaces...";
+        this.list.emptyMessage = "Loading valid interfaces...";
 
         this.search.options = await fetch(`${baseUrl}/neuroconv`)
             .then((res) => res.json())
@@ -93,6 +96,8 @@ export class GuidedStructurePage extends Page {
             )
             .catch((e) => console.error(e));
 
+        this.list.emptyMessage = defaultEmptyMessage
+
         for (const [key, name] of Object.entries(interfaces)) {
             let found = this.search.options?.find((o) => o.value === name);
 

From a7e3e080de4d318b4169d910b383967cac305e44 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:35:17 -0700
Subject: [PATCH 26/60] Fix reference before declaration

---
 src/renderer/src/electron/index.js  |  2 +-
 src/renderer/src/globals.js         | 16 +---------------
 src/renderer/src/progress/index.js  |  3 ++-
 src/renderer/src/progress/update.js |  3 ++-
 src/renderer/utils/url.js           | 14 ++++++++++++++
 5 files changed, 20 insertions(+), 18 deletions(-)
 create mode 100644 src/renderer/utils/url.js

diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 49545692f..a20b50acc 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -1,4 +1,4 @@
-import { updateURLParams } from "../globals.js";
+import { updateURLParams } from "../../utils/url.js";
 import isElectron from "./check.js";
 
 export { isElectron };
diff --git a/src/renderer/src/globals.js b/src/renderer/src/globals.js
index 1cb3ad5bf..89dc5af42 100644
--- a/src/renderer/src/globals.js
+++ b/src/renderer/src/globals.js
@@ -12,18 +12,4 @@ export let runOnLoad = (fn) => {
 // Base Request URL for Python Server
 export const baseUrl = `http://127.0.0.1:${port}`;
 
-export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;
-
-export function updateURLParams(paramsToUpdate) {
-    const params = new URLSearchParams(location.search);
-    for (let key in paramsToUpdate) {
-        const value = paramsToUpdate[key];
-        if (value == undefined) params.delete(key);
-        else params.set(key, value);
-    }
-
-    // Update browser history state
-    const value = `${location.pathname}?${params}`;
-    if (history.state) Object.assign(history.state, paramsToUpdate);
-    window.history.pushState(history.state, null, value);
-}
+export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;
\ No newline at end of file
diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index 7fa377a83..8e39c7e97 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -9,9 +9,10 @@ import {
     conversionSaveFolderPath,
 } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
-import { joinPath, runOnLoad, updateURLParams } from "../globals.js";
+import { joinPath, runOnLoad } from "../globals.js";
 import { merge } from "../stories/pages/utils.js";
 import { updateAppProgress, updateFile } from "./update.js";
+import { updateURLParams } from "../../utils/url.js";
 
 export * from "./update";
 
diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 5c4f72aea..8756db83a 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -1,6 +1,7 @@
+import { updateURLParams } from "../../utils/url.js";
 import { guidedProgressFilePath } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
-import { joinPath, updateURLParams } from "../globals.js";
+import { joinPath } from "../globals.js";
 import { get } from "./index.js";
 
 export const update = (newDatasetName, previousDatasetName) => {
diff --git a/src/renderer/utils/url.js b/src/renderer/utils/url.js
new file mode 100644
index 000000000..9ed9089dc
--- /dev/null
+++ b/src/renderer/utils/url.js
@@ -0,0 +1,14 @@
+
+export function updateURLParams(paramsToUpdate) {
+    const params = new URLSearchParams(location.search);
+    for (let key in paramsToUpdate) {
+        const value = paramsToUpdate[key];
+        if (value == undefined) params.delete(key);
+        else params.set(key, value);
+    }
+
+    // Update browser history state
+    const value = `${location.pathname}?${params}`;
+    if (history.state) Object.assign(history.state, paramsToUpdate);
+    window.history.pushState(history.state, null, value);
+}

From 400ced50cfffecf05cc2b5ab75afb19498eabbac Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 17:50:33 +0000
Subject: [PATCH 27/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/globals.js                                 | 2 +-
 .../src/stories/pages/guided-mode/data/GuidedStructure.js   | 6 +++---
 src/renderer/utils/url.js                                   | 1 -
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/globals.js b/src/renderer/src/globals.js
index 89dc5af42..b235577dd 100644
--- a/src/renderer/src/globals.js
+++ b/src/renderer/src/globals.js
@@ -12,4 +12,4 @@ export let runOnLoad = (fn) => {
 // Base Request URL for Python Server
 export const baseUrl = `http://127.0.0.1:${port}`;
 
-export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;
\ No newline at end of file
+export const supportedInterfaces = guideGlobalMetadata.supported_interfaces;
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 410d7c9fb..c735b6161 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -8,7 +8,7 @@ import { Search } from "../../../Search.js";
 import { Modal } from "../../../Modal";
 import { List } from "../../../List";
 
-const defaultEmptyMessage = "No interfaces selected"
+const defaultEmptyMessage = "No interfaces selected";
 
 export class GuidedStructurePage extends Page {
     constructor(...args) {
@@ -35,7 +35,7 @@ export class GuidedStructurePage extends Page {
 
     list = new List({
         emptyMessage: defaultEmptyMessage,
-        onChange: () => this.unsavedUpdates = true
+        onChange: () => (this.unsavedUpdates = true),
     });
 
     addButton = new Button();
@@ -96,7 +96,7 @@ export class GuidedStructurePage extends Page {
             )
             .catch((e) => console.error(e));
 
-        this.list.emptyMessage = defaultEmptyMessage
+        this.list.emptyMessage = defaultEmptyMessage;
 
         for (const [key, name] of Object.entries(interfaces)) {
             let found = this.search.options?.find((o) => o.value === name);
diff --git a/src/renderer/utils/url.js b/src/renderer/utils/url.js
index 9ed9089dc..502e427f9 100644
--- a/src/renderer/utils/url.js
+++ b/src/renderer/utils/url.js
@@ -1,4 +1,3 @@
-
 export function updateURLParams(paramsToUpdate) {
     const params = new URLSearchParams(location.search);
     for (let key in paramsToUpdate) {

From 516b0e1c77d979383f20cb4fa2ad7f3d2e7fbe70 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:55:22 -0700
Subject: [PATCH 28/60] Fix upload url used for Guided Mode and break out
 staging determination

---
 .../pages/guided-mode/options/GuidedUpload.js |  6 ++---
 .../guided-mode/results/GuidedResults.js      |  7 +++---
 .../src/stories/pages/uploads/UploadsPage.js  | 24 +++++++++++--------
 3 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
index 13987af4b..213902f54 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -47,12 +47,12 @@ export class GuidedUploadPage extends Page {
                 if (!result || !result.isConfirmed) return this.to(1);
             }
 
-            const results = await uploadToDandi.call(this, {
+            globalUploadInfo.results = await uploadToDandi.call(this, {
                 ...globalUploadInfo.info,
                 project: globalState.project.name,
             });
 
-            globalUploadInfo.results = results; // Save the preview results
+            global.data.uploads = {};
 
             this.unsavedUpdates = true; // Ensure that this saves automatically
 
@@ -61,7 +61,7 @@ export class GuidedUploadPage extends Page {
     };
 
     render() {
-        const state = (this.localState = merge(this.info.globalState.upload ?? { info: {}, results: null }, {}));
+        const state = (this.localState = merge(this.info.globalState.upload ?? { info: {} }, {}));
 
         this.form = new JSONSchemaForm({
             schema: dandiUploadSchema,
diff --git a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
index fc3d64df2..17c27432b 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -2,6 +2,7 @@ import { css, html } from "lit";
 import { Page } from "../../Page.js";
 
 import { get } from "dandi";
+import { isStaging } from "../../uploads/UploadsPage.js";
 
 export class GuidedResultsPage extends Page {
     constructor(...args) {
@@ -23,15 +24,13 @@ export class GuidedResultsPage extends Page {
             }
         };
 
-        const { dandiset_id, staging } = this.info.globalState.upload?.info ?? {};
+        const { dandiset_id } = this.info.globalState.upload?.info ?? {};
 
         const elIds = ["name", "modified"];
 
         const otherElIds = ["embargo_status"];
 
-        const liveId = dandiset_id; // '000552' // From Huszar
-        const isStaging = staging; //false
-        const dandiset = await get(liveId, isStaging ? "staging" : undefined);
+        const dandiset = await get(dandiset_id, isStaging(dandiset_id) ? "staging" : undefined);
 
         otherElIds.forEach((str) => handleId(str, dandiset));
         elIds.forEach((str) => handleId(str, dandiset.draft_version));
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index a21742392..2114c07b3 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -14,7 +14,9 @@ import { run } from "../guided-mode/options/utils.js";
 import { notyf } from "../../../dependencies/globals.js";
 import Swal from "sweetalert2";
 
-export async function uploadToDandi(info) {
+export const isStaging = (id) => parseInt(id) >= 100000; // Automatically detect staging IDs
+
+export async function uploadToDandi(info, type = 'project' in info ? '' : "folder") {
     if (!global.data.DANDI?.api_key) {
         await Swal.fire({
             title: "Your DANDI API key is not configured.",
@@ -26,13 +28,21 @@ export async function uploadToDandi(info) {
         return this.to("settings");
     }
 
-    info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs
+    info.staging = isStaging(info.dandiset_id);
     info.api_key = global.data.DANDI.api_key;
 
-    return await run("upload/folder", info, { title: "Uploading to DANDI" }).catch((e) => {
+    const result = await run(type ? `upload/${type}` : 'upload', info, { title: "Uploading to DANDI" }).catch((e) => {
         this.notify(e.message, "error");
         throw e;
     });
+
+
+    if (result) notyf.open({
+        type: "success",
+        message: `${info.project ?? info.nwb_folder_path} successfully uploaded to Dandiset ${info.dandiset_id}`,
+    });
+
+    return result
 }
 
 export class UploadsPage extends Page {
@@ -48,13 +58,7 @@ export class UploadsPage extends Page {
             label: defaultButtonMessage,
             onClick: async () => {
                 await this.form.validate(); // Will throw an error in the callback
-                const results = await uploadToDandi.call(this, { ...global.data.uploads });
-                if (results)
-                    notyf.open({
-                        type: "success",
-                        message: `${global.data.uploads.nwb_folder_path} successfully uploaded to Dandiset ${global.data.uploads.dandiset_id}`,
-                    });
-
+                await uploadToDandi.call(this, { ...global.data.uploads });
                 global.data.uploads = {};
                 global.save();
                 this.requestUpdate();

From e0c8b77b1279bc57d5a6373608c5a23d3c8ba694 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:56:37 -0700
Subject: [PATCH 29/60] Update GuidedUpload.js

---
 .../src/stories/pages/guided-mode/options/GuidedUpload.js     | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
index 213902f54..24a9c3f99 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -52,10 +52,6 @@ export class GuidedUploadPage extends Page {
                 project: globalState.project.name,
             });
 
-            global.data.uploads = {};
-
-            this.unsavedUpdates = true; // Ensure that this saves automatically
-
             this.to(1);
         },
     };

From ea8d2776214ff714bb46e523c065ef8d81c3122c Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 10:59:59 -0700
Subject: [PATCH 30/60] Update DandiResults.js

---
 src/renderer/src/stories/DandiResults.js | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/DandiResults.js b/src/renderer/src/stories/DandiResults.js
index 86cb1e29b..8f1c4cd52 100644
--- a/src/renderer/src/stories/DandiResults.js
+++ b/src/renderer/src/stories/DandiResults.js
@@ -36,8 +36,7 @@ export class DandiResults extends LitElement {
 
         const otherElIds = ["embargo_status"];
 
-        const liveId = this.id; // '000552' // From Huszar
-        const dandiset = await get(liveId, isStaging(this.id) ? "staging" : undefined);
+        const dandiset = await get(this.id, isStaging(this.id) ? "staging" : undefined);
 
         otherElIds.forEach((str) => handleId(str, dandiset));
         elIds.forEach((str) => handleId(str, dandiset.draft_version));

From a56b6939f4aa624aae1dcfde5c583a08709342dc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 18:00:16 +0000
Subject: [PATCH 31/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/pages/uploads/UploadsPage.js   | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 5ba0e8a9b..d141a438d 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -32,7 +32,7 @@ export async function uploadToDandi(info) {
     }
 
     const result = await run(
-        type ? `upload/${type}` : 'upload',
+        type ? `upload/${type}` : "upload",
         {
             ...info,
             staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
@@ -42,18 +42,18 @@ export async function uploadToDandi(info) {
     ).catch((e) => {
         notyf.open({
             type: "error",
-            message: e.message
-        })
+            message: e.message,
+        });
         throw e;
     });
 
+    if (result)
+        notyf.open({
+            type: "success",
+            message: `${info.project ?? info.nwb_folder_path} successfully uploaded to Dandiset ${info.dandiset_id}`,
+        });
 
-    if (result) notyf.open({
-        type: "success",
-        message: `${info.project ?? info.nwb_folder_path} successfully uploaded to Dandiset ${info.dandiset_id}`,
-    });
-
-    return result
+    return result;
 }
 
 export class UploadsPage extends Page {

From 97bd3133bf3ac78f85698506dff8a535766366fd Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 11:03:24 -0700
Subject: [PATCH 32/60] Fix results page and type toggle after merge

---
 .../src/stories/pages/guided-mode/results/GuidedResults.js    | 4 ++--
 src/renderer/src/stories/pages/uploads/UploadsPage.js         | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
index 43e5ad642..882041d34 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -9,14 +9,14 @@ export class GuidedResultsPage extends Page {
     }
 
     render() {
-        const { conversion } = this.info.globalState.conversion;
+        const { conversion } = this.info.globalState;
 
         if (!conversion)
             return html`<div style="text-align: center;"><p>Your conversion failed. Please try again.</p></div>`;
 
         const { dandiset_id } = this.info.globalState.upload?.info ?? {};
 
-        return DandiResults({ id: dandiset_id, files: conversion });
+        return new DandiResults({ id: dandiset_id, files: conversion });
     }
 }
 
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 5ba0e8a9b..0f0f3f1a0 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -18,7 +18,7 @@ import { DandiResults } from "../../DandiResults.js";
 
 export const isStaging = (id) => parseInt(id) >= 100000;
 
-export async function uploadToDandi(info) {
+export async function uploadToDandi(info, type = 'project' in info ? '' : 'folder') {
     const api_key = global.data.DANDI?.api_key;
     if (!api_key) {
         await Swal.fire({

From c2d076585a68607602913b522248897688458843 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 18:03:48 +0000
Subject: [PATCH 33/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/pages/uploads/UploadsPage.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index e4f7c3736..2e4691212 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -18,7 +18,7 @@ import { DandiResults } from "../../DandiResults.js";
 
 export const isStaging = (id) => parseInt(id) >= 100000;
 
-export async function uploadToDandi(info, type = 'project' in info ? '' : 'folder') {
+export async function uploadToDandi(info, type = "project" in info ? "" : "folder") {
     const api_key = global.data.DANDI?.api_key;
     if (!api_key) {
         await Swal.fire({

From e396301ba44c6dcb059694a4b57b72754e3778b3 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:09:00 -0400
Subject: [PATCH 34/60] Update package.json

---
 package.json | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index 3bcb3133a..bd6b39419 100644
--- a/package.json
+++ b/package.json
@@ -12,20 +12,20 @@
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
+    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator",
-    "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.",
+    "build:flask": "python -m PyInstaller nwb-guide.spec",
+    "build:flask:spec:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
+    "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
-    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
-    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",
@@ -57,7 +57,7 @@
       {
         "ext": "nwb",
         "name": "NWB File",
-        "role": "Viewer"
+        "role": "Editor"
       }
     ],
     "files": [

From d5812fb45fcee2beb9440baa713a712cd4bd5607 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:10:53 -0400
Subject: [PATCH 35/60] fix alterations

---
 package.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index bd6b39419..2b3d60ea6 100644
--- a/package.json
+++ b/package.json
@@ -25,6 +25,7 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
+    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
     "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
@@ -57,7 +58,7 @@
       {
         "ext": "nwb",
         "name": "NWB File",
-        "role": "Editor"
+        "role": "Viewer"
       }
     ],
     "files": [

From 9e83ca7cad85855100418d2c5bdcaa2ec29d4205 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:13:42 -0400
Subject: [PATCH 36/60] restore other

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 2b3d60ea6..d93b2d6d8 100644
--- a/package.json
+++ b/package.json
@@ -26,7 +26,7 @@
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
     "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
-    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",

From 02b57d790ac25c0ea7e5380d4385b2ef11d7247e Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 11:28:56 -0700
Subject: [PATCH 37/60] Update main.ts

---
 src/main/main.ts | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 39001a2e4..5e0b68347 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -70,6 +70,7 @@ let globals: {
   },
 
   set mainWindowReady(v) {
+    if (globals.mainWindow) throw new Error('Main window cannot be ready. It does not exist...')
     mainWindowReady = v
     if (v) readyQueue.forEach(f => onWindowReady(f))
     readyQueue = []
@@ -80,7 +81,7 @@ function send(this: BrowserWindow, ...args: any[]) {
   return this.webContents.send(...args)
 }
 
-const onWindowReady = (f: (win: BrowserWindow) => any) => (mainWindowReady) ? f(globals.mainWindow) : readyQueue.push(f)
+const onWindowReady = (f: (win: BrowserWindow) => any) => (globals.mainWindowReady) ? f(globals.mainWindow) : readyQueue.push(f)
 
 
 // Pass all important log functions to the application
@@ -361,7 +362,7 @@ function isValidFile(filepath: string) {
 
 function onFileOpened(_, filepath: string) {
     restoreWindow() || initialize(); // Ensure the application is properly visible
-    onWindowReady((win) => win.webContents.send('fileOpened', filepath))
+    onWindowReady((win) => send.call(win, 'fileOpened', filepath))
 }
 
 if (isWindows && process.argv.length >= 2) {

From cb98081e6567c581f9438eae927c16f57e345e43 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 14:54:47 -0400
Subject: [PATCH 38/60] add spec file for windows

---
 .gitignore             |  2 --
 nwb-guide-windows.spec | 70 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 2 deletions(-)
 create mode 100644 nwb-guide-windows.spec

diff --git a/.gitignore b/.gitignore
index 852548470..0cda7e019 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,8 +19,6 @@ semantic.json
 build/
 yarn.lock
 
-*.spec
-
 *.pyc
 src/.DS_Store
 .DS_Store
diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
new file mode 100644
index 000000000..09f97562f
--- /dev/null
+++ b/nwb-guide-windows.spec
@@ -0,0 +1,70 @@
+# -*- mode: python ; coding: utf-8 -*-
+import sys
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
+from PyInstaller.utils.hooks import collect_data_files
+from PyInstaller.utils.hooks import collect_all
+
+datas = [('./paths.config.json', '.'), ('./package.json', '.')]
+binaries = []
+hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils']
+datas += collect_data_files('jsonschema_specifications')
+tmp_ret = collect_all('nwbinspector')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('neuroconv')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('pynwb')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('hdmf')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ci_info')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+
+
+block_cipher = None
+
+
+a = Analysis(
+    ['pyflask\\app.py'],
+    pathex=[],
+    binaries=binaries,
+    datas=datas,
+    hiddenimports=hiddenimports,
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    win_no_prefer_redirects=False,
+    win_private_assemblies=False,
+    cipher=block_cipher,
+    noarchive=False,
+)
+pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='nwb-guide',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=True,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.zipfiles,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='nwb-guide',
+)

From 0e1e839b492f704299cd1b0ab7a787b8b47a9a1c Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 14:55:52 -0400
Subject: [PATCH 39/60] new commands

---
 package.json | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/package.json b/package.json
index d93b2d6d8..6e2db7464 100644
--- a/package.json
+++ b/package.json
@@ -12,12 +12,13 @@
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
+    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask": "python -m PyInstaller nwb-guide.spec",
-    "build:flask:spec:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
-    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
+    "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
+    "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",

From 610de05202970455f985c8130de9f792cee2c9e5 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:03:09 -0400
Subject: [PATCH 40/60] add other renames

---
 package.json | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/package.json b/package.json
index 6e2db7464..602798335 100644
--- a/package.json
+++ b/package.json
@@ -20,6 +20,12 @@
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
+    "rename:spec:mac": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:mac": "npm run build:flask:spec:mac && npm run rename:spec:mac",
+    "rename:spec:mac-arm64": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac-arm64.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:mac-arm64": "npm run build:flask:spec:mac-arm64 && npm run rename:spec:mac-arm64",
+    "rename:spec:linux": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-linux.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:linux": "npm run build:flask:spec:unix && npm run rename:spec:linux",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From cf691191a8b7313c7f79b8719b1bb9bcf42ab63d Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:04:23 -0400
Subject: [PATCH 41/60] add other build calls

---
 package.json | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/package.json b/package.json
index 602798335..4f6278343 100644
--- a/package.json
+++ b/package.json
@@ -16,6 +16,9 @@
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",

From a807e65c5fe33d08671d0feb9c96574dddf283eb Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:05:14 -0400
Subject: [PATCH 42/60] propagate to top level

---
 package.json | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 4f6278343..d475f4018 100644
--- a/package.json
+++ b/package.json
@@ -13,8 +13,9 @@
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
-    "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
+    "build:mac": "npm run build && npm run build:flask:mac && npm run build:electron:mac",
+    "build:mac-arm64": "npm run build && npm run build:flask:mac-arm64 && npm run build:electron:mac",
+    "build:linux": "npm run build && npm run build:flask:linux && npm run build:electron:linux",
     "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",

From 69efd18daac7cddf7dbcc6371329d350be4c3471 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 15:28:30 -0400
Subject: [PATCH 43/60] forgot hidden import

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index d475f4018..f8efae261 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",

From 1f97066df8744344e58572664ed373e723c2d595 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:55:06 -0400
Subject: [PATCH 44/60] update spec file, duh

---
 nwb-guide-windows.spec | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index 09f97562f..1b46759fa 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -1,13 +1,10 @@
 # -*- mode: python ; coding: utf-8 -*-
-import sys
-sys.setrecursionlimit(sys.getrecursionlimit() * 5)
-
 from PyInstaller.utils.hooks import collect_data_files
 from PyInstaller.utils.hooks import collect_all
 
 datas = [('./paths.config.json', '.'), ('./package.json', '.')]
 binaries = []
-hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils']
+hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils', 'email_validator']
 datas += collect_data_files('jsonschema_specifications')
 tmp_ret = collect_all('nwbinspector')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]

From f63745268221efdc43390b87f8af633e35bdb75d Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 13:57:44 -0700
Subject: [PATCH 45/60] Fix window recognition

---
 src/main/main.ts | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 5e0b68347..1c5ff5cc6 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -70,7 +70,7 @@ let globals: {
   },
 
   set mainWindowReady(v) {
-    if (globals.mainWindow) throw new Error('Main window cannot be ready. It does not exist...')
+    if (!globals.mainWindow) throw new Error('Main window cannot be ready. It does not exist...')
     mainWindowReady = v
     if (v) readyQueue.forEach(f => onWindowReady(f))
     readyQueue = []
@@ -309,6 +309,7 @@ function initialize() {
     };
 
     globals.mainWindow = new BrowserWindow(windowOptions);
+    console.log('SETTING MAIN WINDOW')
     main.enable(globals.mainWindow.webContents);
 
   // HMR for renderer base on electron-vite cli.
@@ -317,6 +318,7 @@ function initialize() {
   else globals.mainWindow.loadFile(path.join(__dirname, '../renderer/index.html'))
 
     globals.mainWindow.once("closed", () => {
+      console.log('DELETING MAIN WINDOW')
       delete globals.mainWindow
     })
 

From 37e1090e34477faaea3f74dc92cb3fe958637221 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 14:04:14 -0700
Subject: [PATCH 46/60] Fix merge

---
 src/renderer/src/stories/JSONSchemaForm.js         | 5 -----
 src/renderer/src/stories/JSONSchemaForm.stories.js | 1 +
 src/renderer/src/stories/JSONSchemaInput.js        | 2 ++
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5f06e8627..aa2912722 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -416,11 +416,6 @@ export class JSONSchemaForm extends LitElement {
             >
                 <label class="guided--form-label">${header(name)}</label>
                 ${interactiveInput}
-                ${info.description
-                    ? html`<p class="guided--text-input-instructions">
-                          ${unsafeHTML(capitalize(info.description))}${info.description.slice(-1)[0] === "." ? "" : "."}
-                      </p>`
-                    : ""}
                 <div class="errors"></div>
                 <div class="warnings"></div>
             </div>
diff --git a/src/renderer/src/stories/JSONSchemaForm.stories.js b/src/renderer/src/stories/JSONSchemaForm.stories.js
index 97dad2eb3..a59857ef8 100644
--- a/src/renderer/src/stories/JSONSchemaForm.stories.js
+++ b/src/renderer/src/stories/JSONSchemaForm.stories.js
@@ -22,6 +22,7 @@ const defaultSchema = {
         test: {
             type: "string",
             default: true,
+            description: "This is a test description",
         },
         warn: {
             type: "string",
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index b6bfd37cd..fde0b43af 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -77,6 +77,8 @@ export class JSONSchemaInput extends LitElement {
                 width: 100%;
                 padding-top: 4px;
                 color: dimgray !important;
+                margin: 0 0 1em;
+                line-height: 1.4285em;
             }
         `;
     }

From e0a249083ada20d0aeaaa62f0eb7f3d774c10b4f Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 13 Sep 2023 14:27:20 -0700
Subject: [PATCH 47/60] Update main.ts

---
 src/main/main.ts | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 1c5ff5cc6..582090189 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -309,7 +309,6 @@ function initialize() {
     };
 
     globals.mainWindow = new BrowserWindow(windowOptions);
-    console.log('SETTING MAIN WINDOW')
     main.enable(globals.mainWindow.webContents);
 
   // HMR for renderer base on electron-vite cli.
@@ -318,7 +317,6 @@ function initialize() {
   else globals.mainWindow.loadFile(path.join(__dirname, '../renderer/index.html'))
 
     globals.mainWindow.once("closed", () => {
-      console.log('DELETING MAIN WINDOW')
       delete globals.mainWindow
     })
 

From b3a68d68b52b81da266ce05adf68f38e5e53da53 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 21:43:55 -0400
Subject: [PATCH 48/60] re-add recursion limit hack, duh

---
 nwb-guide-windows.spec | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index 1b46759fa..e3a9a731d 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -1,4 +1,7 @@
 # -*- mode: python ; coding: utf-8 -*-
+import sys
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
 from PyInstaller.utils.hooks import collect_data_files
 from PyInstaller.utils.hooks import collect_all
 

From 6e1e1ef3b5f63c0fc13d4f241140f9948eb4176f Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 22:08:27 -0400
Subject: [PATCH 49/60] re-add ndx-icephys

---
 nwb-guide-windows.spec | 2 ++
 package.json           | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index e3a9a731d..93640b066 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -17,6 +17,8 @@ tmp_ret = collect_all('pynwb')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 tmp_ret = collect_all('hdmf')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ndx_dandi_icephys')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 tmp_ret = collect_all('ci_info')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 
diff --git a/package.json b/package.json
index f8efae261..c6f5b1487 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ndx_dandi_icephys --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",

From 7c1c3c0a7becd8b6ff5591c421df7d11c298db0e Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 23:46:00 -0400
Subject: [PATCH 50/60] simpify cross-platform; update workflows

---
 .github/workflows/Build-and-deploy-mac.yml    |  1 -
 .../pyflask-build-and-dist-tests.yml          | 17 ++---------
 nwb-guide-windows.spec => nwb-guide.spec      |  0
 package.json                                  | 23 ++++----------
 prepare_pyinstaller_spec.py                   | 30 +++++++++++++++++++
 5 files changed, 39 insertions(+), 32 deletions(-)
 rename nwb-guide-windows.spec => nwb-guide.spec (100%)
 create mode 100644 prepare_pyinstaller_spec.py

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index dd7a77988..7e8afcfe5 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -22,7 +22,6 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: nwb-guide
-          #mamba-version: "*"
           environment-file: environments/environment-MAC.yml
           auto-activate-base: false
 
diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 5fbea858d..b2b89d50b 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -30,19 +30,16 @@ jobs:
             os: ubuntu-latest
             label: environments/environment-Linux.yml
             prefix: /usr/share/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: macos-latest
             label: environments/environment-Mac.yml
             prefix: /Users/runner/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: windows-latest
             label: environments/environment-Windows.yml
             prefix: C:\Miniconda3\envs\nwb-guide
-            shorthand: win
 
     steps:
       - uses: actions/checkout@v3
@@ -88,15 +85,7 @@ jobs:
         run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
-        run: npm run build:flask:${{ matrix.shorthand }}
-
-      #- if: matrix.os == 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
-
-      #- if: matrix.os != 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
+        run: npm run build:flask
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js
diff --git a/nwb-guide-windows.spec b/nwb-guide.spec
similarity index 100%
rename from nwb-guide-windows.spec
rename to nwb-guide.spec
diff --git a/package.json b/package.json
index c6f5b1487..28727a469 100644
--- a/package.json
+++ b/package.json
@@ -11,25 +11,14 @@
     "dev:app": "vite src/renderer",
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
+    "echo": "python -c \"print('hello')\"",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:mac && npm run build:electron:mac",
-    "build:mac-arm64": "npm run build && npm run build:flask:mac-arm64 && npm run build:electron:mac",
-    "build:linux": "npm run build && npm run build:flask:linux && npm run build:electron:linux",
-    "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
+    "build:linux": "npm run build && npm run build:flask && npm run build:electron:linux",
+    "build:flask": "python -m PyInstaller nwb-guide.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ndx_dandi_icephys --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
-    "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
-    "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
-    "rename:spec:mac": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:mac": "npm run build:flask:spec:mac && npm run rename:spec:mac",
-    "rename:spec:mac-arm64": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac-arm64.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:mac-arm64": "npm run build:flask:spec:mac-arm64 && npm run rename:spec:mac-arm64",
-    "rename:spec:linux": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-linux.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:linux": "npm run build:flask:spec:unix && npm run rename:spec:linux",
+    "build:flask:spec": "npm run build:flask:spec:base && python prepare_pyinstaller_spec.py",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
new file mode 100644
index 000000000..41d2cc6d6
--- /dev/null
+++ b/prepare_pyinstaller_spec.py
@@ -0,0 +1,30 @@
+"""
+Calling `pyi-makespec` regenerates the base spec file, but we need to extend the recursion limit.
+
+This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
+"""
+
+
+def test():
+    from pathlib import Path
+
+    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
+        lines = io.readlines()
+
+    lines.insert(1, "import sys\n")
+    lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+    lines.insert(3, "\n")
+
+    # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
+    # The spec file is, however, the same across platforms
+    data_line_index = lines.index("datas = []\n")
+    lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
+
+    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
+        io.writelines(lines)
+
+    print("Sucessfully injected recursion depth extension and json paths!")
+
+
+if __name__ == "__main__":
+    test()

From a9ddea5f8f250dbff3208fdfaaa59673e3f1e436 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 23:48:18 -0400
Subject: [PATCH 51/60] simplify python

---
 prepare_pyinstaller_spec.py | 33 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 20 deletions(-)

diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
index 41d2cc6d6..2e69cb49e 100644
--- a/prepare_pyinstaller_spec.py
+++ b/prepare_pyinstaller_spec.py
@@ -3,28 +3,21 @@
 
 This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
 """
+from pathlib import Path
 
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
+    lines = io.readlines()
 
-def test():
-    from pathlib import Path
+lines.insert(1, "import sys\n")
+lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(3, "\n")
 
-    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
-        lines = io.readlines()
+# Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
+# The spec file is, however, the same across platforms
+data_line_index = lines.index("datas = []\n")
+lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
-    lines.insert(1, "import sys\n")
-    lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
-    lines.insert(3, "\n")
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
+    io.writelines(lines)
 
-    # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
-    # The spec file is, however, the same across platforms
-    data_line_index = lines.index("datas = []\n")
-    lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
-
-    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
-        io.writelines(lines)
-
-    print("Sucessfully injected recursion depth extension and json paths!")
-
-
-if __name__ == "__main__":
-    test()
+print("Sucessfully injected recursion depth extension and json paths!")

From 1d5579b21220a023404c421840bb35cf0e2d729f Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Thu, 14 Sep 2023 00:22:19 -0400
Subject: [PATCH 52/60] modify spec to be platform indepedent

---
 nwb-guide.spec              | 4 +++-
 prepare_pyinstaller_spec.py | 9 ++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/nwb-guide.spec b/nwb-guide.spec
index 93640b066..8b4f5649d 100644
--- a/nwb-guide.spec
+++ b/nwb-guide.spec
@@ -1,5 +1,7 @@
 # -*- mode: python ; coding: utf-8 -*-
 import sys
+from pathlib import Path
+
 sys.setrecursionlimit(sys.getrecursionlimit() * 5)
 
 from PyInstaller.utils.hooks import collect_data_files
@@ -27,7 +29,7 @@ block_cipher = None
 
 
 a = Analysis(
-    ['pyflask\\app.py'],
+    [f"{Path('pyflask') / 'app.py'}"],
     pathex=[],
     binaries=binaries,
     datas=datas,
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
index 2e69cb49e..db06d8e91 100644
--- a/prepare_pyinstaller_spec.py
+++ b/prepare_pyinstaller_spec.py
@@ -9,14 +9,21 @@
     lines = io.readlines()
 
 lines.insert(1, "import sys\n")
-lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(2, "from pathlib import Path\n")
 lines.insert(3, "\n")
+lines.insert(4, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(5, "\n")
 
 # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
 # The spec file is, however, the same across platforms
 data_line_index = lines.index("datas = []\n")
 lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
+# Another platform specific difference is the app.py location
+app_py_line_index = next(index for index, line in enumerate(lines) if "app.py" in line)
+app_py_line = "    [f\"{Path('pyflask') / 'app.py'}\"],\n"
+lines[app_py_line_index] = app_py_line
+
 with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
     io.writelines(lines)
 

From b99b3391edee2a546593a32f9ed7331dbe18a626 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 10:07:12 -0700
Subject: [PATCH 53/60] DANDI upload updates

---
 schemas/json/dandi/global.json                | 22 ++++++++++++++-----
 src/renderer/src/stories/JSONSchemaForm.js    | 22 ++++++++++++++++---
 src/renderer/src/stories/JSONSchemaInput.js   |  3 ++-
 src/renderer/src/stories/forms/utils.ts       |  4 +++-
 src/renderer/src/stories/pages/Page.js        |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |  5 +++--
 .../guided-mode/data/GuidedSourceData.js      |  1 +
 .../stories/pages/settings/SettingsPage.js    |  4 ++--
 .../src/stories/pages/uploads/UploadsPage.js  | 11 +++++++---
 9 files changed, 55 insertions(+), 19 deletions(-)

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
index c841a1cf8..1680fd34d 100644
--- a/schemas/json/dandi/global.json
+++ b/schemas/json/dandi/global.json
@@ -1,10 +1,20 @@
 {
+    "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>The main archive</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>the staging (testing) server</a> have different API keys.</small>",
     "properties": {
-        "api_key": {
-            "type": "string",
-            "format": "password",
-            "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>The main archive</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>the staging (testing) server</a> have different API keys.</small>"
+        "api_keys": {
+            "properties": {
+                "main_api_key": {
+                    "type": "string",
+                    "format": "password",
+                    "description": "From the <a href='https://dandiarchive.org' target='_blank'>main archive</a>"
+                },
+                "staging_api_key": {
+                    "type": "string",
+                    "format": "password",
+                    "description": "From the <a href='https://gui-staging.dandiarchive.org' target='_blank'>staging (testing) server</a>"
+                }
+            },
+            "required": ["main_api_key", "staging_api_key"]
         }
-    },
-    "required": ["api_key"]
+    }
 }
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index aa2912722..bbd554182 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -114,6 +114,22 @@ pre {
   .required.conditional label:after {
     color: transparent;
   }
+
+  h4 { 
+    margin: 0;
+    margin-bottom: 5px;
+    padding-bottom: 5px;
+    border-bottom: 1px solid gainsboro;
+  }
+
+  .guided--text-input-instructions {
+    font-size: 13px;
+    width: 100%;
+    padding-top: 4px;
+    color: dimgray !important;
+    margin: 0 0 1em;
+    line-height: 1.4285em;
+}
 `;
 
 document.addEventListener("dragover", (e) => {
@@ -238,10 +254,10 @@ export class JSONSchemaForm extends LitElement {
 
         // NOTE: Forms with nested forms will handle their own state updates
         if (!value) {
-            delete resultParent[name];
+            if (fullPath.length === 1) delete resultParent[name];
             delete resolvedParent[name];
         } else {
-            resultParent[name] = value;
+            if (fullPath.length === 1) resultParent[name] = value;
             resolvedParent[name] = value;
         }
 
@@ -836,7 +852,7 @@ export class JSONSchemaForm extends LitElement {
 
         return html`
             <div>
-                ${false ? html`<h2>${schema.title}</h2>` : ""} ${false ? html`<p>${schema.description}</p>` : ""}
+                ${schema.description ? html`<h4>Description</h4><p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>` : ""}
                 ${this.#render(schema, this.resolved, this.#requirements)}
             </div>
         `;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index fde0b43af..0a6a7ea07 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,4 +1,5 @@
 import { LitElement, css, html } from "lit";
+import { unsafeHTML } from 'lit/directives/unsafe-html.js'
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
@@ -136,7 +137,7 @@ export class JSONSchemaInput extends LitElement {
             ${input}
             ${info.description
                 ? html`<p class="guided--text-input-instructions">
-                      ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
+                      ${unsafeHTML(capitalize(info.description))}${info.description.slice(-1)[0] === "." ? "" : "."}
                   </p>`
                 : ""}
         `;
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 8a1973675..30660bc4f 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -1,4 +1,6 @@
-export const capitalize = (str: string) => str[0].toUpperCase() + str.slice(1)
+const toCapitalizeAll = ['nwb', 'api', 'id']
+
+export const capitalize = (str: string) => toCapitalizeAll.includes(str.toLowerCase()) ? str.toUpperCase() : str[0].toUpperCase() + str.slice(1)
 
 
 export const header = (headerStr: string) => {
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index c4a52659b..07d3ef6ea 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -17,7 +17,7 @@ export class Page extends LitElement {
     //     );
     // }
 
-    info = { globalState: {} };
+    info = { globalState: {}, states: { saved: false } };
 
     constructor(info = {}) {
         super();
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
index 583ccbee2..ab9ddeb7b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -58,18 +58,19 @@ export class GuidedMetadataPage extends ManagedPage {
     createForm = ({ subject, session, info }) => {
         // const results = createResults({ subject, info }, this.info.globalState);
 
-        const globalState = this.info.globalState;
+        const { globalState } = this.info;
 
         const results = info.metadata; // Edited form info
 
         // Define the appropriate global metadata to fill empty values in the form
-        const aggregateGlobalMetadata = resolveGlobalOverrides(subject, this.info.globalState);
+        const aggregateGlobalMetadata = resolveGlobalOverrides(subject, globalState);
 
         // Define the correct instance identifier
         const instanceId = `sub-${subject}/ses-${session}`;
 
         // Ignore specific metadata in the form by removing their schema value
         const schema = globalState.schema.metadata[subject][session];
+        delete schema.description;
         delete schema.properties.NWBFile.properties.source_script;
         delete schema.properties.NWBFile.properties.source_script_file_name;
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
index 5abb23272..eacd86b3a 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -104,6 +104,7 @@ export class GuidedSourceDataPage extends ManagedPage {
         const instanceId = `sub-${subject}/ses-${session}`;
 
         const schema = this.info.globalState.schema.source_data;
+        delete schema.description;
 
         const form = new JSONSchemaForm({
             identifier: instanceId,
diff --git a/src/renderer/src/stories/pages/settings/SettingsPage.js b/src/renderer/src/stories/pages/settings/SettingsPage.js
index c0ae474f8..69cef8a23 100644
--- a/src/renderer/src/stories/pages/settings/SettingsPage.js
+++ b/src/renderer/src/stories/pages/settings/SettingsPage.js
@@ -40,7 +40,7 @@ export class SettingsPage extends Page {
             const res = resolved[prop];
             if (propInfo) setUndefinedIfNotDeclared(propInfo, res);
         }
-        if (!("api_key" in resolved.DANDI)) resolved.DANDI.api_key = undefined;
+
         merge(this.form.resolved, global.data);
 
         global.save(); // Save the changes, even if invalid on the form
@@ -69,7 +69,7 @@ export class SettingsPage extends Page {
             onUpdate: () => (this.unsavedUpdates = true),
             validateOnChange: (name, parent) => {
                 const value = parent[name];
-                if (name === "api_key") return dandiAPITokenRegex.test(value);
+                if (name.includes("api_key")) return dandiAPITokenRegex.test(value);
                 return true;
             },
             onThrow,
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 2e4691212..2ed2331d1 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -19,10 +19,15 @@ import { DandiResults } from "../../DandiResults.js";
 export const isStaging = (id) => parseInt(id) >= 100000;
 
 export async function uploadToDandi(info, type = "project" in info ? "" : "folder") {
-    const api_key = global.data.DANDI?.api_key;
+
+    const staging = isStaging(info.dandiset_id) // Automatically detect staging IDs
+
+    const whichAPIKey = staging ? 'staging_api_key' : 'main_api_key'
+    const api_key = global.data.DANDI?.api_keys?.[whichAPIKey];
+
     if (!api_key) {
         await Swal.fire({
-            title: "Your DANDI API key is not configured.",
+            title: `Your DANDI API key (${whichAPIKey}) is not configured.`,
             html: "Edit your settings to include this value.",
             icon: "warning",
             confirmButtonText: "Go to Settings",
@@ -35,7 +40,7 @@ export async function uploadToDandi(info, type = "project" in info ? "" : "folde
         type ? `upload/${type}` : "upload",
         {
             ...info,
-            staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
+            staging,
             api_key,
         },
         { title: "Uploading to DANDI" }

From ec98679b49b4456d11430c21bb10f400356434e4 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 10:10:08 -0700
Subject: [PATCH 54/60] Add description about staging derivation

---
 schemas/json/dandi/upload.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/schemas/json/dandi/upload.json b/schemas/json/dandi/upload.json
index 4ece77105..366e702e9 100644
--- a/schemas/json/dandi/upload.json
+++ b/schemas/json/dandi/upload.json
@@ -1,7 +1,8 @@
 {
     "properties": {
         "dandiset_id": {
-            "type": "string"
+            "type": "string",
+            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main or staging DANDI server."
         },
         "cleanup": {
             "type": "boolean",

From 59925b13604f7be0c2181def57cb88cce4a3e694 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 17:11:19 +0000
Subject: [PATCH 55/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js            | 7 +++++--
 src/renderer/src/stories/JSONSchemaInput.js           | 2 +-
 src/renderer/src/stories/pages/uploads/UploadsPage.js | 5 ++---
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bbd554182..bfd84feed 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -115,7 +115,7 @@ pre {
     color: transparent;
   }
 
-  h4 { 
+  h4 {
     margin: 0;
     margin-bottom: 5px;
     padding-bottom: 5px;
@@ -852,7 +852,10 @@ export class JSONSchemaForm extends LitElement {
 
         return html`
             <div>
-                ${schema.description ? html`<h4>Description</h4><p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>` : ""}
+                ${schema.description
+                    ? html`<h4>Description</h4>
+                          <p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>`
+                    : ""}
                 ${this.#render(schema, this.resolved, this.#requirements)}
             </div>
         `;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 0a6a7ea07..f5293a61b 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,5 +1,5 @@
 import { LitElement, css, html } from "lit";
-import { unsafeHTML } from 'lit/directives/unsafe-html.js'
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 2ed2331d1..7da82c9a6 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -19,10 +19,9 @@ import { DandiResults } from "../../DandiResults.js";
 export const isStaging = (id) => parseInt(id) >= 100000;
 
 export async function uploadToDandi(info, type = "project" in info ? "" : "folder") {
+    const staging = isStaging(info.dandiset_id); // Automatically detect staging IDs
 
-    const staging = isStaging(info.dandiset_id) // Automatically detect staging IDs
-
-    const whichAPIKey = staging ? 'staging_api_key' : 'main_api_key'
+    const whichAPIKey = staging ? "staging_api_key" : "main_api_key";
     const api_key = global.data.DANDI?.api_keys?.[whichAPIKey];
 
     if (!api_key) {

From ff45354e34121d6a0ecdcb5450d9e9939eca8c70 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 14 Sep 2023 10:30:46 -0700
Subject: [PATCH 56/60] Update schemas/json/dandi/upload.json

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 schemas/json/dandi/upload.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/schemas/json/dandi/upload.json b/schemas/json/dandi/upload.json
index 366e702e9..40f130e47 100644
--- a/schemas/json/dandi/upload.json
+++ b/schemas/json/dandi/upload.json
@@ -2,7 +2,7 @@
     "properties": {
         "dandiset_id": {
             "type": "string",
-            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main or staging DANDI server."
+            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main DANDI archive or the development staging server."
         },
         "cleanup": {
             "type": "boolean",

From a62a8e56c2a4bad945eed0881cfd54b6e1224e75 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 13:34:47 -0700
Subject: [PATCH 57/60] Count fields properly (only interactive)

---
 src/renderer/src/stories/JSONSchemaForm.js | 41 +++++++++++++++++-----
 1 file changed, 32 insertions(+), 9 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bfd84feed..d1a7967ea 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -484,18 +484,39 @@ export class JSONSchemaForm extends LitElement {
         }
     };
 
-    #getRenderable = (schema = {}, required, path) => {
+    #getRenderable = (schema = {}, required, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
 
-        return entries.filter(([key, value]) => {
+        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v))
+
+        const flattenRecursedValues = (arr) => {
+            const newArr = []
+            arr.forEach((o) => {
+                if (isArrayOfArrays(o)) newArr.push(...o)
+                else newArr.push(o)
+            })
+
+            return newArr
+        }
+
+        const isRenderable = (key, value) => {
+            if (recursive && value.properties)  return this.#getRenderable(value, required[key], [...path, key], true)
+            
+            else return [key, value]
+        }
+
+        const res = entries.map(([key, value]) => {
             if (!value.properties && key === "definitions") return false; // Skip definitions
             if (this.ignore.includes(key)) return false;
-            if (this.showLevelOverride >= path.length) return true;
-            if (required[key]) return true;
-            if (this.#getLink([...this.#base, ...path, key])) return true;
-            if (!this.onlyRequired) return true;
+            if (this.showLevelOverride >= path.length) return isRenderable(key, value);
+            if (required[key]) return isRenderable(key, value);
+            if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
+            if (!this.onlyRequired) return isRenderable(key, value);
             return false;
-        });
+        }).filter(o => !!o)
+
+        return flattenRecursedValues(res); // Flatten on the last pass
+
     };
 
     validateOnChange = () => {};
@@ -735,6 +756,7 @@ export class JSONSchemaForm extends LitElement {
             if (this.mode === "accordion" && hasMany) {
                 const headerName = header(name);
 
+
                 this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
@@ -770,10 +792,11 @@ export class JSONSchemaForm extends LitElement {
                     base: fullPath,
                 });
 
-                const accordion = new Accordion({
+
+                const accordion = new  Accordion({
                     sections: {
                         [headerName]: {
-                            subtitle: `${this.#getRenderable(info, required[name], fullPath).length} fields`,
+                            subtitle: `${this.#getRenderable(info, required[name], fullPath, true).length} fields`,
                             content: this.#nestedForms[name],
                         },
                     },

From 8b4291f710aaa26b24dd1536f4b78e34cec2a3cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 20:36:18 +0000
Subject: [PATCH 58/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js | 46 +++++++++++-----------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index d1a7967ea..e1902a2a3 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -487,36 +487,36 @@ export class JSONSchemaForm extends LitElement {
     #getRenderable = (schema = {}, required, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
 
-        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v))
+        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v));
 
         const flattenRecursedValues = (arr) => {
-            const newArr = []
+            const newArr = [];
             arr.forEach((o) => {
-                if (isArrayOfArrays(o)) newArr.push(...o)
-                else newArr.push(o)
-            })
+                if (isArrayOfArrays(o)) newArr.push(...o);
+                else newArr.push(o);
+            });
 
-            return newArr
-        }
+            return newArr;
+        };
 
         const isRenderable = (key, value) => {
-            if (recursive && value.properties)  return this.#getRenderable(value, required[key], [...path, key], true)
-            
-            else return [key, value]
-        }
+            if (recursive && value.properties) return this.#getRenderable(value, required[key], [...path, key], true);
+            else return [key, value];
+        };
 
-        const res = entries.map(([key, value]) => {
-            if (!value.properties && key === "definitions") return false; // Skip definitions
-            if (this.ignore.includes(key)) return false;
-            if (this.showLevelOverride >= path.length) return isRenderable(key, value);
-            if (required[key]) return isRenderable(key, value);
-            if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
-            if (!this.onlyRequired) return isRenderable(key, value);
-            return false;
-        }).filter(o => !!o)
+        const res = entries
+            .map(([key, value]) => {
+                if (!value.properties && key === "definitions") return false; // Skip definitions
+                if (this.ignore.includes(key)) return false;
+                if (this.showLevelOverride >= path.length) return isRenderable(key, value);
+                if (required[key]) return isRenderable(key, value);
+                if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
+                if (!this.onlyRequired) return isRenderable(key, value);
+                return false;
+            })
+            .filter((o) => !!o);
 
         return flattenRecursedValues(res); // Flatten on the last pass
-
     };
 
     validateOnChange = () => {};
@@ -756,7 +756,6 @@ export class JSONSchemaForm extends LitElement {
             if (this.mode === "accordion" && hasMany) {
                 const headerName = header(name);
 
-
                 this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
@@ -792,8 +791,7 @@ export class JSONSchemaForm extends LitElement {
                     base: fullPath,
                 });
 
-
-                const accordion = new  Accordion({
+                const accordion = new Accordion({
                     sections: {
                         [headerName]: {
                             subtitle: `${this.#getRenderable(info, required[name], fullPath, true).length} fields`,

From 7e48322912da6cd8b4bcb5bfe532f3ffabc9897b Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 13:39:56 -0700
Subject: [PATCH 59/60] Fix table validation

---
 src/renderer/src/stories/JSONSchemaInput.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 81c5fd6ae..3b0b67376 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -189,7 +189,7 @@ export class JSONSchemaInput extends LitElement {
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && this.#triggerValidation(key, this.form.tables[name], path); // this.form.validateOnChange(key, parent, fullPath, v);
+                        return validateOnChange && ( this.onValidate ? this.onValidate() : this.form ? this.form.validateOnChange(key, parent, fullPath, v) : '');
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements

From cd85235dd1216025b3a630280241151a1edb04ef Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 20:40:20 +0000
Subject: [PATCH 60/60] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 3b0b67376..467cdbb65 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -189,7 +189,14 @@ export class JSONSchemaInput extends LitElement {
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && ( this.onValidate ? this.onValidate() : this.form ? this.form.validateOnChange(key, parent, fullPath, v) : '');
+                        return (
+                            validateOnChange &&
+                            (this.onValidate
+                                ? this.onValidate()
+                                : this.form
+                                ? this.form.validateOnChange(key, parent, fullPath, v)
+                                : "")
+                        );
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements