From 45602312ce403c2e1e32ce2cecc1c53c74865449 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 9 Nov 2023 07:52:56 -0800
Subject: [PATCH 001/133] Enable Ophys and fix table

---
 src/renderer/src/stories/SimpleTable.js       | 41 ++++++++++++-------
 .../pages/guided-mode/data/GuidedMetadata.js  |  2 +-
 2 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 4835f3630..03b1d1d3e 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -1,14 +1,16 @@
-import { LitElement, css, html } from "lit";
+import { LitElement, css, html, unsafeCSS } from "lit";
 import { header } from "./forms/utils";
 import { checkStatus } from "../validation";
 
 import { TableCell } from "./table/Cell";
 import { ContextMenu } from "./table/ContextMenu";
-import { errorHue, warningHue } from "./globals";
+import { emojiFontFamily, errorHue, warningHue } from "./globals";
 
 import { Loader } from "./Loader";
 import { styleMap } from "lit/directives/style-map.js";
+
 import "./Button";
+import tippy from "tippy.js";
 
 var isMac = navigator.platform.toUpperCase().indexOf("MAC") >= 0;
 
@@ -96,7 +98,6 @@ export class SimpleTable extends LitElement {
             }
 
             .table-container {
-                position: relative;
                 overflow: auto;
                 max-height: 400px;
             }
@@ -110,6 +111,7 @@ export class SimpleTable extends LitElement {
                 position: sticky;
                 top: 0;
                 left: 0;
+                z-index: 1;
             }
 
             th {
@@ -140,15 +142,10 @@ export class SimpleTable extends LitElement {
                 user-select: none;
             }
 
-            [title] .relative::after {
-                content: "ℹ️";
-                cursor: help;
-                display: inline-block;
+            .relative .info {
                 margin: 0px 5px;
-                text-align: center;
                 font-size: 80%;
-                font-family: "Twemoji Mozilla", "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol",
-                    "Noto Color Emoji", "EmojiOne Color", "Android Emoji", sans-serif;
+                font-family: ${unsafeCSS(emojiFontFamily)}
             }
         `;
     }
@@ -584,11 +581,27 @@ export class SimpleTable extends LitElement {
         }
     }
 
-    #renderHeaderContent = (str) => html`<div class="relative"><span>${str}</span></div>`;
-
     #renderHeader = (str, { description }) => {
-        if (description) return html`<th title="${description}">${this.#renderHeaderContent(str)}</th>`;
-        return html`<th>${this.#renderHeaderContent(str)}</th>`;
+        const header = document.createElement('th')
+
+        // Inner Content
+        const div = document.createElement("div");
+        div.classList.add("relative");
+        const span = document.createElement("span");
+        span.innerHTML = str
+        div.append(span);
+        header.append(div)
+
+        // Add Description Tooltip
+        if (description) {
+            const span = document.createElement("span");
+            span.classList.add("info");
+            span.innerText = "ℹ️";
+            div.append(span);
+            tippy(span, { content: `${description[0].toUpperCase() + description.slice(1)}` });
+        }
+
+        return header;
     };
 
     #cells = [];
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 cb56c989b..2d843cd46 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -20,7 +20,7 @@ import { globalSchema } from "../../../../../../../schemas/base-metadata.schema"
 import globalIcon from "../../../assets/global.svg?raw";
 
 const propsToIgnore = [
-    "Ophys", // Always ignore ophys metadata (for now)
+    // "Ophys", // Always ignore ophys metadata (for now)
     "Icephys", // Always ignore icephys metadata (for now)
     "Behavior", // Always ignore behavior metadata (for now)
     // new RegExp("ndx-.+"), // Ignore all ndx extensions

From 45aea759c18637d76bb42d85fc4bbdead9e3c2a4 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 9 Nov 2023 09:38:29 -0800
Subject: [PATCH 002/133] Add table in table

---
 src/renderer/src/stories/SimpleTable.js       |  15 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |   2 +
 src/renderer/src/stories/table/Cell.ts        |  17 ++-
 src/renderer/src/stories/table/ContextMenu.ts |   2 +
 src/renderer/src/stories/table/cells/base.ts  |  70 ++++++++--
 .../src/stories/table/cells/renderers/base.ts |   3 +-
 src/renderer/src/stories/table/cells/table.ts | 132 ++++++++++++++++++
 7 files changed, 221 insertions(+), 20 deletions(-)
 create mode 100644 src/renderer/src/stories/table/cells/table.ts

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 03b1d1d3e..df5d86dcd 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -170,6 +170,7 @@ export class SimpleTable extends LitElement {
         onThrow,
         deferLoading,
         maxHeight,
+        contextOptions = {}
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -180,6 +181,8 @@ export class SimpleTable extends LitElement {
         this.deferLoading = deferLoading ?? false;
         this.maxHeight = maxHeight ?? "";
 
+        this.contextOptions = contextOptions;
+
         if (validateOnChange) this.validateOnChange = validateOnChange;
         if (onStatusChange) this.onStatusChange = onStatusChange;
         if (onLoaded) this.onLoaded = onLoaded;
@@ -187,6 +190,7 @@ export class SimpleTable extends LitElement {
         if (onUpdate) this.onUpdate = onUpdate;
 
         this.onmousedown = (ev) => {
+            ev.stopPropagation();
             this.#clearSelected();
             this.#selecting = true;
             const cell = this.#getCellFromEvent(ev);
@@ -451,9 +455,12 @@ export class SimpleTable extends LitElement {
         if (options.column?.add) items.push(this.#menuOptions.column.add);
         if (options.column?.remove) items.push(this.#menuOptions.column.remove);
 
-        this.#context = new ContextMenu({ target: this.shadowRoot.querySelector("table"), items });
+        this.#context = new ContextMenu({ 
+            target: this.shadowRoot.querySelector("table"), 
+            items,
+        });
 
-        this.shadowRoot.append(this.#context); // Insert context menu
+        document.body.append(this.#context); // Insert context menu
     }
 
     #loaded = false;
@@ -500,6 +507,7 @@ export class SimpleTable extends LitElement {
                     add: true,
                     remove: true,
                 },
+                ...this.contextOptions
             });
         }
     };
@@ -664,6 +672,9 @@ export class SimpleTable extends LitElement {
 
         // Track the cell renderer
         const cell = new TableCell({
+            info: { 
+                col: this.colHeaders[info.j],
+            },
             value,
             schema,
             validateOnChange: (value) => {
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 2d843cd46..55addad66 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -202,6 +202,8 @@ export class GuidedMetadataPage extends ManagedPage {
             onThrow,
         });
 
+        setInterval(() => console.log(form.results.Ophys?.ImagingPlane[0]?.optical_channel.length), 1000)
+
         return {
             subject,
             session,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index e258e218f..16f976793 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -1,5 +1,7 @@
 import { LitElement, css, html } from "lit"
 import { ArrayCell } from "./cells/array"
+import { NestedTableCell } from "./cells/table"
+
 import { TableCellBase } from "./cells/base"
 import { DateTimeCell } from "./cells/date-time"
 
@@ -15,6 +17,7 @@ type OnValidateFunction = (info: ValidationResult) => void
 
 type TableCellProps = {
     value: string,
+    info: { col: string }
     schema: {[key: string]: any},
     validateOnChange?: ValidationFunction,
     onValidate?: OnValidateFunction,
@@ -23,6 +26,7 @@ type TableCellProps = {
 export class TableCell extends LitElement {
 
     declare schema: TableCellProps['schema']
+    declare info: TableCellProps['info']
 
     static get styles() {
         return css`
@@ -63,10 +67,12 @@ export class TableCell extends LitElement {
     //     }
     // }
 
-    constructor({ value, schema, validateOnChange, onValidate }: TableCellProps) {
+    constructor({ info, value, schema, validateOnChange, onValidate }: TableCellProps) {
         super()
         this.#value = value
         this.schema = schema
+        this.info = info
+        
         if (validateOnChange) this.validateOnChange = validateOnChange
 
         if (onValidate) this.onValidate = onValidate
@@ -78,7 +84,6 @@ export class TableCell extends LitElement {
         }
 
         this.ondblclick = () => this.input.toggle(true)
-        document.addEventListener('click', () => this.input ? this.input.toggle(false) : false)
 
     }
 
@@ -159,7 +164,11 @@ export class TableCell extends LitElement {
 
         this.interacted = false
 
-        if (this.schema.type === "array") cls = ArrayCell
+        if (this.schema.type === "array") {
+            const items = this.schema.items
+            if (items && items.type === "object") cls = NestedTableCell
+            else cls = ArrayCell
+        }
         else if (this.schema.format === "date-time") cls =  DateTimeCell
 
         // Only actually rerender if new class type
@@ -169,6 +178,8 @@ export class TableCell extends LitElement {
                     if (this.input.interacted) this.interacted = true
                     this.validate()
                 },
+                toggle: (v) => this.input ? this.input.toggle(v) : "",
+                info: this.info,
                 schema: this.schema
             })
         }
diff --git a/src/renderer/src/stories/table/ContextMenu.ts b/src/renderer/src/stories/table/ContextMenu.ts
index 9d20e6611..aa618dd0f 100644
--- a/src/renderer/src/stories/table/ContextMenu.ts
+++ b/src/renderer/src/stories/table/ContextMenu.ts
@@ -85,6 +85,8 @@ export class ContextMenu extends LitElement{
         e.stopPropagation()
         this.#activePath = e.path || e.composedPath()
         this.style.display = 'block';
+
+
         this.style.left = e.pageX + "px";
         this.style.top = e.pageY + "px";
     }
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 3a52c7774..df7c5ccf1 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -2,6 +2,10 @@ import { LitElement, PropertyValueMap, css, html } from "lit"
 import { placeCaretAtEnd } from "../utils"
 
 type BaseTableProps = {
+    info: { 
+        col: string,
+    },
+    toggle: (state?: boolean) => void,
     schema: any,
     onOpen: Function,
     onClose: Function,
@@ -47,20 +51,28 @@ export class TableCellBase extends LitElement {
         `
     }
 
-    schema: any;
+    schema: BaseTableProps['schema'];
+    info: BaseTableProps['info'];
+    editToggle: BaseTableProps['toggle']
 
     interacted = false
 
     constructor({
+        info,
         schema,
         onOpen,
         onClose,
-        onChange
+        onChange,
+        toggle
     }: Partial<BaseTableProps> = {}) {
 
         super()
 
+        this.info = info ?? {}
         this.schema = schema ?? {}
+        
+        this.editToggle = toggle ?? (() => {});
+
         if (onOpen) this.onOpen = onOpen
         if (onChange) this.onChange = onChange
         if (onClose) this.onClose = onClose
@@ -79,20 +91,44 @@ export class TableCellBase extends LitElement {
     onClose: BaseTableProps['onClose'] = () => {}
     onChange: BaseTableProps['onChange'] = () => {}
 
+    #editableClose = () => this.editToggle(false)
+
     toggle (state = !this.#active) {
         if (state === this.#active) return
 
         if (state) {
-            this.#editable.setAttribute('contenteditable', '')
-            this.setAttribute('editing', ''),
+
+            this.setAttribute('editing', '')
+
+            if (this.#editor === this.#editable) {
+                this.#editable.setAttribute('contenteditable', '')
+                this.#editable.style.pointerEvents = 'auto'
+                placeCaretAtEnd(this.#editable)
+                document.addEventListener('click', this.#editableClose)
+            } else {
+                this.#editor.onEditStart()
+
+            }
+
             this.onOpen()
-            this.#editable.style.pointerEvents = 'auto'
-            placeCaretAtEnd(this.#editable)
+
         } else {
-            const current = this.getElementValue(this.#editable)
+
+            let current
             this.removeAttribute('editing')
+
+            if (this.#editor === this.#editable) {
+                current = this.getElementValue(this.#editable)
+                this.#editable.style.pointerEvents = ''
+                document.removeEventListener('click', this.#editableClose)
+            } else {
+                current = this.#editor.value
+                if (this.#editor && this.#editor.onEditEnd) this.#editor.onEditEnd()
+            }
+
             this.onClose()
-            this.#editable.style.pointerEvents = ''
+
+
             this.setText( current )
         }
 
@@ -103,15 +139,20 @@ export class TableCellBase extends LitElement {
 
     #update(current: any) {
         let value = this.getValue(current)
-        if (this.value !== value) {
+        console.log('Updating', this.value, value)
+        // NOTE: Forcing change registration for all cells
+        // if (this.value !== value) {
             this.value = value
             this.onChange(value)
-        }
+        // }
     }
 
     setText(value: any, setOnInput = true) {
         if (setOnInput) [ this.#editor, this.#renderer ].forEach(el => this.setChild(el, value)) // RESETS HISTORY
-        this.#update(`${value}`) // Coerce to string
+
+        if (this.schema.type === 'array') this.#update(value) // Ensure array values are not coerced
+        else this.#update(`${value}`) // Coerce to string
+
     }
 
 
@@ -168,8 +209,11 @@ export class TableCellBase extends LitElement {
 
         const editor = this.#editor = this.#render('editor')
         const renderer = this.#renderer = this.#render('renderer')
-
-        this.addEventListener('blur', () => this.toggle(false))
+        
+        this.addEventListener('blur', (ev) => {
+            ev.stopPropagation()
+            this.toggle(false)
+        })
 
 
         if (!editor || !renderer || renderer === editor) return editor || renderer
diff --git a/src/renderer/src/stories/table/cells/renderers/base.ts b/src/renderer/src/stories/table/cells/renderers/base.ts
index 5d2b5c91e..16046a7cc 100644
--- a/src/renderer/src/stories/table/cells/renderers/base.ts
+++ b/src/renderer/src/stories/table/cells/renderers/base.ts
@@ -10,12 +10,11 @@ export class BaseRenderer extends LitElement {
         }
     }
 
-    constructor({ value = []} = {}) {
+    constructor({ value }: { value: any }) {
         super()
         this.value = value
     }
 
-
     render() {
         return html`${this.value}`
     }
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
new file mode 100644
index 000000000..b8b45438f
--- /dev/null
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -0,0 +1,132 @@
+import { LitElement, css, html } from "lit";
+import { TableCellBase } from "./base";
+import { BaseRenderer } from "./renderers/base";
+import { Modal } from "../../Modal";
+
+import { SimpleTable } from "../../SimpleTable.js";
+import { header } from "../../forms/utils";
+
+export class NestedTableEditor extends LitElement {
+
+
+    static get styles() {
+        return [
+            css`
+            `
+        ]
+    }
+
+    info: any
+    schema: any
+    toggle: any
+
+    constructor(props: any) {
+        super(props)
+        this.schema = props.schema
+        this.info = props.info ?? {}
+        this.toggle = props.toggle
+    }
+
+    #modal = new Modal({
+        header: 'Table Editor',
+        onClose: () => this.toggle(false)
+    })
+
+    #table: SimpleTable
+    
+    onEditStart () {
+        const modal = this.#modal
+
+        if (this.info.col) modal.header = `${header(this.info.col)} Table Editor`
+
+        if (this.#table) this.#table.remove()
+
+
+        const div = document.createElement('div')
+        Object.assign(div.style, {
+            width: `${10}px`,
+            height: `${10}px`,
+            position: 'absolute',
+            zIndex: 1000,
+            background: 'red'
+        })
+
+        document.body.append(div)
+
+
+        const table = this.#table = new SimpleTable({
+            schema: this.schema.items,
+            data: this.#value
+        })
+
+        table.style.padding = '25px 50px'
+
+        modal.append(table)
+
+        modal.open = true
+    }
+
+    #value: any
+
+    set value(value) {
+        this.#value = value
+        if (this.#table) this.#table.data = value
+    }
+
+    get value() {
+        return this.#table.data ?? this.#value
+    }
+
+    onEditEnd = () => {
+        this.#modal.open = false
+        Array.from(this.#modal.children).forEach(child => child.remove())
+    }
+
+    render() { 
+        return this.#modal
+    }
+}
+
+customElements.get("nwb-nested-table-cell-editor") || customElements.define("nwb-nested-table-cell-editor", NestedTableEditor);
+
+
+
+export class NestedTableRenderer extends BaseRenderer {
+
+
+    static get styles() {
+        return [
+            css`
+                :host {
+                    display: block;
+                    text-align: center;
+                    width: 100%;
+                }
+            `
+        ]
+    }
+
+    constructor(...args: any[]) {
+        super(...args)
+    }
+
+    render() { 
+        return html`<small>Click to view table</small>`
+    }
+}
+
+customElements.get("nwb-nested-table-cell-renderer") || customElements.define("nwb-nested-table-cell-renderer", NestedTableRenderer);
+
+
+export class NestedTableCell extends TableCellBase {
+
+    constructor(props: any){
+        super(props)
+    }
+
+    renderer = new NestedTableRenderer({ value: this.value })
+    
+    editor = new NestedTableEditor({ info: this.info, toggle: this.editToggle, value: this.value, schema: this.schema })
+}
+
+customElements.get("nwb-nested-table-cell") || customElements.define("nwb-nested-table-cell", NestedTableCell);

From 67731fd4dd53785f47a9f40520648b69b957f147 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 9 Nov 2023 09:58:41 -0800
Subject: [PATCH 003/133] Update form with new data

---
 src/renderer/src/stories/JSONSchemaInput.js          |  2 ++
 src/renderer/src/stories/SimpleTable.js              |  2 ++
 .../stories/pages/guided-mode/data/GuidedMetadata.js |  2 --
 src/renderer/src/stories/table/Cell.ts               | 10 ++++++++--
 src/renderer/src/stories/table/cells/base.ts         | 12 ++++++------
 src/renderer/src/stories/table/cells/table.ts        |  8 --------
 6 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 4ad9a8742..b67027d4d 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -148,6 +148,7 @@ export class JSONSchemaInput extends LitElement {
 
     #validationTimeout = null;
     #updateData = (fullPath, value, forceUpdate) => {
+
         this.onUpdate ? this.onUpdate(value) : this.form ? this.form.updateData(fullPath, value, forceUpdate) : "";
 
         const path = [...fullPath];
@@ -223,6 +224,7 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema.type === "object" && this.form.createTable) {
+
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 0b37569a3..7679d97cc 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -722,6 +722,8 @@ export class SimpleTable extends LitElement {
             if (this.#selecting) this.#selectCells(cell);
         };
 
+        td.ondblclick = () => cell.toggle(true);
+        
         td.appendChild(cell);
         return td;
     };
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 83071aaec..080b99566 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -203,8 +203,6 @@ export class GuidedMetadataPage extends ManagedPage {
             onThrow,
         });
 
-        setInterval(() => console.log(form.results.Ophys?.ImagingPlane[0]?.optical_channel.length), 1000)
-
         return {
             subject,
             session,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index c49749463..82e843d29 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -38,6 +38,7 @@ export class TableCell extends LitElement {
                 white-space: nowrap;
                 color: black;
                 font-size: 13px;
+                height: 100%;
             }
 
             :host > * {
@@ -85,10 +86,15 @@ export class TableCell extends LitElement {
             this.#validator = (value) => regex.test(value)
         }
 
-        this.ondblclick = () => this.input.toggle(true)
+        this.ondblclick = (ev) => {
+            ev.stopPropagation()
+            this.toggle(true)
+        }
 
     }
 
+    toggle = (v: boolean) => this.input.toggle(v)
+
     get value() {
         return this.input ? this.input.getValue() : this.#value
     }
@@ -181,7 +187,7 @@ export class TableCell extends LitElement {
                     if (this.input.interacted) this.interacted = true
                     this.validate()
                 },
-                toggle: (v) => this.input ? this.input.toggle(v) : "",
+                toggle: (v) => this.toggle(v),
                 info: this.info,
                 schema: this.schema
             })
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index df7c5ccf1..d22c5dec6 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -92,6 +92,7 @@ export class TableCellBase extends LitElement {
     onChange: BaseTableProps['onChange'] = () => {}
 
     #editableClose = () => this.editToggle(false)
+    #originalEditorValue = undefined
 
     toggle (state = !this.#active) {
         if (state === this.#active) return
@@ -107,7 +108,6 @@ export class TableCellBase extends LitElement {
                 document.addEventListener('click', this.#editableClose)
             } else {
                 this.#editor.onEditStart()
-
             }
 
             this.onOpen()
@@ -123,6 +123,7 @@ export class TableCellBase extends LitElement {
                 document.removeEventListener('click', this.#editableClose)
             } else {
                 current = this.#editor.value
+                this.interacted = true 
                 if (this.#editor && this.#editor.onEditEnd) this.#editor.onEditEnd()
             }
 
@@ -137,20 +138,19 @@ export class TableCellBase extends LitElement {
 
     getValue = (input: any = this.value) => input // Process inputs from the editor
 
-    #update(current: any) {
+    #update(current: any, forceUpdate = false) {
         let value = this.getValue(current)
-        console.log('Updating', this.value, value)
         // NOTE: Forcing change registration for all cells
-        // if (this.value !== value) {
+        if (this.value !== value || forceUpdate) {
             this.value = value
             this.onChange(value)
-        // }
+        }
     }
 
     setText(value: any, setOnInput = true) {
         if (setOnInput) [ this.#editor, this.#renderer ].forEach(el => this.setChild(el, value)) // RESETS HISTORY
 
-        if (this.schema.type === 'array') this.#update(value) // Ensure array values are not coerced
+        if (this.schema.type === 'array') this.#update(value, true) // Ensure array values are not coerced
         else this.#update(`${value}`) // Coerce to string
 
     }
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
index b8b45438f..e1b710699 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -8,14 +8,6 @@ import { header } from "../../forms/utils";
 
 export class NestedTableEditor extends LitElement {
 
-
-    static get styles() {
-        return [
-            css`
-            `
-        ]
-    }
-
     info: any
     schema: any
     toggle: any

From 23c90db8ed07f198e821fbe3a083a447edfb0ebf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 9 Nov 2023 18:05:00 +0000
Subject: [PATCH 004/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js   |  2 --
 src/renderer/src/stories/SimpleTable.js       | 20 +++++++++----------
 .../guided-mode/data/GuidedPathExpansion.js   |  2 +-
 .../guided-mode/data/GuidedSourceData.js      |  7 +++----
 .../stories/pages/guided-mode/data/utils.js   |  2 +-
 src/renderer/src/stories/table/Cell.ts        |  2 +-
 src/renderer/src/stories/table/cells/base.ts  |  8 ++++----
 src/renderer/src/stories/table/cells/table.ts |  8 ++++----
 8 files changed, 24 insertions(+), 27 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index b67027d4d..4ad9a8742 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -148,7 +148,6 @@ export class JSONSchemaInput extends LitElement {
 
     #validationTimeout = null;
     #updateData = (fullPath, value, forceUpdate) => {
-
         this.onUpdate ? this.onUpdate(value) : this.form ? this.form.updateData(fullPath, value, forceUpdate) : "";
 
         const path = [...fullPath];
@@ -224,7 +223,6 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema.type === "object" && this.form.createTable) {
-
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 7679d97cc..16437262b 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -145,7 +145,7 @@ export class SimpleTable extends LitElement {
             .relative .info {
                 margin: 0px 5px;
                 font-size: 80%;
-                font-family: ${unsafeCSS(emojiFontFamily)}
+                font-family: ${unsafeCSS(emojiFontFamily)};
             }
         `;
     }
@@ -170,7 +170,7 @@ export class SimpleTable extends LitElement {
         onThrow,
         deferLoading,
         maxHeight,
-        contextOptions = {}
+        contextOptions = {},
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -455,8 +455,8 @@ export class SimpleTable extends LitElement {
         if (options.column?.add) items.push(this.#menuOptions.column.add);
         if (options.column?.remove) items.push(this.#menuOptions.column.remove);
 
-        this.#context = new ContextMenu({ 
-            target: this.shadowRoot.querySelector("table"), 
+        this.#context = new ContextMenu({
+            target: this.shadowRoot.querySelector("table"),
             items,
         });
 
@@ -507,7 +507,7 @@ export class SimpleTable extends LitElement {
                     add: true,
                     remove: true,
                 },
-                ...this.contextOptions
+                ...this.contextOptions,
             });
         }
     };
@@ -590,15 +590,15 @@ export class SimpleTable extends LitElement {
     }
 
     #renderHeader = (str, { description }) => {
-        const header = document.createElement('th')
+        const header = document.createElement("th");
 
         // Inner Content
         const div = document.createElement("div");
         div.classList.add("relative");
         const span = document.createElement("span");
-        span.innerHTML = str
+        span.innerHTML = str;
         div.append(span);
-        header.append(div)
+        header.append(div);
 
         // Add Description Tooltip
         if (description) {
@@ -672,7 +672,7 @@ export class SimpleTable extends LitElement {
 
         // Track the cell renderer
         const cell = new TableCell({
-            info: { 
+            info: {
                 col: this.colHeaders[info.j],
             },
             value,
@@ -723,7 +723,7 @@ export class SimpleTable extends LitElement {
         };
 
         td.ondblclick = () => cell.toggle(true);
-        
+
         td.appendChild(cell);
         return td;
     };
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 90af0a741..3b8fe1c1b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -129,7 +129,7 @@ export class GuidedPathExpansionPage extends Page {
 
                 const source_data = {};
                 for (let key in globalState.interfaces) {
-                    const existing = existingSourceData?.[key]
+                    const existing = existingSourceData?.[key];
                     if (existing) source_data[key] = existing ?? {};
                 }
 
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 01cb001ea..431b4aab7 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -69,7 +69,7 @@ export class GuidedSourceDataPage extends ManagedPage {
                     backdrop: "rgba(0,0,0, 0.4)",
                     timerProgressBar: false,
                     didOpen: () => {
-                        Swal.showLoading(); 
+                        Swal.showLoading();
                     },
                 });
             };
@@ -80,7 +80,6 @@ export class GuidedSourceDataPage extends ManagedPage {
 
             await Promise.all(
                 Object.values(this.forms).map(async ({ subject, session, form }) => {
-                    
                     const info = this.info.globalState.results[subject][session];
 
                     // NOTE: This clears all user-defined results
@@ -187,8 +186,8 @@ export class GuidedSourceDataPage extends ManagedPage {
         const modal = (this.#globalModal = createGlobalFormModal.call(this, {
             header: "Global Source Data",
             propsToRemove: [
-                ...propsToIgnore, 
-                "folder_path", 
+                ...propsToIgnore,
+                "folder_path",
                 "file_path",
                 // NOTE: Still keeping plural path specifications for now
             ],
diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index 44ac392dd..668aa7988 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -2,7 +2,7 @@ import { merge } from "../../utils.js";
 
 // Merge project-wide data into metadata
 export function populateWithProjectMetadata(info, globalState) {
-    const copy = structuredClone(info)
+    const copy = structuredClone(info);
     const toMerge = Object.entries(globalState.project).filter(([_, value]) => value && typeof value === "object");
     toMerge.forEach(([key, value]) => {
         let internalMetadata = copy[key];
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 82e843d29..92ae57d9c 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -75,7 +75,7 @@ export class TableCell extends LitElement {
         this.#value = value
         this.schema = schema
         this.info = info
-        
+
         if (validateOnChange) this.validateOnChange = validateOnChange
 
         if (onValidate) this.onValidate = onValidate
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index d22c5dec6..66d0b68d4 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -2,7 +2,7 @@ import { LitElement, PropertyValueMap, css, html } from "lit"
 import { placeCaretAtEnd } from "../utils"
 
 type BaseTableProps = {
-    info: { 
+    info: {
         col: string,
     },
     toggle: (state?: boolean) => void,
@@ -70,7 +70,7 @@ export class TableCellBase extends LitElement {
 
         this.info = info ?? {}
         this.schema = schema ?? {}
-        
+
         this.editToggle = toggle ?? (() => {});
 
         if (onOpen) this.onOpen = onOpen
@@ -123,7 +123,7 @@ export class TableCellBase extends LitElement {
                 document.removeEventListener('click', this.#editableClose)
             } else {
                 current = this.#editor.value
-                this.interacted = true 
+                this.interacted = true
                 if (this.#editor && this.#editor.onEditEnd) this.#editor.onEditEnd()
             }
 
@@ -209,7 +209,7 @@ export class TableCellBase extends LitElement {
 
         const editor = this.#editor = this.#render('editor')
         const renderer = this.#renderer = this.#render('renderer')
-        
+
         this.addEventListener('blur', (ev) => {
             ev.stopPropagation()
             this.toggle(false)
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
index e1b710699..aac54219e 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -25,7 +25,7 @@ export class NestedTableEditor extends LitElement {
     })
 
     #table: SimpleTable
-    
+
     onEditStart () {
         const modal = this.#modal
 
@@ -74,7 +74,7 @@ export class NestedTableEditor extends LitElement {
         Array.from(this.#modal.children).forEach(child => child.remove())
     }
 
-    render() { 
+    render() {
         return this.#modal
     }
 }
@@ -102,7 +102,7 @@ export class NestedTableRenderer extends BaseRenderer {
         super(...args)
     }
 
-    render() { 
+    render() {
         return html`<small>Click to view table</small>`
     }
 }
@@ -117,7 +117,7 @@ export class NestedTableCell extends TableCellBase {
     }
 
     renderer = new NestedTableRenderer({ value: this.value })
-    
+
     editor = new NestedTableEditor({ info: this.info, toggle: this.editToggle, value: this.value, schema: this.schema })
 }
 

From c6c1a23fbb73c829cde90481e8234a88eaace25a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 9 Nov 2023 23:52:11 +0000
Subject: [PATCH 005/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/pages/utils.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/pages/utils.js b/src/renderer/src/stories/pages/utils.js
index d926792e9..fd1d65e6e 100644
--- a/src/renderer/src/stories/pages/utils.js
+++ b/src/renderer/src/stories/pages/utils.js
@@ -45,7 +45,8 @@ export function merge(toMerge = {}, target = {}, mergeOpts = {}) {
     for (const [k, v] of Object.entries(toMerge)) {
         const targetV = target[k];
         // if (isPrivate(k)) continue;
-        if (mergeOpts.arrays && Array.isArray(v) && Array.isArray(targetV)) target[k] = [...targetV, ...v]; // Merge array entries together
+        if (mergeOpts.arrays && Array.isArray(v) && Array.isArray(targetV))
+            target[k] = [...targetV, ...v]; // Merge array entries together
         else if (v === undefined) {
             delete target[k]; // Remove matched values
             // if (mergeOpts.remove !== false) delete target[k]; // Remove matched values

From 6eeea2627a0ae21920b9f72810b36bd3dc429bb1 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 10:13:15 -0500
Subject: [PATCH 006/133] Improve ignore specificity

---
 src/renderer/src/stories/JSONSchemaForm.js    | 28 ++++++-------
 .../src/stories/forms/GlobalFormModal.ts      | 39 ++++++++++++++----
 src/renderer/src/stories/pages/FormPage.js    |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  | 33 ++++++++++-----
 .../guided-mode/data/GuidedSourceData.js      | 41 ++++++++++++-------
 5 files changed, 97 insertions(+), 46 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 04bc6d906..e6cf5d382 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -209,7 +209,7 @@ export class JSONSchemaForm extends LitElement {
         this.results = (props.base ? structuredClone(props.results) : props.results) ?? {}; // Deep clone results in nested forms
         this.globals = props.globals ?? {};
 
-        this.ignore = props.ignore ?? [];
+        this.ignore = props.ignore ?? {};
         this.required = props.required ?? {};
         this.dialogOptions = props.dialogOptions;
         this.dialogType = props.dialogType;
@@ -585,7 +585,7 @@ export class JSONSchemaForm extends LitElement {
     //     }
     // };
 
-    #getRenderable = (schema = {}, required, path, recursive = false) => {
+    #getRenderable = (schema = {}, required, ignore = {}, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
 
         const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v));
@@ -601,20 +601,20 @@ export class JSONSchemaForm extends LitElement {
         };
 
         const isRenderable = (key, value) => {
-            if (recursive && value.properties) return this.#getRenderable(value, required[key], [...path, key], true);
+
+            if (recursive && value.properties) return this.#getRenderable(value, required[key], {
+                ...ignore[key],
+                "*": {...ignore["*"] ?? {}, ...ignore[key]["*"] ?? {}}, // Accumulate ignore values
+            }, [...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.find((v) => {
-                        if (typeof v === "string") return v === key;
-                        else return v.test(key);
-                    })
-                )
-                    return false;
+                if (this.ignore["*"]?.[key]) return false; // Skip all properties with this name
+                else if (this.ignore[key] === true) return false; // Skip this property
                 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);
@@ -824,10 +824,10 @@ export class JSONSchemaForm extends LitElement {
 
     #accordions = {};
 
-    #render = (schema, results, required = {}, path = []) => {
+    #render = (schema, results, required = {}, ignore = {}, path = []) => {
         let isLink = Symbol("isLink");
         // Filter non-required properties (if specified) and render the sub-schema
-        const renderable = this.#getRenderable(schema, required, path);
+        const renderable = this.#getRenderable(schema, required, ignore, path);
 
         // // Filter non-required properties (if specified) and render the sub-schema
         // const renderable = path.length ? this.#getRenderable(schema, required) : Object.entries(schema.properties ?? {})
@@ -934,7 +934,7 @@ export class JSONSchemaForm extends LitElement {
 
             const headerName = header(name);
 
-            const renderableInside = this.#getRenderable(info, required[name], localPath, true);
+            const renderableInside = this.#getRenderable(info, required[name], ignore, localPath, true);
 
             const __disabled = this.results.__disabled ?? (this.results.__disabled = {});
             const __interacted = __disabled.__interacted ?? (__disabled.__interacted = {});
@@ -1140,7 +1140,7 @@ export class JSONSchemaForm extends LitElement {
                 ? html`<h4>Description</h4>
                       <p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>`
                 : ""}
-            ${this.#render(schema, this.resolved, this.#requirements)}
+            ${this.#render(schema, this.resolved, this.#requirements, this.ignore)}
         `;
     }
 }
diff --git a/src/renderer/src/stories/forms/GlobalFormModal.ts b/src/renderer/src/stories/forms/GlobalFormModal.ts
index f6de21e8b..0e3ea2f3c 100644
--- a/src/renderer/src/stories/forms/GlobalFormModal.ts
+++ b/src/renderer/src/stories/forms/GlobalFormModal.ts
@@ -7,12 +7,20 @@ import { onThrow } from "../../errors";
 import { merge } from "../pages/utils.js";
 import { save } from "../../progress/index.js";
 
+type SingleIgnorePropsLevel = {
+    [x:string]: true,
+}
+
+type IgnorePropsLevel = {
+    ["*"]?: SingleIgnorePropsLevel,
+    [x:string]: true | IgnorePropsLevel,
+}
 
 export function createGlobalFormModal(this: Page, {
     header,
     schema,
-    propsToIgnore = [],
-    propsToRemove = [],
+    propsToIgnore = {},
+    propsToRemove = {},
     key,
     hasInstances = false,
     validateOnChange,
@@ -20,8 +28,8 @@ export function createGlobalFormModal(this: Page, {
 }: {
     header: string
     schema: any
-    propsToIgnore?: string[]
-    propsToRemove?: string[]
+    propsToIgnore?: IgnorePropsLevel
+    propsToRemove?: IgnorePropsLevel
     key?: string,
     hasInstances?: boolean
     validateOnChange?: Function,
@@ -37,11 +45,28 @@ export function createGlobalFormModal(this: Page, {
 
     const schemaCopy = structuredClone(schema) // Ensure no mutation
 
-    function removeProperties(obj: any, props: string[]) {
-        props.forEach(prop =>  delete obj[prop])
+    
+    function removeProperties(obj: any, props: IgnorePropsLevel = {}, extraGlobalProps?: SingleIgnorePropsLevel) {
+
+        if (extraGlobalProps && Object.keys(extraGlobalProps).length > 0) {
+            if (props["*"]) props["*"] = { ...props["*"], ...extraGlobalProps }
+            else props["*"] = extraGlobalProps
+        }
+
+        const globals = props["*"] ?? {}
+
+        // First remove all global properties
+        Object.entries(globals).forEach(([key, value]) => (value === true) ? delete obj[key] : '')
+
+        // Full pass for explicit removal
+        Object.entries(props).forEach(([key, value]) => {
+            if (key === '*') return
+            if (value === true) delete obj[key]
+            else removeProperties(obj[key], value, globals)
+        })
     }
 
-    if (hasInstances) Object.keys(schemaCopy.properties).forEach(i => removeProperties(schemaCopy.properties[i].properties, propsToRemove))
+    if (hasInstances) Object.keys(schemaCopy.properties).forEach(key => removeProperties(schemaCopy.properties[key].properties, propsToRemove[key], propsToRemove["*"]))
     else removeProperties(schemaCopy.properties, propsToRemove)
 
     const globalForm = new JSONSchemaForm({
diff --git a/src/renderer/src/stories/pages/FormPage.js b/src/renderer/src/stories/pages/FormPage.js
index 650a5f2e2..76b9068e0 100644
--- a/src/renderer/src/stories/pages/FormPage.js
+++ b/src/renderer/src/stories/pages/FormPage.js
@@ -33,7 +33,7 @@ export function schemaToPages(schema, globalStatePath, options, transformationCa
                 })
             );
 
-            if (optionsCopy.ignore && optionsCopy.ignore.includes(key)) return null;
+            if (optionsCopy.ignore && optionsCopy.ignore[key]) return null;
             return page;
         })
         .filter((page) => page);
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 c805d1daf..f1c4456e2 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -19,15 +19,28 @@ import { globalSchema } from "../../../../../../../schemas/base-metadata.schema"
 
 import globalIcon from "../../../assets/global.svg?raw";
 
-const propsToIgnore = [
-    // "Ophys", // Always ignore ophys metadata (for now)
-    "Icephys", // Always ignore icephys metadata (for now)
-    "Behavior", // Always ignore behavior metadata (for now)
-    // new RegExp("ndx-.+"), // Ignore all ndx extensions
-    "ndx-dandi-icephys",
-    "subject_id",
-    "session_id",
-];
+const propsToIgnore = {
+    "Ophys": true, // Always ignore ophys metadata (for now)
+    "Icephys": true, // Always ignore icephys metadata (for now)
+    "Behavior": true, // Always ignore behavior metadata (for now)
+    "ndx-dandi-icephys": true,
+    "Subject": {
+        "subject_id": true,
+    },
+    "NWBFile": {
+        "session_id": true,
+    }
+}
+
+// const propsToIgnore = [
+//     // "Ophys", // Always ignore ophys metadata (for now)
+//     "Icephys", // Always ignore icephys metadata (for now)
+//     "Behavior", // Always ignore behavior metadata (for now)
+//     // new RegExp("ndx-.+"), // Ignore all ndx extensions
+//     "ndx-dandi-icephys",
+//     "subject_id",
+//     "session_id",
+// ];
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
 
@@ -97,7 +110,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const modal = (this.#globalModal = createGlobalFormModal.call(this, {
             header: "Global Metadata",
-            propsToRemove: [...propsToIgnore],
+            propsToRemove: propsToIgnore,
             schema: globalSchema, // Provide HARDCODED global schema for metadata properties (not automatically abstracting across sessions)...
             hasInstances: true,
             mergeFunction: function (globalResolved, globals) {
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 b725f134d..189aaf014 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -15,14 +15,25 @@ import { Button } from "../../../Button.js";
 import globalIcon from "../../../assets/global.svg?raw";
 import { run } from "../options/utils.js";
 
-const propsToIgnore = [
-    "verbose",
-    "es_key",
-    "exclude_shanks",
-    "load_sync_channel",
-    "stream_id", // NOTE: May be desired for other interfaces
-    "nsx_override",
-];
+// const propsToIgnore = [
+//     "verbose",
+//     "es_key",
+//     "exclude_shanks",
+//     "load_sync_channel",
+//     "stream_id", // NOTE: May be desired for other interfaces
+//     "nsx_override",
+// ];
+
+const propsToIgnore = {
+    "*": {
+        "verbose": true,
+        "es_key": true,
+        "exclude_shanks": true,
+        "load_sync_channel": true,
+        "stream_id": true, // NOTE: May be desired for other interfaces
+        "nsx_override": true,
+    }
+}
 
 export class GuidedSourceDataPage extends ManagedPage {
     constructor(...args) {
@@ -185,12 +196,14 @@ export class GuidedSourceDataPage extends ManagedPage {
         super.connectedCallback();
         const modal = (this.#globalModal = createGlobalFormModal.call(this, {
             header: "Global Source Data",
-            propsToRemove: [
-                ...propsToIgnore,
-                "folder_path",
-                "file_path",
-                // NOTE: Still keeping plural path specifications for now
-            ],
+            propsToRemove: {
+                "*": {
+                    ...propsToIgnore["*"],
+                    "folder_path": true,
+                    "file_path": true,
+                    // NOTE: Still keeping plural path specifications for now
+                }
+            },
             key: "SourceData",
             schema: this.info.globalState.schema.source_data,
             hasInstances: true,

From 91134a61f74e029036f7d11a04fa57c35b97344b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 11 Nov 2023 15:13:35 +0000
Subject: [PATCH 007/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 17 +++++++++-----
 .../src/stories/forms/GlobalFormModal.ts      |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  | 18 +++++++--------
 .../guided-mode/data/GuidedSourceData.js      | 22 +++++++++----------
 4 files changed, 32 insertions(+), 27 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index e6cf5d382..4ae234828 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -601,12 +601,17 @@ export class JSONSchemaForm extends LitElement {
         };
 
         const isRenderable = (key, value) => {
-
-            if (recursive && value.properties) return this.#getRenderable(value, required[key], {
-                ...ignore[key],
-                "*": {...ignore["*"] ?? {}, ...ignore[key]["*"] ?? {}}, // Accumulate ignore values
-            }, [...path, key], true);
-
+            if (recursive && value.properties)
+                return this.#getRenderable(
+                    value,
+                    required[key],
+                    {
+                        ...ignore[key],
+                        "*": { ...(ignore["*"] ?? {}), ...(ignore[key]["*"] ?? {}) }, // Accumulate ignore values
+                    },
+                    [...path, key],
+                    true
+                );
             else return [key, value];
         };
 
diff --git a/src/renderer/src/stories/forms/GlobalFormModal.ts b/src/renderer/src/stories/forms/GlobalFormModal.ts
index 0e3ea2f3c..38ab3ac80 100644
--- a/src/renderer/src/stories/forms/GlobalFormModal.ts
+++ b/src/renderer/src/stories/forms/GlobalFormModal.ts
@@ -45,7 +45,7 @@ export function createGlobalFormModal(this: Page, {
 
     const schemaCopy = structuredClone(schema) // Ensure no mutation
 
-    
+
     function removeProperties(obj: any, props: IgnorePropsLevel = {}, extraGlobalProps?: SingleIgnorePropsLevel) {
 
         if (extraGlobalProps && Object.keys(extraGlobalProps).length > 0) {
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 f1c4456e2..30f4eedf8 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -20,17 +20,17 @@ import { globalSchema } from "../../../../../../../schemas/base-metadata.schema"
 import globalIcon from "../../../assets/global.svg?raw";
 
 const propsToIgnore = {
-    "Ophys": true, // Always ignore ophys metadata (for now)
-    "Icephys": true, // Always ignore icephys metadata (for now)
-    "Behavior": true, // Always ignore behavior metadata (for now)
+    Ophys: true, // Always ignore ophys metadata (for now)
+    Icephys: true, // Always ignore icephys metadata (for now)
+    Behavior: true, // Always ignore behavior metadata (for now)
     "ndx-dandi-icephys": true,
-    "Subject": {
-        "subject_id": true,
+    Subject: {
+        subject_id: true,
     },
-    "NWBFile": {
-        "session_id": true,
-    }
-}
+    NWBFile: {
+        session_id: true,
+    },
+};
 
 // const propsToIgnore = [
 //     // "Ophys", // Always ignore ophys metadata (for now)
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 189aaf014..14144e2bb 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -26,14 +26,14 @@ import { run } from "../options/utils.js";
 
 const propsToIgnore = {
     "*": {
-        "verbose": true,
-        "es_key": true,
-        "exclude_shanks": true,
-        "load_sync_channel": true,
-        "stream_id": true, // NOTE: May be desired for other interfaces
-        "nsx_override": true,
-    }
-}
+        verbose: true,
+        es_key: true,
+        exclude_shanks: true,
+        load_sync_channel: true,
+        stream_id: true, // NOTE: May be desired for other interfaces
+        nsx_override: true,
+    },
+};
 
 export class GuidedSourceDataPage extends ManagedPage {
     constructor(...args) {
@@ -199,10 +199,10 @@ export class GuidedSourceDataPage extends ManagedPage {
             propsToRemove: {
                 "*": {
                     ...propsToIgnore["*"],
-                    "folder_path": true,
-                    "file_path": true,
+                    folder_path: true,
+                    file_path: true,
                     // NOTE: Still keeping plural path specifications for now
-                }
+                },
             },
             key: "SourceData",
             schema: this.info.globalState.schema.source_data,

From ffcc1f161319cc9202385ac0e0c04065d4244bd8 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 11:00:19 -0500
Subject: [PATCH 008/133] Properly ignore properties in tables

---
 schemas/base-metadata.schema.ts               | 45 +++++++++++++++++++
 src/renderer/src/stories/BasicTable.js        |  6 +++
 src/renderer/src/stories/JSONSchemaForm.js    | 20 +++++++--
 src/renderer/src/stories/JSONSchemaInput.js   |  9 +++-
 src/renderer/src/stories/SimpleTable.js       |  6 +++
 src/renderer/src/stories/Table.js             |  5 +++
 .../pages/guided-mode/data/GuidedMetadata.js  | 19 ++++++--
 7 files changed, 102 insertions(+), 8 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 372979e22..6e3887926 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -1,5 +1,6 @@
 import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }
 
+
 export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     // Add unit to weight
@@ -17,6 +18,50 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     // Override description of keywords
     schema.properties.NWBFile.properties.keywords.description = 'Terms to describe your dataset (e.g. Neural circuits, V1, etc.)' // Add description to keywords
+    
+
+    const ophys = schema.properties.Ophys
+
+    if (ophys) {
+        
+        ophys.properties.TwoPhotonSeries.order = [
+            "name",
+            "description",
+            "scan_line_rate",
+            "field_of_view",
+            "unit",
+            "conversion",
+            "offset"
+        ]
+
+        ophys.properties.ImagingPlane.order = [
+            "name",
+            "description",
+            "device",
+            "optic_channel"
+        ]
+    }    
+
+
+    Object.entries(schema.properties).forEach(([key, value]) => {
+
+        const defs = value.properties.definitions ?? {}
+        
+        Object.entries(value.properties).forEach(([k, v]) => {
+
+            if (k ==='definitions') return
+
+            //  Uniformly grab definitions
+           const ref = defs[k] ?? v.items ?? v
+           if (!ref.properties) return 
+           Object.keys(ref.properties).forEach(k => {
+                const info = ref.properties[k]
+                if (info.description && info.description.includes('DEPRECATED')) delete ref.properties[k] // Remove deprecated properties
+            })
+        })
+    })
+    
+    
     return schema
 
 }
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 5d3396c32..351bb2045 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -105,6 +105,7 @@ export class BasicTable extends LitElement {
     constructor({
         name,
         schema,
+        ignore,
         data,
         keyColumn,
         maxHeight,
@@ -121,6 +122,8 @@ export class BasicTable extends LitElement {
         this.maxHeight = maxHeight ?? "";
         this.validateEmptyCells = validateEmptyCells ?? true;
 
+        this.ignore = ignore ?? {};
+
         if (validateOnChange) this.validateOnChange = validateOnChange;
         if (onStatusChange) this.onStatusChange = onStatusChange;
         if (onLoaded) this.onLoaded = onLoaded;
@@ -340,6 +343,9 @@ export class BasicTable extends LitElement {
 
         const entries = { ...this.schema.properties };
 
+        for (let key in this.ignore) delete entries[key]
+        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
             Object.values(this.data).reduce((acc, v) => {
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index e6cf5d382..f36119aec 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -16,6 +16,21 @@ const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
 };
 
+
+export const getIgnore = (o, path) => {
+    if (typeof path === "string") path = path.split(".");
+    return path.reduce((acc, key) => {
+
+        const info = acc[key] ?? {};
+
+        return {
+            ...info,
+            "*": {...(acc["*"] ?? {}), ...(info["*"] ?? {})}, // Accumulate ignore values
+        }
+
+    }, o)
+}
+
 const selfRequiredSymbol = Symbol();
 
 const componentCSS = `
@@ -602,10 +617,7 @@ export class JSONSchemaForm extends LitElement {
 
         const isRenderable = (key, value) => {
 
-            if (recursive && value.properties) return this.#getRenderable(value, required[key], {
-                ...ignore[key],
-                "*": {...ignore["*"] ?? {}, ...ignore[key]["*"] ?? {}}, // Accumulate ignore values
-            }, [...path, key], true);
+            if (recursive && value.properties) return this.#getRenderable(value, required[key], getIgnore(ignore, key), [...path, key], true);
 
             else return [key, value];
         };
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 4ad9a8742..48a7daf64 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -10,7 +10,7 @@ import { List } from "./List";
 import { Modal } from "./Modal";
 
 import { capitalize } from "./forms/utils";
-import { JSONSchemaForm } from "./JSONSchemaForm";
+import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 
 const isFilesystemSelector = (name, format) => {
     if (Array.isArray(format)) return format.map((f) => isFilesystemSelector(name, f)).every(Boolean) ? format : null;
@@ -223,10 +223,15 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema.type === "object" && this.form.createTable) {
+
+                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name]) : {}
+                
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
 
+                    ignore, 
+
                     onUpdate: () => this.#updateData(fullPath, tableMetadata.data, true), // Ensure change propagates to all forms
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
@@ -254,6 +259,8 @@ export class JSONSchemaInput extends LitElement {
                 };
 
                 const table = this.form.createTable(name, tableMetadata, fullPath); // Try creating table. Otherwise use nested form
+
+
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 16437262b..4af959ec4 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -171,6 +171,7 @@ export class SimpleTable extends LitElement {
         deferLoading,
         maxHeight,
         contextOptions = {},
+        ignore = {}
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -181,6 +182,8 @@ export class SimpleTable extends LitElement {
         this.deferLoading = deferLoading ?? false;
         this.maxHeight = maxHeight ?? "";
 
+        this.ignore = ignore
+
         this.contextOptions = contextOptions;
 
         if (validateOnChange) this.validateOnChange = validateOnChange;
@@ -736,6 +739,9 @@ export class SimpleTable extends LitElement {
 
         const entries = (this.#schema = { ...this.schema.properties });
 
+        for (let key in this.ignore) delete entries[key]
+        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
             Object.values(this.data).reduce((acc, v) => {
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index e88abb036..432943807 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -78,6 +78,7 @@ export class Table extends LitElement {
         onStatusChange,
         onThrow,
         contextMenu,
+        ignore
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -86,6 +87,7 @@ export class Table extends LitElement {
         this.globals = globals ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
         this.contextMenu = contextMenu ?? {};
+        this.ignore = ignore ?? {};
 
         if (onThrow) this.onThrow = onThrow;
         if (onUpdate) this.onUpdate = onUpdate;
@@ -172,6 +174,9 @@ export class Table extends LitElement {
 
         const entries = { ...this.schema.properties };
 
+        for (let key in this.ignore) delete entries[key]
+        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
             Object.values(this.data).reduce((acc, v) => {
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 f1c4456e2..3b00be4de 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -20,7 +20,22 @@ import { globalSchema } from "../../../../../../../schemas/base-metadata.schema"
 import globalIcon from "../../../assets/global.svg?raw";
 
 const propsToIgnore = {
-    "Ophys": true, // Always ignore ophys metadata (for now)
+    "Ophys": {
+        "ImagingPlane": {
+            "manifold": true, 
+            "unit": true, 
+            "conversion": true, 
+        },
+        "TwoPhotonSeries": {
+            "format": true,
+            "starting_frame": true,
+            "starting_time": true,
+            "rate": true,
+            "control": true,
+            "control_description": true,
+            "device": true
+        }
+    }, // Always ignore ophys metadata (for now)
     "Icephys": true, // Always ignore icephys metadata (for now)
     "Behavior": true, // Always ignore behavior metadata (for now)
     "ndx-dandi-icephys": true,
@@ -169,8 +184,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-        console.log(subject, session, results);
-
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,

From e84e8e9f33fdbb76aa74cbcab713affc1bdeaa53 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 11 Nov 2023 16:01:17 +0000
Subject: [PATCH 009/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 schemas/base-metadata.schema.ts               | 14 +++++-----
 src/renderer/src/stories/BasicTable.js        |  4 +--
 src/renderer/src/stories/JSONSchemaForm.js    | 16 +++++-------
 src/renderer/src/stories/JSONSchemaInput.js   |  8 +++---
 src/renderer/src/stories/SimpleTable.js       |  8 +++---
 src/renderer/src/stories/Table.js             |  6 ++---
 .../pages/guided-mode/data/GuidedMetadata.js  | 26 +++++++++----------
 7 files changed, 39 insertions(+), 43 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 6e3887926..3e7c03b27 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -18,12 +18,12 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     // Override description of keywords
     schema.properties.NWBFile.properties.keywords.description = 'Terms to describe your dataset (e.g. Neural circuits, V1, etc.)' // Add description to keywords
-    
+
 
     const ophys = schema.properties.Ophys
 
     if (ophys) {
-        
+
         ophys.properties.TwoPhotonSeries.order = [
             "name",
             "description",
@@ -40,28 +40,28 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
             "device",
             "optic_channel"
         ]
-    }    
+    }
 
 
     Object.entries(schema.properties).forEach(([key, value]) => {
 
         const defs = value.properties.definitions ?? {}
-        
+
         Object.entries(value.properties).forEach(([k, v]) => {
 
             if (k ==='definitions') return
 
             //  Uniformly grab definitions
            const ref = defs[k] ?? v.items ?? v
-           if (!ref.properties) return 
+           if (!ref.properties) return
            Object.keys(ref.properties).forEach(k => {
                 const info = ref.properties[k]
                 if (info.description && info.description.includes('DEPRECATED')) delete ref.properties[k] // Remove deprecated properties
             })
         })
     })
-    
-    
+
+
     return schema
 
 }
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 351bb2045..5563f3740 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -343,8 +343,8 @@ export class BasicTable extends LitElement {
 
         const entries = { ...this.schema.properties };
 
-        for (let key in this.ignore) delete entries[key]
-        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+        for (let key in this.ignore) delete entries[key];
+        for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f36119aec..51e6e5484 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -16,20 +16,17 @@ const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
 };
 
-
 export const getIgnore = (o, path) => {
     if (typeof path === "string") path = path.split(".");
     return path.reduce((acc, key) => {
-
         const info = acc[key] ?? {};
 
         return {
             ...info,
-            "*": {...(acc["*"] ?? {}), ...(info["*"] ?? {})}, // Accumulate ignore values
-        }
-
-    }, o)
-}
+            "*": { ...(acc["*"] ?? {}), ...(info["*"] ?? {}) }, // Accumulate ignore values
+        };
+    }, o);
+};
 
 const selfRequiredSymbol = Symbol();
 
@@ -616,9 +613,8 @@ export class JSONSchemaForm extends LitElement {
         };
 
         const isRenderable = (key, value) => {
-
-            if (recursive && value.properties) return this.#getRenderable(value, required[key], getIgnore(ignore, key), [...path, key], true);
-
+            if (recursive && value.properties)
+                return this.#getRenderable(value, required[key], getIgnore(ignore, key), [...path, key], true);
             else return [key, value];
         };
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 48a7daf64..4e67f36af 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -223,14 +223,15 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema.type === "object" && this.form.createTable) {
+                const ignore = this.form?.ignore
+                    ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
+                    : {};
 
-                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name]) : {}
-                
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
 
-                    ignore, 
+                    ignore,
 
                     onUpdate: () => this.#updateData(fullPath, tableMetadata.data, true), // Ensure change propagates to all forms
 
@@ -260,7 +261,6 @@ export class JSONSchemaInput extends LitElement {
 
                 const table = this.form.createTable(name, tableMetadata, fullPath); // Try creating table. Otherwise use nested form
 
-
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 4af959ec4..815993e89 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -171,7 +171,7 @@ export class SimpleTable extends LitElement {
         deferLoading,
         maxHeight,
         contextOptions = {},
-        ignore = {}
+        ignore = {},
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -182,7 +182,7 @@ export class SimpleTable extends LitElement {
         this.deferLoading = deferLoading ?? false;
         this.maxHeight = maxHeight ?? "";
 
-        this.ignore = ignore
+        this.ignore = ignore;
 
         this.contextOptions = contextOptions;
 
@@ -739,8 +739,8 @@ export class SimpleTable extends LitElement {
 
         const entries = (this.#schema = { ...this.schema.properties });
 
-        for (let key in this.ignore) delete entries[key]
-        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+        for (let key in this.ignore) delete entries[key];
+        for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 432943807..46c741f27 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -78,7 +78,7 @@ export class Table extends LitElement {
         onStatusChange,
         onThrow,
         contextMenu,
-        ignore
+        ignore,
     } = {}) {
         super();
         this.schema = schema ?? {};
@@ -174,8 +174,8 @@ export class Table extends LitElement {
 
         const entries = { ...this.schema.properties };
 
-        for (let key in this.ignore) delete entries[key]
-        for (let key in (this.ignore["*"] ?? {})) delete entries[key]
+        for (let key in this.ignore) delete entries[key];
+        for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional properties to the entries variable if necessary
         if (this.schema.additionalProperties) {
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 9727a05aa..c33fbda6d 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -21,20 +21,20 @@ import globalIcon from "../../../assets/global.svg?raw";
 
 const propsToIgnore = {
     Ophys: {
-        "ImagingPlane": {
-            "manifold": true, 
-            "unit": true, 
-            "conversion": true, 
+        ImagingPlane: {
+            manifold: true,
+            unit: true,
+            conversion: true,
+        },
+        TwoPhotonSeries: {
+            format: true,
+            starting_frame: true,
+            starting_time: true,
+            rate: true,
+            control: true,
+            control_description: true,
+            device: true,
         },
-        "TwoPhotonSeries": {
-            "format": true,
-            "starting_frame": true,
-            "starting_time": true,
-            "rate": true,
-            "control": true,
-            "control_description": true,
-            "device": true
-        }
     }, // Always ignore ophys metadata (for now)
     Icephys: true, // Always ignore icephys metadata (for now)
     Behavior: true, // Always ignore behavior metadata (for now)

From 31b01765f7dbc00853d130d0575baa531a780aea Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 16:40:35 -0500
Subject: [PATCH 010/133] Allow ordering the table columns

---
 schemas/base-metadata.schema.ts         |  6 +-
 src/renderer/src/stories/BasicTable.js  | 12 ++--
 src/renderer/src/stories/SimpleTable.js | 16 +++---
 src/renderer/src/stories/Table.js       | 74 +++++++++++++++----------
 4 files changed, 61 insertions(+), 47 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 3e7c03b27..3ba3a15b9 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -24,7 +24,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     if (ophys) {
 
-        ophys.properties.TwoPhotonSeries.order = [
+        ophys.properties.definitions.TwoPhotonSeries.order = [
             "name",
             "description",
             "scan_line_rate",
@@ -34,11 +34,11 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
             "offset"
         ]
 
-        ophys.properties.ImagingPlane.order = [
+        ophys.properties.definitions.ImagingPlane.order = [
             "name",
             "description",
             "device",
-            "optic_channel"
+            "optical_channel"
         ]
     }
 
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 5563f3740..7af4eb123 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -363,14 +363,10 @@ export class BasicTable extends LitElement {
         // Sort Columns by Key Column and Requirement
         const keys =
             (this.#keys =
-            this.colHeaders =
-                Object.keys(entries).sort((a, b) => {
-                    if (a === this.keyColumn) return -1;
-                    if (b === this.keyColumn) return 1;
-                    if (entries[a].required && !entries[b].required) return -1;
-                    if (!entries[a].required && entries[b].required) return 1;
-                    return 0;
-                }));
+            this.colHeaders = sortTable({
+                ...this.schema,
+                properties: entries
+            }, this.keyColumn, this.schema.order));
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 815993e89..3bdef91cc 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -11,6 +11,7 @@ import { styleMap } from "lit/directives/style-map.js";
 
 import "./Button";
 import tippy from "tippy.js";
+import { sortTable } from "./Table";
 
 var isMac = navigator.platform.toUpperCase().indexOf("MAC") >= 0;
 
@@ -757,13 +758,12 @@ export class SimpleTable extends LitElement {
         }
 
         // Sort Columns by Key Column and Requirement
-        const keys = (this.colHeaders = Object.keys(entries).sort((a, b) => {
-            if (a === this.keyColumn) return -1;
-            if (b === this.keyColumn) return 1;
-            if (entries[a].required && !entries[b].required) return -1;
-            if (!entries[a].required && entries[b].required) return 1;
-            return 0;
-        }));
+        this.colHeaders = sortTable({
+            ...this.schema,
+            properties: entries
+        }, this.keyColumn, this.schema.order)
+
+
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {
@@ -778,7 +778,7 @@ export class SimpleTable extends LitElement {
                 <table cellspacing="0" style=${styleMap({ maxHeight: this.maxHeight })}>
                     <thead>
                         <tr>
-                            ${[...keys].map(header).map((str, i) => this.#renderHeader(str, entries[keys[i]]))}
+                            ${[...this.colHeaders].map(header).map((str, i) => this.#renderHeader(str, entries[this.colHeaders[i]]))}
                         </tr>
                     </thead>
                     <tbody></tbody>
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 46c741f27..f40da4863 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -10,6 +10,43 @@ import "tippy.js/dist/tippy.css";
 
 const maxRows = 20;
 
+const isRequired = (col, schema) => {
+    return schema.required?.includes(col);
+};
+
+export function sortTable(schema, keyColumn, order) {
+
+    const cols = Object.keys(schema.properties)
+
+    //Sort alphabetically
+    .sort((a, b) => {
+        if (a < b) return -1;
+        if (a > b) return 1;
+        return 0;
+    })
+    .sort((a, b) => {
+        const aRequired = isRequired(a, schema);
+        const bRequired = isRequired(b, schema);
+        if (aRequired && bRequired) return 0;
+        if (aRequired) return -1;
+        if (bRequired) return 1;
+        return 0;
+    })
+    .sort((a, b) => {
+        if (a === keyColumn) return -1;
+        if (b === keyColumn) return 1;
+        return 0;
+    });
+
+    return order ? cols.sort((a,b) => {
+        const idxA = order.indexOf(a);
+        const idxB = order.indexOf(b);
+        if (idxA === -1) return 1;
+        if (idxB === -1) return -1;
+        return idxA - idxB;
+    }) : cols;
+}
+
 // Inject scoped stylesheet
 const styles = `
 
@@ -163,10 +200,6 @@ export class Table extends LitElement {
     onOverride = () => {};
     onThrow = () => {};
 
-    isRequired = (col) => {
-        return this.schema?.required?.includes(col);
-    };
-
     updated() {
         const div = (this.shadowRoot ?? this).querySelector("div");
 
@@ -192,26 +225,11 @@ export class Table extends LitElement {
         }
 
         // Sort Columns by Key Column and Requirement
-        const colHeaders = (this.colHeaders = Object.keys(entries)
-            .sort((a, b) => {
-                //Sort alphabetically
-                if (a < b) return -1;
-                if (a > b) return 1;
-                return 0;
-            })
-            .sort((a, b) => {
-                const aRequired = this.isRequired(a);
-                const bRequired = this.isRequired(b);
-                if (aRequired && bRequired) return 0;
-                if (aRequired) return -1;
-                if (bRequired) return 1;
-                return 0;
-            })
-            .sort((a, b) => {
-                if (a === this.keyColumn) return -1;
-                if (b === this.keyColumn) return 1;
-                return 0;
-            }));
+
+        const colHeaders = this.colHeaders = sortTable({
+            ...this.schema,
+            properties: entries,
+        }, this.keyColumn, this.schema.order);
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {
@@ -272,7 +290,7 @@ export class Table extends LitElement {
             };
 
             let ogThis = this;
-            const isRequired = this.isRequired(k);
+            const required = isRequired(k, this.schema);
 
             const validator = async function (value, callback) {
                 const validateEmptyCells = ogThis.validateEmptyCells;
@@ -310,7 +328,7 @@ export class Table extends LitElement {
                     return;
                 }
 
-                if (!value && isRequired) {
+                if (!value && required) {
                     ogThis.#handleValidationResult(
                         [{ message: `${header(k)} is a required property.`, type: "error" }],
                         this.row,
@@ -356,8 +374,8 @@ export class Table extends LitElement {
 
             const rel = TH.querySelector(".relative");
 
-            const isRequired = this.isRequired(col);
-            if (isRequired)
+            const required = isRequired(col, this.schema);
+            if (required)
                 rel.setAttribute(
                     "data-required",
                     this.validateEmptyCells

From 0a3809ebf6182dad3f9476bc2ba7bee85444e7f4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 11 Nov 2023 21:40:52 +0000
Subject: [PATCH 011/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/BasicTable.js  | 13 +++--
 src/renderer/src/stories/SimpleTable.js | 18 ++++---
 src/renderer/src/stories/Table.js       | 69 +++++++++++++------------
 3 files changed, 57 insertions(+), 43 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 7af4eb123..9b08973fa 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -363,10 +363,15 @@ export class BasicTable extends LitElement {
         // Sort Columns by Key Column and Requirement
         const keys =
             (this.#keys =
-            this.colHeaders = sortTable({
-                ...this.schema,
-                properties: entries
-            }, this.keyColumn, this.schema.order));
+            this.colHeaders =
+                sortTable(
+                    {
+                        ...this.schema,
+                        properties: entries,
+                    },
+                    this.keyColumn,
+                    this.schema.order
+                ));
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 3bdef91cc..953a95871 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -758,12 +758,14 @@ export class SimpleTable extends LitElement {
         }
 
         // Sort Columns by Key Column and Requirement
-        this.colHeaders = sortTable({
-            ...this.schema,
-            properties: entries
-        }, this.keyColumn, this.schema.order)
-
-
+        this.colHeaders = sortTable(
+            {
+                ...this.schema,
+                properties: entries,
+            },
+            this.keyColumn,
+            this.schema.order
+        );
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {
@@ -778,7 +780,9 @@ export class SimpleTable extends LitElement {
                 <table cellspacing="0" style=${styleMap({ maxHeight: this.maxHeight })}>
                     <thead>
                         <tr>
-                            ${[...this.colHeaders].map(header).map((str, i) => this.#renderHeader(str, entries[this.colHeaders[i]]))}
+                            ${[...this.colHeaders]
+                                .map(header)
+                                .map((str, i) => this.#renderHeader(str, entries[this.colHeaders[i]]))}
                         </tr>
                     </thead>
                     <tbody></tbody>
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index f40da4863..1ecbd9dc0 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -15,36 +15,37 @@ const isRequired = (col, schema) => {
 };
 
 export function sortTable(schema, keyColumn, order) {
-
     const cols = Object.keys(schema.properties)
 
-    //Sort alphabetically
-    .sort((a, b) => {
-        if (a < b) return -1;
-        if (a > b) return 1;
-        return 0;
-    })
-    .sort((a, b) => {
-        const aRequired = isRequired(a, schema);
-        const bRequired = isRequired(b, schema);
-        if (aRequired && bRequired) return 0;
-        if (aRequired) return -1;
-        if (bRequired) return 1;
-        return 0;
-    })
-    .sort((a, b) => {
-        if (a === keyColumn) return -1;
-        if (b === keyColumn) return 1;
-        return 0;
-    });
-
-    return order ? cols.sort((a,b) => {
-        const idxA = order.indexOf(a);
-        const idxB = order.indexOf(b);
-        if (idxA === -1) return 1;
-        if (idxB === -1) return -1;
-        return idxA - idxB;
-    }) : cols;
+        //Sort alphabetically
+        .sort((a, b) => {
+            if (a < b) return -1;
+            if (a > b) return 1;
+            return 0;
+        })
+        .sort((a, b) => {
+            const aRequired = isRequired(a, schema);
+            const bRequired = isRequired(b, schema);
+            if (aRequired && bRequired) return 0;
+            if (aRequired) return -1;
+            if (bRequired) return 1;
+            return 0;
+        })
+        .sort((a, b) => {
+            if (a === keyColumn) return -1;
+            if (b === keyColumn) return 1;
+            return 0;
+        });
+
+    return order
+        ? cols.sort((a, b) => {
+              const idxA = order.indexOf(a);
+              const idxB = order.indexOf(b);
+              if (idxA === -1) return 1;
+              if (idxB === -1) return -1;
+              return idxA - idxB;
+          })
+        : cols;
 }
 
 // Inject scoped stylesheet
@@ -226,10 +227,14 @@ export class Table extends LitElement {
 
         // Sort Columns by Key Column and Requirement
 
-        const colHeaders = this.colHeaders = sortTable({
-            ...this.schema,
-            properties: entries,
-        }, this.keyColumn, this.schema.order);
+        const colHeaders = (this.colHeaders = sortTable(
+            {
+                ...this.schema,
+                properties: entries,
+            },
+            this.keyColumn,
+            this.schema.order
+        ));
 
         // Try to guess the key column if unspecified
         if (!Array.isArray(this.data) && !this.keyColumn) {

From 9d5babf08c16977c384acbaf203b878fff17a4c5 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 17:06:59 -0500
Subject: [PATCH 012/133] Max height of table cell and other updates

---
 schemas/base-metadata.schema.ts                              | 5 +----
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js     | 3 +++
 src/renderer/src/stories/table/Cell.ts                       | 3 ++-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 3ba3a15b9..cf767717d 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -28,10 +28,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
             "name",
             "description",
             "scan_line_rate",
-            "field_of_view",
-            "unit",
-            "conversion",
-            "offset"
+            "field_of_view"
         ]
 
         ophys.properties.definitions.ImagingPlane.order = [
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 c168bbe12..aed8d3f66 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -34,6 +34,9 @@ const propsToIgnore = {
             control: true,
             control_description: true,
             device: true,
+            unit: true,
+            conversion: true,
+            offset: true
         },
     }, // Always ignore ophys metadata (for now)
     Icephys: true, // Always ignore icephys metadata (for now)
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 92ae57d9c..856c698df 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -35,10 +35,11 @@ export class TableCell extends LitElement {
 
             :host {
                 display: flex;
-                white-space: nowrap;
                 color: black;
                 font-size: 13px;
                 height: 100%;
+                max-height:  100px;
+                overflow-y: scroll;
             }
 
             :host > * {

From 1fe98367d6762aab9ebe93d54769a6ac23f6eb71 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 11 Nov 2023 22:08:59 +0000
Subject: [PATCH 013/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 aed8d3f66..d39787601 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -36,7 +36,7 @@ const propsToIgnore = {
             device: true,
             unit: true,
             conversion: true,
-            offset: true
+            offset: true,
         },
     }, // Always ignore ophys metadata (for now)
     Icephys: true, // Always ignore icephys metadata (for now)

From 9f7891ca046d05700eeeb3fa177a14abf4cfebe4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 11 Nov 2023 22:23:53 +0000
Subject: [PATCH 014/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js               | 1 -
 src/renderer/src/stories/pages/guided-mode/data/utils.js | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 74249b98e..5ea687737 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -294,7 +294,6 @@ export class JSONSchemaForm extends LitElement {
 
     // Track resolved values for the form (data only)
     updateData(localPath, value, forceUpdate = false) {
-       
         const path = [...localPath];
         const name = path.pop();
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index 60b38f93e..4618e17ba 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -40,7 +40,6 @@ export function resolveProperties(properties = {}, target, globals = {}) {
         const props = info.properties;
 
         if (!(name in target)) {
-
             if (target.__disabled?.[name]) continue; // Skip disabled properties
 
             if (props) target[name] = {}; // Regisiter new interfaces in results

From 3d454e957ed8643df3cfb255bad12ccba58192ba Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 17:28:36 -0500
Subject: [PATCH 015/133] Allow segmentation

---
 schemas/base-metadata.schema.ts | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index cf767717d..083728880 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -24,14 +24,16 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     if (ophys) {
 
-        ophys.properties.definitions.TwoPhotonSeries.order = [
+        const defs = ophys.properties.definitions
+
+        if (defs.TwoPhotonSeries) defs.TwoPhotonSeries.order = [
             "name",
             "description",
             "scan_line_rate",
             "field_of_view"
         ]
 
-        ophys.properties.definitions.ImagingPlane.order = [
+        if (defs.ImagingPlane) defs.ImagingPlane.order = [
             "name",
             "description",
             "device",

From d49756545ea70e90c7dda381d02aa9f7404401e0 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 17:29:25 -0500
Subject: [PATCH 016/133] Update GuidedMetadata.js

---
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js       | 3 +++
 1 file changed, 3 insertions(+)

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 d39787601..ab961064c 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -33,6 +33,9 @@ const propsToIgnore = {
             rate: true,
             control: true,
             control_description: true,
+            comments: true,
+            resolution: true,
+            dimension: true,
             device: true,
             unit: true,
             conversion: true,

From ce8d56d4bcd74e138f93107ccd43edb1ec1c00e3 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 17:35:54 -0500
Subject: [PATCH 017/133] Update base-metadata.schema.ts

---
 schemas/base-metadata.schema.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 083728880..986727b72 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -24,16 +24,16 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     if (ophys) {
 
-        const defs = ophys.properties.definitions
+        const getProp = (name: string) => ophys.properties.definitions[name] ?? ophys.properties[name]
 
-        if (defs.TwoPhotonSeries) defs.TwoPhotonSeries.order = [
+        if (getProp("TwoPhotonSeries")) getProp("TwoPhotonSeries").order = [
             "name",
             "description",
             "scan_line_rate",
             "field_of_view"
         ]
 
-        if (defs.ImagingPlane) defs.ImagingPlane.order = [
+        if (getProp("ImagingPlane")) getProp("ImagingPlane").order = [
             "name",
             "description",
             "device",

From 296a17939eda680c1e93c0a005f1c6c88303017c Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sat, 11 Nov 2023 17:37:29 -0500
Subject: [PATCH 018/133] Update base-metadata.schema.ts

---
 schemas/base-metadata.schema.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 986727b72..21511673b 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -24,7 +24,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema) => {
 
     if (ophys) {
 
-        const getProp = (name: string) => ophys.properties.definitions[name] ?? ophys.properties[name]
+        const getProp = (name: string) => ophys.properties.definitions?.[name] ?? ophys.properties[name]
 
         if (getProp("TwoPhotonSeries")) getProp("TwoPhotonSeries").order = [
             "name",

From 66916bb33bc30dcce4b24b4f32228f52145a44e5 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sun, 12 Nov 2023 08:06:24 -0500
Subject: [PATCH 019/133] Update BasicTable.js

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

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 9b08973fa..003b415de 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -7,6 +7,7 @@ import { errorHue, warningHue } from "./globals";
 import * as promises from "../promises";
 
 import "./Button";
+import { sortTable } from "./Table";
 
 export class BasicTable extends LitElement {
     static get styles() {

From b6cefb27bb3ea50d8bfe14c3d703172d90434151 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 21 Nov 2023 20:52:46 +0000
Subject: [PATCH 020/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/pages/Page.js               |  2 +-
 .../src/stories/pages/guided-mode/options/utils.js   | 12 +++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index a0aee18bc..8207918c2 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -170,7 +170,7 @@ export class Page extends LitElement {
         Object.assign(element.style, {
             textAlign: "left",
             display: "block",
-        })
+        });
 
         const progressBar = new ProgressBar();
         elements.progress = progressBar;
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 238681e36..83bef4acc 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/utils.js
@@ -23,12 +23,10 @@ export const openProgressSwal = (options, callback) => {
 };
 
 export const run = async (url, payload, options = {}) => {
+    let internalSwal;
 
-    let internalSwal
-
-    if (options.swal === false) {}
-    else if (!options.swal || options.swal === true) {
-
+    if (options.swal === false) {
+    } else if (!options.swal || options.swal === true) {
         if (!("showCancelButton" in options)) {
             options.showCancelButton = true;
             options.customClass = { actions: "swal-conversion-actions" };
@@ -40,12 +38,12 @@ export const run = async (url, payload, options = {}) => {
             signal: cancelController.signal,
         };
 
-        const popup = internalSwal = await openProgressSwal(options, (result) => {
+        const popup = (internalSwal = await openProgressSwal(options, (result) => {
             if (!result.isConfirmed) cancelController.abort();
         }).then(async (swal) => {
             if (options.onOpen) await options.onOpen(swal);
             return swal;
-        });
+        }));
 
         const element = popup.getHtmlContainer();
         const actions = popup.getActions();

From 5450bf93f0b13ba9cf0fe885426886cbb812b951 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 29 Nov 2023 10:31:30 -0800
Subject: [PATCH 021/133] Update sorting

---
 schemas/base-metadata.schema.ts                            | 7 ++++---
 src/renderer/src/stories/SimpleTable.js                    | 4 ++--
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js   | 3 +++
 .../src/stories/pages/guided-mode/results/GuidedResults.js | 2 --
 src/renderer/src/stories/pages/settings/SettingsPage.js    | 2 --
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 283c665bb..2e7f9863c 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -80,16 +80,17 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     if (ophys) {
 
-        const getProp = (name: string) => ophys.properties.definitions?.[name] ?? ophys.properties[name]
+        const getProp = (name: string, base = true) => base ? ophys.properties[name] : ophys.properties.definitions?.[name]
 
-        if (getProp("TwoPhotonSeries")) getProp("TwoPhotonSeries").order = [
+        if (getProp("TwoPhotonSeries")) getProp("TwoPhotonSeries").items.order = [
             "name",
             "description",
             "scan_line_rate",
             "field_of_view"
         ]
 
-        if (getProp("ImagingPlane")) getProp("ImagingPlane").order = [
+
+        if (getProp("ImagingPlane")) getProp("ImagingPlane").items.order = [
             "name",
             "description",
             "device",
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 953a95871..582fb91b5 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -743,8 +743,8 @@ export class SimpleTable extends LitElement {
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
-        // Add existing additional properties to the entries variable if necessary
-        if (this.schema.additionalProperties) {
+        // Add existing additional / pattern properties to the entries variable if necessary
+        if (this.schema.additionalProperties !== false || this.schema.patternProperties) {
             Object.values(this.data).reduce((acc, v) => {
                 Object.keys(v).forEach((k) =>
                     !(k in entries)
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 1873fd331..13e876b5f 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -18,14 +18,17 @@ import { Button } from "../../../Button.js";
 
 import globalIcon from "../../../assets/global.svg?raw";
 
+const imagingPlaneKey = 'imaging_plane';
 const propsToIgnore = {
     Ophys: {
         ImagingPlane: {
+            [imagingPlaneKey]: true,
             manifold: true,
             unit: true,
             conversion: true,
         },
         TwoPhotonSeries: {
+            [imagingPlaneKey]: true,
             format: true,
             starting_frame: true,
             starting_time: true,
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 34f95a16f..06665b3b3 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -11,8 +11,6 @@ export class GuidedResultsPage extends Page {
     render() {
         const { conversion } = this.info.globalState;
 
-        console.log(this.info.globalState);
-
         if (!conversion)
             return html`<div style="text-align: center;"><p>Your conversion failed. Please try again.</p></div>`;
 
diff --git a/src/renderer/src/stories/pages/settings/SettingsPage.js b/src/renderer/src/stories/pages/settings/SettingsPage.js
index 3266bc508..a4c7c4b25 100644
--- a/src/renderer/src/stories/pages/settings/SettingsPage.js
+++ b/src/renderer/src/stories/pages/settings/SettingsPage.js
@@ -20,8 +20,6 @@ const schema = merge(
     }
 );
 
-console.log(schema);
-
 import { Button } from "../../Button.js";
 import { global } from "../../../progress/index.js";
 import { merge, setUndefinedIfNotDeclared } from "../utils.js";

From cefafc37d811120eb22588e84f9a2c6e1719a1ee Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 29 Nov 2023 18:31:48 +0000
Subject: [PATCH 022/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 13e876b5f..45c366beb 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -18,7 +18,7 @@ import { Button } from "../../../Button.js";
 
 import globalIcon from "../../../assets/global.svg?raw";
 
-const imagingPlaneKey = 'imaging_plane';
+const imagingPlaneKey = "imaging_plane";
 const propsToIgnore = {
     Ophys: {
         ImagingPlane: {

From 95e3b5fc374adb6355491dab68f0afc0964c7e2b Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 29 Nov 2023 16:34:48 -0800
Subject: [PATCH 023/133] Basic patternProperties rendering

---
 src/renderer/src/stories/JSONSchemaForm.js    |  47 ++-
 src/renderer/src/stories/JSONSchemaInput.js   | 357 +++++++++++-------
 src/renderer/src/stories/List.ts              |  33 +-
 src/renderer/src/stories/SimpleTable.js       |   3 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |   6 +-
 .../guided-mode/data/GuidedPathExpansion.js   |   1 -
 .../src/stories/pages/inspect/InspectPage.js  |   2 +-
 .../src/stories/pages/preview/PreviewPage.js  |   2 +-
 .../src/stories/pages/uploads/UploadsPage.js  |   2 +-
 9 files changed, 285 insertions(+), 168 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index aa6bef129..13c827803 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -451,7 +451,7 @@ export class JSONSchemaForm extends LitElement {
         // path = path.slice(this.base.length); // Correct for base path
         if (!path) throw new Error("Path not specified");
         return path.reduce(
-            (acc, curr) => (acc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str])]?.[curr]),
+            (acc, curr) => (acc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str]?.[curr])]?.[curr]),
             object
         );
     };
@@ -473,20 +473,20 @@ export class JSONSchemaForm extends LitElement {
             if (indexOf !== -1) path = path.slice(indexOf + 1);
         }
 
-        const resolved = this.#get(path, schema, ["properties"]);
+        const resolved = this.#get(path, schema, ["properties", "patternProperties"]);
         if (resolved["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
 
         return resolved;
     }
 
-    #renderInteractiveElement = (name, info, required, path = []) => {
+    #renderInteractiveElement = (name, info, required, path = [], value) => {
         let isRequired = required[name];
 
         const localPath = [...path, name];
         const externalPath = [...this.base, ...localPath];
 
         const resolved = this.#get(path, this.resolved);
-        const value = resolved[name];
+        if (value === undefined) value = resolved[name];
 
         const isConditional = this.#getLink(externalPath) || typeof isRequired === "function"; // Check the two possible ways of determining if a field is conditional
 
@@ -504,12 +504,12 @@ export class JSONSchemaForm extends LitElement {
             };
 
         const interactiveInput = new JSONSchemaInput({
-            info,
+            schema: info,
             path: localPath,
             value,
             form: this,
             required: isRequired,
-            validateEmptyValue: this.validateEmptyValues,
+            validateEmptyValue: this.validateEmptyValues
         });
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
@@ -530,7 +530,7 @@ export class JSONSchemaForm extends LitElement {
                     ? "conditional"
                     : ""}"
             >
-                <label class="guided--form-label">${info.title ?? header(name)}</label>
+                <label class="guided--form-label">${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}</label>
                 ${interactiveInput}
                 <div class="errors"></div>
                 <div class="warnings"></div>
@@ -832,13 +832,15 @@ export class JSONSchemaForm extends LitElement {
 
     #render = (schema, results, required = {}, ignore = {}, path = []) => {
         let isLink = Symbol("isLink");
+
+        const hasPatternProperties = !!schema.patternProperties;
+
         // Filter non-required properties (if specified) and render the sub-schema
         const renderable = this.#getRenderable(schema, required, ignore, path);
-
         // // Filter non-required properties (if specified) and render the sub-schema
         // const renderable = path.length ? this.#getRenderable(schema, required) : Object.entries(schema.properties ?? {})
 
-        if (renderable.length === 0) return html`<div id="empty">${this.emptyMessage}</div>`;
+        if (renderable.length === 0 && !hasPatternProperties) return html`<div id="empty">${this.emptyMessage}</div>`;
 
         let renderableWithLinks = renderable.reduce((acc, [name, info]) => {
             const externalPath = [...this.base, ...path, name];
@@ -896,9 +898,12 @@ export class JSONSchemaForm extends LitElement {
 
         const finalSort = this.sort ? sorted.sort(this.sort) : sorted;
 
+
         let rendered = finalSort.map((entry) => {
             const [name, info] = entry;
 
+            const hasPatternProperties = !!info.patternProperties;
+
             // Render linked properties
             if (entry[isLink]) {
                 const linkedProperties = info.properties.map((path) => {
@@ -960,9 +965,10 @@ export class JSONSchemaForm extends LitElement {
             enableToggle.checked = !isDisabled;
 
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
-
+            
             if (renderableInside.length) {
-                this.#nestedForms[name] = new JSONSchemaForm({
+                const ogContext = this
+                const nested = this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
                     results: { ...nestedResults },
@@ -993,7 +999,9 @@ export class JSONSchemaForm extends LitElement {
                         this.nLoaded++;
                         this.checkAllLoaded();
                     },
-                    createTable: (...args) => this.createTable(...args),
+                    createTable: function (...args) {
+                        return ogContext.createTable.call(this, ...args)
+                    },
                     onOverride: (...args) => this.onOverride(...args),
                     base,
                 });
@@ -1006,7 +1014,7 @@ export class JSONSchemaForm extends LitElement {
                 toggleable: hasMany,
                 subtitle: html`<div style="display:flex; align-items: center;">
                     ${explicitlyRequired ? "" : enableToggleContainer}${renderableInside.length
-                        ? `${renderableInside.length} fields`
+                        ? `${hasPatternProperties ? 'Dynamic' : renderableInside.length} fields`
                         : ""}
                 </div>`,
                 content: this.#nestedForms[name],
@@ -1086,6 +1094,19 @@ export class JSONSchemaForm extends LitElement {
             return accordion;
         });
 
+        if (hasPatternProperties) {
+              
+              const patternProps = Object.entries(schema.patternProperties).map(( [ key, schema ] ) => {
+                    return this.#renderInteractiveElement(key, schema, required, path, results) 
+              })
+    
+              return [
+                  ...rendered,
+                  ...patternProps
+              ]
+        }
+
+
         return rendered;
     };
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 69a8242ef..cf20fc690 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -96,10 +96,11 @@ export class JSONSchemaInput extends LitElement {
         `;
     }
 
-    // info,
+    // schema,
     // parent,
     // path,
     // form,
+    // patternProperties
     required = false;
     validateOnChange = true;
 
@@ -116,12 +117,13 @@ export class JSONSchemaInput extends LitElement {
             // Update the actual input element
             const el = this.getElement();
             if (el.type === "checkbox") el.checked = value;
-            else if (el.classList.contains("list"))
-                el.children[0].items = value
-                    ? value.map((value) => {
-                          return { value };
-                      })
-                    : [];
+            else if (el.classList.contains("list")) {
+                const list = el.children[0];
+                el.children[0].items = this.#mapToList({
+                    value,
+                    list
+                }) // NOTE: Make sure this is correct
+            }
             else if (el instanceof Search) el.shadowRoot.querySelector("input").value = value;
             else el.value = value;
         }
@@ -136,7 +138,7 @@ export class JSONSchemaInput extends LitElement {
         return true;
     }
 
-    getElement = () => this.shadowRoot.querySelector(".schema-input");
+    getElement = () => this.shadowRoot.querySelector(".schema-input")
 
     #activateTimeoutValidation = (name, path) => {
         this.#clearTimeoutValidation();
@@ -174,35 +176,176 @@ export class JSONSchemaInput extends LitElement {
     }
 
     render() {
-        const { info } = this;
+        const { schema } = this;
 
         const input = this.#render();
 
         return html`
             ${input}
             <p class="guided--text-input-instructions">
-                ${info.description
-                    ? html`${unsafeHTML(capitalize(info.description))}${info.description.slice(-1)[0] === "."
-                          ? ""
-                          : "."}`
-                    : ""}
+                ${schema.description
+                ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
+                    ? ""
+                    : "."}`
+                : ""}
             </p>
         `;
     }
 
     #onThrow = (...args) => (this.onThrow ? this.onThrow(...args) : this.form?.onThrow(...args));
 
+    #isEditableObject = (schema = this.schema) => schema.type === "object";
+
+
+    #list
+    #mapToList({
+        value = this.value,
+        schema = this.schema,
+        list
+    } = {}) {
+
+        const { path: fullPath } = this;
+        const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
+        const name = path.splice(-1)[0];
+
+        const isEditableObject = this.#isEditableObject()
+        const resolved = isEditableObject ? Object.values(value ?? {}) : value ?? [];
+        let items = resolved ? resolved.map((value) => { return { value } }) : []
+
+
+        if (isEditableObject) {
+
+            let regex;
+            try { regex = new RegExp(name) } catch (e) { }
+
+            items = Object.entries(this.value)
+
+            if (regex) items = items.filter(([key]) => regex.test(key))
+
+            items = items.map(([key, value]) => {
+                return {
+                    key,
+                    value,
+                    controls: [
+                        new Button({
+                            label: 'Edit',
+                            size: "small",
+                            onClick: () => {
+
+                                this.#createModal({
+                                    key,
+                                    schema,
+                                    results: value,
+                                    list: list ?? this.#list
+                                })
+                            }
+                        })
+                    ]
+                }
+            })
+        }
+
+        return items
+    }
+
+    #schemaElement
+    #modal
+
+    async #createModal({
+        key = name,
+        schema,
+        results,
+        list
+    } = {}) {
+
+        const createNewObject = !results
+
+        if (this.#modal) this.#modal.remove();
+
+        const submitButton = new Button({
+            label: "Submit",
+            primary: true,
+        });
+
+        const updateTarget = results ?? {};
+
+        submitButton.addEventListener("click", async () => {
+
+            if (this.#schemaElement instanceof JSONSchemaForm) await this.#schemaElement.validate();
+
+            let value = updateTarget
+
+            if (schema?.format && schema.properties) {
+                let newValue = schema?.format;
+                for (let key in schema.properties) newValue = newValue.replace(`{${key}}`, value[key] ?? "").trim();
+                value = newValue;
+            }
+
+            if (createNewObject) list.add({ value });
+            else list.requestUpdate();
+
+            this.#modal.toggle(false);
+        });
+
+        this.#modal = new Modal({
+            header: header(key),
+            footer: submitButton,
+            showCloseButton: createNewObject
+        });
+
+        const div = document.createElement("div");
+        div.style.padding = "25px";
+
+        console.warn('Creating form', name, results, schema, name)
+
+        const isObject = schema.type === "object" || schema.properties; // NOTE: For formatted strings, this is not an object
+
+        this.#schemaElement = isObject
+            ? new JSONSchemaForm({
+                schema,
+                results: updateTarget,
+                onUpdate: (internalPath, value, forceUpdate) => {
+                    if (createNewObject) updateTarget[key] = value
+                    else {
+                        const path = [key, ...internalPath];
+                        console.log(path, this.path)
+                        this.#updateData(path, value, forceUpdate);
+                    }
+                },
+                onThrow: this.#onThrow,
+            })
+            : new JSONSchemaInput({
+                schema,
+                validateOnChange: false,
+                path: this.path,
+                form: this.form,
+                value: updateTarget,
+                onUpdate: (value) => {
+                    if (createNewObject) updateTarget[key] = value
+                    else this.#updateData(key, value, forceUpdate); // NOTE: Untested
+                },
+            });
+
+        div.append(this.#schemaElement);
+
+        this.#modal.append(div);
+
+        document.body.append(this.#modal);
+
+        setTimeout(() => this.#modal.toggle(true));
+    }
+
     #render() {
-        const { validateOnChange, info, path: fullPath } = this;
+        const { validateOnChange, schema, path: fullPath } = this;
 
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
-        const isArray = info.type === "array"; // Handle string (and related) formats / types
+        const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
-        const hasItemsRef = "items" in info && "$ref" in info.items;
-        if (!("items" in info)) info.items = {};
-        if (!("type" in info.items) && !hasItemsRef) info.items.type = "string";
+        const hasItemsRef = "items" in schema && "$ref" in schema.items;
+        if (!("items" in schema)) schema.items = {};
+        if (!("type" in schema.items) && !hasItemsRef) schema.items.type = "string";
 
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
@@ -220,10 +363,10 @@ export class JSONSchemaInput extends LitElement {
             return el;
         };
 
-        if (isArray) {
+        if (isArray || this.#isEditableObject()) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
-            const itemSchema = this.form ? this.form.getSchema("items", info) : info["items"];
+            const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
 
             const fileSystemFormat = isFilesystemSelector(name, itemSchema.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
@@ -248,8 +391,8 @@ export class JSONSchemaInput extends LitElement {
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
-                                  ? this.form.validateOnChange(key, parent, [...this.form.base, ...fullPath], v)
-                                  : "")
+                                    ? this.form.validateOnChange(key, parent, [...this.form.base, ...fullPath], v)
+                                    : "")
                         );
                     },
 
@@ -270,94 +413,24 @@ export class JSONSchemaInput extends LitElement {
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
 
-            const headerText = document.createElement("span");
-            headerText.innerText = header(name);
-
             const addButton = new Button({
                 size: "small",
             });
 
             addButton.innerText = "Add Item";
 
-            let modal;
-
-            let tempParent = {};
-
-            const itemInfo = info.items;
-            const formProperties = itemInfo.properties;
-
-            let element;
-
             addButton.addEventListener("click", () => {
-                if (modal) modal.remove();
-
-                tempParent[name] = {}; // Wipe previous values
-
-                modal = new Modal({
-                    header: headerText,
-                    footer: submitButton,
-                });
-
-                const div = document.createElement("div");
-                div.style.padding = "25px";
-
-                element = formProperties
-                    ? new JSONSchemaForm({
-                          schema: itemInfo,
-                          results: tempParent[name],
-                          onThrow: this.#onThrow,
-                      })
-                    : new JSONSchemaInput({
-                          info: itemInfo,
-                          validateOnChange: false,
-                          path: this.path,
-                          form: this.form,
-                          onUpdate: (value) => (tempParent[name] = value),
-                      });
-
-                div.append(element);
-
-                modal.append(div);
-
-                addButton.insertAdjacentElement("beforebegin", modal);
-
-                setTimeout(() => modal.toggle(true));
+                this.#createModal({ list, schema: itemSchema });
             });
 
-            const list = new List({
-                items: this.value
-                    ? this.value.map((value) => {
-                          return { value };
-                      })
-                    : [],
+            const list = this.#list = new List({
+                items: this.#mapToList(),
                 onChange: async () => {
                     this.#updateData(fullPath, list.items.length ? list.items.map((o) => o.value) : undefined);
                     if (validateOnChange) await this.#triggerValidation(name, path);
                 },
             });
 
-            const submitButton = new Button({
-                label: "Submit",
-                primary: true,
-            });
-
-            submitButton.addEventListener("click", async () => {
-                let value = tempParent[name];
-
-                if (formProperties) {
-                    await element.validate();
-                    if (itemInfo?.format) {
-                        let newValue = itemInfo?.format;
-                        for (let key in formProperties)
-                            newValue = newValue.replace(`{${key}}`, value[key] ?? "").trim();
-                        value = newValue;
-                    }
-                }
-
-                list.add({ value });
-                modal.toggle(false);
-            });
-
             return html`
                 <div class="schema-input list" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
                     ${list} ${addButton}
@@ -366,14 +439,14 @@ export class JSONSchemaInput extends LitElement {
         }
 
         // Basic enumeration of properties on a select element
-        if (info.enum && info.enum.length) {
-            if (info.strict === false) {
+        if (schema.enum && schema.enum.length) {
+            if (schema.strict === false) {
                 // const category = categories.find(({ test }) => test.test(key))?.value;
 
-                const options = info.enum.map((v) => {
+                const options = schema.enum.map((v) => {
                     return {
                         key: v,
-                        keywords: info.enumKeywords?.[v],
+                        keywords: schema.enumKeywords?.[v],
                     };
                 });
 
@@ -396,19 +469,19 @@ export class JSONSchemaInput extends LitElement {
             return html`
                 <select
                     class="guided--input schema-input"
-                    @input=${(ev) => this.#updateData(fullPath, info.enum[ev.target.value])}
+                    @input=${(ev) => this.#updateData(fullPath, schema.enum[ev.target.value])}
                     @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
                 >
-                    <option disabled selected value>${info.placeholder ?? "Select an option"}</option>
-                    ${info.enum.map(
-                        (item, i) =>
-                            html`<option value=${i} ?selected=${this.value === item}>
-                                ${info.enumLabels?.[item] ?? item}
+                    <option disabled selected value>${schema.placeholder ?? "Select an option"}</option>
+                    ${schema.enum.map(
+                (item, i) =>
+                    html`<option value=${i} ?selected=${this.value === item}>
+                                ${schema.enumLabels?.[item] ?? item}
                             </option>`
-                    )}
+            )}
                 </select>
             `;
-        } else if (info.type === "boolean") {
+        } else if (schema.type === "boolean") {
             return html`<input
                 type="checkbox"
                 class="schema-input"
@@ -416,19 +489,19 @@ export class JSONSchemaInput extends LitElement {
                 ?checked=${this.value ?? false}
                 @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
             />`;
-        } else if (info.type === "string" || info.type === "number" || info.type === "integer") {
-            const isInteger = info.type === "integer";
-            if (isInteger) info.type = "number";
-            const isNumber = info.type === "number";
+        } else if (schema.type === "string" || schema.type === "number" || schema.type === "integer") {
+            const isInteger = schema.type === "integer";
+            if (isInteger) schema.type = "number";
+            const isNumber = schema.type === "number";
 
-            const fileSystemFormat = isFilesystemSelector(name, info.format);
+            const fileSystemFormat = isFilesystemSelector(name, schema.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Handle long string formats
-            else if (info.format === "long" || isArray)
+            else if (schema.format === "long" || isArray)
                 return html`<textarea
                     class="guided--input guided--text-area schema-input"
                     type="text"
-                    placeholder="${info.placeholder ?? ""}"
+                    placeholder="${schema.placeholder ?? ""}"
                     style="height: 7.5em; padding-bottom: 20px"
                     maxlength="255"
                     .value="${this.value ?? ""}"
@@ -440,45 +513,45 @@ export class JSONSchemaInput extends LitElement {
             // Handle other string formats
             else {
                 const type =
-                    info.format === "date-time"
+                    schema.format === "date-time"
                         ? "datetime-local"
-                        : info.format ?? (info.type === "string" ? "text" : info.type);
+                        : schema.format ?? (schema.type === "string" ? "text" : schema.type);
                 return html`
                     <input
-                        class="guided--input schema-input ${info.step === null ? "hideStep" : ""}"
+                        class="guided--input schema-input ${schema.step === null ? "hideStep" : ""}"
                         type="${type}"
-                        step=${isNumber && info.step ? info.step : ""}
-                        placeholder="${info.placeholder ?? ""}"
+                        step=${isNumber && schema.step ? schema.step : ""}
+                        placeholder="${schema.placeholder ?? ""}"
                         .value="${this.value ?? ""}"
                         @input=${(ev) => {
-                            let value = ev.target.value;
-                            let newValue = value;
+                        let value = ev.target.value;
+                        let newValue = value;
 
-                            // const isBlank = value === '';
+                        // const isBlank = value === '';
 
-                            if (isInteger) newValue = parseInt(value);
-                            else if (isNumber) newValue = parseFloat(value);
+                        if (isInteger) newValue = parseInt(value);
+                        else if (isNumber) newValue = parseFloat(value);
 
-                            if (isNumber) {
-                                if ("min" in info && value < info.min) newValue = info.min;
-                                else if ("max" in info && value > info.max) newValue = info.max;
-                            }
+                        if (isNumber) {
+                            if ("min" in schema && value < schema.min) newValue = schema.min;
+                            else if ("max" in schema && value > schema.max) newValue = schema.max;
+                        }
 
-                            if (info.transform) newValue = info.transform(newValue, this.value, info);
+                        if (schema.transform) newValue = schema.transform(newValue, this.value, schema);
 
-                            // // Do not check patter if value is empty
-                            // if (info.pattern && !isBlank) {
-                            //     const regex = new RegExp(info.pattern)
-                            //     if (!regex.test(isNaN(newValue) ? value : newValue)) newValue = this.value // revert to last value
-                            // }
+                        // // Do not check patter if value is empty
+                        // if (schema.pattern && !isBlank) {
+                        //     const regex = new RegExp(schema.pattern)
+                        //     if (!regex.test(isNaN(newValue) ? value : newValue)) newValue = this.value // revert to last value
+                        // }
 
-                            if (!isNaN(newValue) && newValue !== value) {
-                                ev.target.value = newValue;
-                                value = newValue;
-                            }
+                        if (!isNaN(newValue) && newValue !== value) {
+                            ev.target.value = newValue;
+                            value = newValue;
+                        }
 
-                            this.#updateData(fullPath, value);
-                        }}
+                        this.#updateData(fullPath, value);
+                    }}
                         @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
                     />
                 `;
@@ -486,7 +559,7 @@ export class JSONSchemaInput extends LitElement {
         }
 
         // Print out the immutable default value
-        return html`<pre>${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pre>`;
+        return html`<pre>${schema.default ? JSON.stringify(schema.default, null, 2) : "No default value"}</pre>`;
     }
 }
 
diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index bb7521baa..b7b309347 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -6,6 +6,7 @@ type ListItemType = {
   key: string,
   content: string,
   value: any,
+  controls: HTMLElement[]
 }
 
 export interface ListProps {
@@ -87,6 +88,12 @@ export class List extends LitElement {
         height: 25px;
       }
 
+      .controls {  
+        margin-left: 1rem;
+        display: flex;
+        gap: 0.5rem;
+      }
+
     `;
   }
 
@@ -231,6 +238,9 @@ export class List extends LitElement {
       li.append(outerDiv)
       outerDiv.append(div)
 
+      const controlsDiv = document.createElement('div');
+      controlsDiv.classList.add("controls");
+
       let editableElement = document.createElement("span");
 
       let resolvedKey = key;
@@ -238,6 +248,8 @@ export class List extends LitElement {
 
       const isUnordered = !!key
 
+      const isObjectContent = content && typeof content === 'object'
+
       if (isUnordered) {
 
         this.setAttribute('unordered', '')
@@ -253,10 +265,13 @@ export class List extends LitElement {
 
         keyEl.innerText = resolvedKey;
         keyEl.style.cursor = "text";
+        div.append(keyEl);
 
-        const sepEl = document.createElement("span");
-        sepEl.innerHTML = "&nbsp;-&nbsp;";
-        div.append(keyEl, sepEl);
+        if (!isObjectContent) {
+          const sepEl = document.createElement("span");
+          sepEl.innerHTML = "&nbsp;-&nbsp;";
+          div.append(sepEl);
+        }
 
         this.object[resolvedKey] = value;
       }
@@ -271,22 +286,26 @@ export class List extends LitElement {
           valueEl.innerText = content;
           div.appendChild(valueEl);
       }
-      else li.append(editableElement = content)
+
+      // Skip object contents
+      else if (!isObjectContent) li.append(editableElement = content)
 
 
 
       if (div.innerText) li.title = div.innerText
 
+      if (item.controls || this.editable) outerDiv.append(controlsDiv)
+
+      if (item.controls) controlsDiv.appendChild(...item.controls);
 
       if (this.editable) {
+
         const button = new Button({
             label: "Delete",
             size: "small",
         });
 
-        button.style.marginLeft = "1rem";
-
-        outerDiv.appendChild(button);
+        controlsDiv.appendChild(button);
 
         editableElement.contentEditable = true;
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 582fb91b5..6e79f93d1 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -54,6 +54,7 @@ export class SimpleTable extends LitElement {
 
             :host([loading]) tfoot {
                 display: block;
+                position: relative;
             }
 
             :host([loading]) tfoot td {
@@ -519,7 +520,7 @@ export class SimpleTable extends LitElement {
     updated() {
         this.setAttribute("loading", "");
 
-        const data = this.#getData();
+        const data = this.#getData(); // Always render at least one row
         const cells = data.map((row, i) => row.map((v, j) => this.#createCell(v, { i, j }))).flat();
 
         // Trigger load after a short delay if not deferred
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 45c366beb..9e1cf462b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -206,7 +206,11 @@ export class GuidedMetadataPage extends ManagedPage {
             onlyRequired: false,
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
-            createTable: (name, metadata, path) => {
+            createTable: function (name, metadata, path) {
+
+                const parentSchema = this.getSchema(path)
+                if (parentSchema.patternProperties) return false
+
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);
                 else return true; // All other tables are handled by the default behavior
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 76ece0c1d..fbaa87438 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -14,7 +14,6 @@ import { CodeBlock } from "../../../CodeBlock.js";
 import { List } from "../../../List";
 import { fs } from "../../../../electron/index.js";
 import { joinPath } from "../../../../globals.js";
-import { JSONSchemaInput } from "../../../JSONSchemaInput.js";
 
 const exampleFileStructure = `mylab/
     ¦   Subjects/
diff --git a/src/renderer/src/stories/pages/inspect/InspectPage.js b/src/renderer/src/stories/pages/inspect/InspectPage.js
index f8dd22ca3..c67f7043d 100644
--- a/src/renderer/src/stories/pages/inspect/InspectPage.js
+++ b/src/renderer/src/stories/pages/inspect/InspectPage.js
@@ -53,7 +53,7 @@ export class InspectPage extends Page {
 
     input = new JSONSchemaInput({
         path: ["filesystem_paths"],
-        info: {
+        schema: {
             type: "array",
             items: {
                 format: ["file", "directory"],
diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
index be1f00070..454b353fe 100644
--- a/src/renderer/src/stories/pages/preview/PreviewPage.js
+++ b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -27,7 +27,7 @@ export class PreviewPage extends Page {
 
     input = new JSONSchemaInput({
         path: ["file_path"],
-        info: {
+        schema: {
             type: "string",
             format: "file",
             description:
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index a63573ddf..833d3a718 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -65,7 +65,7 @@ export async function uploadToDandi(info, type = "project" in info ? "project" :
 
         const input = new JSONSchemaInput({
             path: [whichAPIKey],
-            info: dandiGlobalSchema.properties.api_keys.properties[whichAPIKey],
+            schema: dandiGlobalSchema.properties.api_keys.properties[whichAPIKey],
         });
 
         input.style.padding = "25px";

From 160c8c1817190373d412efd07a2a4e77805e7bd4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 30 Nov 2023 00:35:05 +0000
Subject: [PATCH 024/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    |  34 ++--
 src/renderer/src/stories/JSONSchemaInput.js   | 185 ++++++++----------
 src/renderer/src/stories/List.ts              |   2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |   5 +-
 4 files changed, 105 insertions(+), 121 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 13c827803..99c6853dc 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -509,7 +509,7 @@ export class JSONSchemaForm extends LitElement {
             value,
             form: this,
             required: isRequired,
-            validateEmptyValue: this.validateEmptyValues
+            validateEmptyValue: this.validateEmptyValues,
         });
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
@@ -530,7 +530,9 @@ export class JSONSchemaForm extends LitElement {
                     ? "conditional"
                     : ""}"
             >
-                <label class="guided--form-label">${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}</label>
+                <label class="guided--form-label"
+                    >${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}</label
+                >
                 ${interactiveInput}
                 <div class="errors"></div>
                 <div class="warnings"></div>
@@ -898,7 +900,6 @@ export class JSONSchemaForm extends LitElement {
 
         const finalSort = this.sort ? sorted.sort(this.sort) : sorted;
 
-
         let rendered = finalSort.map((entry) => {
             const [name, info] = entry;
 
@@ -965,10 +966,10 @@ export class JSONSchemaForm extends LitElement {
             enableToggle.checked = !isDisabled;
 
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
-            
+
             if (renderableInside.length) {
-                const ogContext = this
-                const nested = this.#nestedForms[name] = new JSONSchemaForm({
+                const ogContext = this;
+                const nested = (this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
                     results: { ...nestedResults },
@@ -1000,11 +1001,11 @@ export class JSONSchemaForm extends LitElement {
                         this.checkAllLoaded();
                     },
                     createTable: function (...args) {
-                        return ogContext.createTable.call(this, ...args)
+                        return ogContext.createTable.call(this, ...args);
                     },
                     onOverride: (...args) => this.onOverride(...args),
                     base,
-                });
+                }));
             }
 
             const oldStates = this.#accordions[headerName];
@@ -1014,7 +1015,7 @@ export class JSONSchemaForm extends LitElement {
                 toggleable: hasMany,
                 subtitle: html`<div style="display:flex; align-items: center;">
                     ${explicitlyRequired ? "" : enableToggleContainer}${renderableInside.length
-                        ? `${hasPatternProperties ? 'Dynamic' : renderableInside.length} fields`
+                        ? `${hasPatternProperties ? "Dynamic" : renderableInside.length} fields`
                         : ""}
                 </div>`,
                 content: this.#nestedForms[name],
@@ -1095,17 +1096,12 @@ export class JSONSchemaForm extends LitElement {
         });
 
         if (hasPatternProperties) {
-              
-              const patternProps = Object.entries(schema.patternProperties).map(( [ key, schema ] ) => {
-                    return this.#renderInteractiveElement(key, schema, required, path, results) 
-              })
-    
-              return [
-                  ...rendered,
-                  ...patternProps
-              ]
-        }
+            const patternProps = Object.entries(schema.patternProperties).map(([key, schema]) => {
+                return this.#renderInteractiveElement(key, schema, required, path, results);
+            });
 
+            return [...rendered, ...patternProps];
+        }
 
         return rendered;
     };
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index cf20fc690..8ffeec344 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -121,10 +121,9 @@ export class JSONSchemaInput extends LitElement {
                 const list = el.children[0];
                 el.children[0].items = this.#mapToList({
                     value,
-                    list
-                }) // NOTE: Make sure this is correct
-            }
-            else if (el instanceof Search) el.shadowRoot.querySelector("input").value = value;
+                    list,
+                }); // NOTE: Make sure this is correct
+            } else if (el instanceof Search) el.shadowRoot.querySelector("input").value = value;
             else el.value = value;
         }
 
@@ -138,7 +137,7 @@ export class JSONSchemaInput extends LitElement {
         return true;
     }
 
-    getElement = () => this.shadowRoot.querySelector(".schema-input")
+    getElement = () => this.shadowRoot.querySelector(".schema-input");
 
     #activateTimeoutValidation = (name, path) => {
         this.#clearTimeoutValidation();
@@ -184,10 +183,10 @@ export class JSONSchemaInput extends LitElement {
             ${input}
             <p class="guided--text-input-instructions">
                 ${schema.description
-                ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
-                    ? ""
-                    : "."}`
-                : ""}
+                    ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
+                          ? ""
+                          : "."}`
+                    : ""}
             </p>
         `;
     }
@@ -196,31 +195,29 @@ export class JSONSchemaInput extends LitElement {
 
     #isEditableObject = (schema = this.schema) => schema.type === "object";
 
-
-    #list
-    #mapToList({
-        value = this.value,
-        schema = this.schema,
-        list
-    } = {}) {
-
+    #list;
+    #mapToList({ value = this.value, schema = this.schema, list } = {}) {
         const { path: fullPath } = this;
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
-        const isEditableObject = this.#isEditableObject()
+        const isEditableObject = this.#isEditableObject();
         const resolved = isEditableObject ? Object.values(value ?? {}) : value ?? [];
-        let items = resolved ? resolved.map((value) => { return { value } }) : []
-
+        let items = resolved
+            ? resolved.map((value) => {
+                  return { value };
+              })
+            : [];
 
         if (isEditableObject) {
-
             let regex;
-            try { regex = new RegExp(name) } catch (e) { }
+            try {
+                regex = new RegExp(name);
+            } catch (e) {}
 
-            items = Object.entries(this.value)
+            items = Object.entries(this.value);
 
-            if (regex) items = items.filter(([key]) => regex.test(key))
+            if (regex) items = items.filter(([key]) => regex.test(key));
 
             items = items.map(([key, value]) => {
                 return {
@@ -228,37 +225,30 @@ export class JSONSchemaInput extends LitElement {
                     value,
                     controls: [
                         new Button({
-                            label: 'Edit',
+                            label: "Edit",
                             size: "small",
                             onClick: () => {
-
                                 this.#createModal({
                                     key,
                                     schema,
                                     results: value,
-                                    list: list ?? this.#list
-                                })
-                            }
-                        })
-                    ]
-                }
-            })
+                                    list: list ?? this.#list,
+                                });
+                            },
+                        }),
+                    ],
+                };
+            });
         }
 
-        return items
+        return items;
     }
 
-    #schemaElement
-    #modal
-
-    async #createModal({
-        key = name,
-        schema,
-        results,
-        list
-    } = {}) {
+    #schemaElement;
+    #modal;
 
-        const createNewObject = !results
+    async #createModal({ key = name, schema, results, list } = {}) {
+        const createNewObject = !results;
 
         if (this.#modal) this.#modal.remove();
 
@@ -270,10 +260,9 @@ export class JSONSchemaInput extends LitElement {
         const updateTarget = results ?? {};
 
         submitButton.addEventListener("click", async () => {
-
             if (this.#schemaElement instanceof JSONSchemaForm) await this.#schemaElement.validate();
 
-            let value = updateTarget
+            let value = updateTarget;
 
             if (schema?.format && schema.properties) {
                 let newValue = schema?.format;
@@ -290,41 +279,41 @@ export class JSONSchemaInput extends LitElement {
         this.#modal = new Modal({
             header: header(key),
             footer: submitButton,
-            showCloseButton: createNewObject
+            showCloseButton: createNewObject,
         });
 
         const div = document.createElement("div");
         div.style.padding = "25px";
 
-        console.warn('Creating form', name, results, schema, name)
+        console.warn("Creating form", name, results, schema, name);
 
         const isObject = schema.type === "object" || schema.properties; // NOTE: For formatted strings, this is not an object
 
         this.#schemaElement = isObject
             ? new JSONSchemaForm({
-                schema,
-                results: updateTarget,
-                onUpdate: (internalPath, value, forceUpdate) => {
-                    if (createNewObject) updateTarget[key] = value
-                    else {
-                        const path = [key, ...internalPath];
-                        console.log(path, this.path)
-                        this.#updateData(path, value, forceUpdate);
-                    }
-                },
-                onThrow: this.#onThrow,
-            })
+                  schema,
+                  results: updateTarget,
+                  onUpdate: (internalPath, value, forceUpdate) => {
+                      if (createNewObject) updateTarget[key] = value;
+                      else {
+                          const path = [key, ...internalPath];
+                          console.log(path, this.path);
+                          this.#updateData(path, value, forceUpdate);
+                      }
+                  },
+                  onThrow: this.#onThrow,
+              })
             : new JSONSchemaInput({
-                schema,
-                validateOnChange: false,
-                path: this.path,
-                form: this.form,
-                value: updateTarget,
-                onUpdate: (value) => {
-                    if (createNewObject) updateTarget[key] = value
-                    else this.#updateData(key, value, forceUpdate); // NOTE: Untested
-                },
-            });
+                  schema,
+                  validateOnChange: false,
+                  path: this.path,
+                  form: this.form,
+                  value: updateTarget,
+                  onUpdate: (value) => {
+                      if (createNewObject) updateTarget[key] = value;
+                      else this.#updateData(key, value, forceUpdate); // NOTE: Untested
+                  },
+              });
 
         div.append(this.#schemaElement);
 
@@ -391,8 +380,8 @@ export class JSONSchemaInput extends LitElement {
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
-                                    ? this.form.validateOnChange(key, parent, [...this.form.base, ...fullPath], v)
-                                    : "")
+                                  ? this.form.validateOnChange(key, parent, [...this.form.base, ...fullPath], v)
+                                  : "")
                         );
                     },
 
@@ -423,13 +412,13 @@ export class JSONSchemaInput extends LitElement {
                 this.#createModal({ list, schema: itemSchema });
             });
 
-            const list = this.#list = new List({
+            const list = (this.#list = new List({
                 items: this.#mapToList(),
                 onChange: async () => {
                     this.#updateData(fullPath, list.items.length ? list.items.map((o) => o.value) : undefined);
                     if (validateOnChange) await this.#triggerValidation(name, path);
                 },
-            });
+            }));
 
             return html`
                 <div class="schema-input list" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
@@ -474,11 +463,11 @@ export class JSONSchemaInput extends LitElement {
                 >
                     <option disabled selected value>${schema.placeholder ?? "Select an option"}</option>
                     ${schema.enum.map(
-                (item, i) =>
-                    html`<option value=${i} ?selected=${this.value === item}>
+                        (item, i) =>
+                            html`<option value=${i} ?selected=${this.value === item}>
                                 ${schema.enumLabels?.[item] ?? item}
                             </option>`
-            )}
+                    )}
                 </select>
             `;
         } else if (schema.type === "boolean") {
@@ -524,34 +513,34 @@ export class JSONSchemaInput extends LitElement {
                         placeholder="${schema.placeholder ?? ""}"
                         .value="${this.value ?? ""}"
                         @input=${(ev) => {
-                        let value = ev.target.value;
-                        let newValue = value;
+                            let value = ev.target.value;
+                            let newValue = value;
 
-                        // const isBlank = value === '';
+                            // const isBlank = value === '';
 
-                        if (isInteger) newValue = parseInt(value);
-                        else if (isNumber) newValue = parseFloat(value);
+                            if (isInteger) newValue = parseInt(value);
+                            else if (isNumber) newValue = parseFloat(value);
 
-                        if (isNumber) {
-                            if ("min" in schema && value < schema.min) newValue = schema.min;
-                            else if ("max" in schema && value > schema.max) newValue = schema.max;
-                        }
+                            if (isNumber) {
+                                if ("min" in schema && value < schema.min) newValue = schema.min;
+                                else if ("max" in schema && value > schema.max) newValue = schema.max;
+                            }
 
-                        if (schema.transform) newValue = schema.transform(newValue, this.value, schema);
+                            if (schema.transform) newValue = schema.transform(newValue, this.value, schema);
 
-                        // // Do not check patter if value is empty
-                        // if (schema.pattern && !isBlank) {
-                        //     const regex = new RegExp(schema.pattern)
-                        //     if (!regex.test(isNaN(newValue) ? value : newValue)) newValue = this.value // revert to last value
-                        // }
+                            // // Do not check patter if value is empty
+                            // if (schema.pattern && !isBlank) {
+                            //     const regex = new RegExp(schema.pattern)
+                            //     if (!regex.test(isNaN(newValue) ? value : newValue)) newValue = this.value // revert to last value
+                            // }
 
-                        if (!isNaN(newValue) && newValue !== value) {
-                            ev.target.value = newValue;
-                            value = newValue;
-                        }
+                            if (!isNaN(newValue) && newValue !== value) {
+                                ev.target.value = newValue;
+                                value = newValue;
+                            }
 
-                        this.#updateData(fullPath, value);
-                    }}
+                            this.#updateData(fullPath, value);
+                        }}
                         @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
                     />
                 `;
diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index b7b309347..e69db5434 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -88,7 +88,7 @@ export class List extends LitElement {
         height: 25px;
       }
 
-      .controls {  
+      .controls {
         margin-left: 1rem;
         display: flex;
         gap: 0.5rem;
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 9e1cf462b..90834e2d5 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -207,9 +207,8 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             createTable: function (name, metadata, path) {
-
-                const parentSchema = this.getSchema(path)
-                if (parentSchema.patternProperties) return false
+                const parentSchema = this.getSchema(path);
+                if (parentSchema.patternProperties) return false;
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);

From f0c4821d75bc03de78e082c1f74e49f60b664375 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 30 Nov 2023 11:23:07 -0800
Subject: [PATCH 025/133] Flag additional properties (but avoid for now)

---
 schemas/base-metadata.schema.ts             |  2 ++
 src/renderer/src/stories/JSONSchemaForm.js  | 20 ++++++++++++++++----
 src/renderer/src/stories/JSONSchemaInput.js |  7 +++++--
 src/renderer/src/stories/table/Cell.ts      |  2 +-
 4 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 2e7f9863c..390b3539c 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -39,6 +39,8 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     const copy = structuredClone(schema)
 
+    copy.additionalProperties = false
+
     // Add unit to weight
     const subjectProps = copy.properties.Subject.properties
     subjectProps.weight.unit = 'kg'
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 99c6853dc..bae1a27dd 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -836,13 +836,16 @@ export class JSONSchemaForm extends LitElement {
         let isLink = Symbol("isLink");
 
         const hasPatternProperties = !!schema.patternProperties;
+        const hasAdditionalProperties = schema.additionalProperties !== false;
 
         // Filter non-required properties (if specified) and render the sub-schema
         const renderable = this.#getRenderable(schema, required, ignore, path);
         // // Filter non-required properties (if specified) and render the sub-schema
         // const renderable = path.length ? this.#getRenderable(schema, required) : Object.entries(schema.properties ?? {})
 
-        if (renderable.length === 0 && !hasPatternProperties) return html`<div id="empty">${this.emptyMessage}</div>`;
+        const hasProperties = renderable.length > 0 || hasPatternProperties || hasAdditionalProperties;
+
+        if (!hasProperties) return html`<div id="empty">${this.emptyMessage}</div>`;
 
         let renderableWithLinks = renderable.reduce((acc, [name, info]) => {
             const externalPath = [...this.base, ...path, name];
@@ -1097,12 +1100,21 @@ export class JSONSchemaForm extends LitElement {
 
         if (hasPatternProperties) {
             const patternProps = Object.entries(schema.patternProperties).map(([key, schema]) => {
-                return this.#renderInteractiveElement(key, schema, required, path, results);
+                return this.#renderInteractiveElement(key, {
+                    ...schema,
+                    title: `Pattern Properties <small><small>${key}</small></small>`
+                }, required, path, results);
             });
-
-            return [...rendered, ...patternProps];
+            
+            rendered = [...rendered, ...patternProps];
         }
 
+        // if (hasAdditionalProperties) {
+        //     const additionalList = this.#renderInteractiveElement('Additional Properties', schema, required, path, results)
+        //     rendered = [...rendered, additionalList];
+        // }
+ 
+
         return rendered;
     };
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 8ffeec344..6dbc0d89d 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -218,6 +218,7 @@ export class JSONSchemaInput extends LitElement {
             items = Object.entries(this.value);
 
             if (regex) items = items.filter(([key]) => regex.test(key));
+            else items.filter(([key]) => key in schema.properties);
 
             items = items.map(([key, value]) => {
                 return {
@@ -332,6 +333,8 @@ export class JSONSchemaInput extends LitElement {
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
+        const isEditableObject = this.#isEditableObject()
+
         const hasItemsRef = "items" in schema && "$ref" in schema.items;
         if (!("items" in schema)) schema.items = {};
         if (!("type" in schema.items) && !hasItemsRef) schema.items.type = "string";
@@ -352,7 +355,7 @@ export class JSONSchemaInput extends LitElement {
             return el;
         };
 
-        if (isArray || this.#isEditableObject()) {
+        if (isArray || isEditableObject) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
             const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
@@ -406,7 +409,7 @@ export class JSONSchemaInput extends LitElement {
                 size: "small",
             });
 
-            addButton.innerText = "Add Item";
+            addButton.innerText = `Add ${isEditableObject ? 'Property' : 'Item'}`;
 
             addButton.addEventListener("click", () => {
                 this.#createModal({ list, schema: itemSchema });
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 856c698df..d5c85bc7a 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -39,7 +39,7 @@ export class TableCell extends LitElement {
                 font-size: 13px;
                 height: 100%;
                 max-height:  100px;
-                overflow-y: scroll;
+                overflow-y: auto;
             }
 
             :host > * {

From 425b3029aa014662272a457daa63ac2b267c170e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 30 Nov 2023 19:23:27 +0000
Subject: [PATCH 026/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  | 17 +++++++++++------
 src/renderer/src/stories/JSONSchemaInput.js |  4 ++--
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bae1a27dd..e099665e3 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1100,12 +1100,18 @@ export class JSONSchemaForm extends LitElement {
 
         if (hasPatternProperties) {
             const patternProps = Object.entries(schema.patternProperties).map(([key, schema]) => {
-                return this.#renderInteractiveElement(key, {
-                    ...schema,
-                    title: `Pattern Properties <small><small>${key}</small></small>`
-                }, required, path, results);
+                return this.#renderInteractiveElement(
+                    key,
+                    {
+                        ...schema,
+                        title: `Pattern Properties <small><small>${key}</small></small>`,
+                    },
+                    required,
+                    path,
+                    results
+                );
             });
-            
+
             rendered = [...rendered, ...patternProps];
         }
 
@@ -1113,7 +1119,6 @@ export class JSONSchemaForm extends LitElement {
         //     const additionalList = this.#renderInteractiveElement('Additional Properties', schema, required, path, results)
         //     rendered = [...rendered, additionalList];
         // }
- 
 
         return rendered;
     };
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 6dbc0d89d..d5a7850eb 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -333,7 +333,7 @@ export class JSONSchemaInput extends LitElement {
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
-        const isEditableObject = this.#isEditableObject()
+        const isEditableObject = this.#isEditableObject();
 
         const hasItemsRef = "items" in schema && "$ref" in schema.items;
         if (!("items" in schema)) schema.items = {};
@@ -409,7 +409,7 @@ export class JSONSchemaInput extends LitElement {
                 size: "small",
             });
 
-            addButton.innerText = `Add ${isEditableObject ? 'Property' : 'Item'}`;
+            addButton.innerText = `Add ${isEditableObject ? "Property" : "Item"}`;
 
             addButton.addEventListener("click", () => {
                 this.#createModal({ list, schema: itemSchema });

From 98886d86bfb2ba1ad4c7bc4e204a0348607dac18 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 30 Nov 2023 11:42:51 -0800
Subject: [PATCH 027/133] Encode IDs

---
 src/renderer/src/stories/JSONSchemaForm.js | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bae1a27dd..a0d333aef 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -12,6 +12,8 @@ import { resolveProperties } from "./pages/guided-mode/data/utils";
 import { JSONSchemaInput } from "./JSONSchemaInput";
 import { InspectorListItem } from "./preview/inspector/InspectorList";
 
+const encode = (str) => btoa(str).replace(/\+|\/|\=/g, '_');
+
 const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
 };
@@ -273,7 +275,7 @@ export class JSONSchemaForm extends LitElement {
     getInput = (path) => {
         if (typeof path === "string") path = path.split(".");
 
-        const container = this.shadowRoot.querySelector(`#${path.join("-")}`);
+        const container = this.shadowRoot.querySelector(`#${encode(path.join("-"))}`);
 
         if (!container) return this.getForm(path[0]).getInput(path.slice(1));
         return container?.querySelector("jsonschema-input");
@@ -329,14 +331,14 @@ export class JSONSchemaForm extends LitElement {
 
     #addMessage = (name, message, type) => {
         if (Array.isArray(name)) name = name.join("-"); // Convert array to string
-        const container = this.shadowRoot.querySelector(`#${name} .${type}`);
+        const container = this.shadowRoot.querySelector(`#${encode(name)} .${type}`);
         const item = new InspectorListItem(message);
         container.appendChild(item);
     };
 
     #clearMessages = (localPath, type) => {
         if (Array.isArray(localPath)) localPath = localPath.join("-"); // Convert array to string
-        const container = this.shadowRoot.querySelector(`#${localPath} .${type}`);
+        const container = this.shadowRoot.querySelector(`#${encode(localPath)} .${type}`);
 
         if (container) {
             const nChildren = container.children.length;
@@ -525,7 +527,7 @@ export class JSONSchemaForm extends LitElement {
 
         return html`
             <div
-                id=${localPath.join("-")}
+                id=${encode(localPath.join("-"))}
                 class="form-section ${isRequired || isConditional ? "required" : ""} ${isConditional
                     ? "conditional"
                     : ""}"

From b8004fd833cfa0b814a323b0adeadb26b0a189f3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 30 Nov 2023 19:43:30 +0000
Subject: [PATCH 028/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index de579ee13..79ee8e6d4 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -12,7 +12,7 @@ import { resolveProperties } from "./pages/guided-mode/data/utils";
 import { JSONSchemaInput } from "./JSONSchemaInput";
 import { InspectorListItem } from "./preview/inspector/InspectorList";
 
-const encode = (str) => btoa(str).replace(/\+|\/|\=/g, '_');
+const encode = (str) => btoa(str).replace(/\+|\/|\=/g, "_");
 
 const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);

From e6ecdd446d8c23ae745fe57075ea1eb06465dd29 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 13 Dec 2023 10:16:08 -0800
Subject: [PATCH 029/133] Update data from pattern properties forms

---
 src/renderer/src/stories/JSONSchemaForm.js  | 43 ++++++++++++++++-----
 src/renderer/src/stories/JSONSchemaInput.js | 12 +++---
 2 files changed, 38 insertions(+), 17 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 79ee8e6d4..5cfd7e5f2 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -12,7 +12,14 @@ import { resolveProperties } from "./pages/guided-mode/data/utils";
 import { JSONSchemaInput } from "./JSONSchemaInput";
 import { InspectorListItem } from "./preview/inspector/InspectorList";
 
-const encode = (str) => btoa(str).replace(/\+|\/|\=/g, "_");
+const encode = (str) => {
+    try {
+        document.querySelector(`#${str}`);
+        return str;
+    } catch {
+        return btoa(str).replace(/\+|\/|\=/g, "_");
+    }
+}
 
 const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
@@ -263,11 +270,12 @@ export class JSONSchemaForm extends LitElement {
 
         return this.getForm(copy).getTable(tableName);
     };
-    v;
+
     getForm = (path) => {
         if (typeof path === "string") path = path.split(".");
         const form = this.#nestedForms[path[0]];
-        if (!path.length || !form) return this; // No nested form with this name. Returning self.
+        if (!path.length) return this; // No nested form with this name. Returning self
+        if (!form) throw new Error(`Could not find form with name ${path[0]}`);
 
         return form.getForm(path.slice(1));
     };
@@ -307,6 +315,8 @@ export class JSONSchemaForm extends LitElement {
 
         const globalValue = this.getGlobalValue(localPath);
 
+        console.warn('Updated data (up to Ophys.Fluorescence...)', localPath, value)
+
         // NOTE: Forms with nested forms will handle their own state updates
         if (this.isUndefined(value)) {
             // Continue to resolve and re-render...
@@ -449,11 +459,24 @@ export class JSONSchemaForm extends LitElement {
         return true;
     };
 
-    #get = (path, object = this.resolved, omitted = []) => {
+    #get = (path, object = this.resolved, omitted = [], skipped = []) => {
         // path = path.slice(this.base.length); // Correct for base path
         if (!path) throw new Error("Path not specified");
         return path.reduce(
-            (acc, curr) => (acc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str]?.[curr])]?.[curr]),
+            (acc, curr, i) => {
+                    const tempAcc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str] && acc[str][curr])]?.[curr]
+                    if (tempAcc) return tempAcc
+                    else {
+                        const level1 = acc?.[skipped.find((str) => acc[str])]
+                        if (level1) {
+                            const got = Object.keys(level1).find((key) => {
+                                const result = this.#get(path.slice(i+1), level1[key], omitted, skipped)
+                                return result
+                            })
+                            if (got) return level1[got]
+                        }
+                    }
+                },
             object
         );
     };
@@ -475,7 +498,7 @@ export class JSONSchemaForm extends LitElement {
             if (indexOf !== -1) path = path.slice(indexOf + 1);
         }
 
-        const resolved = this.#get(path, schema, ["properties", "patternProperties"]);
+        const resolved = this.#get(path, schema, ["properties", "patternProperties"], ["patternProperties"]);
         if (resolved["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
 
         return resolved;
@@ -694,7 +717,9 @@ export class JSONSchemaForm extends LitElement {
     #isARequiredPropertyString = `is a required property`;
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
-    triggerValidation = async (name, path = [], checkLinks = true) => {
+    triggerValidation = async (name, path = [], checkLinks = true, input = this.getInput([...path, name])) => {
+
+
         const parent = this.#get(path, this.resolved);
 
         const pathToValidate = [...(this.base ?? []), ...path];
@@ -797,8 +822,6 @@ export class JSONSchemaForm extends LitElement {
         warnings.forEach((info) => this.#addMessage(localPath, info, "warnings"));
         info.forEach((info) => this.#addMessage(localPath, info, "info"));
 
-        const input = this.getInput(localPath);
-
         if (isValid && errors.length === 0) {
             input.classList.remove("invalid");
 
@@ -1106,7 +1129,7 @@ export class JSONSchemaForm extends LitElement {
                     key,
                     {
                         ...schema,
-                        title: `Pattern Properties <small><small>${key}</small></small>`,
+                        title: `Pattern Properties <small><small style="font-weight: normal">${key}</small></small>`,
                     },
                     required,
                     path,
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index d5a7850eb..96ac27ad8 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -142,7 +142,7 @@ export class JSONSchemaInput extends LitElement {
     #activateTimeoutValidation = (name, path) => {
         this.#clearTimeoutValidation();
         this.#validationTimeout = setTimeout(() => {
-            this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path) : "";
+            this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path, undefined, this) : "";
         }, 1000);
     };
 
@@ -164,7 +164,7 @@ export class JSONSchemaInput extends LitElement {
 
     #triggerValidation = (name, path) => {
         this.#clearTimeoutValidation();
-        return this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path) : "";
+        return this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path, this) : "";
     };
 
     updated() {
@@ -286,20 +286,18 @@ export class JSONSchemaInput extends LitElement {
         const div = document.createElement("div");
         div.style.padding = "25px";
 
-        console.warn("Creating form", name, results, schema, name);
-
         const isObject = schema.type === "object" || schema.properties; // NOTE: For formatted strings, this is not an object
 
         this.#schemaElement = isObject
             ? new JSONSchemaForm({
                   schema,
                   results: updateTarget,
-                  onUpdate: (internalPath, value, forceUpdate) => {
+                  onUpdate: (internalPath, value) => {
                       if (createNewObject) updateTarget[key] = value;
                       else {
                           const path = [key, ...internalPath];
                           console.log(path, this.path);
-                          this.#updateData(path, value, forceUpdate);
+                          this.#updateData(path, value, true);
                       }
                   },
                   onThrow: this.#onThrow,
@@ -312,7 +310,7 @@ export class JSONSchemaInput extends LitElement {
                   value: updateTarget,
                   onUpdate: (value) => {
                       if (createNewObject) updateTarget[key] = value;
-                      else this.#updateData(key, value, forceUpdate); // NOTE: Untested
+                      else this.#updateData(key, value); // NOTE: Untested
                   },
               });
 

From 95638076aefcc1204f0a25a0a641955a7e705818 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Dec 2023 18:17:00 +0000
Subject: [PATCH 030/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  | 37 +++++++++------------
 src/renderer/src/stories/JSONSchemaInput.js |  6 +++-
 2 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5cfd7e5f2..dd23f2390 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -19,7 +19,7 @@ const encode = (str) => {
     } catch {
         return btoa(str).replace(/\+|\/|\=/g, "_");
     }
-}
+};
 
 const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
@@ -315,7 +315,7 @@ export class JSONSchemaForm extends LitElement {
 
         const globalValue = this.getGlobalValue(localPath);
 
-        console.warn('Updated data (up to Ophys.Fluorescence...)', localPath, value)
+        console.warn("Updated data (up to Ophys.Fluorescence...)", localPath, value);
 
         // NOTE: Forms with nested forms will handle their own state updates
         if (this.isUndefined(value)) {
@@ -462,23 +462,20 @@ export class JSONSchemaForm extends LitElement {
     #get = (path, object = this.resolved, omitted = [], skipped = []) => {
         // path = path.slice(this.base.length); // Correct for base path
         if (!path) throw new Error("Path not specified");
-        return path.reduce(
-            (acc, curr, i) => {
-                    const tempAcc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str] && acc[str][curr])]?.[curr]
-                    if (tempAcc) return tempAcc
-                    else {
-                        const level1 = acc?.[skipped.find((str) => acc[str])]
-                        if (level1) {
-                            const got = Object.keys(level1).find((key) => {
-                                const result = this.#get(path.slice(i+1), level1[key], omitted, skipped)
-                                return result
-                            })
-                            if (got) return level1[got]
-                        }
-                    }
-                },
-            object
-        );
+        return path.reduce((acc, curr, i) => {
+            const tempAcc = acc?.[curr] ?? acc?.[omitted.find((str) => acc[str] && acc[str][curr])]?.[curr];
+            if (tempAcc) return tempAcc;
+            else {
+                const level1 = acc?.[skipped.find((str) => acc[str])];
+                if (level1) {
+                    const got = Object.keys(level1).find((key) => {
+                        const result = this.#get(path.slice(i + 1), level1[key], omitted, skipped);
+                        return result;
+                    });
+                    if (got) return level1[got];
+                }
+            }
+        }, object);
     };
 
     #checkRequiredAfterChange = async (localPath) => {
@@ -718,8 +715,6 @@ export class JSONSchemaForm extends LitElement {
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
     triggerValidation = async (name, path = [], checkLinks = true, input = this.getInput([...path, name])) => {
-
-
         const parent = this.#get(path, this.resolved);
 
         const pathToValidate = [...(this.base ?? []), ...path];
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 96ac27ad8..5817eccb7 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -142,7 +142,11 @@ export class JSONSchemaInput extends LitElement {
     #activateTimeoutValidation = (name, path) => {
         this.#clearTimeoutValidation();
         this.#validationTimeout = setTimeout(() => {
-            this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path, undefined, this) : "";
+            this.onValidate
+                ? this.onValidate()
+                : this.form
+                  ? this.form.triggerValidation(name, path, undefined, this)
+                  : "";
         }, 1000);
     };
 

From 676e939f57209bacc8363d493bb8c96067162ba2 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 13 Dec 2023 10:32:00 -0800
Subject: [PATCH 031/133] Fix list

---
 src/renderer/src/stories/List.ts                                | 2 +-
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js        | 2 +-
 .../stories/pages/guided-mode/options/GuidedInspectorPage.js    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index e69db5434..1c457d977 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -288,7 +288,7 @@ export class List extends LitElement {
       }
 
       // Skip object contents
-      else if (!isObjectContent) li.append(editableElement = content)
+      else if (content instanceof HTMLElement) li.append(editableElement = content)
 
 
 
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 90834e2d5..f5240718e 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -43,7 +43,7 @@ const propsToIgnore = {
             conversion: true,
             offset: true,
         },
-    }, // Always ignore ophys metadata (for now)
+    },
     Icephys: true, // Always ignore icephys metadata (for now)
     Behavior: true, // Always ignore behavior metadata (for now)
     "ndx-dandi-icephys": true,
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js
index cd4dd6f45..154ddb196 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js
@@ -174,7 +174,7 @@ export class GuidedInspectorPage extends Page {
 
                     return manager;
                 })(),
-                ""
+                "Loading inspector report..."
             )}`;
     }
 }

From 97b1913197b551e6d7328842938b00289f0b8142 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 13 Dec 2023 14:25:55 -0800
Subject: [PATCH 032/133] Add pattern properties

---
 src/renderer/assets/css/global.css            |   1 +
 src/renderer/src/stories/JSONSchemaForm.js    |  22 ++--
 src/renderer/src/stories/JSONSchemaInput.js   | 111 ++++++++++++++----
 src/renderer/src/stories/List.ts              |  58 ++++++++-
 .../pages/guided-mode/data/GuidedMetadata.js  |   2 +
 5 files changed, 157 insertions(+), 37 deletions(-)

diff --git a/src/renderer/assets/css/global.css b/src/renderer/assets/css/global.css
index 3d303d974..912b35d5d 100755
--- a/src/renderer/assets/css/global.css
+++ b/src/renderer/assets/css/global.css
@@ -50,6 +50,7 @@ body {
     margin: 0;
     height: 100%;
     display: flex;
+    overflow: hidden; /* Dashboard without scroll behavior */
 }
 
 a {
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index dd23f2390..dc95729b5 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -314,9 +314,7 @@ export class JSONSchemaForm extends LitElement {
         const hasUpdate = resolvedParent[name] !== value;
 
         const globalValue = this.getGlobalValue(localPath);
-
-        console.warn("Updated data (up to Ophys.Fluorescence...)", localPath, value);
-
+        
         // NOTE: Forms with nested forms will handle their own state updates
         if (this.isUndefined(value)) {
             // Continue to resolve and re-render...
@@ -411,8 +409,11 @@ export class JSONSchemaForm extends LitElement {
         if (flaggedInputs.length) {
             flaggedInputs[0].focus();
             if (!message) {
-                if (flaggedInputs.length === 1)
-                    message = `<b>${header(flaggedInputs[0].path.join("."))}</b> is not valid`;
+                if (flaggedInputs.length === 1) {
+                    const path = flaggedInputs[0].path
+                    const schema = this.getSchema(path);
+                    message = `<b>${header(schema.title ?? path.join('.'))}</b> is not valid`;
+                }
                 else message = `${flaggedInputs.length} invalid form values`;
             }
             message += `${
@@ -496,12 +497,12 @@ export class JSONSchemaForm extends LitElement {
         }
 
         const resolved = this.#get(path, schema, ["properties", "patternProperties"], ["patternProperties"]);
-        if (resolved["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
+        if (resolved?.["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
 
         return resolved;
     }
 
-    #renderInteractiveElement = (name, info, required, path = [], value) => {
+    #renderInteractiveElement = (name, info, required, path = [], value, pattern = false) => {
         let isRequired = required[name];
 
         const localPath = [...path, name];
@@ -532,6 +533,7 @@ export class JSONSchemaForm extends LitElement {
             form: this,
             required: isRequired,
             validateEmptyValue: this.validateEmptyValues,
+            pattern: pattern ? name : undefined,
         });
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
@@ -1004,7 +1006,7 @@ export class JSONSchemaForm extends LitElement {
                     },
 
                     required: required[name], // Scoped to the sub-schema
-                    ignore: this.ignore,
+                    ignore: this.ignore[name],
                     dialogOptions: this.dialogOptions,
                     dialogType: this.dialogType,
                     onlyRequired: this.onlyRequired,
@@ -1120,6 +1122,7 @@ export class JSONSchemaForm extends LitElement {
 
         if (hasPatternProperties) {
             const patternProps = Object.entries(schema.patternProperties).map(([key, schema]) => {
+
                 return this.#renderInteractiveElement(
                     key,
                     {
@@ -1128,7 +1131,8 @@ export class JSONSchemaForm extends LitElement {
                     },
                     required,
                     path,
-                    results
+                    results,
+                    true
                 );
             });
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 5817eccb7..6305be325 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -252,9 +252,24 @@ export class JSONSchemaInput extends LitElement {
     #schemaElement;
     #modal;
 
-    async #createModal({ key = name, schema, results, list } = {}) {
+    async #createModal({ key, schema, results, list } = {}) {
+        
         const createNewObject = !results;
 
+        const isPatternProperties = this.pattern
+        const creatNewPatternProperty = isPatternProperties && createNewObject
+
+        const schemaCopy = structuredClone(schema)
+
+        // Add a property name entry to the schema
+        if (creatNewPatternProperty) {
+            schemaCopy.properties = {
+                __: { title: 'Property Name', type: "string", pattern: this.pattern },
+                ...schemaCopy.properties
+            }
+            schemaCopy.required = [...schemaCopy.required ?? [], '__']
+        } 
+
         if (this.#modal) this.#modal.remove();
 
         const submitButton = new Button({
@@ -269,20 +284,29 @@ export class JSONSchemaInput extends LitElement {
 
             let value = updateTarget;
 
-            if (schema?.format && schema.properties) {
-                let newValue = schema?.format;
-                for (let key in schema.properties) newValue = newValue.replace(`{${key}}`, value[key] ?? "").trim();
+            if (schemaCopy?.format && schemaCopy.properties) {
+                let newValue = schemaCopy?.format;
+                for (let key in schemaCopy.properties) newValue = newValue.replace(`{${key}}`, value[key] ?? "").trim();
                 value = newValue;
             }
 
-            if (createNewObject) list.add({ value });
-            else list.requestUpdate();
+            if (createNewObject) {
+
+                if (creatNewPatternProperty) {
+                    const key = value.__
+                    delete value.__
+                    list.add({ key, value });
+                }
+
+                else list.add({ key, value });
+
+            } else list.requestUpdate();
 
             this.#modal.toggle(false);
         });
 
         this.#modal = new Modal({
-            header: header(key),
+            header: key ? header(key) : 'Property Definition',
             footer: submitButton,
             showCloseButton: createNewObject,
         });
@@ -290,24 +314,22 @@ export class JSONSchemaInput extends LitElement {
         const div = document.createElement("div");
         div.style.padding = "25px";
 
-        const isObject = schema.type === "object" || schema.properties; // NOTE: For formatted strings, this is not an object
+        const isObject = schemaCopy.type === "object" || schemaCopy.properties; // NOTE: For formatted strings, this is not an object
 
         this.#schemaElement = isObject
             ? new JSONSchemaForm({
-                  schema,
+                  schema: schemaCopy,
                   results: updateTarget,
                   onUpdate: (internalPath, value) => {
-                      if (createNewObject) updateTarget[key] = value;
-                      else {
+                      if (!createNewObject) {
                           const path = [key, ...internalPath];
-                          console.log(path, this.path);
-                          this.#updateData(path, value, true);
+                          this.#updateData(path, value, true); // Live updates
                       }
                   },
                   onThrow: this.#onThrow,
               })
             : new JSONSchemaInput({
-                  schema,
+                  schema: schemaCopy,
                   validateOnChange: false,
                   path: this.path,
                   form: this.form,
@@ -337,10 +359,6 @@ export class JSONSchemaInput extends LitElement {
 
         const isEditableObject = this.#isEditableObject();
 
-        const hasItemsRef = "items" in schema && "$ref" in schema.items;
-        if (!("items" in schema)) schema.items = {};
-        if (!("type" in schema.items) && !hasItemsRef) schema.items.type = "string";
-
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
             const el = new FilesystemSelector({
@@ -360,12 +378,22 @@ export class JSONSchemaInput extends LitElement {
         if (isArray || isEditableObject) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
+            const isPatternProperties = this.pattern
+            
+            // Provide default item types
+            if (!isPatternProperties) {
+                const hasItemsRef = "items" in schema && "$ref" in schema.items;
+                if (!("items" in schema)) schema.items = {};
+                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = "string";
+            }
+
             const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
 
-            const fileSystemFormat = isFilesystemSelector(name, itemSchema.format);
+            const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
+
             // Create tables if possible
-            else if (itemSchema.type === "object" && this.form.createTable) {
+            else if (itemSchema?.type === "object" && this.form.createTable) {
                 const ignore = this.form?.ignore
                     ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
                     : {};
@@ -414,13 +442,50 @@ export class JSONSchemaInput extends LitElement {
             addButton.innerText = `Add ${isEditableObject ? "Property" : "Item"}`;
 
             addButton.addEventListener("click", () => {
-                this.#createModal({ list, schema: itemSchema });
+                this.#createModal({ list, schema: isPatternProperties ? schema : itemSchema });
             });
 
             const list = (this.#list = new List({
                 items: this.#mapToList(),
-                onChange: async () => {
-                    this.#updateData(fullPath, list.items.length ? list.items.map((o) => o.value) : undefined);
+                transform: (item) => {
+
+                    if (this.#isEditableObject()) {
+
+                        const { key, value } = item
+                        
+                        item.controls = [
+                            new Button({
+                                label: "Edit",
+                                size: "small",
+                                onClick: () => {
+                                    this.#createModal({
+                                        key,
+                                        schema,
+                                        results: value,
+                                        list,
+                                    });
+                                },
+                            }),
+                        ]
+
+                    }
+                }, 
+                onChange: async ({ object, items }, { object: oldObject }) => {
+
+                    console.log('Changed', list.object, list.items)
+                    if (this.pattern) {
+                        const oldKeys = Object.keys(oldObject)
+                        const newKeys = Object.keys(object)
+                        const removedKeys = oldKeys.filter((k) => !newKeys.includes(k))
+                        const updatedKeys = newKeys.filter((k) => oldObject[k] !== object[k])
+                        removedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], undefined))
+                        updatedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], object[k]))
+                    }
+
+                    else {
+                        this.#updateData(fullPath, items.length ? items.map((o) => o.value) : undefined);
+                    }
+
                     if (validateOnChange) await this.#triggerValidation(name, path);
                 },
             }));
diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index 1c457d977..50cecf4f0 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -16,10 +16,18 @@ export interface ListProps {
   editable?: boolean,
   unordered?: boolean,
   listStyles?: any
+  transform?: (item: ListItemType) => ListItemType
+}
+
+type ListState = {
+  items: ListItemType[],
+  object: {[x:string]: ListItemType['value']}
 }
 
 export class List extends LitElement {
 
+  transform: ListProps['transform']
+
   static get styles() {
     return css`
 
@@ -120,7 +128,7 @@ export class List extends LitElement {
       };
     }
 
-    onChange: () => void = () => {}
+    onChange: (updated: ListState, previous: ListState) => void = () => {}
 
     object: {[x:string]: any} = {}
 
@@ -129,11 +137,22 @@ export class List extends LitElement {
     }
 
     #items: ListItemType[] = []
+
     set items(value) {
-      const oldVal = this.#items
-      this.#items = value
-      this.onChange()
-      this.requestUpdate('items', oldVal)
+      const oldList = this.#items
+      this.#items = value.map(item => this.transform ? this.transform(item) ?? item : item)
+      const oldObject = this.object
+      this.#updateObject()
+
+      this.onChange({
+        items: this.#items,
+        object: this.object
+      },
+      {
+        items: oldList,
+        object: oldObject
+      })
+      this.requestUpdate('items', oldList)
     }
 
     get items() { return this.#items }
@@ -195,6 +214,8 @@ export class List extends LitElement {
       this.unordered = props.unordered ?? false
       this.listStyles = props.listStyles ?? {}
 
+      this.transform = props.transform
+
       if (props.onChange) this.onChange = props.onChange
 
     }
@@ -349,6 +370,33 @@ export class List extends LitElement {
       this.items = []
     }
 
+    #updateObject = () => {
+      
+      this.object = {}
+      this.#items.forEach((item, i) => {
+
+        const { key, value } = item;
+
+        const isUnordered = !!key
+        if (isUnordered) {
+          let resolvedKey = key
+
+          // Ensure no duplicate keys
+          let kI = 0;
+          while (resolvedKey in this.object) {
+              i++;
+              resolvedKey = `${key}_${kI}`;
+          }
+
+          this.object[resolvedKey] = value
+        } 
+        
+        else {
+          this.object[i] = value
+        }
+      })
+    }
+
     render() {
 
       this.removeAttribute('unordered')
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 f5240718e..42591fd1b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -170,6 +170,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
@@ -218,6 +219,7 @@ export class GuidedMetadataPage extends ManagedPage {
             onThrow,
         });
 
+
         return {
             subject,
             session,

From c7dc62c3f9fb2fe29d6fe8f926558cb2722155c3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 13 Dec 2023 22:42:36 +0000
Subject: [PATCH 033/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 10 ++-
 src/renderer/src/stories/JSONSchemaInput.js   | 65 ++++++++-----------
 src/renderer/src/stories/List.ts              |  6 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |  2 -
 4 files changed, 33 insertions(+), 50 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index c2a7f822a..a0883ee8e 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -325,7 +325,7 @@ export class JSONSchemaForm extends LitElement {
         const hasUpdate = resolvedParent[name] !== value;
 
         const globalValue = this.getGlobalValue(localPath);
-        
+
         // NOTE: Forms with nested forms will handle their own state updates
         if (this.isUndefined(value)) {
             // Continue to resolve and re-render...
@@ -423,11 +423,10 @@ export class JSONSchemaForm extends LitElement {
             flaggedInputs[0].focus();
             if (!message) {
                 if (flaggedInputs.length === 1) {
-                    const path = flaggedInputs[0].path
+                    const path = flaggedInputs[0].path;
                     const schema = this.getSchema(path);
-                    message = `<b>${header(schema.title ?? path.join('.'))}</b> is not valid`;
-                }
-                else message = `${flaggedInputs.length} invalid form values`;
+                    message = `<b>${header(schema.title ?? path.join("."))}</b> is not valid`;
+                } else message = `${flaggedInputs.length} invalid form values`;
             }
             message += `${
                 this.base.length ? ` in the <b>${this.base.join(".")}</b> section` : ""
@@ -1170,7 +1169,6 @@ export class JSONSchemaForm extends LitElement {
 
         if (hasPatternProperties) {
             const patternProps = Object.entries(schema.patternProperties).map(([key, schema]) => {
-
                 return this.#renderInteractiveElement(
                     key,
                     {
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e167314b2..b6b4cd432 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -123,7 +123,6 @@ export class JSONSchemaInput extends LitElement {
     // onValidate = () => {}
 
     updateData(value, forceValidate = false) {
-        
         if (!forceValidate) {
             // Update the actual input element
             const el = this.getElement();
@@ -264,22 +263,21 @@ export class JSONSchemaInput extends LitElement {
     #modal;
 
     async #createModal({ key, schema, results, list } = {}) {
-        
         const createNewObject = !results;
 
-        const isPatternProperties = this.pattern
-        const creatNewPatternProperty = isPatternProperties && createNewObject
+        const isPatternProperties = this.pattern;
+        const creatNewPatternProperty = isPatternProperties && createNewObject;
 
-        const schemaCopy = structuredClone(schema)
+        const schemaCopy = structuredClone(schema);
 
         // Add a property name entry to the schema
         if (creatNewPatternProperty) {
             schemaCopy.properties = {
-                __: { title: 'Property Name', type: "string", pattern: this.pattern },
-                ...schemaCopy.properties
-            }
-            schemaCopy.required = [...schemaCopy.required ?? [], '__']
-        } 
+                __: { title: "Property Name", type: "string", pattern: this.pattern },
+                ...schemaCopy.properties,
+            };
+            schemaCopy.required = [...(schemaCopy.required ?? []), "__"];
+        }
 
         if (this.#modal) this.#modal.remove();
 
@@ -302,27 +300,23 @@ export class JSONSchemaInput extends LitElement {
             }
 
             // Skip if not unique
-            if (schemaCopy.uniqueItems && list.items.find((item) => item.value === value)) return this.#modal.toggle(false);
+            if (schemaCopy.uniqueItems && list.items.find((item) => item.value === value))
+                return this.#modal.toggle(false);
 
             // Add to the list
             if (createNewObject) {
-
                 if (creatNewPatternProperty) {
-                    const key = value.__
-                    delete value.__
+                    const key = value.__;
+                    delete value.__;
                     list.add({ key, value });
-                }
-
-                else list.add({ key, value });
-
+                } else list.add({ key, value });
             } else list.requestUpdate();
 
-            
             this.#modal.toggle(false);
         });
 
         this.#modal = new Modal({
-            header: key ? header(key) : 'Property Definition',
+            header: key ? header(key) : "Property Definition",
             footer: submitButton,
             showCloseButton: createNewObject,
         });
@@ -394,8 +388,8 @@ export class JSONSchemaInput extends LitElement {
         if (isArray || isEditableObject) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
-            const isPatternProperties = this.pattern
-            
+            const isPatternProperties = this.pattern;
+
             // Provide default item types
             if (!isPatternProperties) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
@@ -407,7 +401,6 @@ export class JSONSchemaInput extends LitElement {
 
             const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
-
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
                 const ignore = this.form?.ignore
@@ -464,11 +457,9 @@ export class JSONSchemaInput extends LitElement {
             const list = (this.#list = new List({
                 items: this.#mapToList(),
                 transform: (item) => {
-
                     if (this.#isEditableObject()) {
+                        const { key, value } = item;
 
-                        const { key, value } = item
-                        
                         item.controls = [
                             new Button({
                                 label: "Edit",
@@ -482,22 +473,18 @@ export class JSONSchemaInput extends LitElement {
                                     });
                                 },
                             }),
-                        ]
-
+                        ];
                     }
-                }, 
+                },
                 onChange: async ({ object, items }, { object: oldObject }) => {
-
                     if (this.pattern) {
-                        const oldKeys = Object.keys(oldObject)
-                        const newKeys = Object.keys(object)
-                        const removedKeys = oldKeys.filter((k) => !newKeys.includes(k))
-                        const updatedKeys = newKeys.filter((k) => oldObject[k] !== object[k])
-                        removedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], undefined))
-                        updatedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], object[k]))
-                    }
-
-                    else {
+                        const oldKeys = Object.keys(oldObject);
+                        const newKeys = Object.keys(object);
+                        const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
+                        const updatedKeys = newKeys.filter((k) => oldObject[k] !== object[k]);
+                        removedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], undefined));
+                        updatedKeys.forEach((k) => this.#updateData([...fullPath.slice(1), k], object[k]));
+                    } else {
                         this.#updateData(fullPath, items.length ? items.map((o) => o.value) : undefined);
                     }
 
diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index 50cecf4f0..12c315682 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -371,7 +371,7 @@ export class List extends LitElement {
     }
 
     #updateObject = () => {
-      
+
       this.object = {}
       this.#items.forEach((item, i) => {
 
@@ -389,8 +389,8 @@ export class List extends LitElement {
           }
 
           this.object[resolvedKey] = value
-        } 
-        
+        }
+
         else {
           this.object[i] = value
         }
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 56dd51131..1cc28fc6a 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -170,7 +170,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
@@ -224,7 +223,6 @@ export class GuidedMetadataPage extends ManagedPage {
             onThrow,
         });
 
-
         return {
             subject,
             session,

From 7fb923e93f61057d28a911c2b76caa0240ad989c Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Fri, 15 Dec 2023 10:20:00 -0800
Subject: [PATCH 034/133] Correct for merge and patternProperties

---
 src/renderer/src/stories/JSONSchemaForm.js  | 5 ++++-
 src/renderer/src/stories/JSONSchemaInput.js | 6 +++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index a0883ee8e..76782b26c 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -736,9 +736,12 @@ export class JSONSchemaForm extends LitElement {
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, name];
         const schema = this.getSchema(localPath);
+        
+        // NOTE: May need to further correct for pattern properties
+        const validateArgs = input.pattern ? [parent, this.schema] : [parent[name], this.schema.properties[name]]
 
         const jsonSchemaErrors = await v
-            .validate(parent[name], this.schema.properties[name])
+            .validate(...validateArgs)
             .errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` }));
 
         const valid =
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index b6b4cd432..811d9dcfc 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -519,9 +519,9 @@ export class JSONSchemaInput extends LitElement {
                     value: {
                         value: this.value,
                         key: this.value,
-                        category: info.enumCategories?.[this.value],
-                        label: info.enumLabels?.[this.value],
-                        keywords: info.enumKeywords?.[this.value],
+                        category: schema.enumCategories?.[this.value],
+                        label: schema.enumLabels?.[this.value],
+                        keywords: schema.enumKeywords?.[this.value],
                     },
                     showAllWhenEmpty: false,
                     listMode: "click",

From 273b83de1390b6225e177f9c97f1823a82b2e877 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Dec 2023 18:20:16 +0000
Subject: [PATCH 035/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 76782b26c..be7f51720 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -736,9 +736,9 @@ export class JSONSchemaForm extends LitElement {
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, name];
         const schema = this.getSchema(localPath);
-        
+
         // NOTE: May need to further correct for pattern properties
-        const validateArgs = input.pattern ? [parent, this.schema] : [parent[name], this.schema.properties[name]]
+        const validateArgs = input.pattern ? [parent, this.schema] : [parent[name], this.schema.properties[name]];
 
         const jsonSchemaErrors = await v
             .validate(...validateArgs)

From 5a2a18d83e435e066b4e2d1fb81ba87f55ff67b4 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Fri, 15 Dec 2023 10:27:45 -0800
Subject: [PATCH 036/133] Validate only patternProperties when provided

---
 src/renderer/src/stories/JSONSchemaForm.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 76782b26c..f6221458a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -737,8 +737,8 @@ export class JSONSchemaForm extends LitElement {
         const externalPath = [...this.base, name];
         const schema = this.getSchema(localPath);
         
-        // NOTE: May need to further correct for pattern properties
-        const validateArgs = input.pattern ? [parent, this.schema] : [parent[name], this.schema.properties[name]]
+        // Validate pattern properties only when specified (NOTE: May need some additional exclusions)
+        const validateArgs = input.pattern ? [parent, { patternProperties: { [name]: this.schema.patternProperties[name] } }] : [parent[name], this.schema.properties[name]]
 
         const jsonSchemaErrors = await v
             .validate(...validateArgs)

From a7cbd0ae2a5a6492fa198d58d45603631b4e3081 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Dec 2023 18:28:17 +0000
Subject: [PATCH 037/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f6221458a..d81da3d12 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -736,9 +736,11 @@ export class JSONSchemaForm extends LitElement {
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, name];
         const schema = this.getSchema(localPath);
-        
+
         // Validate pattern properties only when specified (NOTE: May need some additional exclusions)
-        const validateArgs = input.pattern ? [parent, { patternProperties: { [name]: this.schema.patternProperties[name] } }] : [parent[name], this.schema.properties[name]]
+        const validateArgs = input.pattern
+            ? [parent, { patternProperties: { [name]: this.schema.patternProperties[name] } }]
+            : [parent[name], this.schema.properties[name]];
 
         const jsonSchemaErrors = await v
             .validate(...validateArgs)

From 067c372214a8733c10155a38f41cbddf1a402b18 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Fri, 15 Dec 2023 11:46:03 -0800
Subject: [PATCH 038/133] Fix table validation

---
 src/renderer/src/stories/JSONSchemaForm.js  | 78 ++++++++++++++++-----
 src/renderer/src/stories/JSONSchemaInput.js | 42 ++++++++---
 2 files changed, 93 insertions(+), 27 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f6221458a..680a6b81a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -498,6 +498,45 @@ export class JSONSchemaForm extends LitElement {
         if (!isValid) return true;
     };
 
+    // Resolve all references on the schema when set (INTERNAL USE ONLY)
+    #schema
+    replaceRefsWithValue = (schema, path = [], parent) => {
+        const copy = { ...schema }
+
+        if (schema && typeof schema === 'object' && !Array.isArray(schema)) {
+            for (let propName in copy) {
+                const prop = copy[propName]
+                if (prop && typeof prop === 'object' && !Array.isArray(prop)) {
+                    const internalCopy = copy[propName] = { ...prop }
+                    if (internalCopy['$ref']) {
+                        const prevItem = path.slice(-1)[0];
+                        const resolved = parent.properties.definitions?.[prevItem]
+                        copy[propName] = resolved;
+                    } else {
+                        for (let key in internalCopy) {
+                            const fullPath = [...path, propName, key]
+                            internalCopy[key] = this.replaceRefsWithValue(internalCopy[key], fullPath, copy);
+                        }
+                    }
+                }
+            }
+        } 
+
+        else return schema
+
+        return copy
+    }
+
+    set schema(schema) {
+        this.#schema = schema;
+        this.#schema = this.replaceRefsWithValue(schema)
+    }
+
+
+    get schema () {
+        return this.#schema;
+    }
+
     getSchema(path, schema = this.schema) {
         if (typeof path === "string") path = path.split(".");
 
@@ -508,8 +547,9 @@ export class JSONSchemaForm extends LitElement {
             if (indexOf !== -1) path = path.slice(indexOf + 1);
         }
 
+        // NOTE: Refs are now pre-resolved
         const resolved = this.#get(path, schema, ["properties", "patternProperties"], ["patternProperties"]);
-        if (resolved?.["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
+        // if (resolved?.["$ref"]) return this.getSchema(resolved["$ref"].split("/").slice(1)); // NOTE: This assumes reference to the root of the schema
 
         return resolved;
     }
@@ -729,27 +769,34 @@ export class JSONSchemaForm extends LitElement {
     #isARequiredPropertyString = `is a required property`;
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
-    triggerValidation = async (name, path = [], checkLinks = true, input = this.getInput([...path, name])) => {
-        const parent = this.#get(path, this.resolved);
+    triggerValidation = async (
+        name, 
+        path = [], 
+        checkLinks = true, 
+        input = this.getInput([...path, name]), 
+        schema = this.getSchema([...path, name]),
+        parent = this.#get(path, this.resolved),
+        {
+            onError,
+            onWarning
+        } = {}
+    ) => {
 
         const pathToValidate = [...(this.base ?? []), ...path];
         const localPath = [...path, name]; // Use basePath to augment the validation
-        const externalPath = [...this.base, name];
-        const schema = this.getSchema(localPath);
+        const externalPath = [...this.base, ...localPath];
         
-        // Validate pattern properties only when specified (NOTE: May need some additional exclusions)
-        const validateArgs = input.pattern ? [parent, { patternProperties: { [name]: this.schema.patternProperties[name] } }] : [parent[name], this.schema.properties[name]]
+        const skipValidation = !this.validateEmptyValues && parent[name] === undefined
+        const validateArgs = input.pattern || skipValidation ? [] : [parent[name], schema]
 
-        const jsonSchemaErrors = await v
-            .validate(...validateArgs)
-            .errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` }));
+        const jsonSchemaErrors = validateArgs.length === 2 ? await v.validate(...validateArgs).errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` })) : [];
 
         const valid =
-            !this.validateEmptyValues && parent[name] === undefined
+        skipValidation
                 ? true
                 : await this.validateOnChange(name, parent, pathToValidate);
 
-        const isRequired = this.#isRequired(localPath);
+        const isRequired = this.#isRequired(localPath) || input.required;
 
         let warnings = Array.isArray(valid)
             ? valid.filter((info) => info.type === "warning" && (!isRequired || !info.missing))
@@ -787,7 +834,6 @@ export class JSONSchemaForm extends LitElement {
             if (isUndefined) {
                 // Throw at least a basic warning if a non-linked property is required and missing
                 if (!hasLinks && isRequired) {
-                    const schema = this.getSchema(localPath);
 
                     if (this.validateEmptyValues) {
                         errors.push({
@@ -854,8 +900,8 @@ export class JSONSchemaForm extends LitElement {
         this.checkStatus();
 
         // Show aggregated errors and warnings (if any)
-        warnings.forEach((info) => this.#addMessage(localPath, info, "warnings"));
-        info.forEach((info) => this.#addMessage(localPath, info, "info"));
+        warnings.forEach((info) => onWarning ? onWarning(info) : this.#addMessage(localPath, info, "warnings"));
+        info.forEach((info) => onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info"));
 
         if (isValid && resolvedErrors.length === 0) {
             input.classList.remove("invalid");
@@ -883,7 +929,7 @@ export class JSONSchemaForm extends LitElement {
                 [...path, name]
             );
 
-            resolvedErrors.forEach((info) => this.#addMessage(localPath, info, "errors"));
+            resolvedErrors.forEach((info) => onError ? onError(info) : this.#addMessage(localPath, info, "errors"));
             // element.title = errors.map((info) => info.message).join("\n"); // Set all errors to show on hover
 
             return false;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 811d9dcfc..77efde395 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -149,13 +149,13 @@ export class JSONSchemaInput extends LitElement {
 
     getElement = () => this.shadowRoot.querySelector(".schema-input");
 
-    #activateTimeoutValidation = (name, path) => {
+    #activateTimeoutValidation = (name, path, hooks) => {
         this.#clearTimeoutValidation();
         this.#validationTimeout = setTimeout(() => {
             this.onValidate
                 ? this.onValidate()
                 : this.form
-                  ? this.form.triggerValidation(name, path, undefined, this)
+                  ? this.form.triggerValidation(name, path, undefined, this, undefined, undefined, hooks)
                   : "";
         }, 1000);
     };
@@ -165,7 +165,7 @@ export class JSONSchemaInput extends LitElement {
     };
 
     #validationTimeout = null;
-    #updateData = (fullPath, value, forceUpdate) => {
+    #updateData = (fullPath, value, forceUpdate, hooks) => {
         this.onUpdate ? this.onUpdate(value) : this.form ? this.form.updateData(fullPath, value, forceUpdate) : "";
 
         const path = [...fullPath];
@@ -173,7 +173,7 @@ export class JSONSchemaInput extends LitElement {
 
         this.value = value; // Update the latest value
 
-        this.#activateTimeoutValidation(name, path);
+        this.#activateTimeoutValidation(name, path, hooks);
     };
 
     #triggerValidation = async (name, path) => {
@@ -413,18 +413,38 @@ export class JSONSchemaInput extends LitElement {
 
                     ignore,
 
-                    onUpdate: () => this.#updateData(fullPath, tableMetadata.data, true), // Ensure change propagates to all forms
+                    onUpdate: () => this.#updateData(fullPath, tableMetadata.data, true, { onError: () => {}, onWarning: () => {} }), // Ensure change propagates to all forms
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
-                    validateOnChange: (key, parent, v) => {
-                        return (
-                            validateOnChange &&
+                    validateOnChange: async (key, parent, v) => {
+
+                        const warnings = []
+                        const errors = []
+
+                        const result = 
+                            await (validateOnChange &&
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
-                                  ? this.form.validateOnChange(key, parent, [...this.form.base, ...fullPath], v)
-                                  : "")
-                        );
+                                  ? this.form.triggerValidation(
+                                    key, 
+                                    fullPath, 
+                                    false, 
+                                    this, 
+                                    itemSchema.properties[key], 
+                                    { ...parent, [key]: v },
+                                    {
+                                        onError: (error) => errors.push(error),
+
+                                        onWarning: (warning) => errors.push(warning),
+                                    }
+                                ) // NOTE: No pattern properties support
+                                  : ""))
+                        
+
+                        const returnedValue = errors.length ? errors : (warnings.length ? warnings : result)
+
+                        return returnedValue
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements

From 9348b1f991c0f5fee6879d72c2008884404bac73 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Dec 2023 19:51:20 +0000
Subject: [PATCH 039/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  | 70 ++++++++++-----------
 src/renderer/src/stories/JSONSchemaInput.js | 49 ++++++++-------
 2 files changed, 57 insertions(+), 62 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 680a6b81a..f3f422eb8 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -499,41 +499,38 @@ export class JSONSchemaForm extends LitElement {
     };
 
     // Resolve all references on the schema when set (INTERNAL USE ONLY)
-    #schema
+    #schema;
     replaceRefsWithValue = (schema, path = [], parent) => {
-        const copy = { ...schema }
+        const copy = { ...schema };
 
-        if (schema && typeof schema === 'object' && !Array.isArray(schema)) {
+        if (schema && typeof schema === "object" && !Array.isArray(schema)) {
             for (let propName in copy) {
-                const prop = copy[propName]
-                if (prop && typeof prop === 'object' && !Array.isArray(prop)) {
-                    const internalCopy = copy[propName] = { ...prop }
-                    if (internalCopy['$ref']) {
+                const prop = copy[propName];
+                if (prop && typeof prop === "object" && !Array.isArray(prop)) {
+                    const internalCopy = (copy[propName] = { ...prop });
+                    if (internalCopy["$ref"]) {
                         const prevItem = path.slice(-1)[0];
-                        const resolved = parent.properties.definitions?.[prevItem]
+                        const resolved = parent.properties.definitions?.[prevItem];
                         copy[propName] = resolved;
                     } else {
                         for (let key in internalCopy) {
-                            const fullPath = [...path, propName, key]
+                            const fullPath = [...path, propName, key];
                             internalCopy[key] = this.replaceRefsWithValue(internalCopy[key], fullPath, copy);
                         }
                     }
                 }
             }
-        } 
+        } else return schema;
 
-        else return schema
-
-        return copy
-    }
+        return copy;
+    };
 
     set schema(schema) {
         this.#schema = schema;
-        this.#schema = this.replaceRefsWithValue(schema)
+        this.#schema = this.replaceRefsWithValue(schema);
     }
 
-
-    get schema () {
+    get schema() {
         return this.#schema;
     }
 
@@ -770,31 +767,29 @@ export class JSONSchemaForm extends LitElement {
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
     triggerValidation = async (
-        name, 
-        path = [], 
-        checkLinks = true, 
-        input = this.getInput([...path, name]), 
+        name,
+        path = [],
+        checkLinks = true,
+        input = this.getInput([...path, name]),
         schema = this.getSchema([...path, name]),
         parent = this.#get(path, this.resolved),
-        {
-            onError,
-            onWarning
-        } = {}
+        { onError, onWarning } = {}
     ) => {
-
         const pathToValidate = [...(this.base ?? []), ...path];
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, ...localPath];
-        
-        const skipValidation = !this.validateEmptyValues && parent[name] === undefined
-        const validateArgs = input.pattern || skipValidation ? [] : [parent[name], schema]
 
-        const jsonSchemaErrors = validateArgs.length === 2 ? await v.validate(...validateArgs).errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` })) : [];
+        const skipValidation = !this.validateEmptyValues && parent[name] === undefined;
+        const validateArgs = input.pattern || skipValidation ? [] : [parent[name], schema];
+
+        const jsonSchemaErrors =
+            validateArgs.length === 2
+                ? await v
+                      .validate(...validateArgs)
+                      .errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` }))
+                : [];
 
-        const valid =
-        skipValidation
-                ? true
-                : await this.validateOnChange(name, parent, pathToValidate);
+        const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate);
 
         const isRequired = this.#isRequired(localPath) || input.required;
 
@@ -834,7 +829,6 @@ export class JSONSchemaForm extends LitElement {
             if (isUndefined) {
                 // Throw at least a basic warning if a non-linked property is required and missing
                 if (!hasLinks && isRequired) {
-
                     if (this.validateEmptyValues) {
                         errors.push({
                             message: `${schema.title ?? header(name)} ${this.#isARequiredPropertyString}.`,
@@ -900,8 +894,8 @@ export class JSONSchemaForm extends LitElement {
         this.checkStatus();
 
         // Show aggregated errors and warnings (if any)
-        warnings.forEach((info) => onWarning ? onWarning(info) : this.#addMessage(localPath, info, "warnings"));
-        info.forEach((info) => onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info"));
+        warnings.forEach((info) => (onWarning ? onWarning(info) : this.#addMessage(localPath, info, "warnings")));
+        info.forEach((info) => (onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info")));
 
         if (isValid && resolvedErrors.length === 0) {
             input.classList.remove("invalid");
@@ -929,7 +923,7 @@ export class JSONSchemaForm extends LitElement {
                 [...path, name]
             );
 
-            resolvedErrors.forEach((info) => onError ? onError(info) : this.#addMessage(localPath, info, "errors"));
+            resolvedErrors.forEach((info) => (onError ? onError(info) : this.#addMessage(localPath, info, "errors")));
             // element.title = errors.map((info) => info.message).join("\n"); // Set all errors to show on hover
 
             return false;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 77efde395..6885379c9 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -413,38 +413,39 @@ export class JSONSchemaInput extends LitElement {
 
                     ignore,
 
-                    onUpdate: () => this.#updateData(fullPath, tableMetadata.data, true, { onError: () => {}, onWarning: () => {} }), // Ensure change propagates to all forms
+                    onUpdate: () =>
+                        this.#updateData(fullPath, tableMetadata.data, true, {
+                            onError: () => {},
+                            onWarning: () => {},
+                        }), // Ensure change propagates to all forms
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: async (key, parent, v) => {
+                        const warnings = [];
+                        const errors = [];
 
-                        const warnings = []
-                        const errors = []
-
-                        const result = 
-                            await (validateOnChange &&
+                        const result = await (validateOnChange &&
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
                                   ? this.form.triggerValidation(
-                                    key, 
-                                    fullPath, 
-                                    false, 
-                                    this, 
-                                    itemSchema.properties[key], 
-                                    { ...parent, [key]: v },
-                                    {
-                                        onError: (error) => errors.push(error),
-
-                                        onWarning: (warning) => errors.push(warning),
-                                    }
-                                ) // NOTE: No pattern properties support
-                                  : ""))
-                        
-
-                        const returnedValue = errors.length ? errors : (warnings.length ? warnings : result)
-
-                        return returnedValue
+                                        key,
+                                        fullPath,
+                                        false,
+                                        this,
+                                        itemSchema.properties[key],
+                                        { ...parent, [key]: v },
+                                        {
+                                            onError: (error) => errors.push(error),
+
+                                            onWarning: (warning) => errors.push(warning),
+                                        }
+                                    ) // NOTE: No pattern properties support
+                                  : ""));
+
+                        const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
+
+                        return returnedValue;
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements

From 6b74de4ee52979aaebd7b9f60789591a28004125 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Fri, 15 Dec 2023 12:59:05 -0800
Subject: [PATCH 040/133] Fix table validation in tests

---
 src/renderer/src/stories/JSONSchemaForm.js  | 11 ++++++++---
 src/renderer/src/stories/JSONSchemaInput.js | 16 ++++++++++------
 src/renderer/src/validation/validation.ts   | 14 ++++++--------
 tests/metadata.test.ts                      |  4 ++--
 4 files changed, 26 insertions(+), 19 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f3f422eb8..ce226fdd8 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -388,6 +388,8 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
+
+        // Validate against the entire JSON Schema 
         const result = await v.validate(resolved, this.schema);
 
         // Check if any required inputs are missing
@@ -779,8 +781,10 @@ export class JSONSchemaForm extends LitElement {
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, ...localPath];
 
-        const skipValidation = !this.validateEmptyValues && parent[name] === undefined;
-        const validateArgs = input.pattern || skipValidation ? [] : [parent[name], schema];
+        const value = parent[name];
+        // const value = this.#get(path, this.resolved)
+        const skipValidation = !this.validateEmptyValues && value === undefined;
+        const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
         const jsonSchemaErrors =
             validateArgs.length === 2
@@ -789,7 +793,8 @@ export class JSONSchemaForm extends LitElement {
                       .errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` }))
                 : [];
 
-        const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate);
+        // const jsonSchemaErrors =[]
+        const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
         const isRequired = this.#isRequired(localPath) || input.required;
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 6885379c9..eb8d895ca 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -13,6 +13,8 @@ import { capitalize } from "./forms/utils";
 import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 
+const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
+
 const isFilesystemSelector = (name, format) => {
     if (Array.isArray(format)) return format.map((f) => isFilesystemSelector(name, f)).every(Boolean) ? format : null;
 
@@ -141,8 +143,8 @@ export class JSONSchemaInput extends LitElement {
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
-        this.#triggerValidation(name, path);
         this.#updateData(fullPath, value);
+        this.#triggerValidation(name, path); // NOTE: Is asynchronous
 
         return true;
     }
@@ -165,7 +167,7 @@ export class JSONSchemaInput extends LitElement {
     };
 
     #validationTimeout = null;
-    #updateData = (fullPath, value, forceUpdate, hooks) => {
+    #updateData = (fullPath, value, forceUpdate, hooks = {}) => {
         this.onUpdate ? this.onUpdate(value) : this.form ? this.form.updateData(fullPath, value, forceUpdate) : "";
 
         const path = [...fullPath];
@@ -173,7 +175,7 @@ export class JSONSchemaInput extends LitElement {
 
         this.value = value; // Update the latest value
 
-        this.#activateTimeoutValidation(name, path, hooks);
+        if (hooks.willTimeout !== false) this.#activateTimeoutValidation(name, path, hooks);
     };
 
     #triggerValidation = async (name, path) => {
@@ -413,11 +415,13 @@ export class JSONSchemaInput extends LitElement {
 
                     ignore,
 
-                    onUpdate: () =>
-                        this.#updateData(fullPath, tableMetadata.data, true, {
+                    onUpdate: () => {
+                        return this.#updateData(fullPath, tableMetadata.data, true, {
+                            // willTimeout: false,
                             onError: () => {},
                             onWarning: () => {},
-                        }), // Ensure change propagates to all forms
+                        }) // Ensure change propagates to all forms
+                    },
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: async (key, parent, v) => {
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 62cc9bfc8..d19985cb9 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -26,23 +26,21 @@ schema.Ecephys.ElectrodeGroup.device = function (this: JSONSchemaForm, name, par
 
 
 // NOTE: Does this maintain separation between multiple sessions?
-schema.Ecephys.ElectrodeGroup.name = function(this: JSONSchemaForm, name, parent, path, value) {
-    const currentGroups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
+schema.Ecephys.ElectrodeGroup.name = function(this: JSONSchemaForm, _, __, ___, value) {
+    const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
 
      // Check if the latest value will be new. Run function after validation
-
-    if (!value || !currentGroups.includes(value)) {
+    if (!value || !groups.includes(value)) {
         return () => {
-            rerender.call(this, ['Ecephys', 'Electrodes'])
+             setTimeout(() => rerender.call(this, ['Ecephys', 'Electrodes'])) // Allow for the updates to occur
         }
     }
 }
 
-schema.Ecephys.Electrodes.group_name = function (this: JSONSchemaForm, name, parent, path) {
+schema.Ecephys.Electrodes.group_name = function (this: JSONSchemaForm, _, __, ___, value) {
 
     const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
-
-    if (groups.includes(parent[name])) return true
+    if (groups.includes(value)) return true
     else {
         return [
             {
diff --git a/tests/metadata.test.ts b/tests/metadata.test.ts
index 2396154bc..a3347efc2 100644
--- a/tests/metadata.test.ts
+++ b/tests/metadata.test.ts
@@ -117,7 +117,7 @@ test('inter-table updates are triggered', async () => {
     await form.rendered
 
     // Validate that the results are incorrect
-    const errors = await form.validate().catch(() => true).catch(e =>  true)
+    const errors = await form.validate().catch(e =>  { return true })
     expect(errors).toBe(true) // Is invalid
 
     // Update the table with the missing electrode group
@@ -135,7 +135,7 @@ test('inter-table updates are triggered', async () => {
 
     // Validate that the new structure is correct
     const hasErrors = await form.validate().then(() => false).catch((e) => {
-        console.error(e)
+        console.log('Final', form.results.Ecephys.Electrodes, form.results.Ecephys.ElectrodeGroup)
         return true
     })
     expect(hasErrors).toBe(false) // Is valid

From 9167be508c8cd1662177d5310c0d88c2fa51082e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 15 Dec 2023 20:59:42 +0000
Subject: [PATCH 041/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index ce226fdd8..79bbd032c 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -388,8 +388,7 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
-
-        // Validate against the entire JSON Schema 
+        // Validate against the entire JSON Schema
         const result = await v.validate(resolved, this.schema);
 
         // Check if any required inputs are missing
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index eb8d895ca..c9ba9dfb3 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -420,7 +420,7 @@ export class JSONSchemaInput extends LitElement {
                             // willTimeout: false,
                             onError: () => {},
                             onWarning: () => {},
-                        }) // Ensure change propagates to all forms
+                        }); // Ensure change propagates to all forms
                     },
 
                     // NOTE: This is likely an incorrect declaration of the table validation call

From 0be825c7e1ffacc5ca931ad908d36516e311438a Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Mon, 18 Dec 2023 10:25:54 -0800
Subject: [PATCH 042/133] Allow editing nested tables

---
 schemas/base-metadata.schema.ts               | 18 ++--
 src/renderer/src/stories/BasicTable.js        | 27 ++++--
 src/renderer/src/stories/JSONSchemaForm.js    |  8 +-
 src/renderer/src/stories/JSONSchemaInput.js   | 22 +++--
 src/renderer/src/stories/SimpleTable.js       | 91 ++++++++++++++-----
 src/renderer/src/stories/Table.js             |  4 +-
 src/renderer/src/stories/table/Cell.ts        | 28 ++++--
 src/renderer/src/stories/table/cells/base.ts  | 20 +++-
 src/renderer/src/stories/table/cells/table.ts | 16 +++-
 9 files changed, 172 insertions(+), 62 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index fb01263d0..d27f7b414 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -88,12 +88,18 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
         ]
 
 
-        if (getProp("ImagingPlane")) getProp("ImagingPlane").items.order = [
-            "name",
-            "description",
-            "device",
-            "optical_channel"
-        ]
+        if (getProp("ImagingPlane")) {
+            const imagingPlane = getProp("ImagingPlane")
+            imagingPlane.items.order = [
+                "name",
+                "description",
+                "device",
+                "optical_channel"
+            ]
+
+            imagingPlane.items.properties.optical_channel.items.order = ["name", "description"]
+
+        }
     }
 
 
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 003b415de..fef7292c0 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -8,6 +8,7 @@ import * as promises from "../promises";
 
 import "./Button";
 import { sortTable } from "./Table";
+import tippy from "tippy.js";
 
 export class BasicTable extends LitElement {
     static get styles() {
@@ -228,7 +229,7 @@ export class BasicTable extends LitElement {
         else if (value !== "" && thisTypeOf !== type)
             result = [{ message: `${col} is expected to be of type ${ogType}, not ${thisTypeOf}`, type: "error" }];
         // Otherwise validate using the specified onChange function
-        else result = this.validateOnChange(col, parent, value);
+        else result = this.validateOnChange( [ col ], parent, value);
 
         // Will run synchronously if not a promise result
         return promises.resolve(result, () => {
@@ -243,14 +244,12 @@ export class BasicTable extends LitElement {
 
             if (result === false) errors.push({ message: "Cell is invalid" });
 
-            if (warnings.length) {
-                info.warning = "";
-                info.title = warnings.map((o) => o.message).join("\n");
-            }
-
             if (errors.length) {
                 info.error = "";
                 info.title = errors.map((o) => o.message).join("\n"); // Class switching handled automatically
+            } else if (warnings.length) {
+                info.warning = "";
+                info.title = warnings.map((o) => o.message).join("\n");
             }
 
             if (typeof result === "function") result(); // Run if returned value is a function
@@ -269,6 +268,22 @@ export class BasicTable extends LitElement {
                     if (info === true) return;
                     const td = this.shadowRoot.getElementById(`i${i}_j${j}`);
                     if (td) {
+
+                        const message = info.title
+                        delete info.title
+
+                        if (td._tippy) {
+                            td._tippy.destroy();
+                            td.removeAttribute("data-message");
+                        }
+                        
+
+                        if (message !== undefined) {
+                            tippy(td, { content: message });
+                            td.setAttribute("data-message", value);
+                        }
+
+
                         for (let key in info) {
                             const value = info[key];
                             if (value === undefined) td.removeAttribute(key);
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 79bbd032c..8252c7ef4 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -789,9 +789,15 @@ export class JSONSchemaForm extends LitElement {
             validateArgs.length === 2
                 ? await v
                       .validate(...validateArgs)
-                      .errors.map((e) => ({ type: "error", message: `${header(name)} ${e.message}.` }))
+                      .errors.map((e) => {
+                        const propName = e.path.slice(-1)[0] ?? name
+                        const rowName = e.path.slice(-2)[0]
+                        return { type: "error", message: `${typeof propName === "string" ? `${header(propName)}${typeof rowName === 'number' ? ` on Row ${rowName}` : ''}` : `Row ${propName}`} ${e.message}.` }
+                      }).filter(v => !!v)
                 : [];
 
+        // console.log(externalPath.join('.'), jsonSchemaErrors, ...validateArgs)
+
         // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index c9ba9dfb3..9f4ff26c7 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -409,14 +409,15 @@ export class JSONSchemaInput extends LitElement {
                     ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
                     : {};
 
+                    const ogThis = this;
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
 
                     ignore,
 
-                    onUpdate: () => {
-                        return this.#updateData(fullPath, tableMetadata.data, true, {
+                    onUpdate: function () {
+                        return ogThis.#updateData(fullPath, this.data, true, {
                             // willTimeout: false,
                             onError: () => {},
                             onWarning: () => {},
@@ -424,21 +425,28 @@ export class JSONSchemaInput extends LitElement {
                     },
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
-                    validateOnChange: async (key, parent, v) => {
+                    validateOnChange: async (path, parent, v, baseSchema = itemSchema) => {
                         const warnings = [];
                         const errors = [];
 
+                        const name = path.slice(-1)[0];
+                        const completePath = [...fullPath, ...path.slice(0, -1)];
+
+                        const itemPropSchema = path.reduce((acc, key) => {
+                            return acc?.properties?.[key] ?? acc?.items?.properties?.[key]
+                        }, baseSchema)
+
                         const result = await (validateOnChange &&
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
                                   ? this.form.triggerValidation(
-                                        key,
-                                        fullPath,
+                                        name,
+                                        completePath,
                                         false,
                                         this,
-                                        itemSchema.properties[key],
-                                        { ...parent, [key]: v },
+                                        itemPropSchema,
+                                        { ...parent, [name]: v },
                                         {
                                             onError: (error) => errors.push(error),
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 6e79f93d1..359f18d53 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -12,6 +12,7 @@ import { styleMap } from "lit/directives/style-map.js";
 import "./Button";
 import tippy from "tippy.js";
 import { sortTable } from "./Table";
+import { NestedTableCell } from "./table/cells/table";
 
 var isMac = navigator.platform.toUpperCase().indexOf("MAC") >= 0;
 
@@ -177,7 +178,7 @@ export class SimpleTable extends LitElement {
     } = {}) {
         super();
         this.schema = schema ?? {};
-        this.data = data ?? [];
+        this.#data = data ?? [];
         this.keyColumn = keyColumn;
         this.globals = globals ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
@@ -268,6 +269,17 @@ export class SimpleTable extends LitElement {
         });
     }
 
+    #data = []
+    get data() {
+        // Remove empty array entries
+        if (Array.isArray(this.#data)) return this.#data.filter((o) => Object.keys(o).length);
+        else return this.#data;
+    }
+
+    set data(val) {
+        this.#data = val;
+    }
+
     #selected = {};
     #selecting = false;
     #firstSelected; // TableCell
@@ -285,7 +297,13 @@ export class SimpleTable extends LitElement {
     #getPath = (ev) => ev.path || ev.composedPath();
     #getCellFromEvent = (ev) => this.#getCellFromPath(this.#getPath(ev));
     #getCellFromPath = (path) => {
-        const found = path.find((el) => el instanceof TableCell || el.children?.[0] instanceof TableCell);
+
+        let inTableCell
+
+        const found = path.find((el) => {
+            if (el instanceof NestedTableCell) inTableCell = true;
+            return !inTableCell && (el instanceof TableCell || el.children?.[0] instanceof TableCell)
+        });
         if (found instanceof HTMLTableCellElement) return found.children[0];
         else return found;
     };
@@ -331,7 +349,7 @@ export class SimpleTable extends LitElement {
     }
 
     #getRowData(row, cols = this.colHeaders) {
-        const hasRow = row in this.data;
+        const hasRow = row in this.#data;
         return cols.map((col, j) => {
             let value;
             if (col === this.keyColumn) {
@@ -339,7 +357,7 @@ export class SimpleTable extends LitElement {
                 else return "";
             } else
                 value =
-                    (hasRow ? this.data[row][col] : undefined) ??
+                    (hasRow ? this.#data[row][col] : undefined) ??
                     this.globals[col] ??
                     this.schema.properties[col].default ??
                     "";
@@ -347,7 +365,7 @@ export class SimpleTable extends LitElement {
         });
     }
 
-    #getData(rows = Object.keys(this.data), cols = this.colHeaders) {
+    #getData(rows = Object.keys(this.#data), cols = this.colHeaders) {
         return rows.map((row, i) => this.#getRowData(row, cols));
     }
 
@@ -421,11 +439,11 @@ export class SimpleTable extends LitElement {
                     const { i, row } = cell.simpleTableInfo; // TODO: Support detecting when the user would like to remove more than one row
 
                     // Validate with empty values before removing (to trigger any dependent validations)
-                    const cols = this.data[row];
+                    const cols = this.#data[row];
                     Object.keys(cols).map((k) => (cols[k] = ""));
                     if (this.validateOnChange)
                         Object.keys(cols).map((k) => {
-                            const res = this.validateOnChange(k, { ...cols }, cols[k]);
+                            const res = this.validateOnChange([ k ], { ...cols }, cols[k]);
                             if (typeof res === "function") res();
                         });
 
@@ -554,10 +572,10 @@ export class SimpleTable extends LitElement {
                 return false;
             }
 
-            const rowHeaders = Object.keys(this.data);
+            const rowHeaders = Object.keys(this.#data);
             range.map((i) => {
                 children[i].remove();
-                delete this.data[rowHeaders[row]];
+                delete this.#data[rowHeaders[row]];
                 delete this.#unresolved[row];
                 delete this.#cells[i];
             });
@@ -631,11 +649,11 @@ export class SimpleTable extends LitElement {
         // NOTE: We would like to allow invalid values to mutate the results
         // if (isValid) {
 
-        const isResolved = rowName in this.data;
-        let target = this.data;
+        const isResolved = rowName in this.#data;
+        let target = this.#data;
 
         if (!isResolved) {
-            if (!this.keyColumn) this.data[rowName] = {}; // Add new row to array
+            if (!this.keyColumn) this.#data[rowName] = {}; // Add new row to array
             else {
                 rowName = row;
                 if (!this.#unresolved[rowName]) this.#unresolved[rowName] = {}; // Ensure row exists
@@ -648,7 +666,7 @@ export class SimpleTable extends LitElement {
             if (value !== rowName) {
                 const old = target[rowName] ?? {};
                 if (value) {
-                    this.data[value] = old; // Allow renaming when different
+                    this.#data[value] = old; // Allow renaming when different
                     delete this.#unresolved[row];
                 } else this.#unresolved[row] = old; // Allow tracking when keyColumn is deleted
 
@@ -661,16 +679,16 @@ export class SimpleTable extends LitElement {
             else target[rowName][header] = value;
         }
 
-        if (cell.interacted) this.onUpdate([rowName, header], value);
+        if (cell.interacted) this.onUpdate([ rowName, header ], value);
     };
 
     #createCell = (value, info) => {
-        const rowNames = Object.keys(this.data);
+        const rowNames = Object.keys(this.#data);
 
         const fullInfo = {
             ...info,
             col: this.colHeaders[info.j],
-            row: Array.isArray(this.data) ? `${info.i}` : rowNames[info.i],
+            row: Array.isArray(this.#data) ? `${info.i}` : rowNames[info.i],
         };
 
         const schema = this.#schema[fullInfo.col];
@@ -682,14 +700,23 @@ export class SimpleTable extends LitElement {
             },
             value,
             schema,
-            validateOnChange: (value) => {
+            validateOnChange: async (
+                value, 
+                path = [], 
+                parent = { ...this.#data[fullInfo.row] }, // A copy of the parent
+                schema
+            ) => {
+
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                const res = this.validateOnChange
+                path = [ fullInfo.col, ...path ];
+
+                const res = await this.validateOnChange
                     ? this.validateOnChange(
-                          fullInfo.col,
-                          { ...this.data[fullInfo.row] }, // Validate on a copy of the parent
-                          value
+                          path,
+                          parent,
+                          value,
+                          schema
                       )
                     : true;
 
@@ -699,6 +726,22 @@ export class SimpleTable extends LitElement {
             onValidate: (info) => {
                 const td = cell.simpleTableInfo.td;
                 if (td) {
+
+                    const message = info.title
+                    delete info.title
+
+
+                    if (td._tippy) {
+                        td._tippy.destroy();
+                        td.removeAttribute("data-message");
+                    }
+                    
+                    if (message !== undefined) {
+                        tippy(td, { content: message });
+                        td.setAttribute("data-message", value);
+                    }
+
+                        
                     for (let key in info) {
                         const value = info[key];
                         if (value === undefined) td.removeAttribute(key);
@@ -746,7 +789,7 @@ export class SimpleTable extends LitElement {
 
         // Add existing additional / pattern properties to the entries variable if necessary
         if (this.schema.additionalProperties !== false || this.schema.patternProperties) {
-            Object.values(this.data).reduce((acc, v) => {
+            Object.values(this.#data).reduce((acc, v) => {
                 Object.keys(v).forEach((k) =>
                     !(k in entries)
                         ? (entries[k] = {
@@ -769,8 +812,8 @@ export class SimpleTable extends LitElement {
         );
 
         // Try to guess the key column if unspecified
-        if (!Array.isArray(this.data) && !this.keyColumn) {
-            const [key, value] = Object.entries(this.data)[0];
+        if (!Array.isArray(this.#data) && !this.keyColumn) {
+            const [key, value] = Object.entries(this.#data)[0];
             const foundKey = Object.keys(value).find((k) => value[k] === key);
             if (foundKey) this.keyColumn = foundKey;
         }
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index eefd38bff..6c24a22db 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -282,7 +282,7 @@ export class Table extends LitElement {
                 try {
                     const valid = this.validateOnChange
                         ? await this.validateOnChange(
-                              k,
+                              [ k ],
                               { ...this.data[rowHeaders[row]] }, // Validate on a copy of the parent
                               value
                           )
@@ -606,7 +606,7 @@ export class Table extends LitElement {
             }
 
             if (message) {
-                tippy(cell, { content: message, theme });
+                tippy(cell, { content: message });
                 cell.setAttribute("data-message", message);
             }
         }
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index d5c85bc7a..74ba18966 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -97,7 +97,16 @@ export class TableCell extends LitElement {
     toggle = (v: boolean) => this.input.toggle(v)
 
     get value() {
-        return this.input ? this.input.getValue() : this.#value
+
+        let v = this.input ? this.input.getValue() : this.#value
+
+        if (this.schema.type === 'number' || this.schema.type === 'integer') {
+            const og = v
+            if (og === '') v = undefined
+            else v = Number(v)
+        }
+
+        return v
     }
 
     set value(v) {
@@ -127,14 +136,14 @@ export class TableCell extends LitElement {
 
         if (result === false) errors.push({ message: 'Cell is invalid' })
 
-        if (warnings.length) {
-            info.warning = ''
-            info.title = warnings.map((o) => o.message).join("\n");
-        }
-
         if (errors.length) {
             info.error = ''
-            info.title = errors.map((o) => o.message).join("\n"); // Class switching handled automatically
+            if (this.#cls === NestedTableCell) info.title = `${errors.length} errors found on this nested table.`
+            else info.title = errors.map((o) => o.message).join("\n\n"); // Class switching handled automatically
+        } else if (warnings.length) {
+            info.warning = ''
+            if (this.#cls === NestedTableCell) info.title = `${warnings.length} warnings found on this nested table.`
+            else info.title = warnings.map((o) => o.message).join("\n");
         }
 
         this.onValidate(info)
@@ -190,7 +199,10 @@ export class TableCell extends LitElement {
                 },
                 toggle: (v) => this.toggle(v),
                 info: this.info,
-                schema: this.schema
+                schema: this.schema,
+                nestedProps: {
+                    validateOnChange: this.validateOnChange,
+                }
             })
         }
 
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 66d0b68d4..1163b76bb 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -9,13 +9,21 @@ type BaseTableProps = {
     schema: any,
     onOpen: Function,
     onClose: Function,
-    onChange: Function
+    onChange: Function,
+    nestedProps: NestedTableCellProps,
+}
+
+
+type NestedTableCellProps = {
+    validateOnChange?: Function,
 }
 
 export class TableCellBase extends LitElement {
 
     declare value: any
 
+    nestedProps: NestedTableCellProps
+
     // Separate editor and renderer
     #editable: HTMLElement = document.createElement('div')
     editor: HTMLElement | Function = this.#editable
@@ -63,7 +71,8 @@ export class TableCellBase extends LitElement {
         onOpen,
         onClose,
         onChange,
-        toggle
+        toggle,
+        nestedProps
     }: Partial<BaseTableProps> = {}) {
 
         super()
@@ -71,6 +80,8 @@ export class TableCellBase extends LitElement {
         this.info = info ?? {}
         this.schema = schema ?? {}
 
+        this.nestedProps = nestedProps ?? {}
+
         this.editToggle = toggle ?? (() => {});
 
         if (onOpen) this.onOpen = onOpen
@@ -129,7 +140,6 @@ export class TableCellBase extends LitElement {
 
             this.onClose()
 
-
             this.setText( current )
         }
 
@@ -140,6 +150,7 @@ export class TableCellBase extends LitElement {
 
     #update(current: any, forceUpdate = false) {
         let value = this.getValue(current)
+
         // NOTE: Forcing change registration for all cells
         if (this.value !== value || forceUpdate) {
             this.value = value
@@ -150,9 +161,8 @@ export class TableCellBase extends LitElement {
     setText(value: any, setOnInput = true) {
         if (setOnInput) [ this.#editor, this.#renderer ].forEach(el => this.setChild(el, value)) // RESETS HISTORY
 
-        if (this.schema.type === 'array') this.#update(value, true) // Ensure array values are not coerced
+        if (this.schema.type === 'array' || this.schema.type === 'object') this.#update(value, true) // Ensure array values are not coerced
         else this.#update(`${value}`) // Coerce to string
-
     }
 
 
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
index aac54219e..8f6fd6115 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -11,12 +11,14 @@ export class NestedTableEditor extends LitElement {
     info: any
     schema: any
     toggle: any
+    validateOnChange
 
     constructor(props: any) {
         super(props)
         this.schema = props.schema
         this.info = props.info ?? {}
         this.toggle = props.toggle
+        this.validateOnChange = props.validateOnChange
     }
 
     #modal = new Modal({
@@ -45,10 +47,12 @@ export class NestedTableEditor extends LitElement {
 
         document.body.append(div)
 
-
         const table = this.#table = new SimpleTable({
             schema: this.schema.items,
-            data: this.#value
+            data: this.#value,
+            validateOnChange: (path, parent, value, schema) => {
+                if (this.validateOnChange) return this.validateOnChange(value, path, parent, schema) // NOTE: Flipped because usually only value is passed
+            }
         })
 
         table.style.padding = '25px 50px'
@@ -118,7 +122,13 @@ export class NestedTableCell extends TableCellBase {
 
     renderer = new NestedTableRenderer({ value: this.value })
 
-    editor = new NestedTableEditor({ info: this.info, toggle: this.editToggle, value: this.value, schema: this.schema })
+    editor = new NestedTableEditor({ 
+        info: this.info, 
+        toggle: this.editToggle, 
+        value: this.value, 
+        schema: this.schema,
+        ...this.nestedProps
+    })
 }
 
 customElements.get("nwb-nested-table-cell") || customElements.define("nwb-nested-table-cell", NestedTableCell);

From b9975a537ac8bc614f9d54a2a7d3296a5929c82a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Dec 2023 18:26:21 +0000
Subject: [PATCH 043/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/BasicTable.js        |  9 ++---
 src/renderer/src/stories/JSONSchemaForm.js    | 16 ++++++---
 src/renderer/src/stories/JSONSchemaInput.js   |  6 ++--
 src/renderer/src/stories/SimpleTable.js       | 36 +++++++------------
 src/renderer/src/stories/Table.js             |  2 +-
 src/renderer/src/stories/table/cells/table.ts |  8 ++---
 6 files changed, 35 insertions(+), 42 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index fef7292c0..f321dae15 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -229,7 +229,7 @@ export class BasicTable extends LitElement {
         else if (value !== "" && thisTypeOf !== type)
             result = [{ message: `${col} is expected to be of type ${ogType}, not ${thisTypeOf}`, type: "error" }];
         // Otherwise validate using the specified onChange function
-        else result = this.validateOnChange( [ col ], parent, value);
+        else result = this.validateOnChange([col], parent, value);
 
         // Will run synchronously if not a promise result
         return promises.resolve(result, () => {
@@ -268,22 +268,19 @@ export class BasicTable extends LitElement {
                     if (info === true) return;
                     const td = this.shadowRoot.getElementById(`i${i}_j${j}`);
                     if (td) {
-
-                        const message = info.title
-                        delete info.title
+                        const message = info.title;
+                        delete info.title;
 
                         if (td._tippy) {
                             td._tippy.destroy();
                             td.removeAttribute("data-message");
                         }
-                        
 
                         if (message !== undefined) {
                             tippy(td, { content: message });
                             td.setAttribute("data-message", value);
                         }
 
-
                         for (let key in info) {
                             const value = info[key];
                             if (value === undefined) td.removeAttribute(key);
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 8252c7ef4..8a2ca63e9 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -790,10 +790,18 @@ export class JSONSchemaForm extends LitElement {
                 ? await v
                       .validate(...validateArgs)
                       .errors.map((e) => {
-                        const propName = e.path.slice(-1)[0] ?? name
-                        const rowName = e.path.slice(-2)[0]
-                        return { type: "error", message: `${typeof propName === "string" ? `${header(propName)}${typeof rowName === 'number' ? ` on Row ${rowName}` : ''}` : `Row ${propName}`} ${e.message}.` }
-                      }).filter(v => !!v)
+                          const propName = e.path.slice(-1)[0] ?? name;
+                          const rowName = e.path.slice(-2)[0];
+                          return {
+                              type: "error",
+                              message: `${
+                                  typeof propName === "string"
+                                      ? `${header(propName)}${typeof rowName === "number" ? ` on Row ${rowName}` : ""}`
+                                      : `Row ${propName}`
+                              } ${e.message}.`,
+                          };
+                      })
+                      .filter((v) => !!v)
                 : [];
 
         // console.log(externalPath.join('.'), jsonSchemaErrors, ...validateArgs)
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 9f4ff26c7..1c6f43b4a 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -409,7 +409,7 @@ export class JSONSchemaInput extends LitElement {
                     ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
                     : {};
 
-                    const ogThis = this;
+                const ogThis = this;
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
@@ -433,8 +433,8 @@ export class JSONSchemaInput extends LitElement {
                         const completePath = [...fullPath, ...path.slice(0, -1)];
 
                         const itemPropSchema = path.reduce((acc, key) => {
-                            return acc?.properties?.[key] ?? acc?.items?.properties?.[key]
-                        }, baseSchema)
+                            return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
+                        }, baseSchema);
 
                         const result = await (validateOnChange &&
                             (this.onValidate
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 359f18d53..78685feb5 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -269,7 +269,7 @@ export class SimpleTable extends LitElement {
         });
     }
 
-    #data = []
+    #data = [];
     get data() {
         // Remove empty array entries
         if (Array.isArray(this.#data)) return this.#data.filter((o) => Object.keys(o).length);
@@ -297,12 +297,11 @@ export class SimpleTable extends LitElement {
     #getPath = (ev) => ev.path || ev.composedPath();
     #getCellFromEvent = (ev) => this.#getCellFromPath(this.#getPath(ev));
     #getCellFromPath = (path) => {
-
-        let inTableCell
+        let inTableCell;
 
         const found = path.find((el) => {
             if (el instanceof NestedTableCell) inTableCell = true;
-            return !inTableCell && (el instanceof TableCell || el.children?.[0] instanceof TableCell)
+            return !inTableCell && (el instanceof TableCell || el.children?.[0] instanceof TableCell);
         });
         if (found instanceof HTMLTableCellElement) return found.children[0];
         else return found;
@@ -443,7 +442,7 @@ export class SimpleTable extends LitElement {
                     Object.keys(cols).map((k) => (cols[k] = ""));
                     if (this.validateOnChange)
                         Object.keys(cols).map((k) => {
-                            const res = this.validateOnChange([ k ], { ...cols }, cols[k]);
+                            const res = this.validateOnChange([k], { ...cols }, cols[k]);
                             if (typeof res === "function") res();
                         });
 
@@ -679,7 +678,7 @@ export class SimpleTable extends LitElement {
             else target[rowName][header] = value;
         }
 
-        if (cell.interacted) this.onUpdate([ rowName, header ], value);
+        if (cell.interacted) this.onUpdate([rowName, header], value);
     };
 
     #createCell = (value, info) => {
@@ -701,24 +700,16 @@ export class SimpleTable extends LitElement {
             value,
             schema,
             validateOnChange: async (
-                value, 
-                path = [], 
+                value,
+                path = [],
                 parent = { ...this.#data[fullInfo.row] }, // A copy of the parent
                 schema
             ) => {
-
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                path = [ fullInfo.col, ...path ];
+                path = [fullInfo.col, ...path];
 
-                const res = await this.validateOnChange
-                    ? this.validateOnChange(
-                          path,
-                          parent,
-                          value,
-                          schema
-                      )
-                    : true;
+                const res = (await this.validateOnChange) ? this.validateOnChange(path, parent, value, schema) : true;
 
                 return res;
             },
@@ -726,22 +717,19 @@ export class SimpleTable extends LitElement {
             onValidate: (info) => {
                 const td = cell.simpleTableInfo.td;
                 if (td) {
-
-                    const message = info.title
-                    delete info.title
-
+                    const message = info.title;
+                    delete info.title;
 
                     if (td._tippy) {
                         td._tippy.destroy();
                         td.removeAttribute("data-message");
                     }
-                    
+
                     if (message !== undefined) {
                         tippy(td, { content: message });
                         td.setAttribute("data-message", value);
                     }
 
-                        
                     for (let key in info) {
                         const value = info[key];
                         if (value === undefined) td.removeAttribute(key);
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 6c24a22db..3a9ea89d9 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -282,7 +282,7 @@ export class Table extends LitElement {
                 try {
                     const valid = this.validateOnChange
                         ? await this.validateOnChange(
-                              [ k ],
+                              [k],
                               { ...this.data[rowHeaders[row]] }, // Validate on a copy of the parent
                               value
                           )
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
index 8f6fd6115..49beb57d6 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -122,10 +122,10 @@ export class NestedTableCell extends TableCellBase {
 
     renderer = new NestedTableRenderer({ value: this.value })
 
-    editor = new NestedTableEditor({ 
-        info: this.info, 
-        toggle: this.editToggle, 
-        value: this.value, 
+    editor = new NestedTableEditor({
+        info: this.info,
+        toggle: this.editToggle,
+        value: this.value,
         schema: this.schema,
         ...this.nestedProps
     })

From 3596b776c20df18267a2861ddf7ca1d7cfd8c4c6 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Mon, 18 Dec 2023 13:30:18 -0800
Subject: [PATCH 044/133] Proper validation of all table properties, including
 nested

---
 src/renderer/src/stories/JSONSchemaForm.js    | 86 +++++++++++++------
 src/renderer/src/stories/JSONSchemaInput.js   | 18 ++--
 src/renderer/src/stories/SimpleTable.js       |  7 +-
 .../pages/guided-mode/setup/GuidedSubjects.js |  2 +-
 src/renderer/src/stories/table/Cell.ts        | 29 +++++--
 5 files changed, 100 insertions(+), 42 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 8a2ca63e9..1a0028096 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -443,11 +443,16 @@ export class JSONSchemaForm extends LitElement {
                 await this.#nestedForms[name].validate(resolved ? resolved[name] : undefined); // Validate nested forms too
         }
 
-        try {
-            for (let key in this.tables) await this.tables[key].validate(resolved ? resolved[key] : undefined); // Validate nested tables too
-        } catch (e) {
-            this.throw(e.message);
-        }
+            for (let key in this.tables) {
+                try {
+                    this.tables[key].validate(resolved ? resolved[key] : undefined); // Validate nested tables too
+                } catch (e) {
+                    const title = this.tables[key].schema.title
+                    const message = e.message.replace('this table', `the <b>${header(title ?? [...this.base, key].join("."))}</b> table`);
+                    this.throw(message);
+                    break;
+                }
+            }
 
         // NOTE: Ensure user is aware of any warnings before moving on
         // const activeWarnings = Array.from(this.shadowRoot.querySelectorAll('.warnings')).map(input => Array.from(input.children)).filter(input => input.length)
@@ -553,7 +558,8 @@ export class JSONSchemaForm extends LitElement {
     }
 
     #renderInteractiveElement = (name, info, required, path = [], value, pattern = false) => {
-        let isRequired = required[name];
+        let isRequired = this.#isRequired([...path, name])
+        
 
         const localPath = [...path, name];
         const externalPath = [...this.base, ...localPath];
@@ -689,7 +695,7 @@ export class JSONSchemaForm extends LitElement {
 
         const isRenderable = (key, value) => {
             if (recursive && value.properties)
-                return this.#getRenderable(value, required[key], getIgnore(ignore, key), [...path, key], true);
+                return this.#getRenderable(value, this.#isRequired([...path, key]), getIgnore(ignore, key), [...path, key], true);
             else return [key, value];
         };
 
@@ -748,8 +754,7 @@ export class JSONSchemaForm extends LitElement {
     #isRequired = (path) => {
         if (typeof path === "string") path = path.split("-");
         // path = path.slice(this.base.length); // Remove base path
-        let res = path.reduce((obj, key) => obj && obj[key], this.#requirements);
-
+        let res = path.reduce((obj, key) => obj?.[key], this.#requirements);
         if (typeof res === "object") res = res[selfRequiredSymbol];
         return res;
     };
@@ -774,8 +779,11 @@ export class JSONSchemaForm extends LitElement {
         input = this.getInput([...path, name]),
         schema = this.getSchema([...path, name]),
         parent = this.#get(path, this.resolved),
-        { onError, onWarning } = {}
+        hooks = {}
     ) => {
+
+        const { onError, onWarning } = hooks
+
         const pathToValidate = [...(this.base ?? []), ...path];
         const localPath = [...path, name]; // Use basePath to augment the validation
         const externalPath = [...this.base, ...localPath];
@@ -804,12 +812,11 @@ export class JSONSchemaForm extends LitElement {
                       .filter((v) => !!v)
                 : [];
 
-        // console.log(externalPath.join('.'), jsonSchemaErrors, ...validateArgs)
 
         // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
-        const isRequired = this.#isRequired(localPath) || input.required;
+        const isRequired = this.#isRequired(localPath) || (!input.table && input.required); // Do not trust required status of table validations
 
         let warnings = Array.isArray(valid)
             ? valid.filter((info) => info.type === "warning" && (!isRequired || !info.missing))
@@ -896,6 +903,10 @@ export class JSONSchemaForm extends LitElement {
                 // Non-Strict Rule
                 if (schema.strict === false && e.message.includes("is not one of enum values")) return;
 
+                if (e.message.includes("is not of a type(s) number")) {
+                    if (Number.isNaN(value)) return
+                }
+
                 // Custom Error Transformations
                 if (this.transformErrors) {
                     const res = this.transformErrors(e, externalPath, parent[name]);
@@ -907,15 +918,20 @@ export class JSONSchemaForm extends LitElement {
             .filter((v) => !!v);
 
         // Track errors and warnings
-        this.#nErrors += resolvedErrors.length;
-        this.#nWarnings += warnings.length;
+
+        const updatedWarnings = warnings.map(info => onWarning ? onWarning(info) : info).filter(v => !!v)
+        const updatedErrors = resolvedErrors.map(info => onError ? onError(info) : info).filter(v => !!v)
+
+
+        this.#nErrors += updatedErrors.length;
+        this.#nWarnings += updatedWarnings.length;
         this.checkStatus();
 
         // Show aggregated errors and warnings (if any)
-        warnings.forEach((info) => (onWarning ? onWarning(info) : this.#addMessage(localPath, info, "warnings")));
+        updatedWarnings.forEach((info) => (onWarning ? '' : this.#addMessage(localPath, info, "warnings")));
         info.forEach((info) => (onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info")));
 
-        if (isValid && resolvedErrors.length === 0) {
+        if (isValid && updatedErrors.length === 0) {
             input.classList.remove("invalid");
 
             const linkEl = this.#getLinkElement(externalPath);
@@ -941,7 +957,7 @@ export class JSONSchemaForm extends LitElement {
                 [...path, name]
             );
 
-            resolvedErrors.forEach((info) => (onError ? onError(info) : this.#addMessage(localPath, info, "errors")));
+            updatedErrors.forEach((info) => (onError ? '' : this.#addMessage(localPath, info, "errors")));
             // element.title = errors.map((info) => info.message).join("\n"); // Set all errors to show on hover
 
             return false;
@@ -980,6 +996,12 @@ export class JSONSchemaForm extends LitElement {
             return acc;
         }, []);
 
+
+        const getRequiredValue = (name) => {
+            const value = required[name]
+            return value && typeof value === 'object' ? value[selfRequiredSymbol] : value
+        }
+
         const sorted = renderableWithLinks
 
             // Sort alphabetically
@@ -998,8 +1020,8 @@ export class JSONSchemaForm extends LitElement {
                 const [name] = e1;
                 const [name2] = e2;
 
-                if (required[name] && !required[name2]) return -1; // first required
-                if (!required[name] && required[name2]) return 1; // second required
+                if (getRequiredValue(name) && !getRequiredValue(name2)) return -1; // first required
+                if (!getRequiredValue(name) && getRequiredValue(name2)) return 1; // second required
 
                 if (e1[isLink] && !e2[isLink]) return -1; // first link
                 if (!e1[isLink] && e2[isLink]) return 1; // second link
@@ -1077,6 +1099,8 @@ export class JSONSchemaForm extends LitElement {
 
             const headerName = header(name);
 
+            const isRequired = this.#isRequired(localPath);
+
             const renderableInside = this.#getRenderable(info, required[name], ignore, localPath, true);
 
             const __disabled = this.results.__disabled ?? (this.results.__disabled = {});
@@ -1125,6 +1149,7 @@ export class JSONSchemaForm extends LitElement {
                     onThrow: (...args) => this.onThrow(...args),
                     validateEmptyValues: this.validateEmptyValues,
                     onStatusChange: (status) => {
+                        console.warn('Nested status changed', status)
                         accordion.setStatus(status);
                         this.checkStatus();
                     }, // Forward status changes to the parent form
@@ -1254,18 +1279,31 @@ export class JSONSchemaForm extends LitElement {
         return rendered;
     };
 
-    #registerRequirements = (schema, requirements = {}, acc = this.#requirements) => {
+    #registerRequirements = (schema, requirements = {}, acc = this.#requirements, path = []) => {
         if (!schema) return;
+
+        const isItem = (schema) => schema.items && schema.items.properties;
+        if (isItem(schema)) schema = schema.items;
+
         if (schema.required) schema.required.forEach((key) => (acc[key] = true));
+        
         for (let key in requirements) acc[key] = requirements[key]; // Overwrite standard requirements with custom requirements
+
         if (schema.properties) {
             Object.entries(schema.properties).forEach(([key, value]) => {
-                if (value.properties) {
+
+                const isPropItem = isItem(value);
+
+                if (
+                    value.properties 
+                    || isPropItem
+                ) {
+
+                    const fullPath = [...path, key];
                     let nextAccumulator = acc[key];
                     const isNotObject = typeof nextAccumulator !== "object";
-                    if (!nextAccumulator || isNotObject)
-                        nextAccumulator = acc[key] = { [selfRequiredSymbol]: !!nextAccumulator };
-                    this.#registerRequirements(value, requirements[key], nextAccumulator);
+                    if (!nextAccumulator || isNotObject) nextAccumulator = acc[key] = { [selfRequiredSymbol]: !!(nextAccumulator && !isPropItem) };
+                    this.#registerRequirements(value, requirements[key], nextAccumulator, fullPath);
                 }
             });
         }
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 1c6f43b4a..215a18d53 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -418,13 +418,12 @@ export class JSONSchemaInput extends LitElement {
 
                     onUpdate: function () {
                         return ogThis.#updateData(fullPath, this.data, true, {
-                            // willTimeout: false,
-                            onError: () => {},
-                            onWarning: () => {},
+                            willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
+                            onError: (e) => e,
+                            onWarning: (e) => e,
                         }); // Ensure change propagates to all forms
                     },
 
-                    // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: async (path, parent, v, baseSchema = itemSchema) => {
                         const warnings = [];
                         const errors = [];
@@ -448,9 +447,12 @@ export class JSONSchemaInput extends LitElement {
                                         itemPropSchema,
                                         { ...parent, [name]: v },
                                         {
-                                            onError: (error) => errors.push(error),
-
-                                            onWarning: (warning) => errors.push(warning),
+                                            onError: (error) => {
+                                                errors.push(error) // Skip counting errors
+                                            },
+                                            onWarning: (warning) => {
+                                                warnings.push(warning) // Skip counting warnings
+                                            },
                                         }
                                     ) // NOTE: No pattern properties support
                                   : ""));
@@ -472,7 +474,7 @@ export class JSONSchemaInput extends LitElement {
                     onThrow: (...args) => this.#onThrow(...args),
                 };
 
-                const table = this.form.createTable(name, tableMetadata, fullPath); // Try creating table. Otherwise use nested form
+                const table = this.table = this.form.createTable(name, tableMetadata, fullPath); // Try creating table. Otherwise use nested form
 
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 78685feb5..e97266a52 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -227,7 +227,11 @@ export class SimpleTable extends LitElement {
             if (key == 8 || key == 46) {
                 const path = this.#getPath(ev);
                 if (path[0] === document.body)
-                    Object.values(this.#selected).forEach((row) => row.forEach((o) => o.setInput("")));
+                    Object.values(this.#selected).forEach((row) => {
+                        row.forEach((o) => {
+                            if (o.type !== 'table') o.setInput("")
+                        })
+                    });
                 return;
             }
 
@@ -277,6 +281,7 @@ export class SimpleTable extends LitElement {
     }
 
     set data(val) {
+        console.warn("Setting data")
         this.#data = val;
     }
 
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
index 571803e28..d05dbfc1a 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -128,7 +128,7 @@ export class GuidedSubjectsPage extends Page {
                 this.unsavedUpdates = "conversions";
             },
             validateOnChange: (key, parent, v) => {
-                if (key === "sessions") {
+                if (key.slice(-1)[0] === "sessions") {
                     if (v?.length) return true;
                     else {
                         return [
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 74ba18966..2bb8b04b9 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -70,6 +70,8 @@ export class TableCell extends LitElement {
     //         value: { reflect: true }
     //     }
     // }
+    
+    type = 'text'
 
     constructor({ info, value, schema, validateOnChange, onValidate }: TableCellProps) {
         super()
@@ -103,7 +105,11 @@ export class TableCell extends LitElement {
         if (this.schema.type === 'number' || this.schema.type === 'integer') {
             const og = v
             if (og === '') v = undefined
-            else v = Number(v)
+            else {
+                if (og === 'NaN' || og === 'None' || og === 'null' || og === 'undefined') v = NaN
+                const possibleValue = Number(og)
+                if (!isNaN(possibleValue)) v = possibleValue
+            }
         }
 
         return v
@@ -138,11 +144,11 @@ export class TableCell extends LitElement {
 
         if (errors.length) {
             info.error = ''
-            if (this.#cls === NestedTableCell) info.title = `${errors.length} errors found on this nested table.`
-            else info.title = errors.map((o) => o.message).join("\n\n"); // Class switching handled automatically
+            if (this.type === 'table' && errors.length > 1) info.title = `${errors.length} errors found on this nested table.`
+            else info.title = errors.map((o) => o.message).join("\n"); // Class switching handled automatically
         } else if (warnings.length) {
             info.warning = ''
-            if (this.#cls === NestedTableCell) info.title = `${warnings.length} warnings found on this nested table.`
+            if (this.type === 'table' && warnings.length > 1) info.title = `${warnings.length} warnings found on this nested table.`
             else info.title = warnings.map((o) => o.message).join("\n");
         }
 
@@ -150,7 +156,6 @@ export class TableCell extends LitElement {
 
         if (typeof result === 'function') result() // Run if returned value is a function
 
-
         return info
     };
 
@@ -185,10 +190,18 @@ export class TableCell extends LitElement {
 
         if (this.schema.type === "array") {
             const items = this.schema.items
-            if (items && items.type === "object") cls = NestedTableCell
-            else cls = ArrayCell
+            if (items && items.type === "object") {
+                cls = NestedTableCell
+                this.type = "table"
+            } else {
+                cls = ArrayCell
+                this.type = "array"
+            }
+        }
+        else if (this.schema.format === "date-time") {
+            cls = DateTimeCell
+            this.type = "date-time"
         }
-        else if (this.schema.format === "date-time") cls =  DateTimeCell
 
         // Only actually rerender if new class type
         if (cls !== this.#cls) {

From e35b970862824f2e60deb858a3aa8cff2590f92a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Dec 2023 21:30:34 +0000
Subject: [PATCH 045/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  | 68 ++++++++++-----------
 src/renderer/src/stories/JSONSchemaInput.js |  6 +-
 src/renderer/src/stories/SimpleTable.js     |  6 +-
 src/renderer/src/stories/table/Cell.ts      |  2 +-
 4 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 1a0028096..3da91c166 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -443,16 +443,19 @@ export class JSONSchemaForm extends LitElement {
                 await this.#nestedForms[name].validate(resolved ? resolved[name] : undefined); // Validate nested forms too
         }
 
-            for (let key in this.tables) {
-                try {
-                    this.tables[key].validate(resolved ? resolved[key] : undefined); // Validate nested tables too
-                } catch (e) {
-                    const title = this.tables[key].schema.title
-                    const message = e.message.replace('this table', `the <b>${header(title ?? [...this.base, key].join("."))}</b> table`);
-                    this.throw(message);
-                    break;
-                }
+        for (let key in this.tables) {
+            try {
+                this.tables[key].validate(resolved ? resolved[key] : undefined); // Validate nested tables too
+            } catch (e) {
+                const title = this.tables[key].schema.title;
+                const message = e.message.replace(
+                    "this table",
+                    `the <b>${header(title ?? [...this.base, key].join("."))}</b> table`
+                );
+                this.throw(message);
+                break;
             }
+        }
 
         // NOTE: Ensure user is aware of any warnings before moving on
         // const activeWarnings = Array.from(this.shadowRoot.querySelectorAll('.warnings')).map(input => Array.from(input.children)).filter(input => input.length)
@@ -558,8 +561,7 @@ export class JSONSchemaForm extends LitElement {
     }
 
     #renderInteractiveElement = (name, info, required, path = [], value, pattern = false) => {
-        let isRequired = this.#isRequired([...path, name])
-        
+        let isRequired = this.#isRequired([...path, name]);
 
         const localPath = [...path, name];
         const externalPath = [...this.base, ...localPath];
@@ -695,7 +697,13 @@ export class JSONSchemaForm extends LitElement {
 
         const isRenderable = (key, value) => {
             if (recursive && value.properties)
-                return this.#getRenderable(value, this.#isRequired([...path, key]), getIgnore(ignore, key), [...path, key], true);
+                return this.#getRenderable(
+                    value,
+                    this.#isRequired([...path, key]),
+                    getIgnore(ignore, key),
+                    [...path, key],
+                    true
+                );
             else return [key, value];
         };
 
@@ -781,8 +789,7 @@ export class JSONSchemaForm extends LitElement {
         parent = this.#get(path, this.resolved),
         hooks = {}
     ) => {
-
-        const { onError, onWarning } = hooks
+        const { onError, onWarning } = hooks;
 
         const pathToValidate = [...(this.base ?? []), ...path];
         const localPath = [...path, name]; // Use basePath to augment the validation
@@ -812,7 +819,6 @@ export class JSONSchemaForm extends LitElement {
                       .filter((v) => !!v)
                 : [];
 
-
         // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
@@ -904,7 +910,7 @@ export class JSONSchemaForm extends LitElement {
                 if (schema.strict === false && e.message.includes("is not one of enum values")) return;
 
                 if (e.message.includes("is not of a type(s) number")) {
-                    if (Number.isNaN(value)) return
+                    if (Number.isNaN(value)) return;
                 }
 
                 // Custom Error Transformations
@@ -919,16 +925,15 @@ export class JSONSchemaForm extends LitElement {
 
         // Track errors and warnings
 
-        const updatedWarnings = warnings.map(info => onWarning ? onWarning(info) : info).filter(v => !!v)
-        const updatedErrors = resolvedErrors.map(info => onError ? onError(info) : info).filter(v => !!v)
-
+        const updatedWarnings = warnings.map((info) => (onWarning ? onWarning(info) : info)).filter((v) => !!v);
+        const updatedErrors = resolvedErrors.map((info) => (onError ? onError(info) : info)).filter((v) => !!v);
 
         this.#nErrors += updatedErrors.length;
         this.#nWarnings += updatedWarnings.length;
         this.checkStatus();
 
         // Show aggregated errors and warnings (if any)
-        updatedWarnings.forEach((info) => (onWarning ? '' : this.#addMessage(localPath, info, "warnings")));
+        updatedWarnings.forEach((info) => (onWarning ? "" : this.#addMessage(localPath, info, "warnings")));
         info.forEach((info) => (onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info")));
 
         if (isValid && updatedErrors.length === 0) {
@@ -957,7 +962,7 @@ export class JSONSchemaForm extends LitElement {
                 [...path, name]
             );
 
-            updatedErrors.forEach((info) => (onError ? '' : this.#addMessage(localPath, info, "errors")));
+            updatedErrors.forEach((info) => (onError ? "" : this.#addMessage(localPath, info, "errors")));
             // element.title = errors.map((info) => info.message).join("\n"); // Set all errors to show on hover
 
             return false;
@@ -996,11 +1001,10 @@ export class JSONSchemaForm extends LitElement {
             return acc;
         }, []);
 
-
         const getRequiredValue = (name) => {
-            const value = required[name]
-            return value && typeof value === 'object' ? value[selfRequiredSymbol] : value
-        }
+            const value = required[name];
+            return value && typeof value === "object" ? value[selfRequiredSymbol] : value;
+        };
 
         const sorted = renderableWithLinks
 
@@ -1149,7 +1153,7 @@ export class JSONSchemaForm extends LitElement {
                     onThrow: (...args) => this.onThrow(...args),
                     validateEmptyValues: this.validateEmptyValues,
                     onStatusChange: (status) => {
-                        console.warn('Nested status changed', status)
+                        console.warn("Nested status changed", status);
                         accordion.setStatus(status);
                         this.checkStatus();
                     }, // Forward status changes to the parent form
@@ -1286,23 +1290,19 @@ export class JSONSchemaForm extends LitElement {
         if (isItem(schema)) schema = schema.items;
 
         if (schema.required) schema.required.forEach((key) => (acc[key] = true));
-        
+
         for (let key in requirements) acc[key] = requirements[key]; // Overwrite standard requirements with custom requirements
 
         if (schema.properties) {
             Object.entries(schema.properties).forEach(([key, value]) => {
-
                 const isPropItem = isItem(value);
 
-                if (
-                    value.properties 
-                    || isPropItem
-                ) {
-
+                if (value.properties || isPropItem) {
                     const fullPath = [...path, key];
                     let nextAccumulator = acc[key];
                     const isNotObject = typeof nextAccumulator !== "object";
-                    if (!nextAccumulator || isNotObject) nextAccumulator = acc[key] = { [selfRequiredSymbol]: !!(nextAccumulator && !isPropItem) };
+                    if (!nextAccumulator || isNotObject)
+                        nextAccumulator = acc[key] = { [selfRequiredSymbol]: !!(nextAccumulator && !isPropItem) };
                     this.#registerRequirements(value, requirements[key], nextAccumulator, fullPath);
                 }
             });
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 215a18d53..5828a3edf 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -448,10 +448,10 @@ export class JSONSchemaInput extends LitElement {
                                         { ...parent, [name]: v },
                                         {
                                             onError: (error) => {
-                                                errors.push(error) // Skip counting errors
+                                                errors.push(error); // Skip counting errors
                                             },
                                             onWarning: (warning) => {
-                                                warnings.push(warning) // Skip counting warnings
+                                                warnings.push(warning); // Skip counting warnings
                                             },
                                         }
                                     ) // NOTE: No pattern properties support
@@ -474,7 +474,7 @@ export class JSONSchemaInput extends LitElement {
                     onThrow: (...args) => this.#onThrow(...args),
                 };
 
-                const table = this.table = this.form.createTable(name, tableMetadata, fullPath); // Try creating table. Otherwise use nested form
+                const table = (this.table = this.form.createTable(name, tableMetadata, fullPath)); // Try creating table. Otherwise use nested form
 
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index e97266a52..8c48d327d 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -229,8 +229,8 @@ export class SimpleTable extends LitElement {
                 if (path[0] === document.body)
                     Object.values(this.#selected).forEach((row) => {
                         row.forEach((o) => {
-                            if (o.type !== 'table') o.setInput("")
-                        })
+                            if (o.type !== "table") o.setInput("");
+                        });
                     });
                 return;
             }
@@ -281,7 +281,7 @@ export class SimpleTable extends LitElement {
     }
 
     set data(val) {
-        console.warn("Setting data")
+        console.warn("Setting data");
         this.#data = val;
     }
 
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 2bb8b04b9..476924ca4 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -70,7 +70,7 @@ export class TableCell extends LitElement {
     //         value: { reflect: true }
     //     }
     // }
-    
+
     type = 'text'
 
     constructor({ info, value, schema, validateOnChange, onValidate }: TableCellProps) {

From 90c9b9d7e7f932b712443606f069ba05666c0203 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Mon, 18 Dec 2023 14:00:59 -0800
Subject: [PATCH 046/133] Allow NaN in forms for numbers

---
 src/renderer/src/stories/JSONSchemaInput.js   | 40 ++++++++++++++++++-
 .../src/stories/pages/uploads/UploadsPage.js  |  2 +
 src/renderer/src/stories/table/Cell.ts        | 18 +++------
 src/renderer/src/stories/table/get.ts         | 19 +++++++++
 4 files changed, 64 insertions(+), 15 deletions(-)
 create mode 100644 src/renderer/src/stories/table/get.ts

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 215a18d53..56a0a405f 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -61,7 +61,7 @@ export class JSONSchemaInput extends LitElement {
             }
 
             .guided--input:disabled {
-                color: dimgray;
+                opacity: 0.5;
                 pointer-events: none;
             }
 
@@ -104,6 +104,18 @@ export class JSONSchemaInput extends LitElement {
                 margin: 0 0 1em;
                 line-height: 1.4285em;
             }
+
+            .nan-handler {
+                display: flex;
+                align-items: center;
+                margin-left: 5px;
+                white-space: nowrap;
+            }
+
+            .nan-handler label {
+                margin-left: 5px;
+                font-size: 12px;
+            }
         `;
     }
 
@@ -601,6 +613,8 @@ export class JSONSchemaInput extends LitElement {
             if (isInteger) schema.type = "number";
             const isNumber = schema.type === "number";
 
+            const isRequiredNumber = isNumber && this.required
+
             const fileSystemFormat = isFilesystemSelector(name, schema.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Handle long string formats
@@ -623,6 +637,8 @@ export class JSONSchemaInput extends LitElement {
                     schema.format === "date-time"
                         ? "datetime-local"
                         : schema.format ?? (schema.type === "string" ? "text" : schema.type);
+
+
                 return html`
                     <input
                         class="guided--input schema-input ${schema.step === null ? "hideStep" : ""}"
@@ -657,10 +673,30 @@ export class JSONSchemaInput extends LitElement {
                                 value = newValue;
                             }
 
+                            if (isRequiredNumber) {
+                                const nanHandler = ev.target.parentNode.querySelector(".nan-handler");
+                                if (!(newValue && Number.isNaN(newValue))) nanHandler.checked = false;
+                            }
+
                             this.#updateData(fullPath, value);
                         }}
                         @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
-                    />
+                    /> ${isRequiredNumber ? html`<div class="nan-handler"><input 
+                        type="checkbox" 
+                        ?checked=${this.value && Number.isNaN(this.value)} 
+                        @change=${(ev) => {
+                            const siblingInput = ev.target.parentNode.previousElementSibling;
+                            if (ev.target.checked) {
+                                this.#updateData(fullPath, NaN);
+                                siblingInput.setAttribute("disabled", true);
+                            }
+                            else {
+                                siblingInput.removeAttribute("disabled");
+                                const ev = new Event("input");
+                                siblingInput.dispatchEvent(ev);
+                            }
+                        }}
+                    ></input><label>I Don't Know</label></div>` : ""}
                 `;
             }
         }
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index eb097689b..0678f11e8 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -81,6 +81,7 @@ export async function createDandiset(results = {}) {
         ],
     });
 
+
     content.append(form);
     modal.append(content);
 
@@ -355,6 +356,7 @@ export class UploadsPage extends Page {
         const promise = ready.cpus
             .then(() => ready.dandisets)
             .then(() => {
+
                 // NOTE: API Keys and Dandiset IDs persist across selected project
                 return (this.form = new JSONSchemaForm({
                     results: globalState,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 2bb8b04b9..f9ef46ef2 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -1,10 +1,13 @@
-import { LitElement, css, html } from "lit"
+import { LitElement, css } from "lit"
 import { ArrayCell } from "./cells/array"
 import { NestedTableCell } from "./cells/table"
 
 import { TableCellBase } from "./cells/base"
 import { DateTimeCell } from "./cells/date-time"
 
+
+import { getValue } from './get'
+
 type ValidationResult = {
     title?: string,
     warning?: string,
@@ -101,18 +104,7 @@ export class TableCell extends LitElement {
     get value() {
 
         let v = this.input ? this.input.getValue() : this.#value
-
-        if (this.schema.type === 'number' || this.schema.type === 'integer') {
-            const og = v
-            if (og === '') v = undefined
-            else {
-                if (og === 'NaN' || og === 'None' || og === 'null' || og === 'undefined') v = NaN
-                const possibleValue = Number(og)
-                if (!isNaN(possibleValue)) v = possibleValue
-            }
-        }
-
-        return v
+        return getValue(v, this.schema)
     }
 
     set value(v) {
diff --git a/src/renderer/src/stories/table/get.ts b/src/renderer/src/stories/table/get.ts
new file mode 100644
index 000000000..828a705fe
--- /dev/null
+++ b/src/renderer/src/stories/table/get.ts
@@ -0,0 +1,19 @@
+
+
+export const getValue = (value: any, schema: any) => {
+    if (schema.type === 'number' || schema.type === 'integer') {
+
+        if (typeof value === 'number') return value
+        
+        const og = value
+        if (og === '') return undefined
+        else {
+            if (og === 'NaN' || og === 'None' || og === 'null' || og === 'undefined') return NaN
+            const possibleValue = Number(og)
+            if (!isNaN(possibleValue)) return possibleValue
+        }
+        
+    }
+
+    return value
+}
\ No newline at end of file

From e2ed87c9fea2d689625c0ca07639ff7c907a5d8d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Dec 2023 22:02:07 +0000
Subject: [PATCH 047/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js     | 17 +++++++++--------
 .../src/stories/pages/uploads/UploadsPage.js    |  2 --
 src/renderer/src/stories/table/get.ts           |  6 +++---
 3 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e709f6441..cdc9744b6 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -613,7 +613,7 @@ export class JSONSchemaInput extends LitElement {
             if (isInteger) schema.type = "number";
             const isNumber = schema.type === "number";
 
-            const isRequiredNumber = isNumber && this.required
+            const isRequiredNumber = isNumber && this.required;
 
             const fileSystemFormat = isFilesystemSelector(name, schema.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
@@ -638,7 +638,6 @@ export class JSONSchemaInput extends LitElement {
                         ? "datetime-local"
                         : schema.format ?? (schema.type === "string" ? "text" : schema.type);
 
-
                 return html`
                     <input
                         class="guided--input schema-input ${schema.step === null ? "hideStep" : ""}"
@@ -681,22 +680,24 @@ export class JSONSchemaInput extends LitElement {
                             this.#updateData(fullPath, value);
                         }}
                         @change=${(ev) => validateOnChange && this.#triggerValidation(name, path)}
-                    /> ${isRequiredNumber ? html`<div class="nan-handler"><input 
-                        type="checkbox" 
-                        ?checked=${this.value && Number.isNaN(this.value)} 
+                    />
+                    ${isRequiredNumber
+                        ? html`<div class="nan-handler"><input
+                        type="checkbox"
+                        ?checked=${this.value && Number.isNaN(this.value)}
                         @change=${(ev) => {
                             const siblingInput = ev.target.parentNode.previousElementSibling;
                             if (ev.target.checked) {
                                 this.#updateData(fullPath, NaN);
                                 siblingInput.setAttribute("disabled", true);
-                            }
-                            else {
+                            } else {
                                 siblingInput.removeAttribute("disabled");
                                 const ev = new Event("input");
                                 siblingInput.dispatchEvent(ev);
                             }
                         }}
-                    ></input><label>I Don't Know</label></div>` : ""}
+                    ></input><label>I Don't Know</label></div>`
+                        : ""}
                 `;
             }
         }
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 0678f11e8..eb097689b 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -81,7 +81,6 @@ export async function createDandiset(results = {}) {
         ],
     });
 
-
     content.append(form);
     modal.append(content);
 
@@ -356,7 +355,6 @@ export class UploadsPage extends Page {
         const promise = ready.cpus
             .then(() => ready.dandisets)
             .then(() => {
-
                 // NOTE: API Keys and Dandiset IDs persist across selected project
                 return (this.form = new JSONSchemaForm({
                     results: globalState,
diff --git a/src/renderer/src/stories/table/get.ts b/src/renderer/src/stories/table/get.ts
index 828a705fe..3ff53cf68 100644
--- a/src/renderer/src/stories/table/get.ts
+++ b/src/renderer/src/stories/table/get.ts
@@ -4,7 +4,7 @@ export const getValue = (value: any, schema: any) => {
     if (schema.type === 'number' || schema.type === 'integer') {
 
         if (typeof value === 'number') return value
-        
+
         const og = value
         if (og === '') return undefined
         else {
@@ -12,8 +12,8 @@ export const getValue = (value: any, schema: any) => {
             const possibleValue = Number(og)
             if (!isNaN(possibleValue)) return possibleValue
         }
-        
+
     }
 
     return value
-}
\ No newline at end of file
+}

From eb1c0ada29114167448b9fefb008af419e6666e6 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 21 Dec 2023 15:10:00 -0600
Subject: [PATCH 048/133] Warn users about changing a device name

---
 src/renderer/src/stories/JSONSchemaForm.js   | 18 ++++--
 src/renderer/src/stories/JSONSchemaInput.js  |  1 +
 src/renderer/src/stories/SimpleTable.js      | 13 ++--
 src/renderer/src/stories/table/Cell.ts       | 22 +++++--
 src/renderer/src/stories/table/cells/base.ts | 16 ++---
 src/renderer/src/validation/index.js         | 21 +++++--
 src/renderer/src/validation/validation.ts    | 63 +++++++++++++++++++-
 7 files changed, 123 insertions(+), 31 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 3da91c166..94d3725b4 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -784,16 +784,23 @@ export class JSONSchemaForm extends LitElement {
         name,
         path = [],
         checkLinks = true,
-        input = this.getInput([...path, name]),
-        schema = this.getSchema([...path, name]),
-        parent = this.#get(path, this.resolved),
+        input,
+        schema,
+        parent,
         hooks = {}
     ) => {
+
+        
         const { onError, onWarning } = hooks;
 
-        const pathToValidate = [...(this.base ?? []), ...path];
-        const localPath = [...path, name]; // Use basePath to augment the validation
+        const og = path
+        const localPath = [...path, name].filter(str => typeof str === 'string'); // Ignore row information
         const externalPath = [...this.base, ...localPath];
+        const pathToValidate = [...this.base, ...path]
+
+        if (!input) input = this.getInput(localPath);
+        if (!parent) parent = this.#get(path, this.resolved);
+        if (!schema) schema = this.getSchema(localPath);
 
         const value = parent[name];
         // const value = this.#get(path, this.resolved)
@@ -821,6 +828,7 @@ export class JSONSchemaForm extends LitElement {
 
         // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
+        if (valid === null) return null // Skip validation / data change if the value is null
 
         const isRequired = this.#isRequired(localPath) || (!input.table && input.required); // Do not trust required status of table validations
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index cdc9744b6..e47ffadf0 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -444,6 +444,7 @@ export class JSONSchemaInput extends LitElement {
                         const completePath = [...fullPath, ...path.slice(0, -1)];
 
                         const itemPropSchema = path.reduce((acc, key) => {
+                            if (typeof key === 'number') return acc // Skip row information
                             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
                         }, baseSchema);
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 8c48d327d..a04514939 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -281,7 +281,6 @@ export class SimpleTable extends LitElement {
     }
 
     set data(val) {
-        console.warn("Setting data");
         this.#data = val;
     }
 
@@ -500,8 +499,10 @@ export class SimpleTable extends LitElement {
         this.removeAttribute("waiting");
 
         const scrollRoot = this.shadowRoot.querySelector("table");
+
         // Add cells to body after the initial table render
         const body = this.shadowRoot.querySelector("tbody");
+        body.innerHTML = ""; // Clear existing render
 
         if (!this.#loaded) {
             const tStart = performance.now();
@@ -540,6 +541,7 @@ export class SimpleTable extends LitElement {
     };
 
     updated() {
+
         this.setAttribute("loading", "");
 
         const data = this.#getData(); // Always render at least one row
@@ -712,9 +714,11 @@ export class SimpleTable extends LitElement {
             ) => {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                path = [fullInfo.col, ...path];
-
-                const res = (await this.validateOnChange) ? this.validateOnChange(path, parent, value, schema) : true;
+                const res = (await this.validateOnChange) ? this.validateOnChange([
+                     info.i, 
+                     fullInfo.col, 
+                     ...path 
+                ], parent, value, schema) : true;
 
                 return res;
             },
@@ -772,6 +776,7 @@ export class SimpleTable extends LitElement {
     #schema = {};
 
     render() {
+
         this.#updateRendered();
         this.#resetLoadState();
 
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index f86cfa398..4d6d16aa3 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -102,14 +102,15 @@ export class TableCell extends LitElement {
     toggle = (v: boolean) => this.input.toggle(v)
 
     get value() {
-
         let v = this.input ? this.input.getValue() : this.#value
         return getValue(v, this.schema)
     }
 
     set value(v) {
         if (this.input) this.input.set(v ?? '')
-        this.#value = this.input ? this.input.getValue() : v // Ensure value is coerced
+        this.#value = this.input 
+                            ? this.input.getValue() // Ensure all operations are undoable / value is coerced 
+                            : v // Silently set value if not rendered yet
      }
 
     validateOnChange?: ValidationFunction
@@ -119,6 +120,8 @@ export class TableCell extends LitElement {
 
     validate = async (v = this.value) => {
 
+        const prevValue = this.#value
+
         const validator = this.validateOnChange ?? this.#validator
         let result = await validator(v)
         if (result === true) result = this.#validator(v)
@@ -129,6 +132,11 @@ export class TableCell extends LitElement {
             error: undefined
         }
 
+        if (result === null) {
+            this.value = prevValue // NOTE: Calls popup twice
+            return;
+        }
+
         const warnings = Array.isArray(result) ? result.filter((info) => info.type === "warning") : [];
         const errors = Array.isArray(result) ? result?.filter((info) => info.type === "error") : [];
 
@@ -153,8 +161,9 @@ export class TableCell extends LitElement {
 
     setInput(value: any) {
         this.interacted = persistentInteraction
-        if (this.input) this.input.set(value)  // Ensure all operations are undoable
-        else this.#value = value // Silently set value if not rendered yet
+        this.value = value
+        // if (this.input) this.input.set(value)  // Ensure all operations are undoable
+        // else this.#value = value // Silently set value if not rendered yet
     }
 
     #value
@@ -198,9 +207,10 @@ export class TableCell extends LitElement {
         // Only actually rerender if new class type
         if (cls !== this.#cls) {
             this.input = new cls({
-                onChange: () => {
+                onChange: async (v) => {
                     if (this.input.interacted) this.interacted = true
-                    this.validate()
+                    const result = await this.validate()
+                    if (result) this.#value = v
                 },
                 toggle: (v) => this.toggle(v),
                 info: this.info,
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 1163b76bb..fb886a768 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -148,21 +148,21 @@ export class TableCellBase extends LitElement {
 
     getValue = (input: any = this.value) => input // Process inputs from the editor
 
-    #update(current: any, forceUpdate = false) {
+    #update(current: any, forceUpdate = false, runOnChange = true) {
         let value = this.getValue(current)
 
         // NOTE: Forcing change registration for all cells
         if (this.value !== value || forceUpdate) {
             this.value = value
-            this.onChange(value)
+            if (runOnChange) this.onChange(value)
         }
     }
 
-    setText(value: any, setOnInput = true) {
+    setText(value: any, setOnInput = true, runOnChange = true) {
         if (setOnInput) [ this.#editor, this.#renderer ].forEach(el => this.setChild(el, value)) // RESETS HISTORY
 
-        if (this.schema.type === 'array' || this.schema.type === 'object') this.#update(value, true) // Ensure array values are not coerced
-        else this.#update(`${value}`) // Coerce to string
+        if (this.schema.type === 'array' || this.schema.type === 'object') this.#update(value, true, runOnChange) // Ensure array values are not coerced
+        else this.#update(`${value}`, undefined, runOnChange) // Coerce to string
     }
 
 
@@ -171,19 +171,19 @@ export class TableCellBase extends LitElement {
         document.execCommand(command, show, value)
     }
 
-    set(value: any) {
+    set(value: any, runOnChange = true) {
 
         if (document.execCommand) {
             this.#editable.setAttribute('contenteditable', '')
             this.#editable.focus();
             document.execCommand('selectAll');
             document.execCommand('insertText', false, value);
-            this.setText(value)
+            this.setText(value, undefined, runOnChange)
             this.#editable.blur();
             this.#editable.removeAttribute('contenteditable')
         }
 
-        else this.setText(value) // Ensure value is still set
+        else this.setText(value, undefined, runOnChange) // Ensure value is still set
     }
 
     #render(property: 'renderer' | 'editor') {
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index beccffbc9..2e5bdf82f 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -9,16 +9,18 @@ export function getMessageType(item) {
     return item.type ?? (isErrorImportance.includes(item.importance) ? "error" : "warning");
 }
 
-export function validateOnChange(name, parent, path, value) {
+export async function validateOnChange(name, parent, path, value) {
     let functions = [];
 
     const fullPath = [...path, name];
 
+    const fullPathNoRows = fullPath.filter((key) => typeof key !== "number");
+
     const copy = { ...parent }; // Validate on a copy of the parent
     if (arguments.length > 3) copy[name] = value; // Update value on copy
 
     let lastResolved;
-    functions = fullPath.reduce((acc, key, i) => {
+    functions = fullPathNoRows.reduce((acc, key, i) => {
         if (acc && key in acc) return (lastResolved = acc[key]);
         else return;
     }, validationSchema); // Pass the top level until it runs out
@@ -29,10 +31,13 @@ export function validateOnChange(name, parent, path, value) {
     if (lastResolved !== false && (functions === undefined || functions === true)) {
         // let overridden = false;
         let lastWildcard;
-        fullPath.reduce((acc, key) => {
+        fullPathNoRows.reduce((acc, key) => {
+
             if (acc && "*" in acc) {
-                if (!acc["*"] && lastWildcard)
+                if (!acc["*"]&& lastWildcard)
                     overridden = true; // Disable if false and a wildcard has already been specified
+                
+                // Otherwise set the last wildcard
                 else {
                     lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
                     overridden = false; // Re-enable if a new one is specified below
@@ -45,6 +50,7 @@ export function validateOnChange(name, parent, path, value) {
         if (lastWildcard) functions = [lastWildcard];
     }
 
+
     if (!functions || (Array.isArray(functions) && functions.length === 0)) return; // No validation for this field
     if (!Array.isArray(functions)) functions = [functions];
 
@@ -66,7 +72,8 @@ export function validateOnChange(name, parent, path, value) {
         }
     });
 
-    return resolveAll(results, (arr) => {
+    const res = resolveAll(results, (arr) => {
+
         const flat = arr.flat();
         if (flat.find((res) => res?.message)) {
             return flat
@@ -80,12 +87,16 @@ export function validateOnChange(name, parent, path, value) {
                 }); // Some of the requests end in errors
         }
 
+        if (flat.some((res) => res === null)) return null
+
         // Allow for providing one function to execute after data update
         const hasFunc = results.find((f) => typeof f === "function");
         if (hasFunc) return hasFunc;
 
         return true;
     });
+
+    return res
 }
 
 export function checkStatus(warnings, errors, items = []) {
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index d19985cb9..f1d63593a 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -1,7 +1,8 @@
 import schema from './validation.json'
 import { JSONSchemaForm } from '../stories/JSONSchemaForm.js'
+import Swal from 'sweetalert2'
 
-function rerender (this: JSONSchemaForm, linkedPath: string[]) {
+function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
     const element = this.getTable(linkedPath)
     if (element) element.requestUpdate() // Re-render table to show updates
     // if (element) setTimeout(() => {
@@ -32,7 +33,7 @@ schema.Ecephys.ElectrodeGroup.name = function(this: JSONSchemaForm, _, __, ___,
      // Check if the latest value will be new. Run function after validation
     if (!value || !groups.includes(value)) {
         return () => {
-             setTimeout(() => rerender.call(this, ['Ecephys', 'Electrodes'])) // Allow for the updates to occur
+             setTimeout(() => rerenderTable.call(this, ['Ecephys', 'Electrodes'])) // Allow for the updates to occur
         }
     }
 }
@@ -60,7 +61,7 @@ schema.Ecephys.ElectrodeColumns = {
         if (!name) return true // Allow blank rows
 
         if (prop === 'name' && !(name in this.schema.properties.Ecephys.properties.Electrodes.items.properties)) {
-            const element = rerender.call(this, ['Ecephys', 'Electrodes'])
+            const element = rerenderTable.call(this, ['Ecephys', 'Electrodes'])
             element.schema.properties[name] = {} // Ensure property is present in the schema now
             element.data.forEach(o => name in o ? undefined : o[name] = '') // Set column value as blank if not existent on row
         }
@@ -81,4 +82,60 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
     ]
 }
 
+// Ophys
+schema.Ophys.Device = {
+    ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
+
+        const prevValue = path.reduce((acc, str) => acc[str], this.results)[name]
+
+        if (prevValue === value) return true // No change
+
+        const result = await Swal.fire({
+            title: `Are you sure you want to rename the ${prevValue} device?`,
+            icon: "warning",
+            text: `Changing this may invalidate a lot of properties.`,
+            heightAuto: false,
+            backdrop: "rgba(0,0,0, 0.4)",
+            confirmButtonText: "I understand",
+            showConfirmButton: true,
+            showCancelButton: true,
+            cancelButtonText: "Cancel"
+        })
+
+        if (!result.isConfirmed) return null
+
+        if (result.isConfirmed) {
+            
+        }
+
+        // Update Dependent Tables
+        const dependencies = [
+            ['Ophys', 'ImagingPlane']
+        ]
+
+        dependencies.forEach(path => {
+            rerenderTable.call(this, path)
+        })
+
+        return true
+    }
+}
+
+schema.Ophys.ImagingPlane = {
+    device: function (this: JSONSchemaForm, name, parent, path, value) {
+        const devices = this.results.Ophys.Device.map(o => o.name)
+        if (devices.includes(parent[name])) return true
+        else {
+            return [
+                {
+                    message: 'Not a valid device',
+                    type: 'error'
+                }
+            ]
+        }
+
+    }
+}
+
+
 export default schema

From af2fda4cf48429af45a7ac8af1b4cbdb1325680f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Dec 2023 21:12:02 +0000
Subject: [PATCH 049/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  | 20 +++++---------------
 src/renderer/src/stories/JSONSchemaInput.js |  2 +-
 src/renderer/src/stories/SimpleTable.js     | 10 +++-------
 src/renderer/src/stories/table/Cell.ts      |  4 ++--
 src/renderer/src/validation/index.js        | 10 +++-------
 src/renderer/src/validation/validation.ts   |  2 +-
 6 files changed, 15 insertions(+), 33 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 94d3725b4..2ac492dca 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -780,23 +780,13 @@ export class JSONSchemaForm extends LitElement {
     #isARequiredPropertyString = `is a required property`;
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
-    triggerValidation = async (
-        name,
-        path = [],
-        checkLinks = true,
-        input,
-        schema,
-        parent,
-        hooks = {}
-    ) => {
-
-        
+    triggerValidation = async (name, path = [], checkLinks = true, input, schema, parent, hooks = {}) => {
         const { onError, onWarning } = hooks;
 
-        const og = path
-        const localPath = [...path, name].filter(str => typeof str === 'string'); // Ignore row information
+        const og = path;
+        const localPath = [...path, name].filter((str) => typeof str === "string"); // Ignore row information
         const externalPath = [...this.base, ...localPath];
-        const pathToValidate = [...this.base, ...path]
+        const pathToValidate = [...this.base, ...path];
 
         if (!input) input = this.getInput(localPath);
         if (!parent) parent = this.#get(path, this.resolved);
@@ -828,7 +818,7 @@ export class JSONSchemaForm extends LitElement {
 
         // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
-        if (valid === null) return null // Skip validation / data change if the value is null
+        if (valid === null) return null; // Skip validation / data change if the value is null
 
         const isRequired = this.#isRequired(localPath) || (!input.table && input.required); // Do not trust required status of table validations
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e47ffadf0..b2800059f 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -444,7 +444,7 @@ export class JSONSchemaInput extends LitElement {
                         const completePath = [...fullPath, ...path.slice(0, -1)];
 
                         const itemPropSchema = path.reduce((acc, key) => {
-                            if (typeof key === 'number') return acc // Skip row information
+                            if (typeof key === "number") return acc; // Skip row information
                             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
                         }, baseSchema);
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index a04514939..9bcbfbc04 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -541,7 +541,6 @@ export class SimpleTable extends LitElement {
     };
 
     updated() {
-
         this.setAttribute("loading", "");
 
         const data = this.#getData(); // Always render at least one row
@@ -714,11 +713,9 @@ export class SimpleTable extends LitElement {
             ) => {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                const res = (await this.validateOnChange) ? this.validateOnChange([
-                     info.i, 
-                     fullInfo.col, 
-                     ...path 
-                ], parent, value, schema) : true;
+                const res = (await this.validateOnChange)
+                    ? this.validateOnChange([info.i, fullInfo.col, ...path], parent, value, schema)
+                    : true;
 
                 return res;
             },
@@ -776,7 +773,6 @@ export class SimpleTable extends LitElement {
     #schema = {};
 
     render() {
-
         this.#updateRendered();
         this.#resetLoadState();
 
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 4d6d16aa3..67d79d0c9 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -108,8 +108,8 @@ export class TableCell extends LitElement {
 
     set value(v) {
         if (this.input) this.input.set(v ?? '')
-        this.#value = this.input 
-                            ? this.input.getValue() // Ensure all operations are undoable / value is coerced 
+        this.#value = this.input
+                            ? this.input.getValue() // Ensure all operations are undoable / value is coerced
                             : v // Silently set value if not rendered yet
      }
 
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index 2e5bdf82f..a56eae6dc 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -32,11 +32,9 @@ export async function validateOnChange(name, parent, path, value) {
         // let overridden = false;
         let lastWildcard;
         fullPathNoRows.reduce((acc, key) => {
-
             if (acc && "*" in acc) {
-                if (!acc["*"]&& lastWildcard)
+                if (!acc["*"] && lastWildcard)
                     overridden = true; // Disable if false and a wildcard has already been specified
-                
                 // Otherwise set the last wildcard
                 else {
                     lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
@@ -50,7 +48,6 @@ export async function validateOnChange(name, parent, path, value) {
         if (lastWildcard) functions = [lastWildcard];
     }
 
-
     if (!functions || (Array.isArray(functions) && functions.length === 0)) return; // No validation for this field
     if (!Array.isArray(functions)) functions = [functions];
 
@@ -73,7 +70,6 @@ export async function validateOnChange(name, parent, path, value) {
     });
 
     const res = resolveAll(results, (arr) => {
-
         const flat = arr.flat();
         if (flat.find((res) => res?.message)) {
             return flat
@@ -87,7 +83,7 @@ export async function validateOnChange(name, parent, path, value) {
                 }); // Some of the requests end in errors
         }
 
-        if (flat.some((res) => res === null)) return null
+        if (flat.some((res) => res === null)) return null;
 
         // Allow for providing one function to execute after data update
         const hasFunc = results.find((f) => typeof f === "function");
@@ -96,7 +92,7 @@ export async function validateOnChange(name, parent, path, value) {
         return true;
     });
 
-    return res
+    return res;
 }
 
 export function checkStatus(warnings, errors, items = []) {
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index f1d63593a..6e3a6e186 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -105,7 +105,7 @@ schema.Ophys.Device = {
         if (!result.isConfirmed) return null
 
         if (result.isConfirmed) {
-            
+
         }
 
         // Update Dependent Tables

From ea811a110d1198518aeede432fdbe6d35ced22a4 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 21 Dec 2023 15:43:29 -0600
Subject: [PATCH 050/133] Proper exclusion of certain JSON Schema errors

---
 src/renderer/src/stories/JSONSchemaForm.js    | 94 ++++++++++---------
 src/renderer/src/stories/JSONSchemaInput.js   |  1 +
 src/renderer/src/stories/SimpleTable.js       | 20 ++--
 .../pages/guided-mode/data/GuidedMetadata.js  |  2 +
 src/renderer/src/stories/table/Cell.ts        |  3 +-
 src/renderer/src/stories/table/get.ts         |  2 +-
 6 files changed, 70 insertions(+), 52 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 94d3725b4..2d29046b0 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -218,8 +218,8 @@ export class JSONSchemaForm extends LitElement {
     #updateRendered = (force) =>
         force || this.#rendered === true
             ? (this.#rendered = new Promise(
-                  (resolve) => (this.#toggleRendered = () => resolve((this.#rendered = true)))
-              ))
+                (resolve) => (this.#toggleRendered = () => resolve((this.#rendered = true)))
+            ))
             : this.#rendered;
 
     resolved = {}; // Keep track of actual resolved values—not just what the user provides as results
@@ -412,8 +412,8 @@ export class JSONSchemaForm extends LitElement {
         let message = isValid
             ? ""
             : requiredButNotSpecified.length === 1
-              ? `<b>${header(requiredButNotSpecified[0])}</b> is not defined`
-              : `${requiredButNotSpecified.length} required inputs are not specified properly`;
+                ? `<b>${header(requiredButNotSpecified[0])}</b> is not defined`
+                : `${requiredButNotSpecified.length} required inputs are not specified properly`;
         if (requiredButNotSpecified.length !== nMissingRequired)
             console.warn("Disagreement about the correct error to throw...");
 
@@ -429,9 +429,8 @@ export class JSONSchemaForm extends LitElement {
                     message = `<b>${header(schema.title ?? path.join("."))}</b> is not valid`;
                 } else message = `${flaggedInputs.length} invalid form values`;
             }
-            message += `${
-                this.base.length ? ` in the <b>${this.base.join(".")}</b> section` : ""
-            }. Please check the highlighted fields.`;
+            message += `${this.base.length ? ` in the <b>${this.base.join(".")}</b> section` : ""
+                }. Please check the highlighted fields.`;
         }
 
         if (message) this.throw(message);
@@ -610,8 +609,8 @@ export class JSONSchemaForm extends LitElement {
             <div
                 id=${encode(localPath.join("-"))}
                 class="form-section ${isRequired || isConditional ? "required" : ""} ${isConditional
-                    ? "conditional"
-                    : ""}"
+                ? "conditional"
+                : ""}"
             >
                 <label class="guided--form-label"
                     >${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}</label
@@ -667,10 +666,10 @@ export class JSONSchemaForm extends LitElement {
     };
 
     // Checks missing required properties and throws an error if any are found
-    onInvalid = () => {};
-    onLoaded = () => {};
-    onUpdate = () => {};
-    onOverride = () => {};
+    onInvalid = () => { };
+    onLoaded = () => { };
+    onUpdate = () => { };
+    onOverride = () => { };
 
     // #deleteExtraneousResults = (results, schema) => {
     //     for (let name in results) {
@@ -723,10 +722,10 @@ export class JSONSchemaForm extends LitElement {
         return flattenRecursedValues(res); // Flatten on the last pass
     };
 
-    validateOnChange = () => {};
-    onStatusChange = () => {};
-    onThrow = () => {};
-    createTable = () => {};
+    validateOnChange = () => { };
+    onStatusChange = () => { };
+    onThrow = () => { };
+    createTable = () => { };
 
     #getLink = (args) => {
         if (typeof args === "string") args = args.split("-");
@@ -790,7 +789,7 @@ export class JSONSchemaForm extends LitElement {
         hooks = {}
     ) => {
 
-        
+
         const { onError, onWarning } = hooks;
 
         const og = path
@@ -810,23 +809,40 @@ export class JSONSchemaForm extends LitElement {
         const jsonSchemaErrors =
             validateArgs.length === 2
                 ? await v
-                      .validate(...validateArgs)
-                      .errors.map((e) => {
-                          const propName = e.path.slice(-1)[0] ?? name;
-                          const rowName = e.path.slice(-2)[0];
-                          return {
-                              type: "error",
-                              message: `${
-                                  typeof propName === "string"
-                                      ? `${header(propName)}${typeof rowName === "number" ? ` on Row ${rowName}` : ""}`
-                                      : `Row ${propName}`
-                              } ${e.message}.`,
-                          };
-                      })
-                      .filter((v) => !!v)
+                    .validate(...validateArgs)
+                    .errors.map((e) => {
+                        const propName = e.path.slice(-1)[0] ?? name;
+                        const rowName = e.path.slice(-2)[0];
+
+                        const isRow = typeof rowName === "number"
+
+                        const resolvedValue = e.path.reduce((acc, token) => acc[token], value)
+
+                        // ------------ Exclude Certain Errors ------------
+                        // Non-Strict Rule
+                        if (schema.strict === false && e.message.includes("is not one of enum values")) return;
+
+                        // Allow referring to floats as null (i.e. JSON NaN representation)
+                        if (e.message === "is not of a type(s) number") {
+                            if (resolvedValue === null) {
+                                console.error('Throwing out...', externalPath.join('.'))
+                                return;
+                            }
+                        }
+
+
+
+                        return {
+                            type: "error",
+                            message: `${typeof propName === "string"
+                                    ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
+                                    : `Row ${propName}`
+                                } ${e.message}.`,
+                        };
+                    })
+                    .filter((v) => !!v)
                 : [];
 
-        // const jsonSchemaErrors =[]
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
         if (valid === null) return null // Skip validation / data change if the value is null
 
@@ -889,9 +905,8 @@ export class JSONSchemaForm extends LitElement {
                 const regex = new RegExp(schema.pattern);
                 if (!regex.test(parent[name])) {
                     errors.push({
-                        message: `${schema.title ?? header(name)} does not match the required pattern (${
-                            schema.pattern
-                        }).`,
+                        message: `${schema.title ?? header(name)} does not match the required pattern (${schema.pattern
+                            }).`,
                         type: "error",
                     });
                 }
@@ -914,12 +929,6 @@ export class JSONSchemaForm extends LitElement {
 
         const resolvedErrors = errors
             .map((e) => {
-                // Non-Strict Rule
-                if (schema.strict === false && e.message.includes("is not one of enum values")) return;
-
-                if (e.message.includes("is not of a type(s) number")) {
-                    if (Number.isNaN(value)) return;
-                }
 
                 // Custom Error Transformations
                 if (this.transformErrors) {
@@ -932,7 +941,6 @@ export class JSONSchemaForm extends LitElement {
             .filter((v) => !!v);
 
         // Track errors and warnings
-
         const updatedWarnings = warnings.map((info) => (onWarning ? onWarning(info) : info)).filter((v) => !!v);
         const updatedErrors = resolvedErrors.map((info) => (onError ? onError(info) : info)).filter((v) => !!v);
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e47ffadf0..22aef76ff 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -422,6 +422,7 @@ export class JSONSchemaInput extends LitElement {
                     : {};
 
                 const ogThis = this;
+
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index a04514939..8be88686f 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -351,6 +351,10 @@ export class SimpleTable extends LitElement {
         };
     }
 
+    #isUndefined(val) {
+        return val === undefined || val === "";
+    }
+
     #getRowData(row, cols = this.colHeaders) {
         const hasRow = row in this.#data;
         return cols.map((col, j) => {
@@ -358,12 +362,14 @@ export class SimpleTable extends LitElement {
             if (col === this.keyColumn) {
                 if (hasRow) value = row;
                 else return "";
-            } else
-                value =
-                    (hasRow ? this.#data[row][col] : undefined) ??
-                    this.globals[col] ??
-                    this.schema.properties[col].default ??
-                    "";
+            } else {
+
+                value = hasRow ? this.#data[row][col] : undefined
+                if (this.#isUndefined(value)) value = this.globals[col]
+                if (this.#isUndefined(value)) value = this.schema.properties[col].default
+                if (this.#isUndefined(value)) value = ""
+                
+            }
             return value;
         });
     }
@@ -681,7 +687,7 @@ export class SimpleTable extends LitElement {
         }
         // Update data on passed object
         else {
-            if (value == undefined || value === "") target[rowName][header] = undefined;
+            if (this.#isUndefined(value)) target[rowName][header] = undefined;
             else target[rowName][header] = value;
         }
 
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 1cc28fc6a..54c3923f2 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -170,6 +170,8 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
+        console.log("results", results)
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 4d6d16aa3..f7817ef20 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -79,6 +79,7 @@ export class TableCell extends LitElement {
     constructor({ info, value, schema, validateOnChange, onValidate }: TableCellProps) {
         super()
         this.#value = value
+
         this.schema = schema
         this.info = info
 
@@ -107,7 +108,7 @@ export class TableCell extends LitElement {
     }
 
     set value(v) {
-        if (this.input) this.input.set(v ?? '')
+        if (this.input) this.input.set(v === null  ? v : ( v ?? '' )) // Allow null to be set directly
         this.#value = this.input 
                             ? this.input.getValue() // Ensure all operations are undoable / value is coerced 
                             : v // Silently set value if not rendered yet
diff --git a/src/renderer/src/stories/table/get.ts b/src/renderer/src/stories/table/get.ts
index 3ff53cf68..9a7a72728 100644
--- a/src/renderer/src/stories/table/get.ts
+++ b/src/renderer/src/stories/table/get.ts
@@ -8,7 +8,7 @@ export const getValue = (value: any, schema: any) => {
         const og = value
         if (og === '') return undefined
         else {
-            if (og === 'NaN' || og === 'None' || og === 'null' || og === 'undefined') return NaN
+            if (og === 'NaN' || og === 'None' || og === 'null') return null
             const possibleValue = Number(og)
             if (!isNaN(possibleValue)) return possibleValue
         }

From aa5f7cd35ef618675ad9d3ced4aa1e0cdf0ad735 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 21 Dec 2023 16:47:41 -0600
Subject: [PATCH 051/133] Show additional properties and block adding them

---
 schemas/json/dandi/global.json                |  4 +-
 schemas/json/project/globals.json             |  4 +-
 schemas/json/tutorial.schema.json             |  2 +
 src/renderer/src/stories/JSONSchemaForm.js    | 31 ++++----
 src/renderer/src/stories/JSONSchemaInput.js   | 77 +++++++++++++++----
 src/renderer/src/stories/SimpleTable.js       |  4 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |  6 +-
 7 files changed, 90 insertions(+), 38 deletions(-)

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
index 081eae1f1..882c1ceaf 100644
--- a/schemas/json/dandi/global.json
+++ b/schemas/json/dandi/global.json
@@ -14,8 +14,10 @@
                     "description": "Your DANDI API key from the <a href='https://gui-staging.dandiarchive.org' target='_blank'>staging server</a>"
                 }
             },
+            "additionalProperties": false,
             "required": ["main_api_key"]
         }
     },
-    "required": ["api_keys"]
+    "required": ["api_keys"],
+    "additionalProperties": false
 }
diff --git a/schemas/json/project/globals.json b/schemas/json/project/globals.json
index 921131734..aeadc6217 100644
--- a/schemas/json/project/globals.json
+++ b/schemas/json/project/globals.json
@@ -5,5 +5,7 @@
             "format": "directory",
             "description": "Provide a custom output location for your NWB files. Will default to ~/NWB_GUIDE/conversions"
         }
-    }
+    },
+
+    "additionalProperties": false
 }
diff --git a/schemas/json/tutorial.schema.json b/schemas/json/tutorial.schema.json
index aa30ca892..c3e7c7ed8 100644
--- a/schemas/json/tutorial.schema.json
+++ b/schemas/json/tutorial.schema.json
@@ -8,5 +8,7 @@
       }
   },
 
+  "additionalProperties": false,
+
   "required": ["test_data_directory_path"]
 }
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 2d29046b0..82da48616 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -559,7 +559,7 @@ export class JSONSchemaForm extends LitElement {
         return resolved;
     }
 
-    #renderInteractiveElement = (name, info, required, path = [], value, pattern = false) => {
+    #renderInteractiveElement = (name, info, required, path = [], value, propertyType) => {
         let isRequired = this.#isRequired([...path, name]);
 
         const localPath = [...path, name];
@@ -591,7 +591,7 @@ export class JSONSchemaForm extends LitElement {
             controls: this.controls[name],
             required: isRequired,
             validateEmptyValue: this.validateEmptyValues,
-            pattern: pattern ? name : undefined,
+            pattern: propertyType === 'pattern' ? name : propertyType ?? undefined,
         });
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
@@ -789,20 +789,22 @@ export class JSONSchemaForm extends LitElement {
         hooks = {}
     ) => {
 
-
         const { onError, onWarning } = hooks;
 
-        const og = path
         const localPath = [...path, name].filter(str => typeof str === 'string'); // Ignore row information
         const externalPath = [...this.base, ...localPath];
         const pathToValidate = [...this.base, ...path]
 
+        const undefinedPathToken = localPath.findIndex((str) => !str && typeof str !== 'number') !== -1;
+        if (undefinedPathToken) return true // Will be unable to get schema anyways (additionalProperties)
+
+
         if (!input) input = this.getInput(localPath);
         if (!parent) parent = this.#get(path, this.resolved);
         if (!schema) schema = this.getSchema(localPath);
 
         const value = parent[name];
-        // const value = this.#get(path, this.resolved)
+
         const skipValidation = !this.validateEmptyValues && value === undefined;
         const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
@@ -824,10 +826,7 @@ export class JSONSchemaForm extends LitElement {
 
                         // Allow referring to floats as null (i.e. JSON NaN representation)
                         if (e.message === "is not of a type(s) number") {
-                            if (resolvedValue === null) {
-                                console.error('Throwing out...', externalPath.join('.'))
-                                return;
-                            }
+                            if (resolvedValue === null) return;
                         }
 
 
@@ -1169,7 +1168,6 @@ export class JSONSchemaForm extends LitElement {
                     onThrow: (...args) => this.onThrow(...args),
                     validateEmptyValues: this.validateEmptyValues,
                     onStatusChange: (status) => {
-                        console.warn("Nested status changed", status);
                         accordion.setStatus(status);
                         this.checkStatus();
                     }, // Forward status changes to the parent form
@@ -1284,17 +1282,20 @@ export class JSONSchemaForm extends LitElement {
                     required,
                     path,
                     results,
-                    true
+                    'pattern'
                 );
             });
 
             rendered = [...rendered, ...patternProps];
         }
 
-        // if (hasAdditionalProperties) {
-        //     const additionalList = this.#renderInteractiveElement('Additional Properties', schema, required, path, results)
-        //     rendered = [...rendered, additionalList];
-        // }
+        if (hasAdditionalProperties) {          
+            const additionalElement = this.#renderInteractiveElement('', {
+                title: `Additional Properties`,
+                ...schema
+            }, required, path, results, 'additional')
+            rendered = [...rendered, additionalElement];
+        }
 
         return rendered;
     };
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 22aef76ff..634e021ac 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -238,15 +238,30 @@ export class JSONSchemaInput extends LitElement {
             : [];
 
         if (isEditableObject) {
-            let regex;
-            try {
-                regex = new RegExp(name);
-            } catch (e) {}
+
+
 
             items = Object.entries(this.value);
 
-            if (regex) items = items.filter(([key]) => regex.test(key));
-            else items.filter(([key]) => key in schema.properties);
+            const isAdditionalProperties = this.#isAdditionalProperties()
+
+            if (this.#isPatternProperties()) {
+                const regex = new RegExp(name)
+                items = items.filter(([key]) => regex.test(key));
+            }
+
+            else if (isAdditionalProperties) {
+                const props = Object.keys(schema.properties ?? {})
+                items = items.filter(([key]) => !props.includes(key));
+
+                const patternProps = Object.keys(schema.patternProperties ?? {})
+                patternProps.forEach((key) => {
+                    const regex = new RegExp(key)
+                    items = items.filter(([k]) => !regex.test(k))
+                })
+            } 
+
+            else items.filter(([key]) => key in schema.properties)
 
             items = items.map(([key, value]) => {
                 return {
@@ -259,7 +274,7 @@ export class JSONSchemaInput extends LitElement {
                             onClick: () => {
                                 this.#createModal({
                                     key,
-                                    schema,
+                                    schema: isAdditionalProperties ? undefined : schema,
                                     results: value,
                                     list: list ?? this.#list,
                                 });
@@ -276,10 +291,23 @@ export class JSONSchemaInput extends LitElement {
     #schemaElement;
     #modal;
 
-    async #createModal({ key, schema, results, list } = {}) {
+    #isPatternProperties(){
+        return this.pattern && !this.#isAdditionalProperties()
+    }
+
+    #isAdditionalProperties(){
+        return this.pattern === 'additional'
+    }
+
+    async #createModal({ key, schema = {}, results, list } = {}) {
         const createNewObject = !results;
 
-        const isPatternProperties = this.pattern;
+        // const schemaProperties = Object.keys(schema.properties ?? {});
+        // const additionalProperties = Object.keys(results).filter((key) => !schemaProperties.includes(key));
+        // // const additionalElement = html`<label class="guided--form-label">Additional Properties</label><small>Cannot edit additional properties (${additionalProperties}) at this time</small>`
+
+        const isPatternProperties = this.#isPatternProperties()
+        const isAdditionalProperties = this.#isAdditionalProperties()
         const creatNewPatternProperty = isPatternProperties && createNewObject;
 
         const schemaCopy = structuredClone(schema);
@@ -354,7 +382,7 @@ export class JSONSchemaInput extends LitElement {
               })
             : new JSONSchemaInput({
                   schema: schemaCopy,
-                  validateOnChange: false,
+                  validateOnChange: isAdditionalProperties,
                   path: this.path,
                   form: this.form,
                   value: updateTarget,
@@ -373,9 +401,15 @@ export class JSONSchemaInput extends LitElement {
         setTimeout(() => this.#modal.toggle(true));
     }
 
+
+    #getType = (value = this.value) => Array.isArray(value) ? 'array' : typeof value
+
     #render() {
         const { validateOnChange, schema, path: fullPath } = this;
 
+        // Do your best to fill in missing schema values
+        if (!('type' in schema)) schema.type = this.#getType()
+
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
@@ -402,13 +436,14 @@ export class JSONSchemaInput extends LitElement {
         if (isArray || isEditableObject) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
-            const isPatternProperties = this.pattern;
+            const isPatternProperties = this.#isPatternProperties()
+            const isAdditionalProperties = this.#isAdditionalProperties()
 
             // Provide default item types
-            if (!isPatternProperties) {
+            if (isArray) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
                 if (!("items" in schema)) schema.items = {};
-                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = "string";
+                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = this.#getType(this.value[0]);
             }
 
             const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
@@ -417,6 +452,7 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
+
                 const ignore = this.form?.ignore
                     ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
                     : {};
@@ -449,7 +485,7 @@ export class JSONSchemaInput extends LitElement {
                             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
                         }, baseSchema);
 
-                        const result = await (validateOnChange &&
+                        const result = await (validateOnChange ?
                             (this.onValidate
                                 ? this.onValidate()
                                 : this.form
@@ -469,7 +505,9 @@ export class JSONSchemaInput extends LitElement {
                                             },
                                         }
                                     ) // NOTE: No pattern properties support
-                                  : ""));
+                                  : "") 
+                                  : true
+                    );
 
                         const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
 
@@ -505,10 +543,12 @@ export class JSONSchemaInput extends LitElement {
 
             const list = (this.#list = new List({
                 items: this.#mapToList(),
+
+                // Add edit button when new items are added
+                // NOTE: Duplicates some code in #mapToList
                 transform: (item) => {
                     if (this.#isEditableObject()) {
                         const { key, value } = item;
-
                         item.controls = [
                             new Button({
                                 label: "Edit",
@@ -541,6 +581,11 @@ export class JSONSchemaInput extends LitElement {
                 },
             }));
 
+            if (isAdditionalProperties) {
+                addButton.setAttribute("disabled", true);
+                addButton.title = "Additional properties cannot be added at this time—as they don't have a predictable structure.";
+            }
+
             return html`
                 <div class="schema-input list" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
                     ${list} ${addButton}
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 8be88686f..bbeced5f7 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -720,7 +720,7 @@ export class SimpleTable extends LitElement {
             ) => {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                const res = (await this.validateOnChange) ? this.validateOnChange([
+                const res = this.validateOnChange ? await this.validateOnChange([
                      info.i, 
                      fullInfo.col, 
                      ...path 
@@ -812,7 +812,7 @@ export class SimpleTable extends LitElement {
                 properties: entries,
             },
             this.keyColumn,
-            this.schema.order
+            this.schema.order ?? [ 'name' ] // Specify the order of the columns
         );
 
         // Try to guess the key column if unspecified
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 54c3923f2..c27481695 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -170,8 +170,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-        console.log("results", results)
-
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
@@ -214,7 +212,9 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             createTable: function (name, metadata, path) {
-                const parentSchema = this.getSchema(path);
+
+                // Do not create tables for patternProperties
+                const parentSchema = this.getSchema(path) ?? {};
                 if (parentSchema.patternProperties) return false;
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors

From 6e1599a932679c1f5b0431e2c9f695169a4b55fb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Dec 2023 22:51:58 +0000
Subject: [PATCH 052/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 135 +++++++++---------
 src/renderer/src/stories/JSONSchemaInput.js   |  59 ++++----
 src/renderer/src/stories/SimpleTable.js       |  20 ++-
 .../pages/guided-mode/data/GuidedMetadata.js  |   1 -
 src/renderer/src/stories/table/Cell.ts        |   4 +-
 5 files changed, 101 insertions(+), 118 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 03c68e0f5..2fe5ea5e7 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -218,8 +218,8 @@ export class JSONSchemaForm extends LitElement {
     #updateRendered = (force) =>
         force || this.#rendered === true
             ? (this.#rendered = new Promise(
-                (resolve) => (this.#toggleRendered = () => resolve((this.#rendered = true)))
-            ))
+                  (resolve) => (this.#toggleRendered = () => resolve((this.#rendered = true)))
+              ))
             : this.#rendered;
 
     resolved = {}; // Keep track of actual resolved values—not just what the user provides as results
@@ -412,8 +412,8 @@ export class JSONSchemaForm extends LitElement {
         let message = isValid
             ? ""
             : requiredButNotSpecified.length === 1
-                ? `<b>${header(requiredButNotSpecified[0])}</b> is not defined`
-                : `${requiredButNotSpecified.length} required inputs are not specified properly`;
+              ? `<b>${header(requiredButNotSpecified[0])}</b> is not defined`
+              : `${requiredButNotSpecified.length} required inputs are not specified properly`;
         if (requiredButNotSpecified.length !== nMissingRequired)
             console.warn("Disagreement about the correct error to throw...");
 
@@ -429,8 +429,9 @@ export class JSONSchemaForm extends LitElement {
                     message = `<b>${header(schema.title ?? path.join("."))}</b> is not valid`;
                 } else message = `${flaggedInputs.length} invalid form values`;
             }
-            message += `${this.base.length ? ` in the <b>${this.base.join(".")}</b> section` : ""
-                }. Please check the highlighted fields.`;
+            message += `${
+                this.base.length ? ` in the <b>${this.base.join(".")}</b> section` : ""
+            }. Please check the highlighted fields.`;
         }
 
         if (message) this.throw(message);
@@ -591,7 +592,7 @@ export class JSONSchemaForm extends LitElement {
             controls: this.controls[name],
             required: isRequired,
             validateEmptyValue: this.validateEmptyValues,
-            pattern: propertyType === 'pattern' ? name : propertyType ?? undefined,
+            pattern: propertyType === "pattern" ? name : propertyType ?? undefined,
         });
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
@@ -609,8 +610,8 @@ export class JSONSchemaForm extends LitElement {
             <div
                 id=${encode(localPath.join("-"))}
                 class="form-section ${isRequired || isConditional ? "required" : ""} ${isConditional
-                ? "conditional"
-                : ""}"
+                    ? "conditional"
+                    : ""}"
             >
                 <label class="guided--form-label"
                     >${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}</label
@@ -666,10 +667,10 @@ export class JSONSchemaForm extends LitElement {
     };
 
     // Checks missing required properties and throws an error if any are found
-    onInvalid = () => { };
-    onLoaded = () => { };
-    onUpdate = () => { };
-    onOverride = () => { };
+    onInvalid = () => {};
+    onLoaded = () => {};
+    onUpdate = () => {};
+    onOverride = () => {};
 
     // #deleteExtraneousResults = (results, schema) => {
     //     for (let name in results) {
@@ -722,10 +723,10 @@ export class JSONSchemaForm extends LitElement {
         return flattenRecursedValues(res); // Flatten on the last pass
     };
 
-    validateOnChange = () => { };
-    onStatusChange = () => { };
-    onThrow = () => { };
-    createTable = () => { };
+    validateOnChange = () => {};
+    onStatusChange = () => {};
+    onThrow = () => {};
+    createTable = () => {};
 
     #getLink = (args) => {
         if (typeof args === "string") args = args.split("-");
@@ -779,25 +780,15 @@ export class JSONSchemaForm extends LitElement {
     #isARequiredPropertyString = `is a required property`;
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
-    triggerValidation = async (
-        name,
-        path = [],
-        checkLinks = true,
-        input,
-        schema,
-        parent,
-        hooks = {}
-    ) => {
-
+    triggerValidation = async (name, path = [], checkLinks = true, input, schema, parent, hooks = {}) => {
         const { onError, onWarning } = hooks;
 
-        const localPath = [...path, name].filter(str => typeof str === 'string'); // Ignore row information
+        const localPath = [...path, name].filter((str) => typeof str === "string"); // Ignore row information
         const externalPath = [...this.base, ...localPath];
         const pathToValidate = [...this.base, ...path];
 
-        const undefinedPathToken = localPath.findIndex((str) => !str && typeof str !== 'number') !== -1;
-        if (undefinedPathToken) return true // Will be unable to get schema anyways (additionalProperties)
-
+        const undefinedPathToken = localPath.findIndex((str) => !str && typeof str !== "number") !== -1;
+        if (undefinedPathToken) return true; // Will be unable to get schema anyways (additionalProperties)
 
         if (!input) input = this.getInput(localPath);
         if (!parent) parent = this.#get(path, this.resolved);
@@ -811,35 +802,34 @@ export class JSONSchemaForm extends LitElement {
         const jsonSchemaErrors =
             validateArgs.length === 2
                 ? await v
-                    .validate(...validateArgs)
-                    .errors.map((e) => {
-                        const propName = e.path.slice(-1)[0] ?? name;
-                        const rowName = e.path.slice(-2)[0];
-
-                        const isRow = typeof rowName === "number"
-
-                        const resolvedValue = e.path.reduce((acc, token) => acc[token], value)
-
-                        // ------------ Exclude Certain Errors ------------
-                        // Non-Strict Rule
-                        if (schema.strict === false && e.message.includes("is not one of enum values")) return;
-
-                        // Allow referring to floats as null (i.e. JSON NaN representation)
-                        if (e.message === "is not of a type(s) number") {
-                            if (resolvedValue === null) return;
-                        }
-
-
-
-                        return {
-                            type: "error",
-                            message: `${typeof propName === "string"
-                                    ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
-                                    : `Row ${propName}`
-                                } ${e.message}.`,
-                        };
-                    })
-                    .filter((v) => !!v)
+                      .validate(...validateArgs)
+                      .errors.map((e) => {
+                          const propName = e.path.slice(-1)[0] ?? name;
+                          const rowName = e.path.slice(-2)[0];
+
+                          const isRow = typeof rowName === "number";
+
+                          const resolvedValue = e.path.reduce((acc, token) => acc[token], value);
+
+                          // ------------ Exclude Certain Errors ------------
+                          // Non-Strict Rule
+                          if (schema.strict === false && e.message.includes("is not one of enum values")) return;
+
+                          // Allow referring to floats as null (i.e. JSON NaN representation)
+                          if (e.message === "is not of a type(s) number") {
+                              if (resolvedValue === null) return;
+                          }
+
+                          return {
+                              type: "error",
+                              message: `${
+                                  typeof propName === "string"
+                                      ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
+                                      : `Row ${propName}`
+                              } ${e.message}.`,
+                          };
+                      })
+                      .filter((v) => !!v)
                 : [];
 
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
@@ -904,8 +894,9 @@ export class JSONSchemaForm extends LitElement {
                 const regex = new RegExp(schema.pattern);
                 if (!regex.test(parent[name])) {
                     errors.push({
-                        message: `${schema.title ?? header(name)} does not match the required pattern (${schema.pattern
-                            }).`,
+                        message: `${schema.title ?? header(name)} does not match the required pattern (${
+                            schema.pattern
+                        }).`,
                         type: "error",
                     });
                 }
@@ -928,7 +919,6 @@ export class JSONSchemaForm extends LitElement {
 
         const resolvedErrors = errors
             .map((e) => {
-
                 // Custom Error Transformations
                 if (this.transformErrors) {
                     const res = this.transformErrors(e, externalPath, parent[name]);
@@ -1282,18 +1272,25 @@ export class JSONSchemaForm extends LitElement {
                     required,
                     path,
                     results,
-                    'pattern'
+                    "pattern"
                 );
             });
 
             rendered = [...rendered, ...patternProps];
         }
 
-        if (hasAdditionalProperties) {          
-            const additionalElement = this.#renderInteractiveElement('', {
-                title: `Additional Properties`,
-                ...schema
-            }, required, path, results, 'additional')
+        if (hasAdditionalProperties) {
+            const additionalElement = this.#renderInteractiveElement(
+                "",
+                {
+                    title: `Additional Properties`,
+                    ...schema,
+                },
+                required,
+                path,
+                results,
+                "additional"
+            );
             rendered = [...rendered, additionalElement];
         }
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f1d6837d9..621b92bca 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -238,30 +238,23 @@ export class JSONSchemaInput extends LitElement {
             : [];
 
         if (isEditableObject) {
-
-
-
             items = Object.entries(this.value);
 
-            const isAdditionalProperties = this.#isAdditionalProperties()
+            const isAdditionalProperties = this.#isAdditionalProperties();
 
             if (this.#isPatternProperties()) {
-                const regex = new RegExp(name)
+                const regex = new RegExp(name);
                 items = items.filter(([key]) => regex.test(key));
-            }
-
-            else if (isAdditionalProperties) {
-                const props = Object.keys(schema.properties ?? {})
+            } else if (isAdditionalProperties) {
+                const props = Object.keys(schema.properties ?? {});
                 items = items.filter(([key]) => !props.includes(key));
 
-                const patternProps = Object.keys(schema.patternProperties ?? {})
+                const patternProps = Object.keys(schema.patternProperties ?? {});
                 patternProps.forEach((key) => {
-                    const regex = new RegExp(key)
-                    items = items.filter(([k]) => !regex.test(k))
-                })
-            } 
-
-            else items.filter(([key]) => key in schema.properties)
+                    const regex = new RegExp(key);
+                    items = items.filter(([k]) => !regex.test(k));
+                });
+            } else items.filter(([key]) => key in schema.properties);
 
             items = items.map(([key, value]) => {
                 return {
@@ -291,12 +284,12 @@ export class JSONSchemaInput extends LitElement {
     #schemaElement;
     #modal;
 
-    #isPatternProperties(){
-        return this.pattern && !this.#isAdditionalProperties()
+    #isPatternProperties() {
+        return this.pattern && !this.#isAdditionalProperties();
     }
 
-    #isAdditionalProperties(){
-        return this.pattern === 'additional'
+    #isAdditionalProperties() {
+        return this.pattern === "additional";
     }
 
     async #createModal({ key, schema = {}, results, list } = {}) {
@@ -306,8 +299,8 @@ export class JSONSchemaInput extends LitElement {
         // const additionalProperties = Object.keys(results).filter((key) => !schemaProperties.includes(key));
         // // const additionalElement = html`<label class="guided--form-label">Additional Properties</label><small>Cannot edit additional properties (${additionalProperties}) at this time</small>`
 
-        const isPatternProperties = this.#isPatternProperties()
-        const isAdditionalProperties = this.#isAdditionalProperties()
+        const isPatternProperties = this.#isPatternProperties();
+        const isAdditionalProperties = this.#isAdditionalProperties();
         const creatNewPatternProperty = isPatternProperties && createNewObject;
 
         const schemaCopy = structuredClone(schema);
@@ -401,14 +394,13 @@ export class JSONSchemaInput extends LitElement {
         setTimeout(() => this.#modal.toggle(true));
     }
 
-
-    #getType = (value = this.value) => Array.isArray(value) ? 'array' : typeof value
+    #getType = (value = this.value) => (Array.isArray(value) ? "array" : typeof value);
 
     #render() {
         const { validateOnChange, schema, path: fullPath } = this;
 
         // Do your best to fill in missing schema values
-        if (!('type' in schema)) schema.type = this.#getType()
+        if (!("type" in schema)) schema.type = this.#getType();
 
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
@@ -436,8 +428,8 @@ export class JSONSchemaInput extends LitElement {
         if (isArray || isEditableObject) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
-            const isPatternProperties = this.#isPatternProperties()
-            const isAdditionalProperties = this.#isAdditionalProperties()
+            const isPatternProperties = this.#isPatternProperties();
+            const isAdditionalProperties = this.#isAdditionalProperties();
 
             // Provide default item types
             if (isArray) {
@@ -452,7 +444,6 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
-
                 const ignore = this.form?.ignore
                     ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
                     : {};
@@ -485,8 +476,8 @@ export class JSONSchemaInput extends LitElement {
                             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
                         }, baseSchema);
 
-                        const result = await (validateOnChange ?
-                            (this.onValidate
+                        const result = await (validateOnChange
+                            ? this.onValidate
                                 ? this.onValidate()
                                 : this.form
                                   ? this.form.triggerValidation(
@@ -505,9 +496,8 @@ export class JSONSchemaInput extends LitElement {
                                             },
                                         }
                                     ) // NOTE: No pattern properties support
-                                  : "") 
-                                  : true
-                    );
+                                  : ""
+                            : true);
 
                         const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
 
@@ -583,7 +573,8 @@ export class JSONSchemaInput extends LitElement {
 
             if (isAdditionalProperties) {
                 addButton.setAttribute("disabled", true);
-                addButton.title = "Additional properties cannot be added at this time—as they don't have a predictable structure.";
+                addButton.title =
+                    "Additional properties cannot be added at this time—as they don't have a predictable structure.";
             }
 
             return html`
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index a998d8b9d..ba46abaa1 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -363,12 +363,10 @@ export class SimpleTable extends LitElement {
                 if (hasRow) value = row;
                 else return "";
             } else {
-
-                value = hasRow ? this.#data[row][col] : undefined
-                if (this.#isUndefined(value)) value = this.globals[col]
-                if (this.#isUndefined(value)) value = this.schema.properties[col].default
-                if (this.#isUndefined(value)) value = ""
-                
+                value = hasRow ? this.#data[row][col] : undefined;
+                if (this.#isUndefined(value)) value = this.globals[col];
+                if (this.#isUndefined(value)) value = this.schema.properties[col].default;
+                if (this.#isUndefined(value)) value = "";
             }
             return value;
         });
@@ -719,11 +717,9 @@ export class SimpleTable extends LitElement {
             ) => {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
-                const res = this.validateOnChange ? await this.validateOnChange([
-                     info.i, 
-                     fullInfo.col, 
-                     ...path 
-                ], parent, value, schema) : true;
+                const res = this.validateOnChange
+                    ? await this.validateOnChange([info.i, fullInfo.col, ...path], parent, value, schema)
+                    : true;
 
                 return res;
             },
@@ -810,7 +806,7 @@ export class SimpleTable extends LitElement {
                 properties: entries,
             },
             this.keyColumn,
-            this.schema.order ?? [ 'name' ] // Specify the order of the columns
+            this.schema.order ?? ["name"] // Specify the order of the columns
         );
 
         // Try to guess the key column if unspecified
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 c27481695..8e7270d97 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -212,7 +212,6 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             createTable: function (name, metadata, path) {
-
                 // Do not create tables for patternProperties
                 const parentSchema = this.getSchema(path) ?? {};
                 if (parentSchema.patternProperties) return false;
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index f7817ef20..5be7afff0 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -109,8 +109,8 @@ export class TableCell extends LitElement {
 
     set value(v) {
         if (this.input) this.input.set(v === null  ? v : ( v ?? '' )) // Allow null to be set directly
-        this.#value = this.input 
-                            ? this.input.getValue() // Ensure all operations are undoable / value is coerced 
+        this.#value = this.input
+                            ? this.input.getValue() // Ensure all operations are undoable / value is coerced
                             : v // Silently set value if not rendered yet
      }
 

From 16aba1ad9449d8744f9cdb4e83b05c6cff0b6dbf Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 28 Dec 2023 09:18:37 -0600
Subject: [PATCH 053/133] Fix validation

---
 src/renderer/src/stories/JSONSchemaForm.js    | 131 +++++++++++-------
 .../pages/guided-mode/data/GuidedMetadata.js  |   3 +-
 .../guided-mode/data/GuidedPathExpansion.js   |   3 +-
 src/renderer/src/validation/index.js          |   7 +
 4 files changed, 91 insertions(+), 53 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 2fe5ea5e7..1deea482a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -23,7 +23,7 @@ const encode = (str) => {
 
 import { Validator } from "jsonschema";
 
-var v = new Validator();
+var validator = new Validator();
 
 const isObject = (o) => {
     return o && typeof o === "object" && !Array.isArray(o);
@@ -387,9 +387,48 @@ export class JSONSchemaForm extends LitElement {
         throw new Error(message);
     };
 
+    validateSchema = async (resolved, schema, name) => {
+        return await validator
+        .validate(resolved, schema)
+        .errors.map((e) => {
+
+            const propName = e.path.slice(-1)[0] ?? name ?? e.property;
+            const rowName = e.path.slice(-2)[0];
+
+            const isRow = typeof rowName === "number";
+
+            const resolvedValue = e.path.reduce((acc, token) => acc[token], resolved);
+
+            // ------------ Exclude Certain Errors ------------
+            // Non-Strict Rule
+            if (schema.strict === false && e.message.includes("is not one of enum values")) return;
+
+            // Allow referring to floats as null (i.e. JSON NaN representation)
+            if (e.message === "is not of a type(s) number") {
+                if (resolvedValue === null) return;
+            }
+
+            return {
+                type: "error",
+                message: `${
+                    typeof propName === "string"
+                        ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
+                        : `Row ${propName}`
+                } ${e.message}.`,
+            };
+        })
+        .filter((v) => !!v)
+    }
+
     validate = async (resolved = this.resolved) => {
+
         // Validate against the entire JSON Schema
-        const result = await v.validate(resolved, this.schema);
+        const copy = structuredClone(resolved);
+        delete copy.__disabled
+
+        const result = await this.validateSchema(copy, this.schema);
+
+        const resolvedErrors = this.#resolveErrors(result, this.base, resolved)
 
         // Check if any required inputs are missing
         const requiredButNotSpecified = await this.#validateRequirements(resolved); // get missing required paths
@@ -398,11 +437,17 @@ export class JSONSchemaForm extends LitElement {
         // Check if all inputs are valid
         const flaggedInputs = this.shadowRoot ? this.shadowRoot.querySelectorAll(".invalid") : [];
 
+        if (resolvedErrors.length) {
+            const len = resolvedErrors.length;
+            if (len === 1) this.throw(resolvedErrors[0].message);
+            else this.throw(`${len} JSON Schema errors on this form.`);
+        }
+
         const allErrors = Array.from(flaggedInputs)
-            .map((el) => {
-                return Array.from(el.nextElementSibling.children).map((li) => li.message);
-            })
-            .flat();
+                .map((el) => {
+                    return Array.from(el.nextElementSibling.children).map((li) => li.message);
+                }).flat()
+
 
         const nMissingRequired = allErrors.reduce((acc, curr) => {
             return (acc += curr.includes(this.#isARequiredPropertyString) ? 1 : 0);
@@ -645,8 +690,8 @@ export class JSONSchemaForm extends LitElement {
         let invalid = [];
 
         for (let name in requirements) {
-            let isRequired = requirements[name];
-
+            let isRequired = this.#isRequired(name, requirements)
+            
             if (this.#accordions[name]?.disabled) continue; // Skip disabled accordions
 
             // // NOTE: Uncomment to block checking requirements inside optional properties
@@ -759,10 +804,10 @@ export class JSONSchemaForm extends LitElement {
         ).reduce((a, b) => a && b, true);
     };
 
-    #isRequired = (path) => {
+    #isRequired = (path, requirements = this.#requirements) => {
         if (typeof path === "string") path = path.split("-");
         // path = path.slice(this.base.length); // Remove base path
-        let res = path.reduce((obj, key) => obj?.[key], this.#requirements);
+        let res = path.reduce((obj, key) => obj?.[key], requirements);
         if (typeof res === "object") res = res[selfRequiredSymbol];
         return res;
     };
@@ -779,6 +824,21 @@ export class JSONSchemaForm extends LitElement {
 
     #isARequiredPropertyString = `is a required property`;
 
+    #resolveErrors = (errors, externalPath, parent) => {
+       return errors
+            .map((e) => {
+                // Custom Error Transformations
+                if (this.transformErrors) {
+                    const name = externalPath.slice(-1)[0];
+                    const res = this.transformErrors(e, externalPath, parent[name]);
+                    if (res === false) return;
+                }
+
+                return e;
+            })
+            .filter((v) => !!v);
+    }
+
     // Assume this is going to return as a Promise—even if the change function isn't returning one
     triggerValidation = async (name, path = [], checkLinks = true, input, schema, parent, hooks = {}) => {
         const { onError, onWarning } = hooks;
@@ -801,38 +861,11 @@ export class JSONSchemaForm extends LitElement {
 
         const jsonSchemaErrors =
             validateArgs.length === 2
-                ? await v
-                      .validate(...validateArgs)
-                      .errors.map((e) => {
-                          const propName = e.path.slice(-1)[0] ?? name;
-                          const rowName = e.path.slice(-2)[0];
-
-                          const isRow = typeof rowName === "number";
-
-                          const resolvedValue = e.path.reduce((acc, token) => acc[token], value);
-
-                          // ------------ Exclude Certain Errors ------------
-                          // Non-Strict Rule
-                          if (schema.strict === false && e.message.includes("is not one of enum values")) return;
-
-                          // Allow referring to floats as null (i.e. JSON NaN representation)
-                          if (e.message === "is not of a type(s) number") {
-                              if (resolvedValue === null) return;
-                          }
-
-                          return {
-                              type: "error",
-                              message: `${
-                                  typeof propName === "string"
-                                      ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
-                                      : `Row ${propName}`
-                              } ${e.message}.`,
-                          };
-                      })
-                      .filter((v) => !!v)
+                ? await this.validateSchema(...validateArgs, name)
                 : [];
 
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
+
         if (valid === null) return null; // Skip validation / data change if the value is null
 
         const isRequired = this.#isRequired(localPath) || (!input.table && input.required); // Do not trust required status of table validations
@@ -917,17 +950,7 @@ export class JSONSchemaForm extends LitElement {
 
         if (!isValid && errors.length === 0) errors.push({ type: "error", message: "Invalid value detected" });
 
-        const resolvedErrors = errors
-            .map((e) => {
-                // Custom Error Transformations
-                if (this.transformErrors) {
-                    const res = this.transformErrors(e, externalPath, parent[name]);
-                    if (res === false) return;
-                }
-
-                return e;
-            })
-            .filter((v) => !!v);
+        const resolvedErrors = this.#resolveErrors(errors, externalPath, parent)
 
         // Track errors and warnings
         const updatedWarnings = warnings.map((info) => (onWarning ? onWarning(info) : info)).filter((v) => !!v);
@@ -1132,6 +1155,12 @@ export class JSONSchemaForm extends LitElement {
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
 
             if (renderableInside.length) {
+
+                const allIgnore = this.ignore["*"] ?? {};
+                const ignore = this.ignore[name] ?? {}
+                if (ignore["*"]) ignore["*"] = { ...allIgnore, ...ignore["*"] }
+                else ignore["*"] = allIgnore
+
                 const ogContext = this;
                 const nested = (this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
@@ -1147,7 +1176,7 @@ export class JSONSchemaForm extends LitElement {
                     transformErrors: this.transformErrors,
 
                     required: required[name], // Scoped to the sub-schema
-                    ignore: this.ignore[name],
+                    ignore,
                     dialogOptions: this.dialogOptions,
                     dialogType: this.dialogType,
                     onlyRequired: this.onlyRequired,
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 8e7270d97..2c037b012 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -182,9 +182,10 @@ export class GuidedMetadataPage extends ManagedPage {
                 this.notify(`<b>${header(name)}</b> has been overriden with a global value.`, "warning", 3000);
             },
 
-            transformErrors: (e) => {
+            transformErrors: (e, externalPath, parent) => {
                 // JSON Schema Exceptions
                 if (e.message.includes('does not conform to the "date-time" format.')) return false;
+                if (e.message.includes('not allowed to have the additional property \"Ecephys\".')) return false; // NOTE: Remove after including Ecephys metadata
             },
 
             conditionalRequirements: [
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index fbaa87438..901aca414 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -270,7 +270,7 @@ export class GuidedPathExpansionPage extends Page {
         if (state === undefined) infoBox.open = true; // Open the info box if no option has been selected
 
         // Require properties for all sources
-        const generatedSchema = { type: "object", properties: {} };
+        const generatedSchema = { type: "object", properties: {}, additionalProperties: false };
         for (let key in this.info.globalState.interfaces)
             generatedSchema.properties[key] = { type: "object", ...pathExpansionSchema };
         structureState.schema = generatedSchema;
@@ -368,6 +368,7 @@ export class GuidedPathExpansionPage extends Page {
             onUpdate: () => (this.unsavedUpdates = "conversions"),
             schema: {
                 type: "object",
+                additionalProperties: false,
                 properties: {
                     keep_existing_data: {
                         type: "boolean",
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index a56eae6dc..1db670d5a 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -70,6 +70,13 @@ export async function validateOnChange(name, parent, path, value) {
     });
 
     const res = resolveAll(results, (arr) => {
+
+        arr = arr.map((v, i) => {
+            const func = functions[i];
+            if (typeof func === "function") return v;
+            else return v === null ? undefined : v;
+        })
+        
         const flat = arr.flat();
         if (flat.find((res) => res?.message)) {
             return flat

From b1532fdceb7d4101dcfc5684c530a4737b010414 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 28 Dec 2023 15:19:00 +0000
Subject: [PATCH 054/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 84 +++++++++----------
 .../pages/guided-mode/data/GuidedMetadata.js  |  2 +-
 src/renderer/src/validation/index.js          |  5 +-
 3 files changed, 42 insertions(+), 49 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 1deea482a..e2bb881f3 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -389,46 +389,44 @@ export class JSONSchemaForm extends LitElement {
 
     validateSchema = async (resolved, schema, name) => {
         return await validator
-        .validate(resolved, schema)
-        .errors.map((e) => {
+            .validate(resolved, schema)
+            .errors.map((e) => {
+                const propName = e.path.slice(-1)[0] ?? name ?? e.property;
+                const rowName = e.path.slice(-2)[0];
 
-            const propName = e.path.slice(-1)[0] ?? name ?? e.property;
-            const rowName = e.path.slice(-2)[0];
+                const isRow = typeof rowName === "number";
 
-            const isRow = typeof rowName === "number";
+                const resolvedValue = e.path.reduce((acc, token) => acc[token], resolved);
 
-            const resolvedValue = e.path.reduce((acc, token) => acc[token], resolved);
+                // ------------ Exclude Certain Errors ------------
+                // Non-Strict Rule
+                if (schema.strict === false && e.message.includes("is not one of enum values")) return;
 
-            // ------------ Exclude Certain Errors ------------
-            // Non-Strict Rule
-            if (schema.strict === false && e.message.includes("is not one of enum values")) return;
-
-            // Allow referring to floats as null (i.e. JSON NaN representation)
-            if (e.message === "is not of a type(s) number") {
-                if (resolvedValue === null) return;
-            }
+                // Allow referring to floats as null (i.e. JSON NaN representation)
+                if (e.message === "is not of a type(s) number") {
+                    if (resolvedValue === null) return;
+                }
 
-            return {
-                type: "error",
-                message: `${
-                    typeof propName === "string"
-                        ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
-                        : `Row ${propName}`
-                } ${e.message}.`,
-            };
-        })
-        .filter((v) => !!v)
-    }
+                return {
+                    type: "error",
+                    message: `${
+                        typeof propName === "string"
+                            ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
+                            : `Row ${propName}`
+                    } ${e.message}.`,
+                };
+            })
+            .filter((v) => !!v);
+    };
 
     validate = async (resolved = this.resolved) => {
-
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
-        delete copy.__disabled
+        delete copy.__disabled;
 
         const result = await this.validateSchema(copy, this.schema);
 
-        const resolvedErrors = this.#resolveErrors(result, this.base, resolved)
+        const resolvedErrors = this.#resolveErrors(result, this.base, resolved);
 
         // Check if any required inputs are missing
         const requiredButNotSpecified = await this.#validateRequirements(resolved); // get missing required paths
@@ -444,10 +442,10 @@ export class JSONSchemaForm extends LitElement {
         }
 
         const allErrors = Array.from(flaggedInputs)
-                .map((el) => {
-                    return Array.from(el.nextElementSibling.children).map((li) => li.message);
-                }).flat()
-
+            .map((el) => {
+                return Array.from(el.nextElementSibling.children).map((li) => li.message);
+            })
+            .flat();
 
         const nMissingRequired = allErrors.reduce((acc, curr) => {
             return (acc += curr.includes(this.#isARequiredPropertyString) ? 1 : 0);
@@ -690,8 +688,8 @@ export class JSONSchemaForm extends LitElement {
         let invalid = [];
 
         for (let name in requirements) {
-            let isRequired = this.#isRequired(name, requirements)
-            
+            let isRequired = this.#isRequired(name, requirements);
+
             if (this.#accordions[name]?.disabled) continue; // Skip disabled accordions
 
             // // NOTE: Uncomment to block checking requirements inside optional properties
@@ -825,7 +823,7 @@ export class JSONSchemaForm extends LitElement {
     #isARequiredPropertyString = `is a required property`;
 
     #resolveErrors = (errors, externalPath, parent) => {
-       return errors
+        return errors
             .map((e) => {
                 // Custom Error Transformations
                 if (this.transformErrors) {
@@ -837,7 +835,7 @@ export class JSONSchemaForm extends LitElement {
                 return e;
             })
             .filter((v) => !!v);
-    }
+    };
 
     // Assume this is going to return as a Promise—even if the change function isn't returning one
     triggerValidation = async (name, path = [], checkLinks = true, input, schema, parent, hooks = {}) => {
@@ -859,10 +857,7 @@ export class JSONSchemaForm extends LitElement {
         const skipValidation = !this.validateEmptyValues && value === undefined;
         const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
-        const jsonSchemaErrors =
-            validateArgs.length === 2
-                ? await this.validateSchema(...validateArgs, name)
-                : [];
+        const jsonSchemaErrors = validateArgs.length === 2 ? await this.validateSchema(...validateArgs, name) : [];
 
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
@@ -950,7 +945,7 @@ export class JSONSchemaForm extends LitElement {
 
         if (!isValid && errors.length === 0) errors.push({ type: "error", message: "Invalid value detected" });
 
-        const resolvedErrors = this.#resolveErrors(errors, externalPath, parent)
+        const resolvedErrors = this.#resolveErrors(errors, externalPath, parent);
 
         // Track errors and warnings
         const updatedWarnings = warnings.map((info) => (onWarning ? onWarning(info) : info)).filter((v) => !!v);
@@ -1155,11 +1150,10 @@ export class JSONSchemaForm extends LitElement {
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
 
             if (renderableInside.length) {
-
                 const allIgnore = this.ignore["*"] ?? {};
-                const ignore = this.ignore[name] ?? {}
-                if (ignore["*"]) ignore["*"] = { ...allIgnore, ...ignore["*"] }
-                else ignore["*"] = allIgnore
+                const ignore = this.ignore[name] ?? {};
+                if (ignore["*"]) ignore["*"] = { ...allIgnore, ...ignore["*"] };
+                else ignore["*"] = allIgnore;
 
                 const ogContext = this;
                 const nested = (this.#nestedForms[name] = new JSONSchemaForm({
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 2c037b012..940d07e83 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -185,7 +185,7 @@ export class GuidedMetadataPage extends ManagedPage {
             transformErrors: (e, externalPath, parent) => {
                 // JSON Schema Exceptions
                 if (e.message.includes('does not conform to the "date-time" format.')) return false;
-                if (e.message.includes('not allowed to have the additional property \"Ecephys\".')) return false; // NOTE: Remove after including Ecephys metadata
+                if (e.message.includes('not allowed to have the additional property "Ecephys".')) return false; // NOTE: Remove after including Ecephys metadata
             },
 
             conditionalRequirements: [
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index 1db670d5a..c539460ef 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -70,13 +70,12 @@ export async function validateOnChange(name, parent, path, value) {
     });
 
     const res = resolveAll(results, (arr) => {
-
         arr = arr.map((v, i) => {
             const func = functions[i];
             if (typeof func === "function") return v;
             else return v === null ? undefined : v;
-        })
-        
+        });
+
         const flat = arr.flat();
         if (flat.find((res) => res?.message)) {
             return flat

From 9c95fbb76c5059ed86f7eadfedbd6c3299ee4566 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sun, 31 Dec 2023 09:03:14 -0600
Subject: [PATCH 055/133] Exclude additionalProperties rendering group if none
 exist on initialization

---
 src/renderer/src/stories/JSONSchemaForm.js  |  15 ++-
 src/renderer/src/stories/JSONSchemaInput.js | 111 +++++++++++---------
 2 files changed, 70 insertions(+), 56 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index e2bb881f3..62bd1b9e4 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -9,7 +9,7 @@ import { resolve } from "../promises";
 import { merge } from "./pages/utils";
 import { resolveProperties } from "./pages/guided-mode/data/utils";
 
-import { JSONSchemaInput } from "./JSONSchemaInput";
+import { JSONSchemaInput, getEditableItems } from "./JSONSchemaInput";
 import { InspectorListItem } from "./preview/inspector/InspectorList";
 
 const encode = (str) => {
@@ -1126,8 +1126,6 @@ export class JSONSchemaForm extends LitElement {
 
             const headerName = header(name);
 
-            const isRequired = this.#isRequired(localPath);
-
             const renderableInside = this.#getRenderable(info, required[name], ignore, localPath, true);
 
             const __disabled = this.results.__disabled ?? (this.results.__disabled = {});
@@ -1303,6 +1301,13 @@ export class JSONSchemaForm extends LitElement {
         }
 
         if (hasAdditionalProperties) {
+
+            const pattern = "additional"
+            const shouldRender = getEditableItems(results, pattern, { schema })
+
+            // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
+            if (!shouldRender.length) return rendered
+
             const additionalElement = this.#renderInteractiveElement(
                 "",
                 {
@@ -1312,9 +1317,9 @@ export class JSONSchemaForm extends LitElement {
                 required,
                 path,
                 results,
-                "additional"
+                pattern
             );
-            rendered = [...rendered, additionalElement];
+            return [...rendered, additionalElement];
         }
 
         return rendered;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 621b92bca..975e0e03c 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -13,6 +13,40 @@ import { capitalize } from "./forms/utils";
 import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 
+const isEditableObject = (schema) => schema.type === "object";
+const isAdditionalProperties = (pattern) => pattern === "additional";
+const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
+
+export const getEditableItems = (
+    value, 
+    pattern,
+    { name, schema } = {}
+) => {
+    let items = Object.entries(value);
+
+    const allowAdditionalProperties = isAdditionalProperties(pattern);
+
+    if (isPatternProperties(pattern)) {
+        const regex = new RegExp(name);
+        items = items.filter(([key]) => regex.test(key));
+    } else if (allowAdditionalProperties) {
+        const props = Object.keys(schema.properties ?? {});
+        items = items.filter(([key]) => !props.includes(key));
+
+        const patternProps = Object.keys(schema.patternProperties ?? {});
+        patternProps.forEach((key) => {
+            const regex = new RegExp(key);
+            items = items.filter(([k]) => !regex.test(k));
+        });
+    } 
+    
+    else items.filter(([key]) => key in schema.properties);
+
+    items = items.filter(([key]) => !key.includes('__')); // Remove secret properties
+
+    return items.map(([key, value]) => { return { key, value } })
+}
+
 const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
 
 const isFilesystemSelector = (name, format) => {
@@ -221,42 +255,18 @@ export class JSONSchemaInput extends LitElement {
 
     #onThrow = (...args) => (this.onThrow ? this.onThrow(...args) : this.form?.onThrow(...args));
 
-    #isEditableObject = (schema = this.schema) => schema.type === "object";
-
     #list;
     #mapToList({ value = this.value, schema = this.schema, list } = {}) {
         const { path: fullPath } = this;
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
-        const isEditableObject = this.#isEditableObject();
-        const resolved = isEditableObject ? Object.values(value ?? {}) : value ?? [];
-        let items = resolved
-            ? resolved.map((value) => {
-                  return { value };
-              })
-            : [];
-
-        if (isEditableObject) {
-            items = Object.entries(this.value);
+        const canAddProperties = isEditableObject(this.schema);
 
-            const isAdditionalProperties = this.#isAdditionalProperties();
-
-            if (this.#isPatternProperties()) {
-                const regex = new RegExp(name);
-                items = items.filter(([key]) => regex.test(key));
-            } else if (isAdditionalProperties) {
-                const props = Object.keys(schema.properties ?? {});
-                items = items.filter(([key]) => !props.includes(key));
-
-                const patternProps = Object.keys(schema.patternProperties ?? {});
-                patternProps.forEach((key) => {
-                    const regex = new RegExp(key);
-                    items = items.filter(([k]) => !regex.test(k));
-                });
-            } else items.filter(([key]) => key in schema.properties);
-
-            items = items.map(([key, value]) => {
+        if (canAddProperties) {
+            const editable =  getEditableItems(this.value, this.pattern, { name, schema })
+            console.log(editable)
+           return editable.map(({ key, value }) => {
                 return {
                     key,
                     value,
@@ -267,7 +277,7 @@ export class JSONSchemaInput extends LitElement {
                             onClick: () => {
                                 this.#createModal({
                                     key,
-                                    schema: isAdditionalProperties ? undefined : schema,
+                                    schema: allowAdditionalProperties ? undefined : schema,
                                     results: value,
                                     list: list ?? this.#list,
                                 });
@@ -276,6 +286,13 @@ export class JSONSchemaInput extends LitElement {
                     ],
                 };
             });
+        } else {
+            const resolved = value ?? [];
+            return resolved
+                ? resolved.map((value) => {
+                      return { value };
+                  })
+                : [];
         }
 
         return items;
@@ -284,14 +301,6 @@ export class JSONSchemaInput extends LitElement {
     #schemaElement;
     #modal;
 
-    #isPatternProperties() {
-        return this.pattern && !this.#isAdditionalProperties();
-    }
-
-    #isAdditionalProperties() {
-        return this.pattern === "additional";
-    }
-
     async #createModal({ key, schema = {}, results, list } = {}) {
         const createNewObject = !results;
 
@@ -299,9 +308,9 @@ export class JSONSchemaInput extends LitElement {
         // const additionalProperties = Object.keys(results).filter((key) => !schemaProperties.includes(key));
         // // const additionalElement = html`<label class="guided--form-label">Additional Properties</label><small>Cannot edit additional properties (${additionalProperties}) at this time</small>`
 
-        const isPatternProperties = this.#isPatternProperties();
-        const isAdditionalProperties = this.#isAdditionalProperties();
-        const creatNewPatternProperty = isPatternProperties && createNewObject;
+        const allowPatternProperties = isPatternProperties(this.pattern);
+        const allowAdditionalProperties = isAdditionalProperties(this.pattern);
+        const creatNewPatternProperty = allowPatternProperties && createNewObject;
 
         const schemaCopy = structuredClone(schema);
 
@@ -375,7 +384,7 @@ export class JSONSchemaInput extends LitElement {
               })
             : new JSONSchemaInput({
                   schema: schemaCopy,
-                  validateOnChange: isAdditionalProperties,
+                  validateOnChange: allowAdditionalProperties,
                   path: this.path,
                   form: this.form,
                   value: updateTarget,
@@ -407,7 +416,7 @@ export class JSONSchemaInput extends LitElement {
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
-        const isEditableObject = this.#isEditableObject();
+        const canAddProperties = isEditableObject(this.schema)
 
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
@@ -425,17 +434,17 @@ export class JSONSchemaInput extends LitElement {
             return el;
         };
 
-        if (isArray || isEditableObject) {
+        if (isArray || canAddProperties) {
             // if ('value' in this && !Array.isArray(this.value)) this.value = [ this.value ]
 
-            const isPatternProperties = this.#isPatternProperties();
-            const isAdditionalProperties = this.#isAdditionalProperties();
+            const allowPatternProperties = isPatternProperties(this.pattern);
+            const allowAdditionalProperties = isAdditionalProperties(this.pattern);
 
             // Provide default item types
             if (isArray) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
                 if (!("items" in schema)) schema.items = {};
-                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = this.#getType(this.value[0]);
+                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = this.#getType(this.value?.[0]);
             }
 
             const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
@@ -525,10 +534,10 @@ export class JSONSchemaInput extends LitElement {
                 size: "small",
             });
 
-            addButton.innerText = `Add ${isEditableObject ? "Property" : "Item"}`;
+            addButton.innerText = `Add ${canAddProperties ? "Property" : "Item"}`;
 
             addButton.addEventListener("click", () => {
-                this.#createModal({ list, schema: isPatternProperties ? schema : itemSchema });
+                this.#createModal({ list, schema: allowPatternProperties ? schema : itemSchema });
             });
 
             const list = (this.#list = new List({
@@ -537,7 +546,7 @@ export class JSONSchemaInput extends LitElement {
                 // Add edit button when new items are added
                 // NOTE: Duplicates some code in #mapToList
                 transform: (item) => {
-                    if (this.#isEditableObject()) {
+                    if (canAddProperties) {
                         const { key, value } = item;
                         item.controls = [
                             new Button({
@@ -571,7 +580,7 @@ export class JSONSchemaInput extends LitElement {
                 },
             }));
 
-            if (isAdditionalProperties) {
+            if (allowAdditionalProperties) {
                 addButton.setAttribute("disabled", true);
                 addButton.title =
                     "Additional properties cannot be added at this time—as they don't have a predictable structure.";

From 17a201c7a633abc048d4ae3893db98fb9fb30781 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 31 Dec 2023 15:03:30 +0000
Subject: [PATCH 056/133] [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 | 26 +++++++++------------
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 62bd1b9e4..d97b3150a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1301,12 +1301,11 @@ export class JSONSchemaForm extends LitElement {
         }
 
         if (hasAdditionalProperties) {
-
-            const pattern = "additional"
-            const shouldRender = getEditableItems(results, pattern, { schema })
+            const pattern = "additional";
+            const shouldRender = getEditableItems(results, pattern, { schema });
 
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
-            if (!shouldRender.length) return rendered
+            if (!shouldRender.length) return rendered;
 
             const additionalElement = this.#renderInteractiveElement(
                 "",
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 975e0e03c..eaeb1893a 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -17,11 +17,7 @@ const isEditableObject = (schema) => schema.type === "object";
 const isAdditionalProperties = (pattern) => pattern === "additional";
 const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
-export const getEditableItems = (
-    value, 
-    pattern,
-    { name, schema } = {}
-) => {
+export const getEditableItems = (value, pattern, { name, schema } = {}) => {
     let items = Object.entries(value);
 
     const allowAdditionalProperties = isAdditionalProperties(pattern);
@@ -38,14 +34,14 @@ export const getEditableItems = (
             const regex = new RegExp(key);
             items = items.filter(([k]) => !regex.test(k));
         });
-    } 
-    
-    else items.filter(([key]) => key in schema.properties);
+    } else items.filter(([key]) => key in schema.properties);
 
-    items = items.filter(([key]) => !key.includes('__')); // Remove secret properties
+    items = items.filter(([key]) => !key.includes("__")); // Remove secret properties
 
-    return items.map(([key, value]) => { return { key, value } })
-}
+    return items.map(([key, value]) => {
+        return { key, value };
+    });
+};
 
 const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
 
@@ -264,9 +260,9 @@ export class JSONSchemaInput extends LitElement {
         const canAddProperties = isEditableObject(this.schema);
 
         if (canAddProperties) {
-            const editable =  getEditableItems(this.value, this.pattern, { name, schema })
-            console.log(editable)
-           return editable.map(({ key, value }) => {
+            const editable = getEditableItems(this.value, this.pattern, { name, schema });
+            console.log(editable);
+            return editable.map(({ key, value }) => {
                 return {
                     key,
                     value,
@@ -416,7 +412,7 @@ export class JSONSchemaInput extends LitElement {
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
-        const canAddProperties = isEditableObject(this.schema)
+        const canAddProperties = isEditableObject(this.schema);
 
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {

From 7e42759d852e91440704d79471b906a0d9d217d7 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sun, 31 Dec 2023 09:11:11 -0600
Subject: [PATCH 057/133] Exclude additional properties from (auto)validated
 object

---
 src/renderer/src/stories/JSONSchemaForm.js | 25 ++++++++++++++++------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 62bd1b9e4..1065c54c7 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -420,6 +420,9 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
+
+        console.log('Resolved', resolved)
+        
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -998,14 +1001,14 @@ export class JSONSchemaForm extends LitElement {
         let isLink = Symbol("isLink");
 
         const hasPatternProperties = !!schema.patternProperties;
-        const hasAdditionalProperties = schema.additionalProperties !== false;
+        const allowAdditionalProperties = schema.additionalProperties !== false;
 
         // Filter non-required properties (if specified) and render the sub-schema
         const renderable = this.#getRenderable(schema, required, ignore, path);
         // // Filter non-required properties (if specified) and render the sub-schema
         // const renderable = path.length ? this.#getRenderable(schema, required) : Object.entries(schema.properties ?? {})
 
-        const hasProperties = renderable.length > 0 || hasPatternProperties || hasAdditionalProperties;
+        const hasProperties = renderable.length > 0 || hasPatternProperties || allowAdditionalProperties;
 
         if (!hasProperties) return html`<div id="empty">${this.emptyMessage}</div>`;
 
@@ -1300,13 +1303,14 @@ export class JSONSchemaForm extends LitElement {
             rendered = [...rendered, ...patternProps];
         }
 
-        if (hasAdditionalProperties) {
+        const additionalPropPattern = "additional"
+        const additionalProps = getEditableItems(results, additionalPropPattern, { schema })
 
-            const pattern = "additional"
-            const shouldRender = getEditableItems(results, pattern, { schema })
+        // Render additional properties
+        if (allowAdditionalProperties) {
 
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
-            if (!shouldRender.length) return rendered
+            if (!additionalProps.length) return rendered
 
             const additionalElement = this.#renderInteractiveElement(
                 "",
@@ -1317,9 +1321,16 @@ export class JSONSchemaForm extends LitElement {
                 required,
                 path,
                 results,
-                pattern
+                additionalPropPattern
             );
             return [...rendered, additionalElement];
+        } 
+        
+        // Delete additional properties off the final results
+        else {
+            additionalProps.forEach(({ key }) => {
+                delete results[key]
+            })
         }
 
         return rendered;

From 780598f1ac7b43574918e94e84284801c6403bd5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 31 Dec 2023 15:12:34 +0000
Subject: [PATCH 058/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 1065c54c7..24cc38bc6 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -420,9 +420,8 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
+        console.log("Resolved", resolved);
 
-        console.log('Resolved', resolved)
-        
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -1303,14 +1302,13 @@ export class JSONSchemaForm extends LitElement {
             rendered = [...rendered, ...patternProps];
         }
 
-        const additionalPropPattern = "additional"
-        const additionalProps = getEditableItems(results, additionalPropPattern, { schema })
+        const additionalPropPattern = "additional";
+        const additionalProps = getEditableItems(results, additionalPropPattern, { schema });
 
         // Render additional properties
         if (allowAdditionalProperties) {
-
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
-            if (!additionalProps.length) return rendered
+            if (!additionalProps.length) return rendered;
 
             const additionalElement = this.#renderInteractiveElement(
                 "",
@@ -1324,13 +1322,13 @@ export class JSONSchemaForm extends LitElement {
                 additionalPropPattern
             );
             return [...rendered, additionalElement];
-        } 
-        
+        }
+
         // Delete additional properties off the final results
         else {
             additionalProps.forEach(({ key }) => {
-                delete results[key]
-            })
+                delete results[key];
+            });
         }
 
         return rendered;

From 02876954f207db0ee6fe6985a380136df8161eb9 Mon Sep 17 00:00:00 2001
From: codycbakerphd <cbaker9@nd.edu>
Date: Sun, 31 Dec 2023 15:37:20 -0500
Subject: [PATCH 059/133] fix bad merge conflict

---
 src/renderer/src/stories/Table.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index d44ba2e11..4202119ce 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -295,7 +295,7 @@ export class Table extends LitElement {
             };
 
             let instanceThis = this;
-            const isRequired = this.isRequired(k);
+            const required = isRequired(k, this.schema);
 
             const validator = async function (value, callback) {
                 const validateEmptyCells = instanceThis.validateEmptyCells;
@@ -333,7 +333,7 @@ export class Table extends LitElement {
                     return;
                 }
 
-                if (!value && isRequired) {
+                if (!value && required) {
                     instanceThis.#handleValidationResult(
                         [{ message: `${header(k)} is a required property.`, type: "error" }],
                         this.row,

From 0d659cd07934a1974b48eba2eb3a75ab0a43b96b Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sun, 31 Dec 2023 14:50:14 -0600
Subject: [PATCH 060/133] Preprocess refs independently from the JSON Schema
 form

---
 schemas/base-metadata.schema.ts            |  4 ++--
 src/renderer/src/stories/JSONSchemaForm.js | 28 ++--------------------
 src/renderer/src/stories/forms/utils.ts    | 26 ++++++++++++++++++++
 3 files changed, 30 insertions(+), 28 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index d27f7b414..1ffa4f6b6 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -1,6 +1,6 @@
 import { serverGlobals, resolve } from '../src/renderer/src/server/globals'
 
-import { header } from '../src/renderer/src/stories/forms/utils'
+import { header, replaceRefsWithValue } from '../src/renderer/src/stories/forms/utils'
 
 import baseMetadataSchema from './json/base_metadata_schema.json' assert { type: "json" }
 
@@ -37,7 +37,7 @@ function getSpeciesInfo(species: any[][] = []) {
 export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, global = false) => {
 
 
-    const copy = structuredClone(schema)
+    const copy = replaceRefsWithValue(structuredClone(schema))
 
     copy.additionalProperties = false
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 24cc38bc6..045d86c58 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -4,7 +4,7 @@ import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { Accordion } from "./Accordion";
 
 import { checkStatus } from "../validation";
-import { header } from "./forms/utils";
+import { header, replaceRefsWithValue } from "./forms/utils";
 import { resolve } from "../promises";
 import { merge } from "./pages/utils";
 import { resolveProperties } from "./pages/guided-mode/data/utils";
@@ -554,34 +554,10 @@ export class JSONSchemaForm extends LitElement {
 
     // Resolve all references on the schema when set (INTERNAL USE ONLY)
     #schema;
-    replaceRefsWithValue = (schema, path = [], parent) => {
-        const copy = { ...schema };
-
-        if (schema && typeof schema === "object" && !Array.isArray(schema)) {
-            for (let propName in copy) {
-                const prop = copy[propName];
-                if (prop && typeof prop === "object" && !Array.isArray(prop)) {
-                    const internalCopy = (copy[propName] = { ...prop });
-                    if (internalCopy["$ref"]) {
-                        const prevItem = path.slice(-1)[0];
-                        const resolved = parent.properties.definitions?.[prevItem];
-                        copy[propName] = resolved;
-                    } else {
-                        for (let key in internalCopy) {
-                            const fullPath = [...path, propName, key];
-                            internalCopy[key] = this.replaceRefsWithValue(internalCopy[key], fullPath, copy);
-                        }
-                    }
-                }
-            }
-        } else return schema;
-
-        return copy;
-    };
 
     set schema(schema) {
         this.#schema = schema;
-        this.#schema = this.replaceRefsWithValue(schema);
+        this.#schema = replaceRefsWithValue(schema);
     }
 
     get schema() {
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index ea3cdfb16..416882a7b 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -12,3 +12,29 @@ export const header = (headerStr: string) => headerStr.split(/[_\s]/).filter(str
 export const textToArray = (value: string) => value.split("\n")
                                             .map((str) => str.trim())
                                             .filter((str) => str) // Only keep strings that are not empty
+
+
+    export const replaceRefsWithValue = (schema: { [x:string]: any }, path = [], parent: { [x:string]: any }) => {
+        const copy = { ...schema };
+
+        if (schema && typeof schema === "object" && !Array.isArray(schema)) {
+            for (let propName in copy) {
+                const prop = copy[propName];
+                if (prop && typeof prop === "object" && !Array.isArray(prop)) {
+                    const internalCopy = (copy[propName] = { ...prop });
+                    if (internalCopy["$ref"]) {
+                        const prevItem = path.slice(-1)[0];
+                        const resolved = parent.properties.definitions?.[prevItem];
+                        copy[propName] = resolved;
+                    } else {
+                        for (let key in internalCopy) {
+                            const fullPath = [...path, propName, key];
+                            internalCopy[key] = replaceRefsWithValue(internalCopy[key], fullPath, copy);
+                        }
+                    }
+                }
+            }
+        } else return schema;
+
+        return copy;
+    }
\ No newline at end of file

From ed453b3ab407438bc1829594713558aa5321dd11 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 31 Dec 2023 20:50:30 +0000
Subject: [PATCH 061/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/forms/utils.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 416882a7b..f3b676746 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -37,4 +37,4 @@ export const textToArray = (value: string) => value.split("\n")
         } else return schema;
 
         return copy;
-    }
\ No newline at end of file
+    }

From a7ea64b2f73edbef460b2166217dab06d6763270 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Sun, 31 Dec 2023 14:56:08 -0600
Subject: [PATCH 062/133] Update typescript

---
 src/renderer/src/stories/forms/utils.ts | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 416882a7b..059657add 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -14,7 +14,12 @@ export const textToArray = (value: string) => value.split("\n")
                                             .filter((str) => str) // Only keep strings that are not empty
 
 
-    export const replaceRefsWithValue = (schema: { [x:string]: any }, path = [], parent: { [x:string]: any }) => {
+    export const replaceRefsWithValue = (
+        schema: any, 
+        path: string[] = [], 
+        parent: { [x:string]: any } = schema
+    ) => {
+
         const copy = { ...schema };
 
         if (schema && typeof schema === "object" && !Array.isArray(schema)) {
@@ -34,7 +39,12 @@ export const textToArray = (value: string) => value.split("\n")
                     }
                 }
             }
-        } else return schema;
 
-        return copy;
+            return copy as { [x:string]: any }
+        } 
+
+        console.log(schema)
+        
+        
+        return schema;
     }
\ No newline at end of file

From 085c9286bb04eb35c61b4ec7e603938308ef7f9a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 31 Dec 2023 21:10:44 +0000
Subject: [PATCH 063/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/forms/utils.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index c76ab7c41..0a881de82 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -15,8 +15,8 @@ export const textToArray = (value: string) => value.split("\n")
 
 
     export const replaceRefsWithValue = (
-        schema: any, 
-        path: string[] = [], 
+        schema: any,
+        path: string[] = [],
         parent: { [x:string]: any } = schema
     ) => {
 
@@ -42,7 +42,7 @@ export const textToArray = (value: string) => value.split("\n")
             }
 
             return copy as { [x:string]: any }
-        }         
-        
+        }
+
         return schema;
     }

From 23d56de00db162934daff8857b45c6ff1c0de295 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 16:07:00 +0000
Subject: [PATCH 064/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js        | 5 +++--
 src/renderer/src/stories/forms/GlobalFormModal.ts | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5b97bf22a..94ed87431 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -657,7 +657,9 @@ export class JSONSchemaForm extends LitElement {
                     ? "conditional"
                     : ""}"
             >
-                <label class="guided--form-label">${(info.title ? unsafeHTML(info.title) : null) ?? header(name)} </label>
+                <label class="guided--form-label"
+                    >${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}
+                </label>
                 ${this.showPath
                     ? html` <small
                           >${externalPath
@@ -666,7 +668,6 @@ export class JSONSchemaForm extends LitElement {
                               .join(".")}</small
                       >`
                     : ""}
-
                 ${interactiveInput}
                 <div class="errors"></div>
                 <div class="warnings"></div>
diff --git a/src/renderer/src/stories/forms/GlobalFormModal.ts b/src/renderer/src/stories/forms/GlobalFormModal.ts
index 71cfe24e5..74f8c7662 100644
--- a/src/renderer/src/stories/forms/GlobalFormModal.ts
+++ b/src/renderer/src/stories/forms/GlobalFormModal.ts
@@ -105,7 +105,7 @@ export function createGlobalFormModal(this: Page, {
 
     propsToRemove = {},
     formProps,
-  
+
     // Global-specific options
     key,
     hasInstances = false,

From 12234dfd6f3ce60cd38e1c6eaddcd0ffef1cf4c6 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 10:07:33 -0600
Subject: [PATCH 065/133] Fix merge

---
 src/renderer/src/stories/JSONSchemaForm.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5b97bf22a..ddbb2b1d1 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -973,8 +973,6 @@ export class JSONSchemaForm extends LitElement {
         updatedWarnings.forEach((info) => (onWarning ? "" : this.#addMessage(localPath, info, "warnings")));
         info.forEach((info) => (onInfo ? onInfo(info) : this.#addMessage(localPath, info, "info")));
 
-        const input = this.getInput(localPath);
-
         const groupEl = this.#getGroupElement(externalPath);
 
         if (groupEl) {

From ed5611d465feadc735ef2b3b6899ea3a10aa7f53 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 10:10:37 -0600
Subject: [PATCH 066/133] Update JSONSchemaInput.js

---
 src/renderer/src/stories/JSONSchemaInput.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 1f82db453..8c8370403 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -280,7 +280,7 @@ export class JSONSchemaInput extends LitElement {
 
         if (canAddProperties) {
             const editable = getEditableItems(this.value, this.pattern, { name, schema });
-            console.log(editable);
+
             return editable.map(({ key, value }) => {
                 return {
                     key,
@@ -292,7 +292,7 @@ export class JSONSchemaInput extends LitElement {
                             onClick: () => {
                                 this.#createModal({
                                     key,
-                                    schema: allowAdditionalProperties ? undefined : schema,
+                                    schema: isAdditionalProperties(this.pattern) ? undefined : schema,
                                     results: value,
                                     list: list ?? this.#list,
                                 });

From b2b073f4fd41bd968b4ade0e91e7fee303167128 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 10:12:54 -0600
Subject: [PATCH 067/133] Update JSONSchemaInput.js

---
 src/renderer/src/stories/JSONSchemaInput.js | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 8c8370403..9a6445ffa 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -165,6 +165,10 @@ export class JSONSchemaInput extends LitElement {
                 margin-left: 5px;
                 font-size: 12px;
             }
+
+            .schema-input.list {
+                width: 100%;
+            }
         `;
     }
 

From 8e1ffbe4817283cdf77bfa4e2d3e2863bc3395a6 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 11:35:27 -0600
Subject: [PATCH 068/133] Fix ignore

---
 schemas/base-metadata.schema.ts             | 25 +++++++++++----------
 src/renderer/src/stories/JSONSchemaInput.js |  2 +-
 src/renderer/src/stories/SimpleTable.js     |  4 ++--
 3 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 9c0f2eb10..b7bfde33f 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -88,14 +88,19 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     if (ophys) {
 
-        const getProp = (name: string, base = true) => base ? ophys.properties[name] : ophys.properties.definitions?.[name]
+        const getProp = (name: string) => ophys.properties[name]
 
-        if (getProp("TwoPhotonSeries")) getProp("TwoPhotonSeries").items.order = [
-            "name",
-            "description",
-            "scan_line_rate",
-            "field_of_view"
-        ]
+        if (getProp("TwoPhotonSeries")) {
+            const tpsItemSchema = getProp("TwoPhotonSeries").items
+            tpsItemSchema.order = [
+                "name",
+                "description",
+                "scan_line_rate",
+                "field_of_view"
+            ]
+
+            tpsItemSchema.properties.pmt_gain.title =  'Photomultiplier Gain'
+        }
 
 
         if (getProp("ImagingPlane")) {
@@ -115,14 +120,10 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
     Object.entries(copy.properties).forEach(([key, value]) => {
 
-        const defs = value.properties.definitions ?? {}
-
         Object.entries(value.properties).forEach(([k, v]) => {
 
-            if (k ==='definitions') return
-
             //  Uniformly grab definitions
-           const ref = defs[k] ?? v.items ?? v
+           const ref = v.items ?? v
            if (!ref.properties) return
            Object.keys(ref.properties).forEach(k => {
                 const info = ref.properties[k]
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 9a6445ffa..d304a2836 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -498,7 +498,7 @@ export class JSONSchemaInput extends LitElement {
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
                 const ignore = this.form?.ignore
-                    ? getIgnore(this.form?.ignore, [...this.form.base, ...path, name])
+                    ? getIgnore(this.form?.ignore, [...path, name])
                     : {};
 
                 const ogThis = this;
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index ba46abaa1..e750b3fe9 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -621,14 +621,14 @@ export class SimpleTable extends LitElement {
         }
     }
 
-    #renderHeader = (str, { description }) => {
+    #renderHeader = (str, { title, description }) => {
         const header = document.createElement("th");
 
         // Inner Content
         const div = document.createElement("div");
         div.classList.add("relative");
         const span = document.createElement("span");
-        span.innerHTML = str;
+        span.innerHTML = title ?? str;
         div.append(span);
         header.append(div);
 

From 2ab1a3412102167749fff16b7a876005026c1708 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 17:35:43 +0000
Subject: [PATCH 069/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index d304a2836..4bf958be3 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -497,9 +497,7 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
-                const ignore = this.form?.ignore
-                    ? getIgnore(this.form?.ignore, [...path, name])
-                    : {};
+                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, [...path, name]) : {};
 
                 const ogThis = this;
 

From 6829a423535280029d3925b9ac96bd22e1e57d59 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 11:38:06 -0600
Subject: [PATCH 070/133] Remove editing test div

---
 src/renderer/src/stories/table/cells/table.ts | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/table.ts
index 49beb57d6..080caa299 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/table.ts
@@ -35,18 +35,6 @@ export class NestedTableEditor extends LitElement {
 
         if (this.#table) this.#table.remove()
 
-
-        const div = document.createElement('div')
-        Object.assign(div.style, {
-            width: `${10}px`,
-            height: `${10}px`,
-            position: 'absolute',
-            zIndex: 1000,
-            background: 'red'
-        })
-
-        document.body.append(div)
-
         const table = this.#table = new SimpleTable({
             schema: this.schema.items,
             data: this.#value,

From 18afec8414971c85afefc43d8d4ea77ade9e15cd Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 11:59:42 -0600
Subject: [PATCH 071/133] Update List.ts

---
 src/renderer/src/stories/List.ts | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/renderer/src/stories/List.ts b/src/renderer/src/stories/List.ts
index 2a1568021..2a136d345 100644
--- a/src/renderer/src/stories/List.ts
+++ b/src/renderer/src/stories/List.ts
@@ -357,8 +357,6 @@ export class List extends LitElement {
                     this.items = [...this.items]
                   }
             }
-
-            this.onChange() // Register that the object has changed
         };
 
         button.onClick = deleteListItem;

From b25caf43e1538212fa23fb4f69b518b01eaa0a43 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 13:14:05 -0600
Subject: [PATCH 072/133] Allow adding row to table without any

---
 src/renderer/src/stories/SimpleTable.js | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index e750b3fe9..7a9059793 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -435,6 +435,7 @@ export class SimpleTable extends LitElement {
                 label: "Add Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
+                    if (!cell) return this.addRow(); // No cell selected
                     const { i } = cell.simpleTableInfo;
                     this.addRow(i); //2) // TODO: Support adding more than one row
                 },
@@ -443,6 +444,8 @@ export class SimpleTable extends LitElement {
                 label: "Remove Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
+                    if (!cell) return; // No cell selected
+                    
                     const { i, row } = cell.simpleTableInfo; // TODO: Support detecting when the user would like to remove more than one row
 
                     // Validate with empty values before removing (to trigger any dependent validations)
@@ -570,17 +573,13 @@ export class SimpleTable extends LitElement {
         const count = Math.abs(nRows);
         const range = Array.from({ length: count }, (_, i) => row + i);
 
-        const children = Array.from(this.shadowRoot.querySelector("tbody").children);
+        const bodyEl = this.shadowRoot.querySelector("tbody")
+        const children = Array.from(bodyEl.children);
 
         const isPositive = Math.sign(nRows) === 1;
 
         // Remove elements and cell entries that correspond to the removed elements
         if (!isPositive) {
-            if (children.length - count < 1) {
-                this.onThrow("You must have at least one row");
-                return false;
-            }
-
             const rowHeaders = Object.keys(this.#data);
             range.map((i) => {
                 children[i].remove();
@@ -612,8 +611,10 @@ export class SimpleTable extends LitElement {
                 const data = this.#getRowData(); // Get information for an undefined row
                 const newRow = document.createElement("tr");
                 newRow.append(...data.map((v, j) => this.#renderCell(v, { i, j })));
-                latest.insertAdjacentElement("afterend", newRow);
-                latest = newRow;
+
+                if (latest)latest.insertAdjacentElement("afterend", newRow);
+                else bodyEl.append(newRow);
+
                 return this.getRow(i);
             });
 

From 38e2a9ee480b0f366f9398f34cda8128f33420e1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 19:14:21 +0000
Subject: [PATCH 073/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 7a9059793..6fbeb654b 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -445,7 +445,7 @@ export class SimpleTable extends LitElement {
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
                     if (!cell) return; // No cell selected
-                    
+
                     const { i, row } = cell.simpleTableInfo; // TODO: Support detecting when the user would like to remove more than one row
 
                     // Validate with empty values before removing (to trigger any dependent validations)
@@ -573,7 +573,7 @@ export class SimpleTable extends LitElement {
         const count = Math.abs(nRows);
         const range = Array.from({ length: count }, (_, i) => row + i);
 
-        const bodyEl = this.shadowRoot.querySelector("tbody")
+        const bodyEl = this.shadowRoot.querySelector("tbody");
         const children = Array.from(bodyEl.children);
 
         const isPositive = Math.sign(nRows) === 1;
@@ -612,7 +612,7 @@ export class SimpleTable extends LitElement {
                 const newRow = document.createElement("tr");
                 newRow.append(...data.map((v, j) => this.#renderCell(v, { i, j })));
 
-                if (latest)latest.insertAdjacentElement("afterend", newRow);
+                if (latest) latest.insertAdjacentElement("afterend", newRow);
                 else bodyEl.append(newRow);
 
                 return this.getRow(i);

From 09e5d847eae7a1c10ca60f5ee15af03f7b11300c Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 13:48:50 -0600
Subject: [PATCH 074/133] Proper NaN representation

---
 pyflask/manageNeuroconv/manage_neuroconv.py         |  2 +-
 src/renderer/src/stories/BasicTable.js              |  2 +-
 src/renderer/src/stories/JSONSchemaForm.js          |  8 +++++---
 src/renderer/src/stories/SimpleTable.js             |  4 ++--
 src/renderer/src/stories/Table.js                   |  4 ++--
 .../pages/guided-mode/data/GuidedMetadata.js        |  2 ++
 src/renderer/src/stories/table/Cell.ts              |  4 ++--
 .../src/stories/table/{get.ts => convert.ts}        | 13 +++++++++++--
 src/renderer/src/validation/validation.ts           |  5 ++++-
 9 files changed, 30 insertions(+), 14 deletions(-)
 rename src/renderer/src/stories/table/{get.ts => convert.ts} (58%)

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index ea3accbb4..bf82fc3d8 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -76,7 +76,7 @@ def coerce_schema_compliance_recursive(obj, schema):
             for key, value in obj.items():
                 if key in schema.get("properties", {}):
                     prop_schema = schema["properties"][key]
-                    if prop_schema.get("type") == "number" and value is None:
+                    if prop_schema.get("type") == "number" and (value is None or value == 'NaN'):
                         obj[
                             key
                         ] = (
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index f321dae15..559e45b79 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -277,7 +277,7 @@ export class BasicTable extends LitElement {
                         }
 
                         if (message !== undefined) {
-                            tippy(td, { content: message });
+                            tippy(td, { content: message, allowHTML: true });
                             td.setAttribute("data-message", value);
                         }
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index aac51d391..5e70315e2 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -21,6 +21,8 @@ const encode = (str) => {
     }
 };
 
+const provideNaNMessage = `<br/><small>Type <b>NaN</b> to represent an unknown value.</small>`
+
 import { Validator } from "jsonschema";
 import { successHue, warningHue, errorHue } from "./globals";
 
@@ -425,7 +427,8 @@ export class JSONSchemaForm extends LitElement {
 
                 // Allow referring to floats as null (i.e. JSON NaN representation)
                 if (e.message === "is not of a type(s) number") {
-                    if (resolvedValue === null) return;
+                    if (resolvedValue === 'NaN') return;
+                    else e.message = `${e.message}. ${provideNaNMessage}`;
                 }
 
                 return {
@@ -441,7 +444,6 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
-        console.log("Resolved", resolved);
 
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
@@ -918,7 +920,7 @@ export class JSONSchemaForm extends LitElement {
                 if (!hasLinks && isRequired) {
                     if (this.validateEmptyValues) {
                         errors.push({
-                            message: `${schema.title ?? header(name)} ${this.#isARequiredPropertyString}.`,
+                            message: `${schema.title ?? header(name)} ${this.#isARequiredPropertyString}. ${schema.type === 'number' ? provideNaNMessage : ''}`,
                             type: "error",
                             missing: true,
                         });
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 6fbeb654b..e6dde9934 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -639,7 +639,7 @@ export class SimpleTable extends LitElement {
             span.classList.add("info");
             span.innerText = "ℹ️";
             div.append(span);
-            tippy(span, { content: `${description[0].toUpperCase() + description.slice(1)}` });
+            tippy(span, { content: `${description[0].toUpperCase() + description.slice(1)}`, allowHTML: true });
         }
 
         return header;
@@ -737,7 +737,7 @@ export class SimpleTable extends LitElement {
                     }
 
                     if (message !== undefined) {
-                        tippy(td, { content: message });
+                        tippy(td, { content: message, allowHTML: true });
                         td.setAttribute("data-message", value);
                     }
 
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 4202119ce..921e21fe9 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -401,7 +401,7 @@ export class Table extends LitElement {
                 }
 
                 if (span._tippy) span._tippy.destroy();
-                tippy(span, { content: `${desc}` });
+                tippy(span, { content: `${desc}`, allowHTML: true });
             }
         };
 
@@ -606,7 +606,7 @@ export class Table extends LitElement {
             }
 
             if (message) {
-                tippy(cell, { content: message });
+                tippy(cell, { content: message, allowHTML: true });
                 cell.setAttribute("data-message", message);
             }
         }
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 121a8724e..aaa726a87 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -172,6 +172,8 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
+        console.log('Got', results, preprocessMetadataSchema(schema))
+        
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 5be7afff0..522a543ea 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -6,7 +6,7 @@ import { TableCellBase } from "./cells/base"
 import { DateTimeCell } from "./cells/date-time"
 
 
-import { getValue } from './get'
+import { getValue, renderValue } from './convert'
 
 type ValidationResult = {
     title?: string,
@@ -108,7 +108,7 @@ export class TableCell extends LitElement {
     }
 
     set value(v) {
-        if (this.input) this.input.set(v === null  ? v : ( v ?? '' )) // Allow null to be set directly
+        if (this.input) this.input.set(renderValue(v, this.schema)) // Allow null to be set directly
         this.#value = this.input
                             ? this.input.getValue() // Ensure all operations are undoable / value is coerced
                             : v // Silently set value if not rendered yet
diff --git a/src/renderer/src/stories/table/get.ts b/src/renderer/src/stories/table/convert.ts
similarity index 58%
rename from src/renderer/src/stories/table/get.ts
rename to src/renderer/src/stories/table/convert.ts
index 9a7a72728..09548a0d1 100644
--- a/src/renderer/src/stories/table/get.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -1,4 +1,10 @@
-
+export const renderValue = (value: any, schema: any) => {
+    if (schema.type === 'number' || schema.type === 'integer') {
+        if (value === null) return ''
+    }
+    
+    return value ?? ''
+}
 
 export const getValue = (value: any, schema: any) => {
     if (schema.type === 'number' || schema.type === 'integer') {
@@ -8,11 +14,14 @@ export const getValue = (value: any, schema: any) => {
         const og = value
         if (og === '') return undefined
         else {
-            if (og === 'NaN' || og === 'None' || og === 'null') return null
+            if (og === 'NaN') return 'NaN'
             const possibleValue = Number(og)
             if (!isNaN(possibleValue)) return possibleValue
         }
 
+        console.log('Returning', value)
+
+
     }
 
     return value
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 6e3a6e186..88e51a4fc 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -86,7 +86,10 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
 schema.Ophys.Device = {
     ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
 
-        const prevValue = path.reduce((acc, str) => acc[str], this.results)[name]
+        const row = path.reduce((acc, str) => acc[str], this.results)
+        if (!row) return true
+        
+        const prevValue = row[name]
 
         if (prevValue === value) return true // No change
 

From 37ae64d00a17b5ec27cbe0f4f01ce3106482c3e9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 19:49:43 +0000
Subject: [PATCH 075/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/manageNeuroconv/manage_neuroconv.py              | 2 +-
 src/renderer/src/stories/JSONSchemaForm.js               | 9 +++++----
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js | 4 ++--
 src/renderer/src/stories/table/convert.ts                | 2 +-
 src/renderer/src/validation/validation.ts                | 2 +-
 5 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index bf82fc3d8..e933f1660 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -76,7 +76,7 @@ def coerce_schema_compliance_recursive(obj, schema):
             for key, value in obj.items():
                 if key in schema.get("properties", {}):
                     prop_schema = schema["properties"][key]
-                    if prop_schema.get("type") == "number" and (value is None or value == 'NaN'):
+                    if prop_schema.get("type") == "number" and (value is None or value == "NaN"):
                         obj[
                             key
                         ] = (
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5e70315e2..c8c004a5d 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -21,7 +21,7 @@ const encode = (str) => {
     }
 };
 
-const provideNaNMessage = `<br/><small>Type <b>NaN</b> to represent an unknown value.</small>`
+const provideNaNMessage = `<br/><small>Type <b>NaN</b> to represent an unknown value.</small>`;
 
 import { Validator } from "jsonschema";
 import { successHue, warningHue, errorHue } from "./globals";
@@ -427,7 +427,7 @@ export class JSONSchemaForm extends LitElement {
 
                 // Allow referring to floats as null (i.e. JSON NaN representation)
                 if (e.message === "is not of a type(s) number") {
-                    if (resolvedValue === 'NaN') return;
+                    if (resolvedValue === "NaN") return;
                     else e.message = `${e.message}. ${provideNaNMessage}`;
                 }
 
@@ -444,7 +444,6 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
-
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -920,7 +919,9 @@ export class JSONSchemaForm extends LitElement {
                 if (!hasLinks && isRequired) {
                     if (this.validateEmptyValues) {
                         errors.push({
-                            message: `${schema.title ?? header(name)} ${this.#isARequiredPropertyString}. ${schema.type === 'number' ? provideNaNMessage : ''}`,
+                            message: `${schema.title ?? header(name)} ${this.#isARequiredPropertyString}. ${
+                                schema.type === "number" ? provideNaNMessage : ""
+                            }`,
                             type: "error",
                             missing: true,
                         });
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 aaa726a87..ba2ee9d32 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -172,8 +172,8 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-        console.log('Got', results, preprocessMetadataSchema(schema))
-        
+        console.log("Got", results, preprocessMetadataSchema(schema));
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
diff --git a/src/renderer/src/stories/table/convert.ts b/src/renderer/src/stories/table/convert.ts
index 09548a0d1..071a6e781 100644
--- a/src/renderer/src/stories/table/convert.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -2,7 +2,7 @@ export const renderValue = (value: any, schema: any) => {
     if (schema.type === 'number' || schema.type === 'integer') {
         if (value === null) return ''
     }
-    
+
     return value ?? ''
 }
 
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 88e51a4fc..52dde0537 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -88,7 +88,7 @@ schema.Ophys.Device = {
 
         const row = path.reduce((acc, str) => acc[str], this.results)
         if (!row) return true
-        
+
         const prevValue = row[name]
 
         if (prevValue === value) return true // No change

From 2dab4b9c118578054648cd33d3a88673639b75ef Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 13:57:34 -0600
Subject: [PATCH 076/133] Auto-update devices on dependencies if changed

---
 src/renderer/src/validation/validation.ts | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 88e51a4fc..07ace56cd 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -87,6 +87,7 @@ schema.Ophys.Device = {
     ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
 
         const row = path.reduce((acc, str) => acc[str], this.results)
+
         if (!row) return true
         
         const prevValue = row[name]
@@ -96,7 +97,7 @@ schema.Ophys.Device = {
         const result = await Swal.fire({
             title: `Are you sure you want to rename the ${prevValue} device?`,
             icon: "warning",
-            text: `Changing this may invalidate a lot of properties.`,
+            text: `We will attempt to auto-update your Ophys devices to reflect this.`,
             heightAuto: false,
             backdrop: "rgba(0,0,0, 0.4)",
             confirmButtonText: "I understand",
@@ -107,16 +108,23 @@ schema.Ophys.Device = {
 
         if (!result.isConfirmed) return null
 
-        if (result.isConfirmed) {
-
-        }
-
         // Update Dependent Tables
         const dependencies = [
-            ['Ophys', 'ImagingPlane']
+            ['Ophys', 'ImagingPlane'],
+            ['Ophys', 'OnePhotonSeries'],
+            ['Ophys', 'TwoPhotonSeries']
         ]
 
         dependencies.forEach(path => {
+            const table = this.getTable(path)
+            if (table) {
+                const data = table.data
+                data.forEach(row => {
+                    if (row.device === prevValue) row.device = value
+                })
+                table.data = data
+            }
+
             rerenderTable.call(this, path)
         })
 

From d90f34f7c573c1d764edbcb739ee5273c2afac81 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 3 Jan 2024 15:34:38 -0600
Subject: [PATCH 077/133] Render pattern properties as tables in the File
 Metadata

---
 src/renderer/src/stories/JSONSchemaForm.js    |   1 +
 src/renderer/src/stories/JSONSchemaInput.js   | 256 +++++++++++++-----
 src/renderer/src/stories/SimpleTable.js       |  11 +
 .../pages/guided-mode/data/GuidedMetadata.js  |   9 +-
 4 files changed, 201 insertions(+), 76 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index c8c004a5d..e084c703b 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1325,6 +1325,7 @@ export class JSONSchemaForm extends LitElement {
         const additionalPropPattern = "additional";
         const additionalProps = getEditableItems(results, additionalPropPattern, { schema });
 
+
         // Render additional properties
         if (allowAdditionalProperties) {
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 4bf958be3..f609eb52a 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -12,6 +12,7 @@ import { Modal } from "./Modal";
 import { capitalize } from "./forms/utils";
 import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
+import tippy from "tippy.js";
 
 const isEditableObject = (schema) => schema.type === "object";
 const isAdditionalProperties = (pattern) => pattern === "additional";
@@ -455,7 +456,8 @@ export class JSONSchemaInput extends LitElement {
         // Do your best to fill in missing schema values
         if (!("type" in schema)) schema.type = this.#getType();
 
-        const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
+        const resolvedFullPath = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath]
+        const path = [...resolvedFullPath];
         const name = path.splice(-1)[0];
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
@@ -484,6 +486,22 @@ export class JSONSchemaInput extends LitElement {
             const allowPatternProperties = isPatternProperties(this.pattern);
             const allowAdditionalProperties = isAdditionalProperties(this.pattern);
 
+            const addButton = new Button({
+                size: "small",
+            });
+
+            addButton.innerText = `Add ${canAddProperties ? "Property" : "Item"}`;
+
+            const buttonDiv = document.createElement('div')
+            Object.assign(buttonDiv.style, {  width: 'fit-content' })
+            buttonDiv.append(addButton)
+
+            const disableButton = ({ message, submessage }) => {
+                addButton.setAttribute("disabled", true);
+                tippy(buttonDiv, { content: `<div style="padding: 10px;">${message} <br><small>${submessage}</small></div>`, allowHTML: true })
+            }
+
+
             // Provide default item types
             if (isArray) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
@@ -497,64 +515,61 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
-                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, [...path, name]) : {};
-
-                const ogThis = this;
-
-                const tableMetadata = {
-                    schema: itemSchema,
-                    data: this.value,
-
-                    ignore,
 
-                    onUpdate: function () {
-                        return ogThis.#updateData(fullPath, this.data, true, {
-                            willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
-                            onError: (e) => e,
-                            onWarning: (e) => e,
-                        }); // Ensure change propagates to all forms
-                    },
+                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, resolvedFullPath) : {};
 
-                    validateOnChange: async (path, parent, v, baseSchema = itemSchema) => {
-                        const warnings = [];
-                        const errors = [];
-
-                        const name = path.slice(-1)[0];
-                        const completePath = [...fullPath, ...path.slice(0, -1)];
-
-                        const itemPropSchema = path.reduce((acc, key) => {
-                            if (typeof key === "number") return acc; // Skip row information
-                            return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
-                        }, baseSchema);
-
-                        const result = await (validateOnChange
-                            ? this.onValidate
-                                ? this.onValidate()
-                                : this.form
-                                  ? this.form.triggerValidation(
-                                        name,
-                                        completePath,
-                                        false,
-                                        this,
-                                        itemPropSchema,
-                                        { ...parent, [name]: v },
-                                        {
-                                            onError: (error) => {
-                                                errors.push(error); // Skip counting errors
-                                            },
-                                            onWarning: (warning) => {
-                                                warnings.push(warning); // Skip counting warnings
-                                            },
-                                        }
-                                    ) // NOTE: No pattern properties support
-                                  : ""
-                            : true);
-
-                        const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
-
-                        return returnedValue;
-                    },
+                const ogThis = this;
 
+                function commonUpdateFunction (path, value = this.data) {
+                    return ogThis.#updateData(path, value, true, {
+                        willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
+                        onError: (e) => e,
+                        onWarning: (e) => e,
+                    }); // Ensure change propagates to all forms
+                }
+
+                const commonValidationFunction = async (tableBasePath, path, parent, v, baseSchema = itemSchema) => {
+
+                    const warnings = [];
+                    const errors = [];
+
+                    const name = path.slice(-1)[0];
+                    const completePath = [...tableBasePath, ...path.slice(0, -1)];
+
+                    const itemPropSchema = path.reduce((acc, key) => {
+                        if (typeof key === "number") return acc; // Skip row information
+                        return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
+                    }, baseSchema);
+
+                    const result = await (validateOnChange
+                        ? this.onValidate
+                            ? this.onValidate()
+                            : this.form
+                            ? this.form.triggerValidation(
+                                    name,
+                                    completePath,
+                                    false,
+                                    this,
+                                    itemPropSchema,
+                                    { ...parent, [name]: v },
+                                    {
+                                        onError: (error) => {
+                                            errors.push(error); // Skip counting errors
+                                        },
+                                        onWarning: (warning) => {
+                                            warnings.push(warning); // Skip counting warnings
+                                        },
+                                    }
+                                ) // NOTE: No pattern properties support
+                            : ""
+                        : true);
+
+                    const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
+
+                    return returnedValue;
+                }
+
+                const commonTableMetadata = {
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements
                     validateEmptyCells: this.form?.validateEmptyValues,
                     deferLoading: this.form?.deferLoading,
@@ -565,6 +580,111 @@ export class JSONSchemaInput extends LitElement {
                         }
                     },
                     onThrow: (...args) => this.#onThrow(...args),
+                }
+
+                const createNestedTable = (propName, value) => { 
+                    const property_key = Math.random().toString(36).substring(7);
+
+                    const rowData = Object.entries(value).map(([key, value]) => {
+                       return {[property_key]: key, ...value}
+                    })
+
+                    const schemaCopy = structuredClone(itemSchema);
+                    if (!schemaCopy.properties) schemaCopy.properties = {}
+                    if (!schemaCopy.required) schemaCopy.required = []
+                    schemaCopy.properties[property_key] = { title: 'Property Key', type: 'string', pattern: name }
+                    schemaCopy.order = [ property_key ]
+                    schemaCopy.required.push(property_key)
+
+                    const resultPath = [...path, propName]
+                    const schemaPath = [...resolvedFullPath, propName]
+
+                    const allRemovedKeys = new Set()
+
+                    const tableMetadata = {
+                        schema: schemaCopy,
+                        data: rowData,
+                        ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
+
+                        onUpdate: function () {
+
+                            const oldKeys = Object.keys(value);
+
+                            const result = this.data.reduce((acc, row) => {
+                                const key = row[property_key]
+                                if (key) {
+                                    const copy = {...row}
+                                    delete copy[property_key]
+                                    acc[key] = copy
+                                }
+                                return acc
+                            }, {})
+
+                            const newKeys = Object.keys(result);
+                            const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
+                            removedKeys.forEach(key => allRemovedKeys.add(key))
+                            newKeys.forEach(key => allRemovedKeys.delete(key))
+                            allRemovedKeys.forEach(key => result[key] = undefined)
+                                                        
+                            return commonUpdateFunction.call(this, resultPath, result) // According to 
+                        },
+
+                        validateOnChange: ( path, parent, v ) => commonValidationFunction(schemaPath, path, parent, v, schemaCopy),
+
+                        ...commonTableMetadata
+                    }
+
+                    const table = (this.table = this.form.createTable(propName, tableMetadata, resolvedFullPath)); // Try creating table. Otherwise use nested form
+                    if (table) {
+                        return html`
+                            <h3>${header(propName)}</h3>
+                            ${this.form.tables[`${resolvedFullPath.slice(-1)[0]}.${propName}`] = table === true ? new BasicTable(tableMetadata) : table}
+                        `
+                    }
+                }
+
+
+                // Possibly multiple tables
+                if (isEditableObject(this.schema)) {
+                    
+                    const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce((acc, { key, value }) => {
+                        acc[key] = value;
+                        return acc;
+                    }, {})
+
+
+                    const tables = Object.entries(data).map(([patternPropName, patternPropValue]) => createNestedTable(patternPropName, patternPropValue)).filter(value => !!value)
+
+                    if (tables.length) {
+                        disableButton({ 
+                            message: "New top-level pattern properties cannot be added at this time.", 
+                            submessage: "They need a unique key to be specified." 
+                        })
+
+                        return html`
+                            <div style="width: 100%;">
+                                ${tables}
+                                ${buttonDiv}
+                            </div>
+                        `
+                    }
+                } 
+                
+                // Normal table parsing
+
+                const tableMetadata = {
+                    schema: itemSchema,
+                    data: this.value,
+
+                    ignore,
+
+                    onUpdate: function () {
+                        return commonUpdateFunction.call(this, fullPath)
+                    },
+
+                    validateOnChange: (...args) => commonValidationFunction(fullPath, ...args),
+
+                    ...commonTableMetadata
                 };
 
                 const table = (this.table = this.form.createTable(name, tableMetadata, fullPath)); // Try creating table. Otherwise use nested form
@@ -572,15 +692,6 @@ export class JSONSchemaInput extends LitElement {
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
 
-            const addButton = new Button({
-                size: "small",
-            });
-
-            addButton.innerText = `Add ${canAddProperties ? "Property" : "Item"}`;
-
-            addButton.addEventListener("click", () => {
-                this.#createModal({ list, schema: allowPatternProperties ? schema : itemSchema });
-            });
 
             const list = (this.#list = new List({
                 items: this.#mapToList(),
@@ -622,15 +733,18 @@ export class JSONSchemaInput extends LitElement {
                 },
             }));
 
-            if (allowAdditionalProperties) {
-                addButton.setAttribute("disabled", true);
-                addButton.title =
-                    "Additional properties cannot be added at this time—as they don't have a predictable structure.";
-            }
+            if (allowAdditionalProperties) disableButton({
+                message: "Additional properties cannot be added at this time.", 
+                submessage: "They don't have a predictable structure."
+            })
+
+            addButton.addEventListener("click", () => {
+                this.#createModal({ list, schema: allowPatternProperties ? schema : itemSchema });
+            });
 
             return html`
                 <div class="schema-input list" @change=${() => validateOnChange && this.#triggerValidation(name, path)}>
-                    ${list} ${addButton}
+                    ${list} ${buttonDiv}
                 </div>
             `;
         }
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index e6dde9934..5bbafba64 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -150,6 +150,14 @@ export class SimpleTable extends LitElement {
                 font-size: 80%;
                 font-family: ${unsafeCSS(emojiFontFamily)};
             }
+
+            h3 {
+                margin: 0;
+                padding: 10px;
+                background: black;
+                color: white;
+                border-radius-top: 5px;
+            }
         `;
     }
 
@@ -618,8 +626,11 @@ export class SimpleTable extends LitElement {
                 return this.getRow(i);
             });
 
+            this.onUpdate([], this.data)
             return mapped;
         }
+
+        this.onUpdate([], this.data)
     }
 
     #renderHeader = (str, { title, description }) => {
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 ba2ee9d32..dc56d2c45 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -172,8 +172,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-        console.log("Got", results, preprocessMetadataSchema(schema));
-
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
@@ -225,9 +223,10 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             createTable: function (name, metadata, path) {
-                // Do not create tables for patternProperties
-                const parentSchema = this.getSchema(path) ?? {};
-                if (parentSchema.patternProperties) return false;
+                
+                // // Do not create tables for patternProperties (OLD)
+                // const parentSchema = this.getSchema(path) ?? {};
+                // if (parentSchema.patternProperties) return false
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);

From 959ee90e1ebd723037dcc54245742caff0b1b219 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Jan 2024 21:36:37 +0000
Subject: [PATCH 078/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    |   1 -
 src/renderer/src/stories/JSONSchemaInput.js   | 140 +++++++++---------
 src/renderer/src/stories/SimpleTable.js       |   4 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |   1 -
 4 files changed, 72 insertions(+), 74 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index e084c703b..c8c004a5d 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1325,7 +1325,6 @@ export class JSONSchemaForm extends LitElement {
         const additionalPropPattern = "additional";
         const additionalProps = getEditableItems(results, additionalPropPattern, { schema });
 
-
         // Render additional properties
         if (allowAdditionalProperties) {
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f609eb52a..9e2ed242f 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -456,7 +456,7 @@ export class JSONSchemaInput extends LitElement {
         // Do your best to fill in missing schema values
         if (!("type" in schema)) schema.type = this.#getType();
 
-        const resolvedFullPath = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath]
+        const resolvedFullPath = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const path = [...resolvedFullPath];
         const name = path.splice(-1)[0];
 
@@ -492,15 +492,17 @@ export class JSONSchemaInput extends LitElement {
 
             addButton.innerText = `Add ${canAddProperties ? "Property" : "Item"}`;
 
-            const buttonDiv = document.createElement('div')
-            Object.assign(buttonDiv.style, {  width: 'fit-content' })
-            buttonDiv.append(addButton)
+            const buttonDiv = document.createElement("div");
+            Object.assign(buttonDiv.style, { width: "fit-content" });
+            buttonDiv.append(addButton);
 
             const disableButton = ({ message, submessage }) => {
                 addButton.setAttribute("disabled", true);
-                tippy(buttonDiv, { content: `<div style="padding: 10px;">${message} <br><small>${submessage}</small></div>`, allowHTML: true })
-            }
-
+                tippy(buttonDiv, {
+                    content: `<div style="padding: 10px;">${message} <br><small>${submessage}</small></div>`,
+                    allowHTML: true,
+                });
+            };
 
             // Provide default item types
             if (isArray) {
@@ -515,12 +517,11 @@ export class JSONSchemaInput extends LitElement {
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.form.createTable) {
-
                 const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, resolvedFullPath) : {};
 
                 const ogThis = this;
 
-                function commonUpdateFunction (path, value = this.data) {
+                function commonUpdateFunction(path, value = this.data) {
                     return ogThis.#updateData(path, value, true, {
                         willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
                         onError: (e) => e,
@@ -529,7 +530,6 @@ export class JSONSchemaInput extends LitElement {
                 }
 
                 const commonValidationFunction = async (tableBasePath, path, parent, v, baseSchema = itemSchema) => {
-
                     const warnings = [];
                     const errors = [];
 
@@ -545,7 +545,7 @@ export class JSONSchemaInput extends LitElement {
                         ? this.onValidate
                             ? this.onValidate()
                             : this.form
-                            ? this.form.triggerValidation(
+                              ? this.form.triggerValidation(
                                     name,
                                     completePath,
                                     false,
@@ -561,13 +561,13 @@ export class JSONSchemaInput extends LitElement {
                                         },
                                     }
                                 ) // NOTE: No pattern properties support
-                            : ""
+                              : ""
                         : true);
 
                     const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
 
                     return returnedValue;
-                }
+                };
 
                 const commonTableMetadata = {
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements
@@ -580,26 +580,26 @@ export class JSONSchemaInput extends LitElement {
                         }
                     },
                     onThrow: (...args) => this.#onThrow(...args),
-                }
+                };
 
-                const createNestedTable = (propName, value) => { 
+                const createNestedTable = (propName, value) => {
                     const property_key = Math.random().toString(36).substring(7);
 
                     const rowData = Object.entries(value).map(([key, value]) => {
-                       return {[property_key]: key, ...value}
-                    })
+                        return { [property_key]: key, ...value };
+                    });
 
                     const schemaCopy = structuredClone(itemSchema);
-                    if (!schemaCopy.properties) schemaCopy.properties = {}
-                    if (!schemaCopy.required) schemaCopy.required = []
-                    schemaCopy.properties[property_key] = { title: 'Property Key', type: 'string', pattern: name }
-                    schemaCopy.order = [ property_key ]
-                    schemaCopy.required.push(property_key)
+                    if (!schemaCopy.properties) schemaCopy.properties = {};
+                    if (!schemaCopy.required) schemaCopy.required = [];
+                    schemaCopy.properties[property_key] = { title: "Property Key", type: "string", pattern: name };
+                    schemaCopy.order = [property_key];
+                    schemaCopy.required.push(property_key);
 
-                    const resultPath = [...path, propName]
-                    const schemaPath = [...resolvedFullPath, propName]
+                    const resultPath = [...path, propName];
+                    const schemaPath = [...resolvedFullPath, propName];
 
-                    const allRemovedKeys = new Set()
+                    const allRemovedKeys = new Set();
 
                     const tableMetadata = {
                         schema: schemaCopy,
@@ -607,69 +607,69 @@ export class JSONSchemaInput extends LitElement {
                         ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
 
                         onUpdate: function () {
-
                             const oldKeys = Object.keys(value);
 
                             const result = this.data.reduce((acc, row) => {
-                                const key = row[property_key]
+                                const key = row[property_key];
                                 if (key) {
-                                    const copy = {...row}
-                                    delete copy[property_key]
-                                    acc[key] = copy
+                                    const copy = { ...row };
+                                    delete copy[property_key];
+                                    acc[key] = copy;
                                 }
-                                return acc
-                            }, {})
+                                return acc;
+                            }, {});
 
                             const newKeys = Object.keys(result);
                             const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
-                            removedKeys.forEach(key => allRemovedKeys.add(key))
-                            newKeys.forEach(key => allRemovedKeys.delete(key))
-                            allRemovedKeys.forEach(key => result[key] = undefined)
-                                                        
-                            return commonUpdateFunction.call(this, resultPath, result) // According to 
+                            removedKeys.forEach((key) => allRemovedKeys.add(key));
+                            newKeys.forEach((key) => allRemovedKeys.delete(key));
+                            allRemovedKeys.forEach((key) => (result[key] = undefined));
+
+                            return commonUpdateFunction.call(this, resultPath, result); // According to
                         },
 
-                        validateOnChange: ( path, parent, v ) => commonValidationFunction(schemaPath, path, parent, v, schemaCopy),
+                        validateOnChange: (path, parent, v) =>
+                            commonValidationFunction(schemaPath, path, parent, v, schemaCopy),
 
-                        ...commonTableMetadata
-                    }
+                        ...commonTableMetadata,
+                    };
 
                     const table = (this.table = this.form.createTable(propName, tableMetadata, resolvedFullPath)); // Try creating table. Otherwise use nested form
                     if (table) {
                         return html`
                             <h3>${header(propName)}</h3>
-                            ${this.form.tables[`${resolvedFullPath.slice(-1)[0]}.${propName}`] = table === true ? new BasicTable(tableMetadata) : table}
-                        `
+                            ${(this.form.tables[`${resolvedFullPath.slice(-1)[0]}.${propName}`] =
+                                table === true ? new BasicTable(tableMetadata) : table)}
+                        `;
                     }
-                }
-
+                };
 
                 // Possibly multiple tables
                 if (isEditableObject(this.schema)) {
-                    
-                    const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce((acc, { key, value }) => {
-                        acc[key] = value;
-                        return acc;
-                    }, {})
-
+                    const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
+                        (acc, { key, value }) => {
+                            acc[key] = value;
+                            return acc;
+                        },
+                        {}
+                    );
 
-                    const tables = Object.entries(data).map(([patternPropName, patternPropValue]) => createNestedTable(patternPropName, patternPropValue)).filter(value => !!value)
+                    const tables = Object.entries(data)
+                        .map(([patternPropName, patternPropValue]) =>
+                            createNestedTable(patternPropName, patternPropValue)
+                        )
+                        .filter((value) => !!value);
 
                     if (tables.length) {
-                        disableButton({ 
-                            message: "New top-level pattern properties cannot be added at this time.", 
-                            submessage: "They need a unique key to be specified." 
-                        })
+                        disableButton({
+                            message: "New top-level pattern properties cannot be added at this time.",
+                            submessage: "They need a unique key to be specified.",
+                        });
 
-                        return html`
-                            <div style="width: 100%;">
-                                ${tables}
-                                ${buttonDiv}
-                            </div>
-                        `
+                        return html` <div style="width: 100%;">${tables} ${buttonDiv}</div> `;
                     }
-                } 
-                
+                }
+
                 // Normal table parsing
 
                 const tableMetadata = {
@@ -679,12 +679,12 @@ export class JSONSchemaInput extends LitElement {
                     ignore,
 
                     onUpdate: function () {
-                        return commonUpdateFunction.call(this, fullPath)
+                        return commonUpdateFunction.call(this, fullPath);
                     },
 
                     validateOnChange: (...args) => commonValidationFunction(fullPath, ...args),
 
-                    ...commonTableMetadata
+                    ...commonTableMetadata,
                 };
 
                 const table = (this.table = this.form.createTable(name, tableMetadata, fullPath)); // Try creating table. Otherwise use nested form
@@ -692,7 +692,6 @@ export class JSONSchemaInput extends LitElement {
                 if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
             }
 
-
             const list = (this.#list = new List({
                 items: this.#mapToList(),
 
@@ -733,10 +732,11 @@ export class JSONSchemaInput extends LitElement {
                 },
             }));
 
-            if (allowAdditionalProperties) disableButton({
-                message: "Additional properties cannot be added at this time.", 
-                submessage: "They don't have a predictable structure."
-            })
+            if (allowAdditionalProperties)
+                disableButton({
+                    message: "Additional properties cannot be added at this time.",
+                    submessage: "They don't have a predictable structure.",
+                });
 
             addButton.addEventListener("click", () => {
                 this.#createModal({ list, schema: allowPatternProperties ? schema : itemSchema });
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 5bbafba64..ea427dd6e 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -626,11 +626,11 @@ export class SimpleTable extends LitElement {
                 return this.getRow(i);
             });
 
-            this.onUpdate([], this.data)
+            this.onUpdate([], this.data);
             return mapped;
         }
 
-        this.onUpdate([], this.data)
+        this.onUpdate([], this.data);
     }
 
     #renderHeader = (str, { title, description }) => {
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 dc56d2c45..3178de940 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -223,7 +223,6 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             createTable: function (name, metadata, path) {
-                
                 // // Do not create tables for patternProperties (OLD)
                 // const parentSchema = this.getSchema(path) ?? {};
                 // if (parentSchema.patternProperties) return false

From ad7a1af55cc634cddb8e12162cdc320566c7f3d2 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 4 Jan 2024 06:37:12 -0600
Subject: [PATCH 079/133] Check unique device names

---
 src/renderer/src/stories/SimpleTable.js   |  2 +-
 src/renderer/src/validation/validation.ts | 47 +++++++++++++++++++++--
 2 files changed, 45 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index ea427dd6e..1b4998faf 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -284,7 +284,7 @@ export class SimpleTable extends LitElement {
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data)) return this.#data.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data)) return this.#data //.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 7804b9303..9ac5cb4ad 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -11,6 +11,35 @@ function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
     return element
 }
 
+const isNotUnique = (key, currentValue, rows, idx) => {
+    const isUnique = rows.filter((o, i) => o[key] === currentValue && i !== idx).length === 0
+
+    if (!isUnique) return [
+        {
+            message: `Not a unique ${key}`,
+            type: 'error'
+        }
+    ]
+
+}
+
+const get = (object: any, path: string[]) => {
+    const values: any[] = []
+
+    const name = path.slice(-1)[0]
+    const finalValue = path.slice(0, -1).reduce((acc, str) => {
+        values.push(acc[str])
+        return acc[str]
+    }, object)
+
+
+
+    return {
+        value: finalValue[name],
+        values
+    }
+}
+
 // Specify JavaScript-side validation
 schema.Ecephys.ElectrodeGroup.device = function (this: JSONSchemaForm, name, parent, path) {
     const devices = this.results.Ecephys.Device.map(o => o.name)
@@ -86,13 +115,25 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
 schema.Ophys.Device = {
     ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
 
-        const row = path.reduce((acc, str) => acc[str], this.results)
+        const { 
+            values, 
+            value: row 
+        } = get(this.results, path)
+        
+        if (!row) return true // Allow blank rows
 
-        if (!row) return true
+        const rows = values.slice(-1)[0]
+        const idx = path.slice(-1)[0]
+        const isUniqueError = isNotUnique(name, value, rows, idx)
+        if (isUniqueError) return isUniqueError
 
         const prevValue = row[name]
+        
+        if (prevValue === value || prevValue === undefined) return true // No change
 
-        if (prevValue === value) return true // No change
+        const prevUniqueError = isNotUnique(name, prevValue, rows, idx)
+        console.log(prevUniqueError)
+        if (prevUniqueError) return true // Register as valid
 
         const result = await Swal.fire({
             title: `Are you sure you want to rename the ${prevValue} device?`,

From 9c776c03ac0ee1b81d3b0d48ce49969ddc9d4b31 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 4 Jan 2024 12:37:49 +0000
Subject: [PATCH 080/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/SimpleTable.js   |  2 +-
 src/renderer/src/validation/validation.ts | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 1b4998faf..947537d89 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -284,7 +284,7 @@ export class SimpleTable extends LitElement {
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data)) return this.#data //.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data)) return this.#data; //.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 9ac5cb4ad..cd86d97f6 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -115,11 +115,11 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
 schema.Ophys.Device = {
     ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
 
-        const { 
-            values, 
-            value: row 
+        const {
+            values,
+            value: row
         } = get(this.results, path)
-        
+
         if (!row) return true // Allow blank rows
 
         const rows = values.slice(-1)[0]
@@ -128,7 +128,7 @@ schema.Ophys.Device = {
         if (isUniqueError) return isUniqueError
 
         const prevValue = row[name]
-        
+
         if (prevValue === value || prevValue === undefined) return true // No change
 
         const prevUniqueError = isNotUnique(name, prevValue, rows, idx)

From 9c1c68a7b0ebd29bd426664265ce561d8478eb02 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 4 Jan 2024 08:17:50 -0600
Subject: [PATCH 081/133] Ensure safe property editing

---
 src/renderer/src/stories/JSONSchemaInput.js | 74 ++++++++++++++++-----
 src/renderer/src/stories/forms/utils.ts     |  2 +
 src/renderer/src/validation/index.js        | 24 +++++--
 src/renderer/src/validation/validation.ts   | 32 ++++++++-
 4 files changed, 107 insertions(+), 25 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 9e2ed242f..ccae63da8 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -3,7 +3,7 @@ import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
-import { header } from "./forms/utils";
+import { header, tempPropertyKey } from "./forms/utils";
 
 import { Button } from "./Button";
 import { List } from "./List";
@@ -14,6 +14,7 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
+
 const isEditableObject = (schema) => schema.type === "object";
 const isAdditionalProperties = (pattern) => pattern === "additional";
 const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
@@ -519,25 +520,30 @@ export class JSONSchemaInput extends LitElement {
             else if (itemSchema?.type === "object" && this.form.createTable) {
                 const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, resolvedFullPath) : {};
 
-                const ogThis = this;
+                const instanceThis = this;
 
                 function commonUpdateFunction(path, value = this.data) {
-                    return ogThis.#updateData(path, value, true, {
+                    return instanceThis.#updateData(path, value, true, {
                         willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
                         onError: (e) => e,
                         onWarning: (e) => e,
                     }); // Ensure change propagates to all forms
                 }
 
-                const commonValidationFunction = async (tableBasePath, path, parent, v, baseSchema = itemSchema) => {
+                const commonValidationFunction = async (tableBasePath, path, parent, newValue, baseSchema = itemSchema, skip = 0) => {
                     const warnings = [];
                     const errors = [];
 
                     const name = path.slice(-1)[0];
                     const completePath = [...tableBasePath, ...path.slice(0, -1)];
 
-                    const itemPropSchema = path.reduce((acc, key) => {
-                        if (typeof key === "number") return acc; // Skip row information
+                    const toIterate = path.slice(skip);
+
+                    const itemPropSchema = toIterate.reduce((acc, key) => {
+                        // if (acc?.patternProperties) {
+                        //     const pattern = Object.keys(acc.patternProperties).find((pattern) => new RegExp(pattern).test(key));
+                        //     if (pattern) return acc.patternProperties[pattern];
+                        // }
                         return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
                     }, baseSchema);
 
@@ -551,7 +557,7 @@ export class JSONSchemaInput extends LitElement {
                                     false,
                                     this,
                                     itemPropSchema,
-                                    { ...parent, [name]: v },
+                                    { ...parent, [name]: newValue },
                                     {
                                         onError: (error) => {
                                             errors.push(error); // Skip counting errors
@@ -583,37 +589,43 @@ export class JSONSchemaInput extends LitElement {
                 };
 
                 const createNestedTable = (propName, value) => {
-                    const property_key = Math.random().toString(36).substring(7);
 
                     const rowData = Object.entries(value).map(([key, value]) => {
-                        return { [property_key]: key, ...value };
+                        return { [tempPropertyKey]: key, ...value };
                     });
 
                     const schemaCopy = structuredClone(itemSchema);
                     if (!schemaCopy.properties) schemaCopy.properties = {};
                     if (!schemaCopy.required) schemaCopy.required = [];
-                    schemaCopy.properties[property_key] = { title: "Property Key", type: "string", pattern: name };
-                    schemaCopy.order = [property_key];
-                    schemaCopy.required.push(property_key);
+                    schemaCopy.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
+                    schemaCopy.order = [tempPropertyKey];
+                    schemaCopy.required.push(tempPropertyKey);
 
                     const resultPath = [...path, propName];
                     const schemaPath = [...resolvedFullPath, propName];
 
                     const allRemovedKeys = new Set();
 
+                    const keyAlreadyExists = (key) => Object.keys(value).includes(key)
+
+
+                    let previousValidValues = {}
+
                     const tableMetadata = {
                         schema: schemaCopy,
                         data: rowData,
                         ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
 
-                        onUpdate: function () {
+                        onUpdate: function (path, newValue) {
                             const oldKeys = Object.keys(value);
 
+                            if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return // Do not overwrite existing keys
+
                             const result = this.data.reduce((acc, row) => {
-                                const key = row[property_key];
+                                const key = row[tempPropertyKey];
                                 if (key) {
                                     const copy = { ...row };
-                                    delete copy[property_key];
+                                    delete copy[tempPropertyKey];
                                     acc[key] = copy;
                                 }
                                 return acc;
@@ -628,9 +640,35 @@ export class JSONSchemaInput extends LitElement {
                             return commonUpdateFunction.call(this, resultPath, result); // According to
                         },
 
-                        validateOnChange: (path, parent, v) =>
-                            commonValidationFunction(schemaPath, path, parent, v, schemaCopy),
+                        validateOnChange: function (path, parent, newValue){
+
+                            const rowIdx = path[0]
+                            const currentKey = this.data[rowIdx][tempPropertyKey]
+                            const updatedPath = [ this.data[rowIdx][tempPropertyKey], ...path.slice(1) ]; // Replace row with key
+
+                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey
 
+                            // Do not overwrite existing keys
+                            if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
+
+                                if (keyAlreadyExists(newValue)) {
+
+
+                                    if (!previousValidValues[rowIdx]) previousValidValues[rowIdx] = resolvedKey
+
+                                    return [
+                                        {
+                                            message: `Key already exists.<br><small>This value is still ${resolvedKey}.</small>`,
+                                            type: "error", 
+                                        }
+                                    ]
+                                } 
+                                
+                                else delete previousValidValues[rowIdx]
+                            }
+
+                            return commonValidationFunction(resultPath, updatedPath, parent, newValue, schemaCopy, 1)
+                        },
                         ...commonTableMetadata,
                     };
 
@@ -682,7 +720,7 @@ export class JSONSchemaInput extends LitElement {
                         return commonUpdateFunction.call(this, fullPath);
                     },
 
-                    validateOnChange: (...args) => commonValidationFunction(fullPath, ...args),
+                    validateOnChange: (...args) => commonValidationFunction(fullPath, ...args, 1),
 
                     ...commonTableMetadata,
                 };
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 0a881de82..44a61f347 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -1,6 +1,8 @@
 const toCapitalizeAll = ['nwb', 'api', 'id']
 const toCapitalizeNone = ['or', 'and']
 
+export const tempPropertyKey = Math.random().toString(36).substring(7);
+
 export const capitalize = (str: string) => {
     const lowerCase = str.toLowerCase()
     return toCapitalizeAll.includes(lowerCase) ? str.toUpperCase() : (toCapitalizeNone.includes(lowerCase) ? lowerCase : str[0].toUpperCase() + str.slice(1))
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index c539460ef..f1b2f2162 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -14,13 +14,13 @@ export async function validateOnChange(name, parent, path, value) {
 
     const fullPath = [...path, name];
 
-    const fullPathNoRows = fullPath.filter((key) => typeof key !== "number");
+    const toIterate = fullPath //fullPathNoRows // fullPath
 
     const copy = { ...parent }; // Validate on a copy of the parent
     if (arguments.length > 3) copy[name] = value; // Update value on copy
 
     let lastResolved;
-    functions = fullPathNoRows.reduce((acc, key, i) => {
+    functions = toIterate.reduce((acc, key, i) => {
         if (acc && key in acc) return (lastResolved = acc[key]);
         else return;
     }, validationSchema); // Pass the top level until it runs out
@@ -31,21 +31,35 @@ export async function validateOnChange(name, parent, path, value) {
     if (lastResolved !== false && (functions === undefined || functions === true)) {
         // let overridden = false;
         let lastWildcard;
-        fullPathNoRows.reduce((acc, key) => {
+        toIterate.reduce((acc, key) => {
+
             if (acc && "*" in acc) {
-                if (!acc["*"] && lastWildcard)
+                if (acc["*"] === false && lastWildcard)
                     overridden = true; // Disable if false and a wildcard has already been specified
+
                 // Otherwise set the last wildcard
                 else {
+                    
                     lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
+
                     overridden = false; // Re-enable if a new one is specified below
                 }
+            } else if (lastWildcard && typeof lastWildcard === "object"){
+
+                    const newWildcard = lastWildcard[key] ?? lastWildcard["*"] ?? lastWildcard["**"] ?? (acc && acc["**"]) // Drill wildcard objects once resolved
+                    // Prioritize continuation of last wildcard
+                    if (newWildcard) lastWildcard = newWildcard; 
             }
+
+
             return acc?.[key];
+
         }, validationSchema);
 
+
         if (overridden && functions !== true) lastWildcard = false; // Disable if not promised to exist
-        if (lastWildcard) functions = [lastWildcard];
+        
+        if (typeof lastWildcard === 'function') functions = [lastWildcard];
     }
 
     if (!functions || (Array.isArray(functions) && functions.length === 0)) return; // No validation for this field
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 9ac5cb4ad..e6ac65789 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -1,6 +1,7 @@
 import schema from './validation.json'
 import { JSONSchemaForm } from '../stories/JSONSchemaForm.js'
 import Swal from 'sweetalert2'
+import { tempPropertyKey } from '../stories/forms/utils'
 
 function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
     const element = this.getTable(linkedPath)
@@ -12,7 +13,11 @@ function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
 }
 
 const isNotUnique = (key, currentValue, rows, idx) => {
-    const isUnique = rows.filter((o, i) => o[key] === currentValue && i !== idx).length === 0
+
+    const array = Array.isArray(rows) ? rows : Object.values(rows)
+    idx = Array.isArray(rows) ? idx : Object.keys(rows).indexOf(idx)
+
+    const isUnique = array.filter((o, i) => o[key] === currentValue && i !== idx).length === 0
 
     if (!isUnique) return [
         {
@@ -111,6 +116,30 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
     ]
 }
 
+function ensureUnique(this: JSONSchemaForm, name, parent, path, value) {
+    const { 
+        values, 
+        value: row 
+    } = get(this.results, path)
+    
+    if (!row) return true // Allow blank rows
+
+    const rows = values.slice(-1)[0]
+    const idx = path.slice(-1)[0]
+    const isUniqueError = isNotUnique(name, value, rows, idx)
+    if (isUniqueError) return isUniqueError
+
+    return true
+}
+
+schema.Ophys = {
+    '*': {
+        '**': {
+            ['name']: ensureUnique,
+        }
+    }
+}
+
 // Ophys
 schema.Ophys.Device = {
     ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
@@ -132,7 +161,6 @@ schema.Ophys.Device = {
         if (prevValue === value || prevValue === undefined) return true // No change
 
         const prevUniqueError = isNotUnique(name, prevValue, rows, idx)
-        console.log(prevUniqueError)
         if (prevUniqueError) return true // Register as valid
 
         const result = await Swal.fire({

From 724a320988e48a61e93b4c1541fa7a01112049e5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 4 Jan 2024 14:18:08 +0000
Subject: [PATCH 082/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 46 ++++++++++-----------
 src/renderer/src/validation/index.js        | 21 ++++------
 src/renderer/src/validation/validation.ts   |  8 ++--
 3 files changed, 33 insertions(+), 42 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index ccae63da8..4c40fea7c 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -14,7 +14,6 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
-
 const isEditableObject = (schema) => schema.type === "object";
 const isAdditionalProperties = (pattern) => pattern === "additional";
 const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
@@ -530,7 +529,14 @@ export class JSONSchemaInput extends LitElement {
                     }); // Ensure change propagates to all forms
                 }
 
-                const commonValidationFunction = async (tableBasePath, path, parent, newValue, baseSchema = itemSchema, skip = 0) => {
+                const commonValidationFunction = async (
+                    tableBasePath,
+                    path,
+                    parent,
+                    newValue,
+                    baseSchema = itemSchema,
+                    skip = 0
+                ) => {
                     const warnings = [];
                     const errors = [];
 
@@ -589,7 +595,6 @@ export class JSONSchemaInput extends LitElement {
                 };
 
                 const createNestedTable = (propName, value) => {
-
                     const rowData = Object.entries(value).map(([key, value]) => {
                         return { [tempPropertyKey]: key, ...value };
                     });
@@ -606,10 +611,9 @@ export class JSONSchemaInput extends LitElement {
 
                     const allRemovedKeys = new Set();
 
-                    const keyAlreadyExists = (key) => Object.keys(value).includes(key)
+                    const keyAlreadyExists = (key) => Object.keys(value).includes(key);
 
-
-                    let previousValidValues = {}
+                    let previousValidValues = {};
 
                     const tableMetadata = {
                         schema: schemaCopy,
@@ -619,7 +623,7 @@ export class JSONSchemaInput extends LitElement {
                         onUpdate: function (path, newValue) {
                             const oldKeys = Object.keys(value);
 
-                            if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return // Do not overwrite existing keys
+                            if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return; // Do not overwrite existing keys
 
                             const result = this.data.reduce((acc, row) => {
                                 const key = row[tempPropertyKey];
@@ -640,34 +644,28 @@ export class JSONSchemaInput extends LitElement {
                             return commonUpdateFunction.call(this, resultPath, result); // According to
                         },
 
-                        validateOnChange: function (path, parent, newValue){
-
-                            const rowIdx = path[0]
-                            const currentKey = this.data[rowIdx][tempPropertyKey]
-                            const updatedPath = [ this.data[rowIdx][tempPropertyKey], ...path.slice(1) ]; // Replace row with key
+                        validateOnChange: function (path, parent, newValue) {
+                            const rowIdx = path[0];
+                            const currentKey = this.data[rowIdx][tempPropertyKey];
+                            const updatedPath = [this.data[rowIdx][tempPropertyKey], ...path.slice(1)]; // Replace row with key
 
-                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey
+                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey;
 
                             // Do not overwrite existing keys
                             if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
-
                                 if (keyAlreadyExists(newValue)) {
-
-
-                                    if (!previousValidValues[rowIdx]) previousValidValues[rowIdx] = resolvedKey
+                                    if (!previousValidValues[rowIdx]) previousValidValues[rowIdx] = resolvedKey;
 
                                     return [
                                         {
                                             message: `Key already exists.<br><small>This value is still ${resolvedKey}.</small>`,
-                                            type: "error", 
-                                        }
-                                    ]
-                                } 
-                                
-                                else delete previousValidValues[rowIdx]
+                                            type: "error",
+                                        },
+                                    ];
+                                } else delete previousValidValues[rowIdx];
                             }
 
-                            return commonValidationFunction(resultPath, updatedPath, parent, newValue, schemaCopy, 1)
+                            return commonValidationFunction(resultPath, updatedPath, parent, newValue, schemaCopy, 1);
                         },
                         ...commonTableMetadata,
                     };
diff --git a/src/renderer/src/validation/index.js b/src/renderer/src/validation/index.js
index f1b2f2162..382706d10 100644
--- a/src/renderer/src/validation/index.js
+++ b/src/renderer/src/validation/index.js
@@ -14,7 +14,7 @@ export async function validateOnChange(name, parent, path, value) {
 
     const fullPath = [...path, name];
 
-    const toIterate = fullPath //fullPathNoRows // fullPath
+    const toIterate = fullPath; //fullPathNoRows // fullPath
 
     const copy = { ...parent }; // Validate on a copy of the parent
     if (arguments.length > 3) copy[name] = value; // Update value on copy
@@ -32,34 +32,27 @@ export async function validateOnChange(name, parent, path, value) {
         // let overridden = false;
         let lastWildcard;
         toIterate.reduce((acc, key) => {
-
             if (acc && "*" in acc) {
                 if (acc["*"] === false && lastWildcard)
                     overridden = true; // Disable if false and a wildcard has already been specified
-
                 // Otherwise set the last wildcard
                 else {
-                    
                     lastWildcard = typeof acc["*"] === "string" ? acc["*"].replace(`{*}`, `${name}`) : acc["*"];
 
                     overridden = false; // Re-enable if a new one is specified below
                 }
-            } else if (lastWildcard && typeof lastWildcard === "object"){
-
-                    const newWildcard = lastWildcard[key] ?? lastWildcard["*"] ?? lastWildcard["**"] ?? (acc && acc["**"]) // Drill wildcard objects once resolved
-                    // Prioritize continuation of last wildcard
-                    if (newWildcard) lastWildcard = newWildcard; 
+            } else if (lastWildcard && typeof lastWildcard === "object") {
+                const newWildcard = lastWildcard[key] ?? lastWildcard["*"] ?? lastWildcard["**"] ?? (acc && acc["**"]); // Drill wildcard objects once resolved
+                // Prioritize continuation of last wildcard
+                if (newWildcard) lastWildcard = newWildcard;
             }
 
-
             return acc?.[key];
-
         }, validationSchema);
 
-
         if (overridden && functions !== true) lastWildcard = false; // Disable if not promised to exist
-        
-        if (typeof lastWildcard === 'function') functions = [lastWildcard];
+
+        if (typeof lastWildcard === "function") functions = [lastWildcard];
     }
 
     if (!functions || (Array.isArray(functions) && functions.length === 0)) return; // No validation for this field
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index ddacf9d5b..4b4ea0b8a 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -117,11 +117,11 @@ schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, p
 }
 
 function ensureUnique(this: JSONSchemaForm, name, parent, path, value) {
-    const { 
-        values, 
-        value: row 
+    const {
+        values,
+        value: row
     } = get(this.results, path)
-    
+
     if (!row) return true // Allow blank rows
 
     const rows = values.slice(-1)[0]

From ab37d93dd306775eb6aea9811028935f3d0fb1bd Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 4 Jan 2024 13:47:17 -0600
Subject: [PATCH 083/133] Render as editable tables

---
 src/renderer/src/stories/JSONSchemaForm.js    |   3 +
 src/renderer/src/stories/JSONSchemaInput.js   | 197 ++++++++++++------
 src/renderer/src/stories/SimpleTable.js       |  31 ++-
 src/renderer/src/stories/forms/utils.ts       |   4 +-
 src/renderer/src/stories/table/Cell.ts        |   7 +-
 .../table/cells/{table.ts => input.ts}        |  50 +++--
 .../src/stories/table/cells/renderers/base.ts |   2 +-
 src/renderer/src/validation/validation.ts     |   3 +-
 8 files changed, 198 insertions(+), 99 deletions(-)
 rename src/renderer/src/stories/table/cells/{table.ts => input.ts} (53%)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index c8c004a5d..9d0085d9b 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -380,6 +380,9 @@ export class JSONSchemaForm extends LitElement {
 
     #clearMessages = (localPath, type) => {
         if (Array.isArray(localPath)) localPath = localPath.join("-"); // Convert array to string
+
+        if (!localPath.length) return
+        
         const container = this.shadowRoot.querySelector(`#${encode(localPath)} .${type}`);
 
         if (container) {
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 4c40fea7c..e18cd7bad 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -3,7 +3,7 @@ import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
-import { header, tempPropertyKey } from "./forms/utils";
+import { header, tempPropertyKey, tempPropertyValueKey } from "./forms/utils";
 
 import { Button } from "./Button";
 import { List } from "./List";
@@ -14,7 +14,10 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
-const isEditableObject = (schema) => schema.type === "object";
+
+// Schema or value indicates editable object
+const isEditableObject = (schema, value) => schema.type === "object" || (value && typeof value === 'object' && !Array.isArray(value))
+;
 const isAdditionalProperties = (pattern) => pattern === "additional";
 const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
@@ -35,7 +38,9 @@ export const getEditableItems = (value, pattern, { name, schema } = {}) => {
             const regex = new RegExp(key);
             items = items.filter(([k]) => !regex.test(k));
         });
-    } else items.filter(([key]) => key in schema.properties);
+    } 
+    
+    else if (schema.properties) items = items.filter(([key]) => key in schema.properties);
 
     items = items.filter(([key]) => !key.includes("__")); // Remove secret properties
 
@@ -222,7 +227,7 @@ export class JSONSchemaInput extends LitElement {
         this.#validationTimeout = setTimeout(() => {
             this.onValidate
                 ? this.onValidate()
-                : this.form
+                : this.form?.triggerValidation
                   ? this.form.triggerValidation(name, path, undefined, this, undefined, undefined, hooks)
                   : "";
         }, 1000);
@@ -234,7 +239,7 @@ export class JSONSchemaInput extends LitElement {
 
     #validationTimeout = null;
     #updateData = (fullPath, value, forceUpdate, hooks = {}) => {
-        this.onUpdate ? this.onUpdate(value) : this.form ? this.form.updateData(fullPath, value, forceUpdate) : "";
+        this.onUpdate ? this.onUpdate(value) : this.form?.updateData ? this.form.updateData(fullPath, value, forceUpdate) : "";
 
         const path = [...fullPath];
         const name = path.splice(-1)[0];
@@ -246,7 +251,7 @@ export class JSONSchemaInput extends LitElement {
 
     #triggerValidation = async (name, path) => {
         this.#clearTimeoutValidation();
-        return this.onValidate ? this.onValidate() : this.form ? this.form.triggerValidation(name, path, this) : "";
+        return this.onValidate ? this.onValidate() : this.form?.triggerValidation ? this.form.triggerValidation(name, path, this) : "";
     };
 
     updated() {
@@ -281,7 +286,7 @@ export class JSONSchemaInput extends LitElement {
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
 
-        const canAddProperties = isEditableObject(this.schema);
+        const canAddProperties = isEditableObject(this.schema, this.value);
 
         if (canAddProperties) {
             const editable = getEditableItems(this.value, this.pattern, { name, schema });
@@ -441,7 +446,7 @@ export class JSONSchemaInput extends LitElement {
     #moveToNextInput = (ev) => {
         if (ev.key === "Enter") {
             ev.preventDefault();
-            if (this.form) {
+            if (this.form?.inputs) {
                 const idx = this.form.inputs.findIndex((input) => input === this);
                 this.#handleNextInput(idx + 1);
             }
@@ -462,7 +467,7 @@ export class JSONSchemaInput extends LitElement {
 
         const isArray = schema.type === "array"; // Handle string (and related) formats / types
 
-        const canAddProperties = isEditableObject(this.schema);
+        const canAddProperties = isEditableObject(this.schema, this.value);
 
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
@@ -511,7 +516,7 @@ export class JSONSchemaInput extends LitElement {
                 if (!("type" in schema.items) && !hasItemsRef) schema.items.type = this.#getType(this.value?.[0]);
             }
 
-            const itemSchema = this.form ? this.form.getSchema("items", schema) : schema["items"];
+            const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
 
             const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
@@ -556,7 +561,7 @@ export class JSONSchemaInput extends LitElement {
                     const result = await (validateOnChange
                         ? this.onValidate
                             ? this.onValidate()
-                            : this.form
+                            : this.form?.triggerValidation
                               ? this.form.triggerValidation(
                                     name,
                                     completePath,
@@ -582,40 +587,120 @@ export class JSONSchemaInput extends LitElement {
                 };
 
                 const commonTableMetadata = {
-                    onStatusChange: () => this.form?.checkStatus(), // Check status on all elements
+                    onStatusChange: () => this.form?.checkStatus && this.form.checkStatus(), // Check status on all elements
                     validateEmptyCells: this.form?.validateEmptyValues,
                     deferLoading: this.form?.deferLoading,
                     onLoaded: () => {
                         if (this.form) {
-                            this.form.nLoaded++;
-                            this.form.checkAllLoaded();
+                            if (this.form.nLoaded)this.form.nLoaded++;
+                            if (this.form.checkAllLoaded) this.form.checkAllLoaded();
                         }
                     },
                     onThrow: (...args) => this.#onThrow(...args),
                 };
 
-                const createNestedTable = (propName, value) => {
-                    const rowData = Object.entries(value).map(([key, value]) => {
-                        return { [tempPropertyKey]: key, ...value };
-                    });
+                const addPropertyKeyToSchema = (schema) => {
+                    const schemaCopy = structuredClone(schema);
+
 
-                    const schemaCopy = structuredClone(itemSchema);
                     if (!schemaCopy.properties) schemaCopy.properties = {};
                     if (!schemaCopy.required) schemaCopy.required = [];
+
                     schemaCopy.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
                     schemaCopy.order = [tempPropertyKey];
+
                     schemaCopy.required.push(tempPropertyKey);
 
-                    const resultPath = [...path, propName];
-                    const schemaPath = [...resolvedFullPath, propName];
+                    if (!schema['items']) {
+                        
+                        const resolvedItemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
+                        if (!resolvedItemSchema) return schemaCopy
+
+                        delete schemaCopy.patternProperties
+
+                        schemaCopy.properties[tempPropertyValueKey] = {
+                            type: 'array',
+                            items: resolvedItemSchema.properties ? addPropertyKeyToSchema(itemSchema) : itemSchema,
+                            title: "Property Value",
+                            __generated: true
+                        };
+
+                        schemaCopy.required.push(tempPropertyValueKey);
+                    }
+
+                    if (schemaCopy.__generated) return schemaCopy['items'] // Only return the relevant items for tables in nested tables
+                
+
+                    return schemaCopy
+
+                }
+
+
+                const createNestedTable = (id, value, { 
+                    name: propName = id, 
+                    schema = itemSchema
+                } = {}) => {
+
+
+                    const schemaCopy = addPropertyKeyToSchema(schema)
+
+                    const resultPath = [...path];
+
+                    const schemaPath = [...resolvedFullPath];
+
+                    const rowData = Object.entries(value).map(([key, value]) => {
+                        return !schema['items'] ? {[tempPropertyKey]: key, [tempPropertyValueKey]: value } : { [tempPropertyKey]: key, ...value };
+                    });
+
+                    if (propName) {
+                        resultPath.push(propName);
+                        schemaPath.push(propName);
+                    }
+
 
                     const allRemovedKeys = new Set();
 
                     const keyAlreadyExists = (key) => Object.keys(value).includes(key);
 
-                    let previousValidValues = {};
+                    const previousValidValues = {};
+
+                    function resolvePath(path, target) {
+                        return path.map((key, i) => {
+                            const ogKey = key
+                            const nextKey = path[i + 1]
+                            if (key === tempPropertyKey) key = target[tempPropertyKey]
+                            if (nextKey === tempPropertyKey) key = []
+
+                            target = target[ogKey] ?? {}
+
+                            if (nextKey === tempPropertyValueKey) return target[tempPropertyKey] // Grab next property key
+                            if (key === tempPropertyValueKey) return []
+
+                            return key
+                        }).flat()
+                    }
+
+                    function setValueOnAccumulator(row, acc) {
+                        const key = row[tempPropertyKey];
+
+                        if (!key) return acc
+
+                        if (tempPropertyValueKey in row) {
+                            const propValue = row[tempPropertyValueKey];
+                            if (Array.isArray(propValue)) acc[key] = propValue.reduce((acc, row) =>  setValueOnAccumulator(row, acc), {})
+                            else acc[key] = propValue;
+                        }
+                        else {
+                            const copy = { ...row };
+                            delete copy[tempPropertyKey];
+                            acc[key] = copy;
+                        }
+
+                        return acc
+                    }
 
                     const tableMetadata = {
+                        keyColumn: tempPropertyKey,
                         schema: schemaCopy,
                         data: rowData,
                         ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
@@ -625,15 +710,7 @@ export class JSONSchemaInput extends LitElement {
 
                             if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return; // Do not overwrite existing keys
 
-                            const result = this.data.reduce((acc, row) => {
-                                const key = row[tempPropertyKey];
-                                if (key) {
-                                    const copy = { ...row };
-                                    delete copy[tempPropertyKey];
-                                    acc[key] = copy;
-                                }
-                                return acc;
-                            }, {});
+                            const result = this.data.reduce((acc, row) =>  setValueOnAccumulator(row, acc), {});
 
                             const newKeys = Object.keys(result);
                             const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
@@ -641,15 +718,19 @@ export class JSONSchemaInput extends LitElement {
                             newKeys.forEach((key) => allRemovedKeys.delete(key));
                             allRemovedKeys.forEach((key) => (result[key] = undefined));
 
-                            return commonUpdateFunction.call(this, resultPath, result); // According to
+
+                            // const resolvedPath = resolvePath(path, this.data)
+                            return commonUpdateFunction.call(this, [], result); // Update all table data
                         },
 
                         validateOnChange: function (path, parent, newValue) {
-                            const rowIdx = path[0];
-                            const currentKey = this.data[rowIdx][tempPropertyKey];
-                            const updatedPath = [this.data[rowIdx][tempPropertyKey], ...path.slice(1)]; // Replace row with key
 
-                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey;
+                            const rowIdx = path[0]
+                            const currentKey = this.data[rowIdx]?.[tempPropertyKey]
+
+                            const updatedPath = resolvePath(path, this.data)
+
+                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey
 
                             // Do not overwrite existing keys
                             if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
@@ -665,23 +746,23 @@ export class JSONSchemaInput extends LitElement {
                                 } else delete previousValidValues[rowIdx];
                             }
 
-                            return commonValidationFunction(resultPath, updatedPath, parent, newValue, schemaCopy, 1);
+                            return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1)
                         },
                         ...commonTableMetadata,
                     };
+ 
 
-                    const table = (this.table = this.form.createTable(propName, tableMetadata, resolvedFullPath)); // Try creating table. Otherwise use nested form
-                    if (table) {
-                        return html`
-                            <h3>${header(propName)}</h3>
-                            ${(this.form.tables[`${resolvedFullPath.slice(-1)[0]}.${propName}`] =
-                                table === true ? new BasicTable(tableMetadata) : table)}
-                        `;
-                    }
+                    const table = this.form.createTable(id, tableMetadata, resolvedFullPath); // Try creating table. Otherwise use nested form
+                    return table
                 };
 
+
+
                 // Possibly multiple tables
-                if (isEditableObject(this.schema)) {
+                if (isEditableObject(schema, this.value)) {
+
+                    
+                    // One table with nested tables for each property
                     const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
                         (acc, { key, value }) => {
                             acc[key] = value;
@@ -690,24 +771,11 @@ export class JSONSchemaInput extends LitElement {
                         {}
                     );
 
-                    const tables = Object.entries(data)
-                        .map(([patternPropName, patternPropValue]) =>
-                            createNestedTable(patternPropName, patternPropValue)
-                        )
-                        .filter((value) => !!value);
-
-                    if (tables.length) {
-                        disableButton({
-                            message: "New top-level pattern properties cannot be added at this time.",
-                            submessage: "They need a unique key to be specified.",
-                        });
-
-                        return html` <div style="width: 100%;">${tables} ${buttonDiv}</div> `;
-                    }
+                    const table = createNestedTable(name, data, { schema })
+                    return table
                 }
 
                 // Normal table parsing
-
                 const tableMetadata = {
                     schema: itemSchema,
                     data: this.value,
@@ -725,7 +793,12 @@ export class JSONSchemaInput extends LitElement {
 
                 const table = (this.table = this.form.createTable(name, tableMetadata, fullPath)); // Try creating table. Otherwise use nested form
 
-                if (table) return (this.form.tables[name] = table === true ? new BasicTable(tableMetadata) : table);
+                if (table) {
+                    const tableEl = table === true ? new BasicTable(tableMetadata) : table;
+                    const tables = this.form?.tables
+                    if (tables) tables[name]  = tableEl
+                    return tableEl
+                }
             }
 
             const list = (this.#list = new List({
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 947537d89..c36de61cc 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -1,5 +1,5 @@
 import { LitElement, css, html, unsafeCSS } from "lit";
-import { header } from "./forms/utils";
+import { header, tempPropertyKey, tempPropertyValueKey } from "./forms/utils";
 import { checkStatus } from "../validation";
 
 import { TableCell } from "./table/Cell";
@@ -12,7 +12,7 @@ import { styleMap } from "lit/directives/style-map.js";
 import "./Button";
 import tippy from "tippy.js";
 import { sortTable } from "./Table";
-import { NestedTableCell } from "./table/cells/table";
+import { NestedInputCell } from "./table/cells/input";
 
 var isMac = navigator.platform.toUpperCase().indexOf("MAC") >= 0;
 
@@ -186,8 +186,9 @@ export class SimpleTable extends LitElement {
     } = {}) {
         super();
         this.schema = schema ?? {};
-        this.#data = data ?? [];
-        this.keyColumn = keyColumn;
+        this.#keyColumn = keyColumn
+        this.data = data ?? [];
+
         this.globals = globals ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
         this.deferLoading = deferLoading ?? false;
@@ -281,15 +282,17 @@ export class SimpleTable extends LitElement {
         });
     }
 
+    #keyColumn
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data)) return this.#data; //.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data)) return this.#data //.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
     set data(val) {
         this.#data = val;
+        this.keyColumn = Array.isArray(this.#data) ? undefined : this.#keyColumn ?? "Property Key";
     }
 
     #selected = {};
@@ -309,11 +312,11 @@ export class SimpleTable extends LitElement {
     #getPath = (ev) => ev.path || ev.composedPath();
     #getCellFromEvent = (ev) => this.#getCellFromPath(this.#getPath(ev));
     #getCellFromPath = (path) => {
-        let inTableCell;
+        let inInputCell;
 
         const found = path.find((el) => {
-            if (el instanceof NestedTableCell) inTableCell = true;
-            return !inTableCell && (el instanceof TableCell || el.children?.[0] instanceof TableCell);
+            if (el instanceof NestedInputCell) inInputCell = true;
+            return !inInputCell && (el instanceof TableCell || el.children?.[0] instanceof TableCell);
         });
         if (found instanceof HTMLTableCellElement) return found.children[0];
         else return found;
@@ -373,7 +376,7 @@ export class SimpleTable extends LitElement {
             } else {
                 value = hasRow ? this.#data[row][col] : undefined;
                 if (this.#isUndefined(value)) value = this.globals[col];
-                if (this.#isUndefined(value)) value = this.schema.properties[col].default;
+                if (this.#isUndefined(value)) value = this.schema.properties?.[col]?.default;
                 if (this.#isUndefined(value)) value = "";
             }
             return value;
@@ -706,10 +709,12 @@ export class SimpleTable extends LitElement {
     #createCell = (value, info) => {
         const rowNames = Object.keys(this.#data);
 
+        const row = Array.isArray(this.#data) ? info.i : rowNames[info.i]
+
         const fullInfo = {
             ...info,
             col: this.colHeaders[info.j],
-            row: Array.isArray(this.#data) ? `${info.i}` : rowNames[info.i],
+            row: `${row}`
         };
 
         const schema = this.#schema[fullInfo.col];
@@ -717,6 +722,10 @@ export class SimpleTable extends LitElement {
         // Track the cell renderer
         const cell = new TableCell({
             info: {
+                title: header(
+                    fullInfo.col === tempPropertyValueKey 
+                    ? 'Property' // outerParent[tempPropertyKey] // NOTE: For new rows, this will be unresolved at instantiation
+                    : fullInfo.col),
                 col: this.colHeaders[info.j],
             },
             value,
@@ -730,7 +739,7 @@ export class SimpleTable extends LitElement {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
                 const res = this.validateOnChange
-                    ? await this.validateOnChange([info.i, fullInfo.col, ...path], parent, value, schema)
+                    ? await this.validateOnChange([row, fullInfo.col, ...path], parent, value, schema)
                     : true;
 
                 return res;
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 44a61f347..1fc2466e5 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -1,7 +1,9 @@
 const toCapitalizeAll = ['nwb', 'api', 'id']
 const toCapitalizeNone = ['or', 'and']
 
-export const tempPropertyKey = Math.random().toString(36).substring(7);
+const createRandomString = () => Math.random().toString(36).substring(7);
+export const tempPropertyKey = createRandomString();
+export const tempPropertyValueKey = createRandomString();
 
 export const capitalize = (str: string) => {
     const lowerCase = str.toLowerCase()
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 522a543ea..ccd4e3858 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -1,6 +1,6 @@
 import { LitElement, css } from "lit"
 import { ArrayCell } from "./cells/array"
-import { NestedTableCell } from "./cells/table"
+import { NestedInputCell } from "./cells/input"
 
 import { TableCellBase } from "./cells/base"
 import { DateTimeCell } from "./cells/date-time"
@@ -193,7 +193,7 @@ export class TableCell extends LitElement {
         if (this.schema.type === "array") {
             const items = this.schema.items
             if (items && items.type === "object") {
-                cls = NestedTableCell
+                cls = NestedInputCell
                 this.type = "table"
             } else {
                 cls = ArrayCell
@@ -203,6 +203,9 @@ export class TableCell extends LitElement {
         else if (this.schema.format === "date-time") {
             cls = DateTimeCell
             this.type = "date-time"
+        } else if (this.schema.type === "object") {
+            cls = NestedInputCell
+            this.type = "table"
         }
 
         // Only actually rerender if new class type
diff --git a/src/renderer/src/stories/table/cells/table.ts b/src/renderer/src/stories/table/cells/input.ts
similarity index 53%
rename from src/renderer/src/stories/table/cells/table.ts
rename to src/renderer/src/stories/table/cells/input.ts
index 080caa299..c5911bed2 100644
--- a/src/renderer/src/stories/table/cells/table.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -4,9 +4,11 @@ import { BaseRenderer } from "./renderers/base";
 import { Modal } from "../../Modal";
 
 import { SimpleTable } from "../../SimpleTable.js";
+import { JSONSchemaInput } from "../../JSONSchemaInput";
+
 import { header } from "../../forms/utils";
 
-export class NestedTableEditor extends LitElement {
+export class NestedEditor extends LitElement {
 
     info: any
     schema: any
@@ -22,30 +24,38 @@ export class NestedTableEditor extends LitElement {
     }
 
     #modal = new Modal({
-        header: 'Table Editor',
+        header: 'Editor',
         onClose: () => this.toggle(false)
     })
 
-    #table: SimpleTable
+    #input: JSONSchemaInput
 
     onEditStart () {
         const modal = this.#modal
 
-        if (this.info.col) modal.header = `${header(this.info.col)} Table Editor`
+        if (this.info.col) modal.header = `${this.schema.title ?? header(this.info.col)} Editor`
+
+        if (this.#input) this.#input.remove()
+
+        const data = this.#value || (this.schema.type === 'array' ? [] : (this.schema.type === 'object' ? {} : this.schema.default))
 
-        if (this.#table) this.#table.remove()
+        console.log('Schema',  modal.header, this.schema)
 
-        const table = this.#table = new SimpleTable({
-            schema: this.schema.items,
-            data: this.#value,
+        const input = this.#input = new JSONSchemaInput({
+            schema: this.schema,
+            value: data,
+            path: [ this.info.col ],
             validateOnChange: (path, parent, value, schema) => {
                 if (this.validateOnChange) return this.validateOnChange(value, path, parent, schema) // NOTE: Flipped because usually only value is passed
+            },
+            form: {
+                createTable: (name, metadata, path) => new SimpleTable(metadata), // If possible to render as a table, do so
             }
         })
 
-        table.style.padding = '25px 50px'
+        input.style.padding = '25px 50px'
 
-        modal.append(table)
+        modal.append(input)
 
         modal.open = true
     }
@@ -54,11 +64,11 @@ export class NestedTableEditor extends LitElement {
 
     set value(value) {
         this.#value = value
-        if (this.#table) this.#table.data = value
+        if (this.#input) this.#input.value = value
     }
 
     get value() {
-        return this.#table.data ?? this.#value
+        return this.#input.value ?? this.#value
     }
 
     onEditEnd = () => {
@@ -71,11 +81,11 @@ export class NestedTableEditor extends LitElement {
     }
 }
 
-customElements.get("nwb-nested-table-cell-editor") || customElements.define("nwb-nested-table-cell-editor", NestedTableEditor);
+customElements.get("nwb-nested-input-editor") || customElements.define("nwb-nested-input-editor", NestedEditor);
 
 
 
-export class NestedTableRenderer extends BaseRenderer {
+export class NestedRenderer extends BaseRenderer {
 
 
     static get styles() {
@@ -95,22 +105,22 @@ export class NestedTableRenderer extends BaseRenderer {
     }
 
     render() {
-        return html`<small>Click to view table</small>`
+        return html`<small>Click to view cell</small>`
     }
 }
 
-customElements.get("nwb-nested-table-cell-renderer") || customElements.define("nwb-nested-table-cell-renderer", NestedTableRenderer);
+customElements.get("nwb-nested-input-renderer") || customElements.define("nwb-nested-input-renderer", NestedRenderer);
 
 
-export class NestedTableCell extends TableCellBase {
+export class NestedInputCell extends TableCellBase {
 
     constructor(props: any){
         super(props)
     }
 
-    renderer = new NestedTableRenderer({ value: this.value })
+    renderer = new NestedRenderer({ value: this.value })
 
-    editor = new NestedTableEditor({
+    editor = new NestedEditor({
         info: this.info,
         toggle: this.editToggle,
         value: this.value,
@@ -119,4 +129,4 @@ export class NestedTableCell extends TableCellBase {
     })
 }
 
-customElements.get("nwb-nested-table-cell") || customElements.define("nwb-nested-table-cell", NestedTableCell);
+customElements.get("nwb-nested-input-cell") || customElements.define("nwb-nested-input-cell", NestedInputCell);
diff --git a/src/renderer/src/stories/table/cells/renderers/base.ts b/src/renderer/src/stories/table/cells/renderers/base.ts
index 16046a7cc..728aa4e1c 100644
--- a/src/renderer/src/stories/table/cells/renderers/base.ts
+++ b/src/renderer/src/stories/table/cells/renderers/base.ts
@@ -10,7 +10,7 @@ export class BaseRenderer extends LitElement {
         }
     }
 
-    constructor({ value }: { value: any }) {
+    constructor({ value }: { value: any } = {}) {
         super()
         this.value = value
     }
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 4b4ea0b8a..6c04174e7 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -1,7 +1,6 @@
 import schema from './validation.json'
 import { JSONSchemaForm } from '../stories/JSONSchemaForm.js'
 import Swal from 'sweetalert2'
-import { tempPropertyKey } from '../stories/forms/utils'
 
 function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
     const element = this.getTable(linkedPath)
@@ -40,7 +39,7 @@ const get = (object: any, path: string[]) => {
 
 
     return {
-        value: finalValue[name],
+        value: finalValue?.[name],
         values
     }
 }

From 6aab853e8b5911a16867aab5176037f73434350a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 4 Jan 2024 19:48:26 +0000
Subject: [PATCH 084/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js  |   4 +-
 src/renderer/src/stories/JSONSchemaInput.js | 125 +++++++++-----------
 src/renderer/src/stories/SimpleTable.js     |  17 +--
 3 files changed, 70 insertions(+), 76 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 9d0085d9b..fe6dac235 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -381,8 +381,8 @@ export class JSONSchemaForm extends LitElement {
     #clearMessages = (localPath, type) => {
         if (Array.isArray(localPath)) localPath = localPath.join("-"); // Convert array to string
 
-        if (!localPath.length) return
-        
+        if (!localPath.length) return;
+
         const container = this.shadowRoot.querySelector(`#${encode(localPath)} .${type}`);
 
         if (container) {
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e18cd7bad..44f6d560e 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -14,10 +14,9 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
-
 // Schema or value indicates editable object
-const isEditableObject = (schema, value) => schema.type === "object" || (value && typeof value === 'object' && !Array.isArray(value))
-;
+const isEditableObject = (schema, value) =>
+    schema.type === "object" || (value && typeof value === "object" && !Array.isArray(value));
 const isAdditionalProperties = (pattern) => pattern === "additional";
 const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
@@ -38,9 +37,7 @@ export const getEditableItems = (value, pattern, { name, schema } = {}) => {
             const regex = new RegExp(key);
             items = items.filter(([k]) => !regex.test(k));
         });
-    } 
-    
-    else if (schema.properties) items = items.filter(([key]) => key in schema.properties);
+    } else if (schema.properties) items = items.filter(([key]) => key in schema.properties);
 
     items = items.filter(([key]) => !key.includes("__")); // Remove secret properties
 
@@ -239,7 +236,11 @@ export class JSONSchemaInput extends LitElement {
 
     #validationTimeout = null;
     #updateData = (fullPath, value, forceUpdate, hooks = {}) => {
-        this.onUpdate ? this.onUpdate(value) : this.form?.updateData ? this.form.updateData(fullPath, value, forceUpdate) : "";
+        this.onUpdate
+            ? this.onUpdate(value)
+            : this.form?.updateData
+              ? this.form.updateData(fullPath, value, forceUpdate)
+              : "";
 
         const path = [...fullPath];
         const name = path.splice(-1)[0];
@@ -251,7 +252,11 @@ export class JSONSchemaInput extends LitElement {
 
     #triggerValidation = async (name, path) => {
         this.#clearTimeoutValidation();
-        return this.onValidate ? this.onValidate() : this.form?.triggerValidation ? this.form.triggerValidation(name, path, this) : "";
+        return this.onValidate
+            ? this.onValidate()
+            : this.form?.triggerValidation
+              ? this.form.triggerValidation(name, path, this)
+              : "";
     };
 
     updated() {
@@ -592,7 +597,7 @@ export class JSONSchemaInput extends LitElement {
                     deferLoading: this.form?.deferLoading,
                     onLoaded: () => {
                         if (this.form) {
-                            if (this.form.nLoaded)this.form.nLoaded++;
+                            if (this.form.nLoaded) this.form.nLoaded++;
                             if (this.form.checkAllLoaded) this.form.checkAllLoaded();
                         }
                     },
@@ -602,7 +607,6 @@ export class JSONSchemaInput extends LitElement {
                 const addPropertyKeyToSchema = (schema) => {
                     const schemaCopy = structuredClone(schema);
 
-
                     if (!schemaCopy.properties) schemaCopy.properties = {};
                     if (!schemaCopy.required) schemaCopy.required = [];
 
@@ -611,45 +615,40 @@ export class JSONSchemaInput extends LitElement {
 
                     schemaCopy.required.push(tempPropertyKey);
 
-                    if (!schema['items']) {
-                        
-                        const resolvedItemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
-                        if (!resolvedItemSchema) return schemaCopy
+                    if (!schema["items"]) {
+                        const resolvedItemSchema = this.form?.getSchema
+                            ? this.form.getSchema("items", schema)
+                            : schema["items"];
+                        if (!resolvedItemSchema) return schemaCopy;
 
-                        delete schemaCopy.patternProperties
+                        delete schemaCopy.patternProperties;
 
                         schemaCopy.properties[tempPropertyValueKey] = {
-                            type: 'array',
+                            type: "array",
                             items: resolvedItemSchema.properties ? addPropertyKeyToSchema(itemSchema) : itemSchema,
                             title: "Property Value",
-                            __generated: true
+                            __generated: true,
                         };
 
                         schemaCopy.required.push(tempPropertyValueKey);
                     }
 
-                    if (schemaCopy.__generated) return schemaCopy['items'] // Only return the relevant items for tables in nested tables
-                
-
-                    return schemaCopy
-
-                }
-
-
-                const createNestedTable = (id, value, { 
-                    name: propName = id, 
-                    schema = itemSchema
-                } = {}) => {
+                    if (schemaCopy.__generated) return schemaCopy["items"]; // Only return the relevant items for tables in nested tables
 
+                    return schemaCopy;
+                };
 
-                    const schemaCopy = addPropertyKeyToSchema(schema)
+                const createNestedTable = (id, value, { name: propName = id, schema = itemSchema } = {}) => {
+                    const schemaCopy = addPropertyKeyToSchema(schema);
 
                     const resultPath = [...path];
 
                     const schemaPath = [...resolvedFullPath];
 
                     const rowData = Object.entries(value).map(([key, value]) => {
-                        return !schema['items'] ? {[tempPropertyKey]: key, [tempPropertyValueKey]: value } : { [tempPropertyKey]: key, ...value };
+                        return !schema["items"]
+                            ? { [tempPropertyKey]: key, [tempPropertyValueKey]: value }
+                            : { [tempPropertyKey]: key, ...value };
                     });
 
                     if (propName) {
@@ -657,7 +656,6 @@ export class JSONSchemaInput extends LitElement {
                         schemaPath.push(propName);
                     }
 
-
                     const allRemovedKeys = new Set();
 
                     const keyAlreadyExists = (key) => Object.keys(value).includes(key);
@@ -665,38 +663,40 @@ export class JSONSchemaInput extends LitElement {
                     const previousValidValues = {};
 
                     function resolvePath(path, target) {
-                        return path.map((key, i) => {
-                            const ogKey = key
-                            const nextKey = path[i + 1]
-                            if (key === tempPropertyKey) key = target[tempPropertyKey]
-                            if (nextKey === tempPropertyKey) key = []
+                        return path
+                            .map((key, i) => {
+                                const ogKey = key;
+                                const nextKey = path[i + 1];
+                                if (key === tempPropertyKey) key = target[tempPropertyKey];
+                                if (nextKey === tempPropertyKey) key = [];
 
-                            target = target[ogKey] ?? {}
+                                target = target[ogKey] ?? {};
 
-                            if (nextKey === tempPropertyValueKey) return target[tempPropertyKey] // Grab next property key
-                            if (key === tempPropertyValueKey) return []
+                                if (nextKey === tempPropertyValueKey) return target[tempPropertyKey]; // Grab next property key
+                                if (key === tempPropertyValueKey) return [];
 
-                            return key
-                        }).flat()
+                                return key;
+                            })
+                            .flat();
                     }
 
                     function setValueOnAccumulator(row, acc) {
                         const key = row[tempPropertyKey];
 
-                        if (!key) return acc
+                        if (!key) return acc;
 
                         if (tempPropertyValueKey in row) {
                             const propValue = row[tempPropertyValueKey];
-                            if (Array.isArray(propValue)) acc[key] = propValue.reduce((acc, row) =>  setValueOnAccumulator(row, acc), {})
+                            if (Array.isArray(propValue))
+                                acc[key] = propValue.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
                             else acc[key] = propValue;
-                        }
-                        else {
+                        } else {
                             const copy = { ...row };
                             delete copy[tempPropertyKey];
                             acc[key] = copy;
                         }
 
-                        return acc
+                        return acc;
                     }
 
                     const tableMetadata = {
@@ -710,7 +710,7 @@ export class JSONSchemaInput extends LitElement {
 
                             if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return; // Do not overwrite existing keys
 
-                            const result = this.data.reduce((acc, row) =>  setValueOnAccumulator(row, acc), {});
+                            const result = this.data.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
 
                             const newKeys = Object.keys(result);
                             const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
@@ -718,19 +718,17 @@ export class JSONSchemaInput extends LitElement {
                             newKeys.forEach((key) => allRemovedKeys.delete(key));
                             allRemovedKeys.forEach((key) => (result[key] = undefined));
 
-
                             // const resolvedPath = resolvePath(path, this.data)
                             return commonUpdateFunction.call(this, [], result); // Update all table data
                         },
 
                         validateOnChange: function (path, parent, newValue) {
+                            const rowIdx = path[0];
+                            const currentKey = this.data[rowIdx]?.[tempPropertyKey];
 
-                            const rowIdx = path[0]
-                            const currentKey = this.data[rowIdx]?.[tempPropertyKey]
-
-                            const updatedPath = resolvePath(path, this.data)
+                            const updatedPath = resolvePath(path, this.data);
 
-                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey
+                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey;
 
                             // Do not overwrite existing keys
                             if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
@@ -746,22 +744,17 @@ export class JSONSchemaInput extends LitElement {
                                 } else delete previousValidValues[rowIdx];
                             }
 
-                            return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1)
+                            return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1);
                         },
                         ...commonTableMetadata,
                     };
- 
 
                     const table = this.form.createTable(id, tableMetadata, resolvedFullPath); // Try creating table. Otherwise use nested form
-                    return table
+                    return table;
                 };
 
-
-
                 // Possibly multiple tables
                 if (isEditableObject(schema, this.value)) {
-
-                    
                     // One table with nested tables for each property
                     const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
                         (acc, { key, value }) => {
@@ -771,8 +764,8 @@ export class JSONSchemaInput extends LitElement {
                         {}
                     );
 
-                    const table = createNestedTable(name, data, { schema })
-                    return table
+                    const table = createNestedTable(name, data, { schema });
+                    return table;
                 }
 
                 // Normal table parsing
@@ -795,9 +788,9 @@ export class JSONSchemaInput extends LitElement {
 
                 if (table) {
                     const tableEl = table === true ? new BasicTable(tableMetadata) : table;
-                    const tables = this.form?.tables
-                    if (tables) tables[name]  = tableEl
-                    return tableEl
+                    const tables = this.form?.tables;
+                    if (tables) tables[name] = tableEl;
+                    return tableEl;
                 }
             }
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index c36de61cc..f657f0e89 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -186,7 +186,7 @@ export class SimpleTable extends LitElement {
     } = {}) {
         super();
         this.schema = schema ?? {};
-        this.#keyColumn = keyColumn
+        this.#keyColumn = keyColumn;
         this.data = data ?? [];
 
         this.globals = globals ?? {};
@@ -282,11 +282,11 @@ export class SimpleTable extends LitElement {
         });
     }
 
-    #keyColumn
+    #keyColumn;
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data)) return this.#data //.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data)) return this.#data; //.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
@@ -709,12 +709,12 @@ export class SimpleTable extends LitElement {
     #createCell = (value, info) => {
         const rowNames = Object.keys(this.#data);
 
-        const row = Array.isArray(this.#data) ? info.i : rowNames[info.i]
+        const row = Array.isArray(this.#data) ? info.i : rowNames[info.i];
 
         const fullInfo = {
             ...info,
             col: this.colHeaders[info.j],
-            row: `${row}`
+            row: `${row}`,
         };
 
         const schema = this.#schema[fullInfo.col];
@@ -723,9 +723,10 @@ export class SimpleTable extends LitElement {
         const cell = new TableCell({
             info: {
                 title: header(
-                    fullInfo.col === tempPropertyValueKey 
-                    ? 'Property' // outerParent[tempPropertyKey] // NOTE: For new rows, this will be unresolved at instantiation
-                    : fullInfo.col),
+                    fullInfo.col === tempPropertyValueKey
+                        ? "Property" // outerParent[tempPropertyKey] // NOTE: For new rows, this will be unresolved at instantiation
+                        : fullInfo.col
+                ),
                 col: this.colHeaders[info.j],
             },
             value,

From 6a7b50b8fb48a4b1d3c58538dae471571385f792 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Mon, 8 Jan 2024 11:39:19 -0800
Subject: [PATCH 085/133] Pass schema appropriately from all tables

---
 src/renderer/src/stories/BasicTable.js | 2 +-
 src/renderer/src/stories/Table.js      | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 559e45b79..6342b3ac1 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -229,7 +229,7 @@ export class BasicTable extends LitElement {
         else if (value !== "" && thisTypeOf !== type)
             result = [{ message: `${col} is expected to be of type ${ogType}, not ${thisTypeOf}`, type: "error" }];
         // Otherwise validate using the specified onChange function
-        else result = this.validateOnChange([col], parent, value);
+        else result = this.validateOnChange([col], parent, value, this.schema.properties[col]);
 
         // Will run synchronously if not a promise result
         return promises.resolve(result, () => {
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 921e21fe9..cfa1d3e3c 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -284,7 +284,8 @@ export class Table extends LitElement {
                         ? await this.validateOnChange(
                               [k],
                               { ...this.data[rowHeaders[row]] }, // Validate on a copy of the parent
-                              value
+                              value,
+                              info.properties[k]
                           )
                         : true; // Return true if validation errored out on the JavaScript side (e.g. server is down)
 

From 1ba664766c6e50d046848dd023ee4e838ae34542 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 9 Jan 2024 10:01:41 -0800
Subject: [PATCH 086/133] Fix validation

---
 src/renderer/src/stories/JSONSchemaForm.js    |  54 ++--
 src/renderer/src/stories/JSONSchemaInput.js   |   4 +-
 .../guided-mode/data/GuidedPathExpansion.js   |   6 +-
 .../pages/guided-mode/options/GuidedUpload.js |   2 +-
 .../src/stories/pages/uploads/UploadsPage.js  |   6 +-
 src/renderer/src/stories/table/cells/input.ts |   2 -
 src/renderer/src/stories/table/convert.ts     |   3 -
 src/renderer/src/validation/validation.ts     | 260 ++++++++++--------
 tests/metadata.test.ts                        |  13 +-
 9 files changed, 179 insertions(+), 171 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index fe6dac235..f6cce3b89 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -291,37 +291,36 @@ export class JSONSchemaForm extends LitElement {
         if (props.base) this.base = props.base;
     }
 
-    getTable = (path) => {
+
+    // Get the form element defined by the path (stops before table cells)
+    getFormElement = (path, { forms = true, tables = true, inputs = true } = {}) => {
         if (typeof path === "string") path = path.split(".");
+        if (!path.length) return this
 
-        if (path.length === 1) return this.tables[path[0]]; // return table if accessible
+        const name = path[0];
+        const updatedPath = path.slice(1)
 
-        const copy = [...path];
-        const tableName = copy.pop();
 
-        return this.getForm(copy).getTable(tableName);
-    };
+        const form = this.#nestedForms[name] // Check forms
+        if (!form) {
+            const table = this.tables[name] // Check tables
+            if (table && tables) return table // Skip table cells
+        } 
+        
+        else if (!updatedPath.length && forms) return form
 
-    getForm = (path) => {
-        if (typeof path === "string") path = path.split(".");
-        const form = this.#nestedForms[path[0]];
-        if (!path.length) return this; // No nested form with this name. Returning self
-        if (!form) throw new Error(`Could not find form with name ${path[0]}`);
+        // Check Inputs
+        // const inputContainer = this.shadowRoot.querySelector(`#${encode(path.join("-"))}`);
+        // if (inputContainer && inputs) return inputContainer.querySelector("jsonschema-input");;
 
-        return form.getForm(path.slice(1));
-    };
+        const foundInput = this.inputs[path.join(".")] // Check Inputs
+        if (foundInput && inputs) return foundInput;
 
-    getInput = (path) => {
-        if (typeof path === "string") path = path.split(".");
 
-        const container = this.shadowRoot.querySelector(`#${encode(path.join("-"))}`);
+        // Check Nested Form Inputs
+        return form?.getFormElement(updatedPath, { forms, tables, inputs });
 
-        if (!container) {
-            if (path.length > 1) return this.getForm(path[0]).getInput(path.slice(1));
-            else return;
-        }
-        return container?.querySelector("jsonschema-input");
-    };
+    }
 
     #requirements = {};
 
@@ -354,7 +353,7 @@ export class JSONSchemaForm extends LitElement {
             // Continue to resolve and re-render...
             if (globalValue) {
                 value = resolvedParent[name] = globalValue;
-                const input = this.getInput(localPath);
+                const input = this.getFormElement(localPath);
                 if (input) {
                     input.updateData(globalValue);
                     this.onOverride(name, globalValue, path);
@@ -447,6 +446,7 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
+
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -641,8 +641,7 @@ export class JSONSchemaForm extends LitElement {
             pattern: propertyType === "pattern" ? name : propertyType ?? undefined,
         });
 
-        this.inputs.push(interactiveInput);
-
+        this.inputs[localPath.join("-")] = interactiveInput;
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
 
         // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("jsonschema-input")).map(input => input.children)
@@ -867,7 +866,7 @@ export class JSONSchemaForm extends LitElement {
         const undefinedPathToken = localPath.findIndex((str) => !str && typeof str !== "number") !== -1;
         if (undefinedPathToken) return true; // Will be unable to get schema anyways (additionalProperties)
 
-        if (!input) input = this.getInput(localPath);
+        if (!input) input = this.getFormElement(localPath, { forms: false, tables: false });
         if (!parent) parent = this.#get(path, this.resolved);
         if (!schema) schema = this.getSchema(localPath);
 
@@ -998,6 +997,7 @@ export class JSONSchemaForm extends LitElement {
 
             return true;
         } else {
+
             // Add new invalid classes and errors
             input.classList.add("invalid");
 
@@ -1391,7 +1391,7 @@ export class JSONSchemaForm extends LitElement {
     #resetLoadState() {
         this.#loaded = false;
         this.nLoaded = 0;
-        this.inputs = [];
+        this.inputs = {};
     }
 
     // Check if everything is internally rendered
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 44f6d560e..7a7b70fca 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -436,7 +436,7 @@ export class JSONSchemaInput extends LitElement {
     #getType = (value = this.value) => (Array.isArray(value) ? "array" : typeof value);
 
     #handleNextInput = (idx) => {
-        const next = this.form.inputs[idx];
+        const next = Object.values(this.form.inputs)[idx];
         if (next) {
             const el = getFirstFocusableElement(next);
             if (el) {
@@ -452,7 +452,7 @@ export class JSONSchemaInput extends LitElement {
         if (ev.key === "Enter") {
             ev.preventDefault();
             if (this.form?.inputs) {
-                const idx = this.form.inputs.findIndex((input) => input === this);
+                const idx = Object.values(this.form.inputs).findIndex((input) => input === this);
                 this.#handleNextInput(idx + 1);
             }
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 901aca414..fdf1dfbb8 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -290,8 +290,8 @@ export class GuidedPathExpansionPage extends Page {
                 const name = parentPath.pop();
 
                 if (name === "base_directory") {
-                    form.getInput([...parentPath, "base_directory"]).value = value; // Update value pre-emptively
-                    const input = form.getInput([...parentPath, "format_string_path"]);
+                    form.getFormElement([...parentPath, "base_directory"]).value = value; // Update value pre-emptively
+                    const input = form.getFormElement([...parentPath, "format_string_path"]);
                     if (input.value) input.updateData(input.value, true);
                 }
             },
@@ -299,7 +299,7 @@ export class GuidedPathExpansionPage extends Page {
                 const value = parent[name];
 
                 if (fs) {
-                    const baseDir = form.getInput([...parentPath, "base_directory"]);
+                    const baseDir = form.getFormElement([...parentPath, "base_directory"]);
                     if (name === "format_string_path") {
                         if (value && baseDir && !baseDir.value) {
                             return [
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 4b6aeecac..f2205cabe 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -69,7 +69,7 @@ export class GuidedUploadPage extends Page {
                 merge(apiKeys, global.data.DANDI.api_keys);
                 global.save();
                 await regenerateDandisets();
-                const input = this.form.getInput(["dandiset "]);
+                const input = this.form.getFormElement(["dandiset "]);
                 input.requestUpdate();
             },
             formProps: {
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 1d6dbc857..dda722fab 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -129,7 +129,7 @@ export async function createDandiset(results = {}) {
 
                 await addDandiset(res);
 
-                const input = this.form.getInput(["dandiset"]);
+                const input = this.form.getFormElement(["dandiset"]);
                 input.updateData(id);
                 input.requestUpdate();
 
@@ -303,7 +303,7 @@ export class UploadsPage extends Page {
                 merge(apiKeys, global.data.DANDI.api_keys);
                 global.save();
                 await regenerateDandisets();
-                const input = this.form.getInput(["dandiset "]);
+                const input = this.form.getFormElement(["dandiset "]);
                 input.requestUpdate();
             },
             formProps: {
@@ -382,7 +382,7 @@ export class UploadsPage extends Page {
                         if (id === folderPathKey) {
                             const keysToUpdate = ["dandiset"];
                             keysToUpdate.forEach((k) => {
-                                const input = this.form.getInput([k]);
+                                const input = this.form.getFormElement([k]);
                                 if (input.value) input.updateData("");
                             });
                         }
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index c5911bed2..9aa36078f 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -39,8 +39,6 @@ export class NestedEditor extends LitElement {
 
         const data = this.#value || (this.schema.type === 'array' ? [] : (this.schema.type === 'object' ? {} : this.schema.default))
 
-        console.log('Schema',  modal.header, this.schema)
-
         const input = this.#input = new JSONSchemaInput({
             schema: this.schema,
             value: data,
diff --git a/src/renderer/src/stories/table/convert.ts b/src/renderer/src/stories/table/convert.ts
index 071a6e781..62b437483 100644
--- a/src/renderer/src/stories/table/convert.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -19,9 +19,6 @@ export const getValue = (value: any, schema: any) => {
             if (!isNaN(possibleValue)) return possibleValue
         }
 
-        console.log('Returning', value)
-
-
     }
 
     return value
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 6c04174e7..71b8fc134 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -3,7 +3,7 @@ import { JSONSchemaForm } from '../stories/JSONSchemaForm.js'
 import Swal from 'sweetalert2'
 
 function rerenderTable (this: JSONSchemaForm, linkedPath: string[]) {
-    const element = this.getTable(linkedPath)
+    const element = this.getFormElement(linkedPath)
     if (element) element.requestUpdate() // Re-render table to show updates
     // if (element) setTimeout(() => {
     //     element.requestUpdate()
@@ -44,77 +44,86 @@ const get = (object: any, path: string[]) => {
     }
 }
 
-// Specify JavaScript-side validation
-schema.Ecephys.ElectrodeGroup.device = function (this: JSONSchemaForm, name, parent, path) {
-    const devices = this.results.Ecephys.Device.map(o => o.name)
-    if (devices.includes(parent[name])) return true
-    else {
-        return [
-            {
-                message: 'Not a valid device',
-                type: 'error'
-            }
-        ]
-    }
-}
-
-
 // NOTE: Does this maintain separation between multiple sessions?
-schema.Ecephys.ElectrodeGroup.name = function(this: JSONSchemaForm, _, __, ___, value) {
-    const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
-
-     // Check if the latest value will be new. Run function after validation
-    if (!value || !groups.includes(value)) {
-        return () => {
-             setTimeout(() => rerenderTable.call(this, ['Ecephys', 'Electrodes'])) // Allow for the updates to occur
+schema.Ecephys.ElectrodeGroup = {
+    ["*"]: {
+        name: function (this: JSONSchemaForm, _, __, ___, value) {
+            const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
+        
+                // Check if the latest value will be new. Run function after validation
+            if (!value || !groups.includes(value)) {
+                return () => {
+                        setTimeout(() => rerenderTable.call(this, ['Ecephys', 'Electrodes'])) // Allow for the updates to occur
+                }
+            }
+        },
+        
+        device: function (this: JSONSchemaForm, name, parent, path) {
+            const devices = this.results.Ecephys.Device.map(o => o.name)
+            if (devices.includes(parent[name])) return true
+            else {
+                return [
+                    {
+                        message: 'Not a valid device',
+                        type: 'error'
+                    }
+                ]
+            }
         }
     }
 }
 
-schema.Ecephys.Electrodes.group_name = function (this: JSONSchemaForm, _, __, ___, value) {
+schema.Ecephys.Electrodes = {
+    ["*"]:{
 
-    const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
-    if (groups.includes(value)) return true
-    else {
-        return [
-            {
-                message: 'Not a valid group name',
-                type: 'error'
+        // Label columns as invalid if not registered on the ElectrodeColumns table
+        // NOTE: If not present in the schema, these are not being rendered...
+        ['*']: function (this: JSONSchemaForm, name, parent, path) {
+            if (!this.results.Ecephys.ElectrodeColumns.find((o: any) => o.name === name)) return [
+                {
+                    message: 'Not a valid column',
+                    type: 'error'
+                }
+            ]
+        },
+
+        group_name: function (this: JSONSchemaForm, _, __, ___, value) {
+
+            const groups = this.results.Ecephys.ElectrodeGroup.map(o => o.name)
+            if (groups.includes(value)) return true
+            else {
+                return [
+                    {
+                        message: 'Not a valid group name',
+                        type: 'error'
+                    }
+                ]
             }
-        ]
+        }
     }
 }
 
 
 // Update the columns available on the Electrodes table when there is a new name in the ElectrodeColumns table
 schema.Ecephys.ElectrodeColumns = {
-    '*': function (this: JSONSchemaForm, prop, parent, path) {
-
-        const name = parent['name']
-        if (!name) return true // Allow blank rows
-
-        if (prop === 'name' && !(name in this.schema.properties.Ecephys.properties.Electrodes.items.properties)) {
-            const element = rerenderTable.call(this, ['Ecephys', 'Electrodes'])
-            element.schema.properties[name] = {} // Ensure property is present in the schema now
-            element.data.forEach(o => name in o ? undefined : o[name] = '') // Set column value as blank if not existent on row
+    ['*']: {
+        ['*']: function (this: JSONSchemaForm, prop, parent, path) {
+
+            const name = parent['name']
+            if (!name) return true // Allow blank rows
+    
+            if (prop === 'name' && !(name in this.schema.properties.Ecephys.properties.Electrodes.items.properties)) {
+                const element = rerenderTable.call(this, ['Ecephys', 'Electrodes'])
+                element.schema.properties[name] = {} // Ensure property is present in the schema now
+                element.data.forEach(o => name in o ? undefined : o[name] = '') // Set column value as blank if not existent on row
+            }
+    
+            this.schema.properties.Ecephys.properties.Electrodes.items.properties[name][prop] = parent[prop] // Update the actual schema for this (e.g. to update visible descriptions)
+            return true
         }
-
-        this.schema.properties.Ecephys.properties.Electrodes.items.properties[name][prop] = parent[prop] // Update the actual schema for this (e.g. to update visible descriptions)
-        return true
     }
 }
 
-// Label columns as invalid if not registered on the ElectrodeColumns table
-// NOTE: If not present in the schema, these are not being rendered...
-schema.Ecephys.Electrodes["*"] = function (this: JSONSchemaForm, name, parent, path) {
-    if (!this.results.Ecephys.ElectrodeColumns.find((o: any) => o.name === name)) return [
-        {
-            message: 'Not a valid column',
-            type: 'error'
-        }
-    ]
-}
-
 function ensureUnique(this: JSONSchemaForm, name, parent, path, value) {
     const {
         values,
@@ -132,7 +141,7 @@ function ensureUnique(this: JSONSchemaForm, name, parent, path, value) {
 }
 
 schema.Ophys = {
-    '*': {
+    ['*']: {
         '**': {
             ['name']: ensureUnique,
         }
@@ -141,78 +150,85 @@ schema.Ophys = {
 
 // Ophys
 schema.Ophys.Device = {
-    ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
-
-        const {
-            values,
-            value: row
-        } = get(this.results, path)
-
-        if (!row) return true // Allow blank rows
-
-        const rows = values.slice(-1)[0]
-        const idx = path.slice(-1)[0]
-        const isUniqueError = isNotUnique(name, value, rows, idx)
-        if (isUniqueError) return isUniqueError
-
-        const prevValue = row[name]
-
-        if (prevValue === value || prevValue === undefined) return true // No change
-
-        const prevUniqueError = isNotUnique(name, prevValue, rows, idx)
-        if (prevUniqueError) return true // Register as valid
-
-        const result = await Swal.fire({
-            title: `Are you sure you want to rename the ${prevValue} device?`,
-            icon: "warning",
-            text: `We will attempt to auto-update your Ophys devices to reflect this.`,
-            heightAuto: false,
-            backdrop: "rgba(0,0,0, 0.4)",
-            confirmButtonText: "I understand",
-            showConfirmButton: true,
-            showCancelButton: true,
-            cancelButtonText: "Cancel"
-        })
-
-        if (!result.isConfirmed) return null
-
-        // Update Dependent Tables
-        const dependencies = [
-            ['Ophys', 'ImagingPlane'],
-            ['Ophys', 'OnePhotonSeries'],
-            ['Ophys', 'TwoPhotonSeries']
-        ]
-
-        dependencies.forEach(path => {
-            const table = this.getTable(path)
-            if (table) {
-                const data = table.data
-                data.forEach(row => {
-                    if (row.device === prevValue) row.device = value
-                })
-                table.data = data
-            }
-
-            rerenderTable.call(this, path)
-        })
+    ["*"]: {
+
+        ['name']: async function (this: JSONSchemaForm, name, parent, path, value) {
+
+            const {
+                values,
+                value: row
+            } = get(this.results, path)
+    
+            console.log('row', values, row)
+    
+            if (!row) return true // Allow blank rows
+    
+            const rows = values.slice(-1)[0]
+            const idx = path.slice(-1)[0]
+            const isUniqueError = isNotUnique(name, value, rows, idx)
+            if (isUniqueError) return isUniqueError
+    
+            const prevValue = row[name]
+    
+            if (prevValue === value || prevValue === undefined) return true // No change
+    
+            const prevUniqueError = isNotUnique(name, prevValue, rows, idx)
+            if (prevUniqueError) return true // Register as valid
+    
+            const result = await Swal.fire({
+                title: `Are you sure you want to rename the ${prevValue} device?`,
+                icon: "warning",
+                text: `We will attempt to auto-update your Ophys devices to reflect this.`,
+                heightAuto: false,
+                backdrop: "rgba(0,0,0, 0.4)",
+                confirmButtonText: "I understand",
+                showConfirmButton: true,
+                showCancelButton: true,
+                cancelButtonText: "Cancel"
+            })
+    
+            if (!result.isConfirmed) return null
+    
+            // Update Dependent Tables
+            const dependencies = [
+                ['Ophys', 'ImagingPlane'],
+                ['Ophys', 'OnePhotonSeries'],
+                ['Ophys', 'TwoPhotonSeries']
+            ]
+    
+            dependencies.forEach(path => {
+                const table = this.getFormElement(path)
+                if (table) {
+                    const data = table.data
+                    data.forEach(row => {
+                        if (row.device === prevValue) row.device = value
+                    })
+                    table.data = data
+                }
+    
+                rerenderTable.call(this, path)
+            })
+    
+            return true
+        }
 
-        return true
     }
 }
 
 schema.Ophys.ImagingPlane = {
-    device: function (this: JSONSchemaForm, name, parent, path, value) {
-        const devices = this.results.Ophys.Device.map(o => o.name)
-        if (devices.includes(parent[name])) return true
-        else {
-            return [
-                {
-                    message: 'Not a valid device',
-                    type: 'error'
-                }
-            ]
+    ["*"]: {
+        device: function (this: JSONSchemaForm, name, parent, path, value) {
+            const devices = this.results.Ophys.Device.map(o => o.name)
+            if (devices.includes(parent[name])) return true
+            else {
+                return [
+                    {
+                        message: 'Not a valid device',
+                        type: 'error'
+                    }
+                ]
+            }
         }
-
     }
 }
 
diff --git a/tests/metadata.test.ts b/tests/metadata.test.ts
index a3347efc2..d1fdd2ec5 100644
--- a/tests/metadata.test.ts
+++ b/tests/metadata.test.ts
@@ -121,7 +121,7 @@ test('inter-table updates are triggered', async () => {
     expect(errors).toBe(true) // Is invalid
 
     // Update the table with the missing electrode group
-    const table = form.getTable(['Ecephys', 'ElectrodeGroup']) // This is a SimpleTable where rows can be added
+    const table = form.getFormElement(['Ecephys', 'ElectrodeGroup']) // This is a SimpleTable where rows can be added
     const row = table.addRow()
 
     const baseRow = table.getRow(0)
@@ -134,10 +134,7 @@ test('inter-table updates are triggered', async () => {
     await new Promise((res) => setTimeout(() => res(true), 1000))
 
     // Validate that the new structure is correct
-    const hasErrors = await form.validate().then(() => false).catch((e) => {
-        console.log('Final', form.results.Ecephys.Electrodes, form.results.Ecephys.ElectrodeGroup)
-        return true
-    })
+    const hasErrors = await form.validate().then(() => false).catch((e) => true)
     expect(hasErrors).toBe(false) // Is valid
 })
 
@@ -193,9 +190,9 @@ test('changes are resolved correctly', async () => {
     await form.validate().catch(e => errors = true)
     expect(errors).toBe(true) // Is invalid
 
-    const input1 = form.getInput(['v0'])
-    const input2 = form.getInput(['l1', 'v1'])
-    const input3 = form.getInput(['l1', 'l2', 'l3', 'v2'])
+    const input1 = form.getFormElement(['v0'])
+    const input2 = form.getFormElement(['l1', 'v1'])
+    const input3 = form.getFormElement(['l1', 'l2', 'l3', 'v2'])
 
     input1.updateData('test')
     input2.updateData('test')

From 95f71ea374b80e4d0d1231f99fc9337e8267dba9 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 11 Jan 2024 12:51:02 -0800
Subject: [PATCH 087/133] Fix plane metadata

---
 src/renderer/src/stories/JSONSchemaForm.js    |  92 +--
 src/renderer/src/stories/JSONSchemaInput.js   | 627 ++++++++++--------
 .../pages/guided-mode/data/GuidedMetadata.js  |  68 +-
 src/renderer/src/stories/table/cells/input.ts |   4 +-
 src/renderer/src/validation/validation.ts     |   4 +-
 tests/metadata.test.ts                        |   2 +-
 6 files changed, 450 insertions(+), 347 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f6cce3b89..7154830dd 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -72,32 +72,8 @@ const componentCSS = `
       line-height: 1.4285em;
     }
 
-    .guided--form-label {
-      display: block;
-      width: 100%;
-      margin: 1.45rem 0 0 0;
-      color: black;
-      font-weight: 600;
-    }
-
-    .form-section:first-child .guided--form-label {
-      margin-top: 0;
-    }
-
-    jsonschema-input {
-        margin-top: 0.5rem;
-    }
-
-    .guided--form-label {
-      font-size: 1.2em !important;
-    }
-
-    .guided--form-label.centered {
-      text-align: center;
-    }
-
-    .guided--form-label.header {
-      font-size: 1.5em !important;
+    *:first-child jsonschema-input {
+      margin: 0;
     }
 
     .link {
@@ -158,28 +134,12 @@ const componentCSS = `
         color: DimGray;
     }
 
-  .required label:after {
-    content: "*";
-    color: #ff0033;
-
-  }
-
-  :host(:not([validateemptyvalues])) .required label:after {
-    color: gray;
-
-  }
-
-
-  .required.conditional label:after {
-    color: transparent;
-  }
-
-  h4 {
-    margin: 0;
-    margin-bottom: 5px;
-    padding-bottom: 5px;
-    border-bottom: 1px solid gainsboro;
-  }
+    h4 {
+        margin: 0;
+        margin-bottom: 5px;
+        padding-bottom: 5px;
+        border-bottom: 1px solid gainsboro;
+    }
 
     .guided--text-input-instructions {
         font-size: 13px;
@@ -261,8 +221,6 @@ export class JSONSchemaForm extends LitElement {
         this.dialogType = props.dialogType;
         this.deferLoading = props.deferLoading ?? false;
 
-        this.showPath = props.showPath ?? false;
-
         this.controls = props.controls ?? {};
 
         this.transformErrors = props.transformErrors;
@@ -283,7 +241,8 @@ export class JSONSchemaForm extends LitElement {
         if (props.onThrow) this.onThrow = props.onThrow;
         if (props.onLoaded) this.onLoaded = props.onLoaded;
         if (props.onUpdate) this.onUpdate = props.onUpdate;
-        if (props.createTable) this.createTable = props.createTable;
+        if (props.renderTable) this.renderTable = props.renderTable;
+        if (props.renderCustomHTML) this.renderCustomHTML = props.renderCustomHTML;
         if (props.onOverride) this.onOverride = props.onOverride;
 
         if (props.onStatusChange) this.onStatusChange = props.onStatusChange;
@@ -637,8 +596,12 @@ export class JSONSchemaForm extends LitElement {
             form: this,
             controls: this.controls[name],
             required: isRequired,
+            conditional: isConditional,
             validateEmptyValue: this.validateEmptyValues,
             pattern: propertyType === "pattern" ? name : propertyType ?? undefined,
+            renderTable: this.renderTable,
+            renderCustomHTML: this.renderCustomHTML,
+            showLabel: true
         });
 
         this.inputs[localPath.join("-")] = interactiveInput;
@@ -656,21 +619,8 @@ export class JSONSchemaForm extends LitElement {
         return html`
             <div
                 id=${encode(localPath.join("-"))}
-                class="form-section ${isRequired || isConditional ? "required" : ""} ${isConditional
-                    ? "conditional"
-                    : ""}"
+                class="form-section"
             >
-                <label class="guided--form-label"
-                    >${(info.title ? unsafeHTML(info.title) : null) ?? header(name)}
-                </label>
-                ${this.showPath
-                    ? html` <small
-                          >${externalPath
-                              .slice(0, -1)
-                              .map((str) => header(str ?? ""))
-                              .join(".")}</small
-                      >`
-                    : ""}
                 ${interactiveInput}
                 <div class="errors"></div>
                 <div class="warnings"></div>
@@ -781,7 +731,8 @@ export class JSONSchemaForm extends LitElement {
     validateOnChange = () => {};
     onStatusChange = () => {};
     onThrow = () => {};
-    createTable = () => {};
+    renderTable = () => {};
+    renderCustomHTML = () => {};
 
     #getLink = (args) => {
         if (typeof args === "string") args = args.split("-");
@@ -1030,7 +981,6 @@ export class JSONSchemaForm extends LitElement {
         const hasProperties = renderable.length > 0 || hasPatternProperties || allowAdditionalProperties;
 
         if (!hasProperties) return html`<div id="empty">${this.emptyMessage}</div>`;
-
         let renderableWithLinks = renderable.reduce((acc, [name, info]) => {
             const externalPath = [...this.base, ...path, name];
             const link = this.#getGroup(externalPath); // Use the base path to find a link
@@ -1193,7 +1143,6 @@ export class JSONSchemaForm extends LitElement {
 
                     required: required[name], // Scoped to the sub-schema
                     ignore,
-                    showPath: this.showPath,
                     dialogOptions: this.dialogOptions,
                     dialogType: this.dialogType,
                     onlyRequired: this.onlyRequired,
@@ -1212,8 +1161,11 @@ export class JSONSchemaForm extends LitElement {
                         this.nLoaded++;
                         this.checkAllLoaded();
                     },
-                    createTable: function (...args) {
-                        return ogContext.createTable.call(this, ...args);
+                    renderCustomHTML: function (...args) {
+                        return ogContext.renderCustomHTML.call(this, ...args);
+                    },
+                    renderTable: function (...args) {
+                        return ogContext.renderTable.call(this, ...args);
                     },
                     onOverride: (...args) => this.onOverride(...args),
                     base,
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 7a7b70fca..0dc212a02 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,3 +1,4 @@
+
 import { LitElement, css, html } from "lit";
 import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
@@ -14,11 +15,286 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
+
+
+export function createTable(fullPath, {
+    onUpdate,
+    onThrow,
+    forceItems = false
+}){
+
+    const path = [...fullPath];
+    const name = path.splice(-1)[0];
+    const schema = this.schema;
+    const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
+    const validateOnChange = this.validateOnChange;
+
+    const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : {};
+
+    const commonValidationFunction = async (
+        tableBasePath,
+        path,
+        parent,
+        newValue,
+        baseSchema = itemSchema,
+        skip = 0
+    ) => {
+        const warnings = [];
+        const errors = [];
+
+        const name = path.slice(-1)[0];
+        const completePath = [...tableBasePath, ...path.slice(0, -1)];
+
+        const toIterate = path.slice(skip);
+
+        const itemPropSchema = toIterate.reduce((acc, key) => {
+            return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
+        }, baseSchema);
+
+        const result = await (validateOnChange
+            ? this.onValidate
+                ? this.onValidate()
+                : this.form?.triggerValidation
+                  ? this.form.triggerValidation(
+                        name,
+                        completePath,
+                        false,
+                        this,
+                        itemPropSchema,
+                        { ...parent, [name]: newValue },
+                        {
+                            onError: (error) => {
+                                errors.push(error); // Skip counting errors
+                            },
+                            onWarning: (warning) => {
+                                warnings.push(warning); // Skip counting warnings
+                            },
+                        }
+                    ) // NOTE: No pattern properties support
+                  : ""
+            : true);
+
+        const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
+
+        return returnedValue;
+    };
+
+    const commonTableMetadata = {
+        onStatusChange: () => this.form?.checkStatus && this.form.checkStatus(), // Check status on all elements
+        validateEmptyCells: this.validateEmptyValue,
+        deferLoading: this.form?.deferLoading,
+        onLoaded: () => {
+            if (this.form) {
+                if (this.form.nLoaded) this.form.nLoaded++;
+                if (this.form.checkAllLoaded) this.form.checkAllLoaded();
+            }
+        },
+        onThrow: (...args) => onThrow(...args),
+    };
+
+    const addPropertyKeyToSchema = (schema) => {
+        const schemaCopy = structuredClone(schema);
+
+        const schemaRef = forceItems ? schemaCopy["items"] : schemaCopy;
+
+        if (!schemaRef.properties) schemaRef.properties = {};
+        if (!schemaRef.required) schemaRef.required = [];
+
+        schemaRef.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
+        if (!schemaRef.order) schemaRef.order = [];
+        schemaRef.order.unshift(tempPropertyKey);
+
+        schemaRef.required.push(tempPropertyKey);
+
+        if (!schema["items"]) {
+            const resolvedItemSchema = this.form?.getSchema
+                ? this.form.getSchema("items", schema)
+                : schema["items"];
+            if (!resolvedItemSchema) return schemaRef;
+
+            delete schemaRef.patternProperties;
+
+            schemaRef.properties[tempPropertyValueKey] = {
+                type: "array",
+                items: resolvedItemSchema.properties ? addPropertyKeyToSchema(itemSchema) : itemSchema,
+                title: "Property Value",
+                __generated: true,
+            };
+
+            schemaRef.required.push(tempPropertyValueKey);
+        }
+
+        if (schemaRef.__generated) return schemaRef["items"]; // Only return the relevant items for tables in nested tables
+
+        return schemaRef;
+    };
+
+    const createNestedTable = (id, value, { name: propName = id, schema = itemSchema } = {}) => {
+        const schemaCopy = addPropertyKeyToSchema(schema);
+
+        const resultPath = [...path];
+
+        const schemaPath = [...fullPath];
+
+        const rowData = Object.entries(value).map(([key, value]) => {
+            return !schema["items"]
+                ? { [tempPropertyKey]: key, [tempPropertyValueKey]: value }
+                : { [tempPropertyKey]: key, ...value };
+        });
+
+        if (propName) {
+            resultPath.push(propName);
+            schemaPath.push(propName);
+        }
+
+        const allRemovedKeys = new Set();
+
+        const keyAlreadyExists = (key) => Object.keys(value).includes(key);
+
+        const previousValidValues = {};
+
+        function resolvePath(path, target) {
+            return path
+                .map((key, i) => {
+                    const ogKey = key;
+                    const nextKey = path[i + 1];
+                    if (key === tempPropertyKey) key = target[tempPropertyKey];
+                    if (nextKey === tempPropertyKey) key = [];
+
+                    target = target[ogKey] ?? {};
+
+                    if (nextKey === tempPropertyValueKey) return target[tempPropertyKey]; // Grab next property key
+                    if (key === tempPropertyValueKey) return [];
+
+                    return key;
+                })
+                .flat();
+        }
+
+        function setValueOnAccumulator(row, acc) {
+            const key = row[tempPropertyKey];
+
+            if (!key) return acc;
+
+            if (tempPropertyValueKey in row) {
+                const propValue = row[tempPropertyValueKey];
+                if (Array.isArray(propValue))
+                    acc[key] = propValue.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
+                else acc[key] = propValue;
+            } else {
+                const copy = { ...row };
+                delete copy[tempPropertyKey];
+                acc[key] = copy;
+            }
+
+            return acc;
+        }
+
+        const tableMetadata = {
+            keyColumn: tempPropertyKey,
+            schema: schemaCopy,
+            data: rowData,
+            ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
+
+            onUpdate: function (path, newValue) {
+                const oldKeys = Object.keys(value);
+
+                if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return; // Do not overwrite existing keys
+
+                const result = this.data.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
+
+                const newKeys = Object.keys(result);
+                const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
+                removedKeys.forEach((key) => allRemovedKeys.add(key));
+                newKeys.forEach((key) => allRemovedKeys.delete(key));
+                allRemovedKeys.forEach((key) => (result[key] = undefined));
+
+                // const resolvedPath = resolvePath(path, this.data)
+                return onUpdate.call(this, [], result); // Update all table data
+            },
+
+            validateOnChange: function (path, parent, newValue) {
+                const rowIdx = path[0];
+                const currentKey = this.data[rowIdx]?.[tempPropertyKey];
+
+                const updatedPath = resolvePath(path, this.data);
+
+                const resolvedKey = previousValidValues[rowIdx] ?? currentKey;
+
+                // Do not overwrite existing keys
+                if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
+                    if (keyAlreadyExists(newValue)) {
+                        if (!previousValidValues[rowIdx]) previousValidValues[rowIdx] = resolvedKey;
+
+                        return [
+                            {
+                                message: `Key already exists.<br><small>This value is still ${resolvedKey}.</small>`,
+                                type: "error",
+                            },
+                        ];
+                    } else delete previousValidValues[rowIdx];
+                }
+
+                return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1);
+            },
+            ...commonTableMetadata,
+        };
+
+        const table = this.renderTable(id, tableMetadata, fullPath); 
+        return table // Try rendering as a nested table with a fake property key (otherwise use nested forms)
+    };
+
+    // Possibly multiple tables
+    if (isEditableObject(schema, this.value)) {
+        
+        // One table with nested tables for each property
+        const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
+            (acc, { key, value }) => {
+                acc[key] = value;
+                return acc;
+            },
+            {}
+        );
+
+        const table = createNestedTable(name, data, { schema });
+        if (table) return table;
+    }
+
+    // Normal table parsing
+    const tableMetadata = {
+        schema: itemSchema,
+        data: this.value,
+
+        ignore,
+
+        onUpdate: function () {
+            return onUpdate.call(this, fullPath);
+        },
+
+        validateOnChange: (...args) => commonValidationFunction(fullPath, ...args, 1),
+
+        ...commonTableMetadata,
+    };
+
+    const table = (this.table = this.renderTable(name, tableMetadata, path)); // Try creating table. Otherwise use nested form
+
+    if (table) {
+        const tableEl = table === true ? new BasicTable(tableMetadata) : table;
+        const tables = this.form?.tables;
+        if (tables) tables[name] = tableEl;
+        return tableEl;
+    }
+}
+
+
+
+
+
 // Schema or value indicates editable object
-const isEditableObject = (schema, value) =>
+export const isEditableObject = (schema, value) =>
     schema.type === "object" || (value && typeof value === "object" && !Array.isArray(value));
 const isAdditionalProperties = (pattern) => pattern === "additional";
-const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
+export const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
 export const getEditableItems = (value, pattern, { name, schema } = {}) => {
     let items = Object.entries(value);
@@ -83,6 +359,7 @@ export class JSONSchemaInput extends LitElement {
             }
 
             :host {
+                margin-top: 1.45rem;
                 display: block;
             }
 
@@ -92,6 +369,7 @@ export class JSONSchemaInput extends LitElement {
 
             main {
                 display: flex;
+                margin-top: 0.5rem;
             }
 
             #controls {
@@ -172,14 +450,63 @@ export class JSONSchemaInput extends LitElement {
             .schema-input.list {
                 width: 100%;
             }
+
+            .guided--form-label {
+                display: block;
+                width: 100%;
+                margin: 0;
+                color: black;
+                font-weight: 600;
+                font-size: 1.2em !important;
+              }
+              
+            .guided--form-label.centered {
+                text-align: center;
+            }
+        
+            .guided--form-label.header {
+                font-size: 1.5em !important;
+            }
+
+            .required label:after {
+                content: " *";
+                color: #ff0033;
+            }
+            
+            :host(:not([validateemptyvalue])) .required label:after {
+                color: gray;
+            }
+            
+            .required.conditional label:after {
+                color: transparent;
+            }
+
+            hr {
+                display: block;
+                height: 1px;
+                border: 0;
+                border-top: 1px solid #ccc;
+                padding: 0;
+                margin-bottom: 1em;
+            }
+          
         `;
     }
 
+    static get properties() {
+        return {
+            schema: { type: Object, reflect: false },
+            validateEmptyValue: { type: Boolean, reflect: true },
+        };
+    }
+
+
     // schema,
     // parent,
     // path,
     // form,
     // pattern
+    // showLabel
     controls = [];
     required = false;
     validateOnChange = true;
@@ -272,14 +599,21 @@ export class JSONSchemaInput extends LitElement {
         const input = this.#render();
 
         return html`
-            <main>${input}${this.controls ? html`<div id="controls">${this.controls}</div>` : ""}</main>
-            <p class="guided--text-input-instructions">
-                ${schema.description
-                    ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
-                          ? ""
-                          : "."}`
-                    : ""}
-            </p>
+            <div class="${this.required || this.conditional ? "required" : ""} ${this.conditional
+                ? "conditional"
+                : ""}">
+            
+                ${this.showLabel ? html`<label class="guided--form-label">${(schema.title ? unsafeHTML(schema.title) : null) ?? header(this.path.slice(-1)[0])}` : ''}
+                </label>
+                <main>${input}${this.controls ? html`<div id="controls">${this.controls}</div>` : ""}</main>
+                <p class="guided--text-input-instructions">
+                    ${schema.description
+                        ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
+                            ? ""
+                            : "."}`
+                        : ""}
+                </p>
+            </div>
         `;
     }
 
@@ -410,6 +744,7 @@ export class JSONSchemaInput extends LitElement {
                           this.#updateData(path, value, true); // Live updates
                       }
                   },
+                  renderTable: this.renderTable,
                   onThrow: this.#onThrow,
               })
             : new JSONSchemaInput({
@@ -418,6 +753,7 @@ export class JSONSchemaInput extends LitElement {
                   path: this.path,
                   form: this.form,
                   value: updateTarget,
+                  renderTable: this.renderTable,
                   onUpdate: (value) => {
                       if (createNewObject) updateTarget[key] = value;
                       else this.#updateData(key, value); // NOTE: Untested
@@ -474,6 +810,12 @@ export class JSONSchemaInput extends LitElement {
 
         const canAddProperties = isEditableObject(this.schema, this.value);
 
+        if (this.renderCustomHTML){
+            const custom = this.renderCustomHTML(name, schema, path, { onUpdate: this.#updateData, onThrow: this.#onThrow });
+            if (custom) return custom;
+        }
+
+
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
             const el = new FilesystemSelector({
@@ -523,275 +865,28 @@ export class JSONSchemaInput extends LitElement {
 
             const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
 
+
             const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
-            else if (itemSchema?.type === "object" && this.form.createTable) {
-                const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, resolvedFullPath) : {};
+            else if (itemSchema?.type === "object" && this.renderTable) {
 
                 const instanceThis = this;
 
-                function commonUpdateFunction(path, value = this.data) {
+                function updateFunction (path, value = this.data) {
                     return instanceThis.#updateData(path, value, true, {
                         willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
                         onError: (e) => e,
                         onWarning: (e) => e,
-                    }); // Ensure change propagates to all forms
+                    })
                 }
 
-                const commonValidationFunction = async (
-                    tableBasePath,
-                    path,
-                    parent,
-                    newValue,
-                    baseSchema = itemSchema,
-                    skip = 0
-                ) => {
-                    const warnings = [];
-                    const errors = [];
-
-                    const name = path.slice(-1)[0];
-                    const completePath = [...tableBasePath, ...path.slice(0, -1)];
-
-                    const toIterate = path.slice(skip);
-
-                    const itemPropSchema = toIterate.reduce((acc, key) => {
-                        // if (acc?.patternProperties) {
-                        //     const pattern = Object.keys(acc.patternProperties).find((pattern) => new RegExp(pattern).test(key));
-                        //     if (pattern) return acc.patternProperties[pattern];
-                        // }
-                        return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
-                    }, baseSchema);
-
-                    const result = await (validateOnChange
-                        ? this.onValidate
-                            ? this.onValidate()
-                            : this.form?.triggerValidation
-                              ? this.form.triggerValidation(
-                                    name,
-                                    completePath,
-                                    false,
-                                    this,
-                                    itemPropSchema,
-                                    { ...parent, [name]: newValue },
-                                    {
-                                        onError: (error) => {
-                                            errors.push(error); // Skip counting errors
-                                        },
-                                        onWarning: (warning) => {
-                                            warnings.push(warning); // Skip counting warnings
-                                        },
-                                    }
-                                ) // NOTE: No pattern properties support
-                              : ""
-                        : true);
-
-                    const returnedValue = errors.length ? errors : warnings.length ? warnings : result;
-
-                    return returnedValue;
-                };
-
-                const commonTableMetadata = {
-                    onStatusChange: () => this.form?.checkStatus && this.form.checkStatus(), // Check status on all elements
-                    validateEmptyCells: this.form?.validateEmptyValues,
-                    deferLoading: this.form?.deferLoading,
-                    onLoaded: () => {
-                        if (this.form) {
-                            if (this.form.nLoaded) this.form.nLoaded++;
-                            if (this.form.checkAllLoaded) this.form.checkAllLoaded();
-                        }
-                    },
-                    onThrow: (...args) => this.#onThrow(...args),
-                };
-
-                const addPropertyKeyToSchema = (schema) => {
-                    const schemaCopy = structuredClone(schema);
-
-                    if (!schemaCopy.properties) schemaCopy.properties = {};
-                    if (!schemaCopy.required) schemaCopy.required = [];
-
-                    schemaCopy.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
-                    schemaCopy.order = [tempPropertyKey];
-
-                    schemaCopy.required.push(tempPropertyKey);
-
-                    if (!schema["items"]) {
-                        const resolvedItemSchema = this.form?.getSchema
-                            ? this.form.getSchema("items", schema)
-                            : schema["items"];
-                        if (!resolvedItemSchema) return schemaCopy;
-
-                        delete schemaCopy.patternProperties;
-
-                        schemaCopy.properties[tempPropertyValueKey] = {
-                            type: "array",
-                            items: resolvedItemSchema.properties ? addPropertyKeyToSchema(itemSchema) : itemSchema,
-                            title: "Property Value",
-                            __generated: true,
-                        };
-
-                        schemaCopy.required.push(tempPropertyValueKey);
-                    }
-
-                    if (schemaCopy.__generated) return schemaCopy["items"]; // Only return the relevant items for tables in nested tables
-
-                    return schemaCopy;
-                };
-
-                const createNestedTable = (id, value, { name: propName = id, schema = itemSchema } = {}) => {
-                    const schemaCopy = addPropertyKeyToSchema(schema);
-
-                    const resultPath = [...path];
-
-                    const schemaPath = [...resolvedFullPath];
+                const table = createTable.call(this, resolvedFullPath, {
+                    onUpdate: updateFunction,
+                    onThrow: this.#onThrow
+                }); // Ensure change propagates
 
-                    const rowData = Object.entries(value).map(([key, value]) => {
-                        return !schema["items"]
-                            ? { [tempPropertyKey]: key, [tempPropertyValueKey]: value }
-                            : { [tempPropertyKey]: key, ...value };
-                    });
-
-                    if (propName) {
-                        resultPath.push(propName);
-                        schemaPath.push(propName);
-                    }
-
-                    const allRemovedKeys = new Set();
-
-                    const keyAlreadyExists = (key) => Object.keys(value).includes(key);
-
-                    const previousValidValues = {};
-
-                    function resolvePath(path, target) {
-                        return path
-                            .map((key, i) => {
-                                const ogKey = key;
-                                const nextKey = path[i + 1];
-                                if (key === tempPropertyKey) key = target[tempPropertyKey];
-                                if (nextKey === tempPropertyKey) key = [];
-
-                                target = target[ogKey] ?? {};
-
-                                if (nextKey === tempPropertyValueKey) return target[tempPropertyKey]; // Grab next property key
-                                if (key === tempPropertyValueKey) return [];
-
-                                return key;
-                            })
-                            .flat();
-                    }
-
-                    function setValueOnAccumulator(row, acc) {
-                        const key = row[tempPropertyKey];
-
-                        if (!key) return acc;
-
-                        if (tempPropertyValueKey in row) {
-                            const propValue = row[tempPropertyValueKey];
-                            if (Array.isArray(propValue))
-                                acc[key] = propValue.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
-                            else acc[key] = propValue;
-                        } else {
-                            const copy = { ...row };
-                            delete copy[tempPropertyKey];
-                            acc[key] = copy;
-                        }
-
-                        return acc;
-                    }
-
-                    const tableMetadata = {
-                        keyColumn: tempPropertyKey,
-                        schema: schemaCopy,
-                        data: rowData,
-                        ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
-
-                        onUpdate: function (path, newValue) {
-                            const oldKeys = Object.keys(value);
-
-                            if (path.slice(-1)[0] === tempPropertyKey && keyAlreadyExists(newValue)) return; // Do not overwrite existing keys
-
-                            const result = this.data.reduce((acc, row) => setValueOnAccumulator(row, acc), {});
-
-                            const newKeys = Object.keys(result);
-                            const removedKeys = oldKeys.filter((k) => !newKeys.includes(k));
-                            removedKeys.forEach((key) => allRemovedKeys.add(key));
-                            newKeys.forEach((key) => allRemovedKeys.delete(key));
-                            allRemovedKeys.forEach((key) => (result[key] = undefined));
-
-                            // const resolvedPath = resolvePath(path, this.data)
-                            return commonUpdateFunction.call(this, [], result); // Update all table data
-                        },
-
-                        validateOnChange: function (path, parent, newValue) {
-                            const rowIdx = path[0];
-                            const currentKey = this.data[rowIdx]?.[tempPropertyKey];
-
-                            const updatedPath = resolvePath(path, this.data);
-
-                            const resolvedKey = previousValidValues[rowIdx] ?? currentKey;
-
-                            // Do not overwrite existing keys
-                            if (path.slice(-1)[0] === tempPropertyKey && resolvedKey !== newValue) {
-                                if (keyAlreadyExists(newValue)) {
-                                    if (!previousValidValues[rowIdx]) previousValidValues[rowIdx] = resolvedKey;
-
-                                    return [
-                                        {
-                                            message: `Key already exists.<br><small>This value is still ${resolvedKey}.</small>`,
-                                            type: "error",
-                                        },
-                                    ];
-                                } else delete previousValidValues[rowIdx];
-                            }
-
-                            return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1);
-                        },
-                        ...commonTableMetadata,
-                    };
-
-                    const table = this.form.createTable(id, tableMetadata, resolvedFullPath); // Try creating table. Otherwise use nested form
-                    return table;
-                };
-
-                // Possibly multiple tables
-                if (isEditableObject(schema, this.value)) {
-                    // One table with nested tables for each property
-                    const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
-                        (acc, { key, value }) => {
-                            acc[key] = value;
-                            return acc;
-                        },
-                        {}
-                    );
-
-                    const table = createNestedTable(name, data, { schema });
-                    return table;
-                }
-
-                // Normal table parsing
-                const tableMetadata = {
-                    schema: itemSchema,
-                    data: this.value,
-
-                    ignore,
-
-                    onUpdate: function () {
-                        return commonUpdateFunction.call(this, fullPath);
-                    },
-
-                    validateOnChange: (...args) => commonValidationFunction(fullPath, ...args, 1),
-
-                    ...commonTableMetadata,
-                };
-
-                const table = (this.table = this.form.createTable(name, tableMetadata, fullPath)); // Try creating table. Otherwise use nested form
-
-                if (table) {
-                    const tableEl = table === true ? new BasicTable(tableMetadata) : table;
-                    const tables = this.form?.tables;
-                    if (tables) tables[name] = tableEl;
-                    return tableEl;
-                }
+                if (table) return table
             }
 
             const list = (this.#list = new List({
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 3178de940..be98a86ab 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -56,6 +56,8 @@ const propsToIgnore = {
 };
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
+import { JSONSchemaInput, createTable, getEditableItems, isEditableObject, isPatternProperties } from "../../../JSONSchemaInput.js";
+import { html } from "lit";
 
 const getInfoFromId = (key) => {
     let [subject, session] = key.split("/");
@@ -172,6 +174,14 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
+        const patternPropsToRetitle = [
+            'Ophys.Fluorescence',
+            'Ophys.DfOverF',
+            'Ophys.SegmentationImages'
+        ]
+
+        const customSymbol = Symbol("custom");
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
@@ -222,10 +232,60 @@ export class GuidedMetadataPage extends ManagedPage {
             onlyRequired: false,
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
-            createTable: function (name, metadata, path) {
-                // // Do not create tables for patternProperties (OLD)
-                // const parentSchema = this.getSchema(path) ?? {};
-                // if (parentSchema.patternProperties) return false
+            renderCustomHTML: function (name, inputSchema, localPath, { onUpdate, onThrow }) {
+
+                if (isPatternProperties(this.pattern)) {
+                    if (patternPropsToRetitle.includes(this.form.base.join('.'))) {
+
+                            const schemaCopy = { ...inputSchema };
+                            inputSchema.title = 'Plane Metadata<hr>';
+
+                            // One table with nested tables for each property
+                            const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
+                                (acc, { key, value }) => {
+                                    acc[key] = value;
+                                    return acc;
+                                },
+                                {}
+                            );
+
+                            const nProps = Object.keys(data).length;
+
+                            return Object.entries(data).map(([ name, value ]) => {
+                                return Object.entries(schemaCopy.patternProperties).map(([ pattern, schema ]) => {
+
+                                    const mockInput = {
+                                        schema: {
+                                            type: "object",
+                                            items: schema,
+                                        },
+                                        renderTable: this.renderTable,
+                                        value: value,
+                                        pattern: pattern
+                                    }
+
+                                    return html`
+                                    <div style="width: 100%;">
+                                        ${nProps > 1 ? html`<h3>${header(name)}</h3>` : ''}
+                                        ${createTable.call(mockInput, [...localPath], {
+                                            forceItems: true,
+                                            onUpdate: (localPath, value) => onUpdate([ name, ...localPath ], value, true, {
+                                                willTimeout: false,
+                                                onError: (e) => e,
+                                                onWarning: (e) => e,
+                                            }),
+                                            onThrow: onThrow,
+                                        })}
+                                    </div>
+                                    `
+                                })
+                            }).flat()
+
+                    }
+                }
+            },
+
+            renderTable: function (name, metadata) {
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index 9aa36078f..110e867fb 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -46,9 +46,7 @@ export class NestedEditor extends LitElement {
             validateOnChange: (path, parent, value, schema) => {
                 if (this.validateOnChange) return this.validateOnChange(value, path, parent, schema) // NOTE: Flipped because usually only value is passed
             },
-            form: {
-                createTable: (name, metadata, path) => new SimpleTable(metadata), // If possible to render as a table, do so
-            }
+            renderTable: (name, metadata, path) => new SimpleTable(metadata) // NOTE: Would be most ideal to have a reference to the containing input...
         })
 
         input.style.padding = '25px 50px'
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 71b8fc134..5b7972d9d 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -158,9 +158,7 @@ schema.Ophys.Device = {
                 values,
                 value: row
             } = get(this.results, path)
-    
-            console.log('row', values, row)
-    
+        
             if (!row) return true // Allow blank rows
     
             const rows = values.slice(-1)[0]
diff --git a/tests/metadata.test.ts b/tests/metadata.test.ts
index d1fdd2ec5..af471654b 100644
--- a/tests/metadata.test.ts
+++ b/tests/metadata.test.ts
@@ -106,7 +106,7 @@ test('inter-table updates are triggered', async () => {
         schema,
         results,
         validateOnChange,
-        createTable: (name, metadata, path) => {
+        renderTable: (name, metadata, path) => {
             if (name !== "Electrodes") return new SimpleTable(metadata);
             else return true
         },

From efb4a02e0a773107b396bbe6714de67c4e4a7e06 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jan 2024 21:02:10 +0000
Subject: [PATCH 088/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 31 ++----
 src/renderer/src/stories/JSONSchemaInput.js   | 94 +++++++++----------
 .../pages/guided-mode/data/GuidedMetadata.js  | 90 +++++++++---------
 .../guided-mode/data/GuidedSourceData.js      |  1 -
 src/renderer/src/validation/validation.ts     | 26 ++---
 5 files changed, 110 insertions(+), 132 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 4c1d0f53f..a9a5a706a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -250,36 +250,30 @@ export class JSONSchemaForm extends LitElement {
         if (props.base) this.base = props.base;
     }
 
-
     // Get the form element defined by the path (stops before table cells)
     getFormElement = (path, { forms = true, tables = true, inputs = true } = {}) => {
         if (typeof path === "string") path = path.split(".");
-        if (!path.length) return this
+        if (!path.length) return this;
 
         const name = path[0];
-        const updatedPath = path.slice(1)
-
+        const updatedPath = path.slice(1);
 
-        const form = this.#nestedForms[name] // Check forms
+        const form = this.#nestedForms[name]; // Check forms
         if (!form) {
-            const table = this.tables[name] // Check tables
-            if (table && tables) return table // Skip table cells
-        } 
-        
-        else if (!updatedPath.length && forms) return form
+            const table = this.tables[name]; // Check tables
+            if (table && tables) return table; // Skip table cells
+        } else if (!updatedPath.length && forms) return form;
 
         // Check Inputs
         // const inputContainer = this.shadowRoot.querySelector(`#${encode(path.join("-"))}`);
         // if (inputContainer && inputs) return inputContainer.querySelector("jsonschema-input");;
 
-        const foundInput = this.inputs[path.join(".")] // Check Inputs
+        const foundInput = this.inputs[path.join(".")]; // Check Inputs
         if (foundInput && inputs) return foundInput;
 
-
         // Check Nested Form Inputs
         return form?.getFormElement(updatedPath, { forms, tables, inputs });
-
-    }
+    };
 
     #requirements = {};
 
@@ -405,7 +399,6 @@ export class JSONSchemaForm extends LitElement {
     };
 
     validate = async (resolved = this.resolved) => {
-
         // Validate against the entire JSON Schema
         const copy = structuredClone(resolved);
         delete copy.__disabled;
@@ -580,7 +573,7 @@ export class JSONSchemaForm extends LitElement {
             pattern: propertyType === "pattern" ? name : propertyType ?? undefined,
             renderTable: this.renderTable,
             renderCustomHTML: this.renderCustomHTML,
-            showLabel: true
+            showLabel: true,
         });
 
         this.inputs[localPath.join("-")] = interactiveInput;
@@ -596,10 +589,7 @@ export class JSONSchemaForm extends LitElement {
         // console.log(interactiveInput)
 
         return html`
-            <div
-                id=${encode(localPath.join("-"))}
-                class="form-section"
-            >
+            <div id=${encode(localPath.join("-"))} class="form-section">
                 ${interactiveInput}
                 <div class="errors"></div>
                 <div class="warnings"></div>
@@ -927,7 +917,6 @@ export class JSONSchemaForm extends LitElement {
 
             return true;
         } else {
-
             // Add new invalid classes and errors
             input.classList.add("invalid");
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 43415eb94..445713d73 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,4 +1,3 @@
-
 import { LitElement, css, html } from "lit";
 import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
@@ -15,14 +14,7 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 
-
-
-export function createTable(fullPath, {
-    onUpdate,
-    onThrow,
-    forceItems = false
-}){
-
+export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
     const path = [...fullPath];
     const name = path.splice(-1)[0];
     const schema = this.schema;
@@ -107,9 +99,7 @@ export function createTable(fullPath, {
         schemaRef.required.push(tempPropertyKey);
 
         if (!schema["items"]) {
-            const resolvedItemSchema = this.form?.getSchema
-                ? this.form.getSchema("items", schema)
-                : schema["items"];
+            const resolvedItemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
             if (!resolvedItemSchema) return schemaRef;
 
             delete schemaRef.patternProperties;
@@ -240,21 +230,17 @@ export function createTable(fullPath, {
             ...commonTableMetadata,
         };
 
-        const table = this.renderTable(id, tableMetadata, fullPath); 
-        return table // Try rendering as a nested table with a fake property key (otherwise use nested forms)
+        const table = this.renderTable(id, tableMetadata, fullPath);
+        return table; // Try rendering as a nested table with a fake property key (otherwise use nested forms)
     };
 
     // Possibly multiple tables
     if (isEditableObject(schema, this.value)) {
-        
         // One table with nested tables for each property
-        const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce(
-            (acc, { key, value }) => {
-                acc[key] = value;
-                return acc;
-            },
-            {}
-        );
+        const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce((acc, { key, value }) => {
+            acc[key] = value;
+            return acc;
+        }, {});
 
         const table = createNestedTable(name, data, { schema });
         if (table) return table;
@@ -286,10 +272,6 @@ export function createTable(fullPath, {
     }
 }
 
-
-
-
-
 // Schema or value indicates editable object
 export const isEditableObject = (schema, value) =>
     schema.type === "object" || (value && typeof value === "object" && !Array.isArray(value));
@@ -461,12 +443,12 @@ export class JSONSchemaInput extends LitElement {
                 color: black;
                 font-weight: 600;
                 font-size: 1.2em !important;
-              }
-              
+            }
+
             .guided--form-label.centered {
                 text-align: center;
             }
-        
+
             .guided--form-label.header {
                 font-size: 1.5em !important;
             }
@@ -475,11 +457,11 @@ export class JSONSchemaInput extends LitElement {
                 content: " *";
                 color: #ff0033;
             }
-            
+
             :host(:not([validateemptyvalue])) .required label:after {
                 color: gray;
             }
-            
+
             .required.conditional label:after {
                 color: transparent;
             }
@@ -492,7 +474,6 @@ export class JSONSchemaInput extends LitElement {
                 padding: 0;
                 margin-bottom: 1em;
             }
-          
         `;
     }
 
@@ -503,7 +484,6 @@ export class JSONSchemaInput extends LitElement {
         };
     }
 
-
     // schema,
     // parent,
     // path,
@@ -600,19 +580,29 @@ export class JSONSchemaInput extends LitElement {
         const input = this.#render();
 
         return html`
-            <div class="${this.required || this.conditional ? "required" : ""} ${this.conditional
-                ? "conditional"
-                : ""}">
-            
-                ${this.showLabel ? html`<label class="guided--form-label">${(schema.title ? unsafeHTML(schema.title) : null) ?? header(this.path.slice(-1)[0])}` : ''}
+            <div class="${this.required || this.conditional ? "required" : ""} ${
+                this.conditional ? "conditional" : ""
+            }">
+
+                ${
+                    this.showLabel
+                        ? html`<label class="guided--form-label"
+                              >${(schema.title ? unsafeHTML(schema.title) : null) ??
+                              header(this.path.slice(-1)[0])}</label
+                          >`
+                        : ""
+                }
                 </label>
                 <main>${input}${this.controls ? html`<div id="controls">${this.controls}</div>` : ""}</main>
                 <p class="guided--text-input-instructions">
-                    ${schema.description
-                        ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] === "."
-                            ? ""
-                            : "."}`
-                        : ""}
+                    ${
+                        schema.description
+                            ? html`${unsafeHTML(capitalize(schema.description))}${schema.description.slice(-1)[0] ===
+                              "."
+                                  ? ""
+                                  : "."}`
+                            : ""
+                    }
                 </p>
             </div>
         `;
@@ -809,12 +799,14 @@ export class JSONSchemaInput extends LitElement {
 
         const canAddProperties = isEditableObject(this.schema, this.value);
 
-        if (this.renderCustomHTML){
-            const custom = this.renderCustomHTML(name, schema, path, { onUpdate: this.#updateData, onThrow: this.#onThrow });
+        if (this.renderCustomHTML) {
+            const custom = this.renderCustomHTML(name, schema, path, {
+                onUpdate: this.#updateData,
+                onThrow: this.#onThrow,
+            });
             if (custom) return custom;
         }
 
-
         // Handle file and directory formats
         const createFilesystemSelector = (format) => {
             const filesystemSelectorElement = new FilesystemSelector({
@@ -864,28 +856,26 @@ export class JSONSchemaInput extends LitElement {
 
             const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
 
-
             const fileSystemFormat = isFilesystemSelector(name, itemSchema?.format);
             if (fileSystemFormat) return createFilesystemSelector(fileSystemFormat);
             // Create tables if possible
             else if (itemSchema?.type === "object" && this.renderTable) {
-
                 const instanceThis = this;
 
-                function updateFunction (path, value = this.data) {
+                function updateFunction(path, value = this.data) {
                     return instanceThis.#updateData(path, value, true, {
                         willTimeout: false, // Since there is a special validation function, do not trigger a timeout validation call
                         onError: (e) => e,
                         onWarning: (e) => e,
-                    })
+                    });
                 }
 
                 const table = createTable.call(this, resolvedFullPath, {
                     onUpdate: updateFunction,
-                    onThrow: this.#onThrow
+                    onThrow: this.#onThrow,
                 }); // Ensure change propagates
 
-                if (table) return table
+                if (table) return table;
             }
 
             const list = (this.#list = new List({
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 a914a630a..442ef585d 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -56,7 +56,13 @@ const propsToIgnore = {
 };
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
-import { JSONSchemaInput, createTable, getEditableItems, isEditableObject, isPatternProperties } from "../../../JSONSchemaInput.js";
+import {
+    JSONSchemaInput,
+    createTable,
+    getEditableItems,
+    isEditableObject,
+    isPatternProperties,
+} from "../../../JSONSchemaInput.js";
 import { html } from "lit";
 
 const getInfoFromId = (key) => {
@@ -174,11 +180,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveResults(subject, session, globalState);
 
-        const patternPropsToRetitle = [
-            'Ophys.Fluorescence',
-            'Ophys.DfOverF',
-            'Ophys.SegmentationImages'
-        ]
+        const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
 
         const customSymbol = Symbol("custom");
 
@@ -233,27 +235,25 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             renderCustomHTML: function (name, inputSchema, localPath, { onUpdate, onThrow }) {
-
                 if (isPatternProperties(this.pattern)) {
-                    if (patternPropsToRetitle.includes(this.form.base.join('.'))) {
-
-                            const schemaCopy = { ...inputSchema };
-                            inputSchema.title = 'Plane Metadata<hr>';
-
-                            // One table with nested tables for each property
-                            const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
-                                (acc, { key, value }) => {
-                                    acc[key] = value;
-                                    return acc;
-                                },
-                                {}
-                            );
-
-                            const nProps = Object.keys(data).length;
-
-                            return Object.entries(data).map(([ name, value ]) => {
-                                return Object.entries(schemaCopy.patternProperties).map(([ pattern, schema ]) => {
-
+                    if (patternPropsToRetitle.includes(this.form.base.join("."))) {
+                        const schemaCopy = { ...inputSchema };
+                        inputSchema.title = "Plane Metadata<hr>";
+
+                        // One table with nested tables for each property
+                        const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
+                            (acc, { key, value }) => {
+                                acc[key] = value;
+                                return acc;
+                            },
+                            {}
+                        );
+
+                        const nProps = Object.keys(data).length;
+
+                        return Object.entries(data)
+                            .map(([name, value]) => {
+                                return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
                                     const mockInput = {
                                         schema: {
                                             type: "object",
@@ -261,32 +261,32 @@ export class GuidedMetadataPage extends ManagedPage {
                                         },
                                         renderTable: this.renderTable,
                                         value: value,
-                                        pattern: pattern
-                                    }
+                                        pattern: pattern,
+                                    };
 
                                     return html`
-                                    <div style="width: 100%;">
-                                        ${nProps > 1 ? html`<h3>${header(name)}</h3>` : ''}
-                                        ${createTable.call(mockInput, [...localPath], {
-                                            forceItems: true,
-                                            onUpdate: (localPath, value) => onUpdate([ name, ...localPath ], value, true, {
-                                                willTimeout: false,
-                                                onError: (e) => e,
-                                                onWarning: (e) => e,
-                                            }),
-                                            onThrow: onThrow,
-                                        })}
-                                    </div>
-                                    `
-                                })
-                            }).flat()
-
+                                        <div style="width: 100%;">
+                                            ${nProps > 1 ? html`<h3>${header(name)}</h3>` : ""}
+                                            ${createTable.call(mockInput, [...localPath], {
+                                                forceItems: true,
+                                                onUpdate: (localPath, value) =>
+                                                    onUpdate([name, ...localPath], value, true, {
+                                                        willTimeout: false,
+                                                        onError: (e) => e,
+                                                        onWarning: (e) => e,
+                                                    }),
+                                                onThrow: onThrow,
+                                            })}
+                                        </div>
+                                    `;
+                                });
+                            })
+                            .flat();
                     }
                 }
             },
 
             renderTable: function (name, metadata) {
-
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);
                 else return true; // All other tables are handled by the default behavior
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 9d2d8d517..a1ba18163 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -15,7 +15,6 @@ import globalIcon from "../../../assets/global.svg?raw";
 
 import { baseUrl } from "../../../../server/globals";
 
-
 const propsToIgnore = {
     "*": {
         verbose: true,
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 0448fd450..8a9b0f20c 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -49,7 +49,7 @@ schema.Ecephys.ElectrodeGroup = {
     ["*"]: {
         name: function (this: JSONSchemaForm, _, __, ___, value) {
             const groups = this.results.Ecephys.ElectrodeGroup.map(({ name }) => name)
-        
+
                 // Check if the latest value will be new. Run function after validation
             if (!value || !groups.includes(value)) {
                 return () => {
@@ -57,7 +57,7 @@ schema.Ecephys.ElectrodeGroup = {
                 }
             }
         },
-        
+
         device: function (this: JSONSchemaForm, name, parent, path) {
             const devices = this.results.Ecephys.Device.map(({ name }) => name)
             if (devices.includes(parent[name])) return true
@@ -155,21 +155,21 @@ schema.Ophys.Device = {
                 values,
                 value: row
             } = get(this.results, path)
-        
+
             if (!row) return true // Allow blank rows
-    
+
             const rows = values.slice(-1)[0]
             const idx = path.slice(-1)[0]
             const isUniqueError = isNotUnique(name, value, rows, idx)
             if (isUniqueError) return isUniqueError
-    
+
             const prevValue = row[name]
-    
+
             if (prevValue === value || prevValue === undefined) return true // No change
-    
+
             const prevUniqueError = isNotUnique(name, prevValue, rows, idx)
             if (prevUniqueError) return true // Register as valid
-    
+
             const result = await Swal.fire({
                 title: `Are you sure you want to rename the ${prevValue} device?`,
                 icon: "warning",
@@ -181,16 +181,16 @@ schema.Ophys.Device = {
                 showCancelButton: true,
                 cancelButtonText: "Cancel"
             })
-    
+
             if (!result.isConfirmed) return null
-    
+
             // Update Dependent Tables
             const dependencies = [
                 ['Ophys', 'ImagingPlane'],
                 ['Ophys', 'OnePhotonSeries'],
                 ['Ophys', 'TwoPhotonSeries']
             ]
-    
+
             dependencies.forEach(path => {
                 const table = this.getFormElement(path)
                 if (table) {
@@ -200,10 +200,10 @@ schema.Ophys.Device = {
                     })
                     table.data = data
                 }
-    
+
                 rerenderTable.call(this, path)
             })
-    
+
             return true
         }
 

From 8e04428a4b6b99cd25aacf69b37cebac3dde36a0 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 11 Jan 2024 14:13:22 -0800
Subject: [PATCH 089/133] Ensure pipelines are consistent with new structure

---
 src/renderer/src/progress/index.js  | 28 ++++++++++++++++++++++------
 src/renderer/src/progress/update.js |  2 +-
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index ed7b03601..efe461fc6 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -120,10 +120,29 @@ export const getEntries = () => {
     return progressFiles.filter((path) => path.slice(-5) === ".json");
 };
 
+const oldConversionsPath = "conversion";
+const convertOldPath = (path) => {
+    if (path && path.slice(0, oldConversionsPath.length) === oldConversionsPath)return `/${path.slice(oldConversionsPath.length)}`;
+    else return path
+}
+
+const transformProgressFile = (progressFile) => {
+    progressFile["page-before-exit"] = convertOldPath(progressFile["page-before-exit"]);
+    Object.values(progressFile.sections).forEach((section) => {
+        const pages = {}
+        Object.entries(section.pages).forEach(([ page, value ]) => {
+            pages[convertOldPath(page)] = value
+        })
+        section.pages = pages
+    })
+
+    return progressFile
+
+}
 export const getAll = (progressFiles) => {
     return progressFiles.map((progressFile) => {
         let progressFilePath = joinPath(guidedProgressFilePath, progressFile);
-        return JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath));
+        return transformProgressFile(JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)));
     });
 };
 
@@ -134,6 +153,7 @@ export const getCurrentProjectName = () => {
 
 export const get = (name) => {
     if (!name) {
+        console.error('No name provided to get()')
         const params = new URLSearchParams(location.search);
         const projectName = params.get("project");
         if (!projectName) {
@@ -155,19 +175,15 @@ export const get = (name) => {
     let progressFilePath = joinPath(guidedProgressFilePath, name + ".json");
 
     const exists = fs ? fs.existsSync(progressFilePath) : localStorage.getItem(progressFilePath) !== null;
-    return exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {};
+    return transformProgressFile(exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {});
 };
 
-const oldConversionsPath = "conversion";
 export function resume(name) {
     const global = this ? this.load(name) : get(name);
 
     let commandToResume = global["page-before-exit"] || "//start";
     updateURLParams({ project: name });
 
-    if (commandToResume.slice(0, oldConversionsPath.length) === oldConversionsPath)
-        commandToResume = `/${commandToResume.slice(oldConversionsPath.length)}`;
-
     if (this) this.onTransition(commandToResume);
 
     return commandToResume;
diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 2eafc52a3..02b6946d0 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -28,7 +28,7 @@ export const updateAppProgress = (
     dataOrProjectName = {},
     projectName = typeof dataOrProjectName === "string" ? dataOrProjectName : undefined
 ) => {
-    const transitionOffPipeline = pageId && pageId.split("/")[0] !== "conversion";
+    const transitionOffPipeline = pageId && pageId.slice(0, 2) !== '//'
 
     if (transitionOffPipeline) {
         updateURLParams({ project: undefined });

From 56e0eccbcda852431d5e26167fc77aa7e1a3fa0f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jan 2024 22:16:01 +0000
Subject: [PATCH 090/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/progress/index.js  | 34 ++++++++++++++++-------------
 src/renderer/src/progress/update.js |  2 +-
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index efe461fc6..4c738f13f 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -122,27 +122,29 @@ export const getEntries = () => {
 
 const oldConversionsPath = "conversion";
 const convertOldPath = (path) => {
-    if (path && path.slice(0, oldConversionsPath.length) === oldConversionsPath)return `/${path.slice(oldConversionsPath.length)}`;
-    else return path
-}
+    if (path && path.slice(0, oldConversionsPath.length) === oldConversionsPath)
+        return `/${path.slice(oldConversionsPath.length)}`;
+    else return path;
+};
 
 const transformProgressFile = (progressFile) => {
     progressFile["page-before-exit"] = convertOldPath(progressFile["page-before-exit"]);
     Object.values(progressFile.sections).forEach((section) => {
-        const pages = {}
-        Object.entries(section.pages).forEach(([ page, value ]) => {
-            pages[convertOldPath(page)] = value
-        })
-        section.pages = pages
-    })
-
-    return progressFile
+        const pages = {};
+        Object.entries(section.pages).forEach(([page, value]) => {
+            pages[convertOldPath(page)] = value;
+        });
+        section.pages = pages;
+    });
 
-}
+    return progressFile;
+};
 export const getAll = (progressFiles) => {
     return progressFiles.map((progressFile) => {
         let progressFilePath = joinPath(guidedProgressFilePath, progressFile);
-        return transformProgressFile(JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)));
+        return transformProgressFile(
+            JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath))
+        );
     });
 };
 
@@ -153,7 +155,7 @@ export const getCurrentProjectName = () => {
 
 export const get = (name) => {
     if (!name) {
-        console.error('No name provided to get()')
+        console.error("No name provided to get()");
         const params = new URLSearchParams(location.search);
         const projectName = params.get("project");
         if (!projectName) {
@@ -175,7 +177,9 @@ export const get = (name) => {
     let progressFilePath = joinPath(guidedProgressFilePath, name + ".json");
 
     const exists = fs ? fs.existsSync(progressFilePath) : localStorage.getItem(progressFilePath) !== null;
-    return transformProgressFile(exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {});
+    return transformProgressFile(
+        exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {}
+    );
 };
 
 export function resume(name) {
diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 02b6946d0..f0302a0c4 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -28,7 +28,7 @@ export const updateAppProgress = (
     dataOrProjectName = {},
     projectName = typeof dataOrProjectName === "string" ? dataOrProjectName : undefined
 ) => {
-    const transitionOffPipeline = pageId && pageId.slice(0, 2) !== '//'
+    const transitionOffPipeline = pageId && pageId.slice(0, 2) !== "//";
 
     if (transitionOffPipeline) {
         updateURLParams({ project: undefined });

From 95bcfb71b9573acbd21a04db2305a5137f8acd24 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 11 Jan 2024 14:21:01 -0800
Subject: [PATCH 091/133] Update GuidedMetadata.js

---
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js        | 2 --
 1 file changed, 2 deletions(-)

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 442ef585d..ca0f3ff39 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -182,8 +182,6 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
 
-        const customSymbol = Symbol("custom");
-
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,

From 2692aa94a67b0ba9e792b97dea86eeb8a8a189f1 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 11 Jan 2024 14:36:46 -0800
Subject: [PATCH 092/133] Update BasicTable.js

---
 src/renderer/src/stories/BasicTable.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 401898325..d29669a71 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -246,10 +246,10 @@ export class BasicTable extends LitElement {
 
             if (errors.length) {
                 info.error = "";
-                info.title = errors.map((o) => error.message).join("\n"); // Class switching handled automatically
+                info.title = errors.map((error) => error.message).join("\n"); // Class switching handled automatically
             } else if (warnings.length) {
                 info.warning = "";
-                info.title = warnings.map((o) => warning.message).join("\n");
+                info.title = warnings.map((warning) => warning.message).join("\n");
             }
 
             if (typeof result === "function") result(); // Run if returned value is a function

From 0b361013f86069545099df1825f2393d7536a582 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 11 Jan 2024 14:47:00 -0800
Subject: [PATCH 093/133] Fix variables

---
 src/renderer/src/stories/BasicTable.js  | 2 +-
 src/renderer/src/stories/SimpleTable.js | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index d29669a71..976524ed7 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -278,7 +278,7 @@ export class BasicTable extends LitElement {
 
                         if (message !== undefined) {
                             tippy(td, { content: message, allowHTML: true });
-                            td.setAttribute("data-message", value);
+                            td.setAttribute("data-message", message);
                         }
 
                         for (let key in info) {
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 85c189569..d82a2a075 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -761,7 +761,7 @@ export class SimpleTable extends LitElement {
 
                     if (message !== undefined) {
                         tippy(td, { content: message, allowHTML: true });
-                        td.setAttribute("data-message", value);
+                        td.setAttribute("data-message", message);
                     }
 
                     for (let key in info) {

From 5390233c937bd54b5f47b8198c4fe34b967cc428 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 17 Jan 2024 12:16:24 -0800
Subject: [PATCH 094/133] Fix ignore and click instruction

---
 src/renderer/src/stories/JSONSchemaInput.js   | 4 +++-
 src/renderer/src/stories/table/cells/input.ts | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 445713d73..ffb65c561 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -180,6 +180,8 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
             return acc;
         }
 
+
+        
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,
@@ -251,7 +253,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         schema: itemSchema,
         data: this.value,
 
-        ignore,
+        ignore: ignore?.[name], // According to schema
 
         onUpdate: function () {
             return onUpdate.call(this, fullPath);
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index 110e867fb..2b7c0b908 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -101,7 +101,7 @@ export class NestedRenderer extends BaseRenderer {
     }
 
     render() {
-        return html`<small>Click to view cell</small>`
+        return html`<small>Double-click to view cell</small>`
     }
 }
 

From df79b82c658beedec6ae326d2ae41282a1febc04 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 17 Jan 2024 20:17:13 +0000
Subject: [PATCH 095/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index ffb65c561..72e70d076 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -180,8 +180,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
             return acc;
         }
 
-
-        
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,

From 6fe8c8021bdf36a1a82a9b4d9aac7104b9a86a65 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 17 Jan 2024 12:46:24 -0800
Subject: [PATCH 096/133] Fix nested validation

---
 src/renderer/src/stories/JSONSchemaForm.js    |  1 +
 src/renderer/src/stories/JSONSchemaInput.js   |  7 ++++---
 src/renderer/src/stories/table/cells/input.ts | 14 ++++++++++----
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index a9a5a706a..f9b70c258 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -792,6 +792,7 @@ export class JSONSchemaForm extends LitElement {
 
         const value = parent[name];
 
+
         const skipValidation = !this.validateEmptyValues && value === undefined;
         const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index ffb65c561..178d97199 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -37,7 +37,8 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         const name = path.slice(-1)[0];
         const completePath = [...tableBasePath, ...path.slice(0, -1)];
 
-        const toIterate = path.slice(skip);
+        // const toIterate = path.slice(skip);
+        const toIterate = path.filter(value => typeof value === 'string')
 
         const itemPropSchema = toIterate.reduce((acc, key) => {
             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
@@ -259,7 +260,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
             return onUpdate.call(this, fullPath);
         },
 
-        validateOnChange: (...args) => commonValidationFunction(fullPath, ...args, 1),
+        validateOnChange: (...args) => commonValidationFunction(fullPath, ...args),
 
         ...commonTableMetadata,
     };
@@ -308,7 +309,7 @@ export const getEditableItems = (value, pattern, { name, schema } = {}) => {
 
 const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
 
-const isFilesystemSelector = (name, format) => {
+const isFilesystemSelector = (name = '', format) => {
     if (Array.isArray(format)) return format.map((f) => isFilesystemSelector(name, f)).every(Boolean) ? format : null;
 
     const matched = name.match(/(.+_)?(.+)_paths?/);
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index 2b7c0b908..dfee1f1bf 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -39,12 +39,18 @@ export class NestedEditor extends LitElement {
 
         const data = this.#value || (this.schema.type === 'array' ? [] : (this.schema.type === 'object' ? {} : this.schema.default))
 
+        const schema = this.schema
+
         const input = this.#input = new JSONSchemaInput({
-            schema: this.schema,
+            schema,
             value: data,
-            path: [ this.info.col ],
-            validateOnChange: (path, parent, value, schema) => {
-                if (this.validateOnChange) return this.validateOnChange(value, path, parent, schema) // NOTE: Flipped because usually only value is passed
+            path: [],
+            form: {
+                triggerValidation: (name, completePath, _, __, schema, parent) => {
+                    const path = [ ...completePath, name ] 
+                    const value = parent[name]
+                    if (this.validateOnChange) return this.validateOnChange(value, path, parent) // NOTE: Flipped because usually only value is passed
+                }
             },
             renderTable: (name, metadata, path) => new SimpleTable(metadata) // NOTE: Would be most ideal to have a reference to the containing input...
         })

From 272fe9ff15f123fa84935654f51a5d5fbb6ea124 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 18 Jan 2024 00:00:05 +0000
Subject: [PATCH 097/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    | 1 -
 src/renderer/src/stories/JSONSchemaInput.js   | 4 ++--
 src/renderer/src/stories/table/cells/input.ts | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index f9b70c258..a9a5a706a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -792,7 +792,6 @@ export class JSONSchemaForm extends LitElement {
 
         const value = parent[name];
 
-
         const skipValidation = !this.validateEmptyValues && value === undefined;
         const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 6c6c29127..f9968e951 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -38,7 +38,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         const completePath = [...tableBasePath, ...path.slice(0, -1)];
 
         // const toIterate = path.slice(skip);
-        const toIterate = path.filter(value => typeof value === 'string')
+        const toIterate = path.filter((value) => typeof value === "string");
 
         const itemPropSchema = toIterate.reduce((acc, key) => {
             return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
@@ -307,7 +307,7 @@ export const getEditableItems = (value, pattern, { name, schema } = {}) => {
 
 const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
 
-const isFilesystemSelector = (name = '', format) => {
+const isFilesystemSelector = (name = "", format) => {
     if (Array.isArray(format)) return format.map((f) => isFilesystemSelector(name, f)).every(Boolean) ? format : null;
 
     const matched = name.match(/(.+_)?(.+)_paths?/);
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index dfee1f1bf..ee18c06b5 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -47,7 +47,7 @@ export class NestedEditor extends LitElement {
             path: [],
             form: {
                 triggerValidation: (name, completePath, _, __, schema, parent) => {
-                    const path = [ ...completePath, name ] 
+                    const path = [ ...completePath, name ]
                     const value = parent[name]
                     if (this.validateOnChange) return this.validateOnChange(value, path, parent) // NOTE: Flipped because usually only value is passed
                 }

From 167caaa1e66cb91271e047de10aa5dff32e453d7 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 17 Jan 2024 16:05:49 -0800
Subject: [PATCH 098/133] Intermediate update for ignore improvements

---
 src/renderer/src/stories/JSONSchemaInput.js          | 12 ++++++++++--
 src/renderer/src/stories/SimpleTable.js              |  1 +
 .../stories/pages/guided-mode/data/GuidedMetadata.js | 11 ++++++++---
 src/renderer/src/stories/table/Cell.ts               |  6 +++++-
 src/renderer/src/stories/table/cells/input.ts        |  5 +++++
 5 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 6c6c29127..962a1ee1f 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -181,11 +181,16 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
             return acc;
         }
 
+
+        
+        const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}
+        console.error('Nested Ignore (2)', schemaPath, nestedIgnore, this.form)
+
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,
             data: rowData,
-            ignore: this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}, // According to schema
+            ignore: nestedIgnore, // According to schema
 
             onUpdate: function (path, newValue) {
                 const oldKeys = Object.keys(value);
@@ -247,12 +252,15 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         if (table) return table;
     }
 
+    const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : ignore?.[name];
+    console.log('Nested Ignore', name, nestedIgnore)
+
     // Normal table parsing
     const tableMetadata = {
         schema: itemSchema,
         data: this.value,
 
-        ignore: ignore?.[name], // According to schema
+        ignore: nestedIgnore, // According to schema
 
         onUpdate: function () {
             return onUpdate.call(this, fullPath);
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index d82a2a075..5edd29100 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -733,6 +733,7 @@ export class SimpleTable extends LitElement {
             },
             value,
             schema,
+            ignore: this.ignore,
             validateOnChange: async (
                 value,
                 path = [],
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 ca0f3ff39..d3da2e454 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -19,8 +19,15 @@ import { Button } from "../../../Button.js";
 import globalIcon from "../../../assets/global.svg?raw";
 
 const imagingPlaneKey = "imaging_plane";
+
 const propsToIgnore = {
     Ophys: {
+
+        // NOTE: Get this to work
+        '*': {
+            starting_time: true,
+            rate: true
+        },
         ImagingPlane: {
             [imagingPlaneKey]: true,
             manifold: true,
@@ -31,8 +38,6 @@ const propsToIgnore = {
             [imagingPlaneKey]: true,
             format: true,
             starting_frame: true,
-            starting_time: true,
-            rate: true,
             control: true,
             control_description: true,
             comments: true,
@@ -42,7 +47,7 @@ const propsToIgnore = {
             unit: true,
             conversion: true,
             offset: true,
-        },
+        }
     },
     Icephys: true, // Always ignore icephys metadata (for now)
     Behavior: true, // Always ignore behavior metadata (for now)
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 43b192cb9..5bd2c9a3c 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -76,7 +76,7 @@ export class TableCell extends LitElement {
 
     type = 'text'
 
-    constructor({ info, value, schema, validateOnChange, onValidate }: TableCellProps) {
+    constructor({ info, value, schema, validateOnChange, ignore, onValidate }: TableCellProps) {
         super()
         this.#value = value
 
@@ -84,6 +84,7 @@ export class TableCell extends LitElement {
         this.info = info
 
         if (validateOnChange) this.validateOnChange = validateOnChange
+        if (ignore) this.ignore = ignore
 
         if (onValidate) this.onValidate = onValidate
 
@@ -115,6 +116,8 @@ export class TableCell extends LitElement {
      }
 
     validateOnChange?: ValidationFunction
+    ignore?: { [key: string]: boolean } = {}
+    
     onValidate: OnValidateFunction = () => {}
 
     #validator: ValidationFunction = () => true
@@ -221,6 +224,7 @@ export class TableCell extends LitElement {
                 schema: this.schema,
                 nestedProps: {
                     validateOnChange: this.validateOnChange,
+                    ignore: this.ignore
                 }
             })
         }
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index dfee1f1bf..555091941 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -14,12 +14,14 @@ export class NestedEditor extends LitElement {
     schema: any
     toggle: any
     validateOnChange
+    ignore: any
 
     constructor(props: any) {
         super(props)
         this.schema = props.schema
         this.info = props.info ?? {}
         this.toggle = props.toggle
+        this.ignore = props.ignore
         this.validateOnChange = props.validateOnChange
     }
 
@@ -41,10 +43,13 @@ export class NestedEditor extends LitElement {
 
         const schema = this.schema
 
+        console.error('FIX THIS', this.ignore)
+        
         const input = this.#input = new JSONSchemaInput({
             schema,
             value: data,
             path: [],
+            ignore: this.ignore,
             form: {
                 triggerValidation: (name, completePath, _, __, schema, parent) => {
                     const path = [ ...completePath, name ] 

From 2d4c2bad30708c804afa555ab14b58ea79818697 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 18 Jan 2024 00:06:11 +0000
Subject: [PATCH 099/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js               | 8 +++-----
 .../src/stories/pages/guided-mode/data/GuidedMetadata.js  | 7 +++----
 src/renderer/src/stories/table/Cell.ts                    | 2 +-
 src/renderer/src/stories/table/cells/input.ts             | 2 +-
 4 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f4a151333..4f44e58be 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -181,10 +181,8 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
             return acc;
         }
 
-
-        
-        const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {}
-        console.error('Nested Ignore (2)', schemaPath, nestedIgnore, this.form)
+        const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
+        console.error("Nested Ignore (2)", schemaPath, nestedIgnore, this.form);
 
         const tableMetadata = {
             keyColumn: tempPropertyKey,
@@ -253,7 +251,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
     }
 
     const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : ignore?.[name];
-    console.log('Nested Ignore', name, nestedIgnore)
+    console.log("Nested Ignore", name, nestedIgnore);
 
     // Normal table parsing
     const tableMetadata = {
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 d3da2e454..550bc9bb2 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -22,11 +22,10 @@ const imagingPlaneKey = "imaging_plane";
 
 const propsToIgnore = {
     Ophys: {
-
         // NOTE: Get this to work
-        '*': {
+        "*": {
             starting_time: true,
-            rate: true
+            rate: true,
         },
         ImagingPlane: {
             [imagingPlaneKey]: true,
@@ -47,7 +46,7 @@ const propsToIgnore = {
             unit: true,
             conversion: true,
             offset: true,
-        }
+        },
     },
     Icephys: true, // Always ignore icephys metadata (for now)
     Behavior: true, // Always ignore behavior metadata (for now)
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 5bd2c9a3c..a7a7fd58e 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -117,7 +117,7 @@ export class TableCell extends LitElement {
 
     validateOnChange?: ValidationFunction
     ignore?: { [key: string]: boolean } = {}
-    
+
     onValidate: OnValidateFunction = () => {}
 
     #validator: ValidationFunction = () => true
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index cb5c0e142..aed7ee7ab 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -44,7 +44,7 @@ export class NestedEditor extends LitElement {
         const schema = this.schema
 
         console.error('FIX THIS', this.ignore)
-        
+
         const input = this.#input = new JSONSchemaInput({
             schema,
             value: data,

From 83f950f16b2494c92069526a8f7ba83de78b115c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 01:48:01 +0000
Subject: [PATCH 100/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/Accordion.js                      | 3 ++-
 src/renderer/src/stories/FileSystemSelector.js             | 7 ++++---
 src/renderer/src/stories/JSONSchemaForm.js                 | 3 ++-
 src/renderer/src/stories/SimpleTable.js                    | 6 ++++--
 src/renderer/src/stories/Table.js                          | 3 ++-
 src/renderer/src/stories/pages/Page.js                     | 6 ++++--
 .../stories/pages/guided-mode/data/GuidedPathExpansion.js  | 6 ++++--
 src/renderer/src/stories/pages/utils.js                    | 3 ++-
 8 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/src/renderer/src/stories/Accordion.js b/src/renderer/src/stories/Accordion.js
index b4f502944..d4711e82d 100644
--- a/src/renderer/src/stories/Accordion.js
+++ b/src/renderer/src/stories/Accordion.js
@@ -234,7 +234,8 @@ export class Accordion extends LitElement {
     };
 
     toOpen = (state = this.open) => {
-        if (!this.toggleable) return true; // Force open if not toggleable
+        if (!this.toggleable)
+            return true; // Force open if not toggleable
         else if (this.disabled) return false; // Force closed if disabled
         return state;
     };
diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index 507ff0bac..831fbe236 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -167,9 +167,10 @@ export class FilesystemSelector extends LitElement {
             // const path = file.filePath ?? file.filePaths?.[0];
             this.#handleFiles(results.filePath ?? results.filePaths, type);
         } else {
-            let handles = await (type === "directory"
-                ? window.showDirectoryPicker()
-                : window.showOpenFilePicker({ multiple: this.multiple })
+            let handles = await (
+                type === "directory"
+                    ? window.showDirectoryPicker()
+                    : window.showOpenFilePicker({ multiple: this.multiple })
             ).catch(() => []); // Call using the same options
 
             const result = Array.isArray(handles) ? handles.map(({ name }) => name) : handles.name;
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index a9a5a706a..0875dffa1 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -684,7 +684,8 @@ export class JSONSchemaForm extends LitElement {
         const res = entries
             .map(([key, value]) => {
                 if (!value.properties && key === "definitions") return false; // Skip definitions
-                if (this.ignore["*"]?.[key]) return false; // Skip all properties with this name
+                if (this.ignore["*"]?.[key])
+                    return false; // Skip all properties with this name
                 else if (this.ignore[key] === true) return false; // Skip this property
                 if (this.showLevelOverride >= path.length) return isRenderable(key, value);
                 if (required[key]) return isRenderable(key, value);
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 5edd29100..9449df371 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -286,7 +286,8 @@ export class SimpleTable extends LitElement {
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data)) return this.#data; //.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data))
+            return this.#data; //.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
@@ -679,7 +680,8 @@ export class SimpleTable extends LitElement {
         let target = this.#data;
 
         if (!isResolved) {
-            if (!this.keyColumn) this.#data[rowName] = {}; // Add new row to array
+            if (!this.keyColumn)
+                this.#data[rowName] = {}; // Add new row to array
             else {
                 rowName = row;
                 if (!this.#unresolved[rowName]) this.#unresolved[rowName] = {}; // Ensure row exists
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 0c5269329..0d56e0da6 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -473,7 +473,8 @@ export class Table extends LitElement {
                 let target = this.data;
 
                 if (!isResolved) {
-                    if (!this.keyColumn) this.data[rowName] = {}; // Add new row to array
+                    if (!this.keyColumn)
+                        this.data[rowName] = {}; // Add new row to array
                     else {
                         rowName = row;
                         if (!unresolved[rowName]) unresolved[rowName] = {}; // Ensure row exists
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index e1655d055..d1881c2fd 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -66,7 +66,8 @@ export class Page extends LitElement {
                 transition === 1 && // Only ensure save for standard forward progression
                 !this.info.states.saved)
         ) {
-            if (transition === 1) await this.save(); // Save before a single forward transition
+            if (transition === 1)
+                await this.save(); // Save before a single forward transition
             else {
                 await Swal.fire({
                     title: "You have unsaved data on this page.",
@@ -144,7 +145,8 @@ export class Page extends LitElement {
         if (!Array.isArray(toRun)) toRun = this.mapSessions();
 
         // Filter the sessions to run
-        if (typeof original === "number") toRun = randomizeElements(toRun, original); // Grab a random set of sessions
+        if (typeof original === "number")
+            toRun = randomizeElements(toRun, original); // Grab a random set of sessions
         else if (typeof original === "string") toRun = toRun.filter(({ subject }) => subject === original);
         else if (typeof original === "function") toRun = toRun.filter(original);
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 29b91d1f5..182a10eb2 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -189,12 +189,14 @@ export class GuidedPathExpansionPage extends Page {
             if (!keepExistingData) {
                 for (let sub in globalResults) {
                     const subRef = results[sub];
-                    if (!subRef) delete globalResults[sub]; // Delete removed subjects
+                    if (!subRef)
+                        delete globalResults[sub]; // Delete removed subjects
                     else {
                         for (let ses in globalResults[sub]) {
                             const sesRef = subRef[ses];
 
-                            if (!sesRef) delete globalResults[sub][ses]; // Delete removed sessions
+                            if (!sesRef)
+                                delete globalResults[sub][ses]; // Delete removed sessions
                             else {
                                 const globalSesRef = globalResults[sub][ses];
 
diff --git a/src/renderer/src/stories/pages/utils.js b/src/renderer/src/stories/pages/utils.js
index d793377d7..492de2fb9 100644
--- a/src/renderer/src/stories/pages/utils.js
+++ b/src/renderer/src/stories/pages/utils.js
@@ -53,7 +53,8 @@ export function merge(toMerge = {}, target = {}, mergeOptions = {}) {
         } else if (isObject(value)) {
             if (isObject(targetValue)) target[k] = merge(value, targetValue, mergeOptions);
             else {
-                if (mergeOptions.clone) target[k] = merge(value, {}, mergeOptions); // Replace primitive values
+                if (mergeOptions.clone)
+                    target[k] = merge(value, {}, mergeOptions); // Replace primitive values
                 else target[k] = value; // Replace object values
             }
         } else target[k] = value; // Replace primitive values

From e955c6950079a7f03027a8f7c244be3315b96004 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 23 Jan 2024 09:01:49 -0800
Subject: [PATCH 101/133] Fix deep ignore passing. Don't render empty
 TwoPhotonSeries. Reorder some properties

---
 schemas/base-metadata.schema.ts                 | 11 ++++++++++-
 src/renderer/src/stories/JSONSchemaForm.js      |  6 ++----
 src/renderer/src/stories/JSONSchemaInput.js     | 14 ++++++++------
 src/renderer/src/stories/SimpleTable.js         |  5 ++++-
 .../pages/guided-mode/data/GuidedMetadata.js    | 17 +++++++++++++++--
 src/renderer/src/stories/table/cells/input.ts   |  3 +--
 6 files changed, 40 insertions(+), 16 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index b7bfde33f..ab22bbb18 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -109,7 +109,16 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
                 "name",
                 "description",
                 "device",
-                "optical_channel"
+                "optical_channel",
+                "excitation_lambda",
+                "indicator",
+                "location",
+                "reference_frame",
+                "imaging_rate",
+                'grid_spacing',
+                "grid_spacing_unit",
+                "origin_coords",
+                'origin_coords_unit'
             ]
 
             imagingPlane.items.properties.optical_channel.items.order = ["name", "description"]
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 0875dffa1..8835204fe 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1091,10 +1091,8 @@ export class JSONSchemaForm extends LitElement {
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
 
             if (renderableInside.length) {
-                const allIgnore = this.ignore["*"] ?? {};
-                const ignore = this.ignore[name] ?? {};
-                if (ignore["*"]) ignore["*"] = { ...allIgnore, ...ignore["*"] };
-                else ignore["*"] = allIgnore;
+
+                const ignore = getIgnore(this.ignore, name)
 
                 const ogContext = this;
                 const nested = (this.#nestedForms[name] = new JSONSchemaForm({
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 9e7bbf9f1..c871f1e00 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -15,8 +15,10 @@ import { Search } from "./Search";
 import tippy from "tippy.js";
 
 export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
-    const path = [...fullPath];
-    const name = path.splice(-1)[0];
+
+    const name = fullPath.slice(-1)[0]
+    const path = fullPath.slice(0, -1);
+    
     const schema = this.schema;
     const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
     const validateOnChange = this.validateOnChange;
@@ -182,7 +184,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         }
 
         const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
-        console.error("Nested Ignore (2)", schemaPath, nestedIgnore, this.form);
 
         const tableMetadata = {
             keyColumn: tempPropertyKey,
@@ -250,8 +251,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         if (table) return table;
     }
 
-    const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : ignore?.[name];
-    console.log("Nested Ignore", name, nestedIgnore);
+    const nestedIgnore = getIgnore(ignore, fullPath)
 
     // Normal table parsing
     const tableMetadata = {
@@ -586,6 +586,8 @@ export class JSONSchemaInput extends LitElement {
 
         const input = this.#render();
 
+        if (input === null) return null; // Hide rendering
+
         return html`
             <div class="${this.required || this.conditional ? "required" : ""} ${
                 this.conditional ? "conditional" : ""
@@ -811,7 +813,7 @@ export class JSONSchemaInput extends LitElement {
                 onUpdate: this.#updateData,
                 onThrow: this.#onThrow,
             });
-            if (custom) return custom;
+            if (custom || custom === null) return custom;
         }
 
         // Handle file and directory formats
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 9449df371..b4a5f4dc0 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -13,6 +13,7 @@ import "./Button";
 import tippy from "tippy.js";
 import { sortTable } from "./Table";
 import { NestedInputCell } from "./table/cells/input";
+import { getIgnore } from "./JSONSchemaForm";
 
 var isMac = navigator.platform.toUpperCase().indexOf("MAC") >= 0;
 
@@ -723,6 +724,8 @@ export class SimpleTable extends LitElement {
 
         const schema = this.#schema[fullInfo.col];
 
+        const ignore = getIgnore(this.ignore, [ fullInfo.col ]);
+
         // Track the cell renderer
         const cell = new TableCell({
             info: {
@@ -735,7 +738,7 @@ export class SimpleTable extends LitElement {
             },
             value,
             schema,
-            ignore: this.ignore,
+            ignore,
             validateOnChange: async (
                 value,
                 path = [],
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 1d93e0c5d..9d1e045ac 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -61,10 +61,8 @@ const propsToIgnore = {
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
 import {
-    JSONSchemaInput,
     createTable,
     getEditableItems,
-    isEditableObject,
     isPatternProperties,
 } from "../../../JSONSchemaInput.js";
 import { html } from "lit";
@@ -237,7 +235,11 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             renderCustomHTML: function (name, inputSchema, localPath, { onUpdate, onThrow }) {
+
+                if (name === "TwoPhotonSeries" && (!this.value || !this.value.length)) return null
+
                 if (isPatternProperties(this.pattern)) {
+
                     if (patternPropsToRetitle.includes(this.form.base.join("."))) {
                         const schemaCopy = { ...inputSchema };
                         inputSchema.title = "Plane Metadata<hr>";
@@ -256,6 +258,8 @@ export class GuidedMetadataPage extends ManagedPage {
                         return Object.entries(data)
                             .map(([name, value]) => {
                                 return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
+
+                                    // NOTE: No name can be passed into createTable without side effects...
                                     const mockInput = {
                                         schema: {
                                             type: "object",
@@ -264,6 +268,9 @@ export class GuidedMetadataPage extends ManagedPage {
                                         renderTable: this.renderTable,
                                         value: value,
                                         pattern: pattern,
+                                        form: {
+                                            ignore: this.form.ignore
+                                        }
                                     };
 
                                     return html`
@@ -289,6 +296,12 @@ export class GuidedMetadataPage extends ManagedPage {
             },
 
             renderTable: function (name, metadata) {
+
+                // Ignore all additional properties—even if specified in the data
+                const updatedSchema = structuredClone(metadata.schema);
+                updatedSchema.additionalProperties = false;
+                metadata.schema = updatedSchema;
+                
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);
                 else return true; // All other tables are handled by the default behavior
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index aed7ee7ab..18ffbdbd5 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -43,14 +43,13 @@ export class NestedEditor extends LitElement {
 
         const schema = this.schema
 
-        console.error('FIX THIS', this.ignore)
 
         const input = this.#input = new JSONSchemaInput({
             schema,
             value: data,
             path: [],
-            ignore: this.ignore,
             form: {
+                ignore: this.ignore,
                 triggerValidation: (name, completePath, _, __, schema, parent) => {
                     const path = [ ...completePath, name ]
                     const value = parent[name]

From 09e3793fbc29a338194b0a99ff3083b12b9aa211 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 17:02:05 +0000
Subject: [PATCH 102/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js     |  3 +--
 src/renderer/src/stories/JSONSchemaInput.js    |  7 +++----
 src/renderer/src/stories/SimpleTable.js        |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js   | 18 +++++-------------
 4 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 8835204fe..a42ea18dc 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1091,8 +1091,7 @@ export class JSONSchemaForm extends LitElement {
             const nestedResults = __disabled[name] ?? results[name] ?? this.results[name]; // One or the other will exist—depending on global or local disabling
 
             if (renderableInside.length) {
-
-                const ignore = getIgnore(this.ignore, name)
+                const ignore = getIgnore(this.ignore, name);
 
                 const ogContext = this;
                 const nested = (this.#nestedForms[name] = new JSONSchemaForm({
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index c871f1e00..ae8733b99 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -15,10 +15,9 @@ import { Search } from "./Search";
 import tippy from "tippy.js";
 
 export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
-
-    const name = fullPath.slice(-1)[0]
+    const name = fullPath.slice(-1)[0];
     const path = fullPath.slice(0, -1);
-    
+
     const schema = this.schema;
     const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
     const validateOnChange = this.validateOnChange;
@@ -251,7 +250,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         if (table) return table;
     }
 
-    const nestedIgnore = getIgnore(ignore, fullPath)
+    const nestedIgnore = getIgnore(ignore, fullPath);
 
     // Normal table parsing
     const tableMetadata = {
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index b4a5f4dc0..0d5da283e 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -724,7 +724,7 @@ export class SimpleTable extends LitElement {
 
         const schema = this.#schema[fullInfo.col];
 
-        const ignore = getIgnore(this.ignore, [ fullInfo.col ]);
+        const ignore = getIgnore(this.ignore, [fullInfo.col]);
 
         // Track the cell renderer
         const cell = new TableCell({
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 9d1e045ac..3e205a665 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -60,11 +60,7 @@ const propsToIgnore = {
 };
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
-import {
-    createTable,
-    getEditableItems,
-    isPatternProperties,
-} from "../../../JSONSchemaInput.js";
+import { createTable, getEditableItems, isPatternProperties } from "../../../JSONSchemaInput.js";
 import { html } from "lit";
 
 const getInfoFromId = (key) => {
@@ -235,11 +231,9 @@ export class GuidedMetadataPage extends ManagedPage {
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
 
             renderCustomHTML: function (name, inputSchema, localPath, { onUpdate, onThrow }) {
-
-                if (name === "TwoPhotonSeries" && (!this.value || !this.value.length)) return null
+                if (name === "TwoPhotonSeries" && (!this.value || !this.value.length)) return null;
 
                 if (isPatternProperties(this.pattern)) {
-
                     if (patternPropsToRetitle.includes(this.form.base.join("."))) {
                         const schemaCopy = { ...inputSchema };
                         inputSchema.title = "Plane Metadata<hr>";
@@ -258,7 +252,6 @@ export class GuidedMetadataPage extends ManagedPage {
                         return Object.entries(data)
                             .map(([name, value]) => {
                                 return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
-
                                     // NOTE: No name can be passed into createTable without side effects...
                                     const mockInput = {
                                         schema: {
@@ -269,8 +262,8 @@ export class GuidedMetadataPage extends ManagedPage {
                                         value: value,
                                         pattern: pattern,
                                         form: {
-                                            ignore: this.form.ignore
-                                        }
+                                            ignore: this.form.ignore,
+                                        },
                                     };
 
                                     return html`
@@ -296,12 +289,11 @@ export class GuidedMetadataPage extends ManagedPage {
             },
 
             renderTable: function (name, metadata) {
-
                 // Ignore all additional properties—even if specified in the data
                 const updatedSchema = structuredClone(metadata.schema);
                 updatedSchema.additionalProperties = false;
                 metadata.schema = updatedSchema;
-                
+
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors
                 if (name !== "Electrodes") return new SimpleTable(metadata);
                 else return true; // All other tables are handled by the default behavior

From a0edf0df0cd144b96495e1cf7da56108d754222b Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 23 Jan 2024 14:37:58 -0800
Subject: [PATCH 103/133] Handle additional properties like custom pattern
 properties

---
 src/renderer/src/stories/JSONSchemaForm.js    |   6 +-
 src/renderer/src/stories/JSONSchemaInput.js   |  11 +-
 .../pages/guided-mode/data/GuidedMetadata.js  | 126 +++++++++++++++---
 3 files changed, 117 insertions(+), 26 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index a42ea18dc..464d902ca 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -21,6 +21,8 @@ const encode = (str) => {
     }
 };
 
+const additionalPropPattern = "additional";
+
 const provideNaNMessage = `<br/><small>Type <b>NaN</b> to represent an unknown value.</small>`;
 
 import { Validator } from "jsonschema";
@@ -1243,11 +1245,11 @@ export class JSONSchemaForm extends LitElement {
             rendered = [...rendered, ...patternProps];
         }
 
-        const additionalPropPattern = "additional";
         const additionalProps = getEditableItems(results, additionalPropPattern, { schema });
 
         // Render additional properties
         if (allowAdditionalProperties) {
+            
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
             if (!additionalProps.length) return rendered;
 
@@ -1262,7 +1264,9 @@ export class JSONSchemaForm extends LitElement {
                 results,
                 additionalPropPattern
             );
+
             return [...rendered, additionalElement];
+
         }
 
         // Delete additional properties off the final results
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index ae8733b99..1f157782e 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -15,6 +15,7 @@ import { Search } from "./Search";
 import tippy from "tippy.js";
 
 export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
+
     const name = fullPath.slice(-1)[0];
     const path = fullPath.slice(0, -1);
 
@@ -260,7 +261,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         ignore: nestedIgnore, // According to schema
 
         onUpdate: function () {
-            return onUpdate.call(this, fullPath);
+            return onUpdate.call(this, fullPath, this.data); // Update all table data
         },
 
         validateOnChange: (...args) => commonValidationFunction(fullPath, ...args),
@@ -268,6 +269,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         ...commonTableMetadata,
     };
 
+
     const table = (this.table = this.renderTable(name, tableMetadata, path)); // Try creating table. Otherwise use nested form
 
     if (table) {
@@ -281,7 +283,10 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 // Schema or value indicates editable object
 export const isEditableObject = (schema, value) =>
     schema.type === "object" || (value && typeof value === "object" && !Array.isArray(value));
-const isAdditionalProperties = (pattern) => pattern === "additional";
+
+
+
+export const isAdditionalProperties = (pattern) => pattern === "additional";
 export const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
 export const getEditableItems = (value, pattern, { name, schema } = {}) => {
@@ -310,8 +315,6 @@ export const getEditableItems = (value, pattern, { name, schema } = {}) => {
     });
 };
 
-const sleep = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
-
 const isFilesystemSelector = (name = "", format) => {
     if (Array.isArray(format)) return format.map((f) => isFilesystemSelector(name, f)).every(Boolean) ? format : null;
 
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 3e205a665..797320281 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -7,7 +7,7 @@ import { Modal } from "../../../Modal";
 import { validateOnChange } from "../../../../validation/index.js";
 import { resolveGlobalOverrides, resolveMetadata } from "./utils.js";
 import Swal from "sweetalert2";
-import { SimpleTable } from "../../../SimpleTable.js";
+import { SimpleTable } from "../../../SimpleTable";
 import { onThrow } from "../../../../errors";
 import { merge } from "../../utils.js";
 import { NWBFilePreview } from "../../../preview/NWBFilePreview.js";
@@ -60,7 +60,7 @@ const propsToIgnore = {
 };
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
-import { createTable, getEditableItems, isPatternProperties } from "../../../JSONSchemaInput.js";
+import { createTable, getEditableItems, isPatternProperties, isAdditionalProperties } from "../../../JSONSchemaInput.js";
 import { html } from "lit";
 
 const getInfoFromId = (key) => {
@@ -178,7 +178,15 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveMetadata(subject, session, globalState);
 
-        const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
+        const additionalPropertiesToRetitle = [
+            "Ophys.ImageSegmentation",
+        ]
+
+        const patternPropsToRetitle = [
+            "Ophys.Fluorescence", 
+            "Ophys.DfOverF", 
+            "Ophys.SegmentationImages"
+        ];
 
         // Create the form
         const form = new JSONSchemaForm({
@@ -233,33 +241,83 @@ export class GuidedMetadataPage extends ManagedPage {
             renderCustomHTML: function (name, inputSchema, localPath, { onUpdate, onThrow }) {
                 if (name === "TwoPhotonSeries" && (!this.value || !this.value.length)) return null;
 
-                if (isPatternProperties(this.pattern)) {
-                    if (patternPropsToRetitle.includes(this.form.base.join("."))) {
-                        const schemaCopy = { ...inputSchema };
-                        inputSchema.title = "Plane Metadata<hr>";
+                const isAdditional = isAdditionalProperties(this.pattern);
+                const isPattern = isPatternProperties(this.pattern);
+                
+
+                if (isAdditional || isPattern) {
 
-                        // One table with nested tables for each property
-                        const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
-                            (acc, { key, value }) => {
-                                acc[key] = value;
-                                return acc;
-                            },
-                            {}
-                        );
+                    // One table with nested tables for each property
+                    const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
+                        (acc, { key, value }) => {
+                            acc[key] = value;
+                            return acc;
+                        },
+                        {}
+                    );
 
-                        const nProps = Object.keys(data).length;
+                    const nProps = Object.keys(data).length;
+
+                    const schemaCopy = { ...inputSchema };
+
+                    if (additionalPropertiesToRetitle.includes(this.form.base.join("."))) {
+                        inputSchema.title = "";
+                        
+                        return Object.entries(data)
+                        .map(([name, value]) => {
+
+                            const mockInput = {
+                                schema: {
+                                    type: "array",
+                                    items: {
+                                        type: "object",
+                                        additionalProperties: true
+                                    },
+                                },
+                                renderTable: this.renderTable,
+                                value,
+                                form: {
+                                    ignore: this.form.ignore,
+                                },
+                            };
+
+
+                            const table = createTable.call(mockInput, [...localPath], {
+                                onUpdate: (localPath, value) => {
+                                    onUpdate([name, ...localPath], value, true, {
+                                        willTimeout: false,
+                                        onError: (e) => e,
+                                        onWarning: (e) => e,
+                                    })
+                                },
+                                onThrow: onThrow,
+                            })
+
+                            return html`
+                                <div style="width: 100%;">
+                                <h3>${header(name)}</h3>
+                                    ${table}
+                                </div>
+                            `;
+
+                        })
+                    }
+                      
+                    if (patternPropsToRetitle.includes(this.form.base.join("."))) {
+                        
+                        inputSchema.title = "Plane Metadata<hr>";
 
                         return Object.entries(data)
                             .map(([name, value]) => {
-                                return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
-                                    // NOTE: No name can be passed into createTable without side effects...
+
+                                const createNestedTable = (value, pattern, schema) => {
                                     const mockInput = {
                                         schema: {
                                             type: "object",
                                             items: schema,
                                         },
                                         renderTable: this.renderTable,
-                                        value: value,
+                                        value,
                                         pattern: pattern,
                                         form: {
                                             ignore: this.form.ignore,
@@ -281,17 +339,43 @@ export class GuidedMetadataPage extends ManagedPage {
                                             })}
                                         </div>
                                     `;
+                                }
+
+                                if (isAdditional) {
+                                    console.warn(value)
+                                    const data = value.reduce((acc, item) => {
+                                        const name = item.name
+                                        acc[name] = item;
+                                        return acc;
+                                    }, {})
+                                    console.error(data)
+                                    return createNestedTable(data, undefined, {
+                                        type: "object",
+                                        items: {
+                                            type: "object",
+                                            additionalProperties: true
+                                        }
+                                    })
+                                }
+
+
+                                return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
+                                    return createNestedTable(value, pattern, schema)
                                 });
                             })
                             .flat();
+
+
                     }
                 }
             },
 
             renderTable: function (name, metadata) {
-                // Ignore all additional properties—even if specified in the data
+
                 const updatedSchema = structuredClone(metadata.schema);
-                updatedSchema.additionalProperties = false;
+
+                if (updatedSchema.additionalProperties !== true) updatedSchema.additionalProperties = false; // Indicate all additional properties are false (if not true)
+
                 metadata.schema = updatedSchema;
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors

From 1ca496007d14ecc3580a699cfbd0e64e4e2a55da Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 22:38:47 +0000
Subject: [PATCH 104/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js    |  2 -
 src/renderer/src/stories/JSONSchemaInput.js   |  4 --
 .../pages/guided-mode/data/GuidedMetadata.js  | 61 ++++++++-----------
 3 files changed, 24 insertions(+), 43 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 464d902ca..6574a466a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -1249,7 +1249,6 @@ export class JSONSchemaForm extends LitElement {
 
         // Render additional properties
         if (allowAdditionalProperties) {
-            
             // NOTE: If no pre-existing additional properties exist, exclude the entire rendering group
             if (!additionalProps.length) return rendered;
 
@@ -1266,7 +1265,6 @@ export class JSONSchemaForm extends LitElement {
             );
 
             return [...rendered, additionalElement];
-
         }
 
         // Delete additional properties off the final results
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 1f157782e..f39a5c9bd 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -15,7 +15,6 @@ import { Search } from "./Search";
 import tippy from "tippy.js";
 
 export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
-
     const name = fullPath.slice(-1)[0];
     const path = fullPath.slice(0, -1);
 
@@ -269,7 +268,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         ...commonTableMetadata,
     };
 
-
     const table = (this.table = this.renderTable(name, tableMetadata, path)); // Try creating table. Otherwise use nested form
 
     if (table) {
@@ -284,8 +282,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 export const isEditableObject = (schema, value) =>
     schema.type === "object" || (value && typeof value === "object" && !Array.isArray(value));
 
-
-
 export const isAdditionalProperties = (pattern) => pattern === "additional";
 export const isPatternProperties = (pattern) => pattern && !isAdditionalProperties(pattern);
 
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 797320281..0427a23d8 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -60,7 +60,12 @@ const propsToIgnore = {
 };
 
 import { preprocessMetadataSchema } from "../../../../../../../schemas/base-metadata.schema";
-import { createTable, getEditableItems, isPatternProperties, isAdditionalProperties } from "../../../JSONSchemaInput.js";
+import {
+    createTable,
+    getEditableItems,
+    isPatternProperties,
+    isAdditionalProperties,
+} from "../../../JSONSchemaInput.js";
 import { html } from "lit";
 
 const getInfoFromId = (key) => {
@@ -178,15 +183,9 @@ export class GuidedMetadataPage extends ManagedPage {
 
         resolveMetadata(subject, session, globalState);
 
-        const additionalPropertiesToRetitle = [
-            "Ophys.ImageSegmentation",
-        ]
+        const additionalPropertiesToRetitle = ["Ophys.ImageSegmentation"];
 
-        const patternPropsToRetitle = [
-            "Ophys.Fluorescence", 
-            "Ophys.DfOverF", 
-            "Ophys.SegmentationImages"
-        ];
+        const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
 
         // Create the form
         const form = new JSONSchemaForm({
@@ -243,10 +242,8 @@ export class GuidedMetadataPage extends ManagedPage {
 
                 const isAdditional = isAdditionalProperties(this.pattern);
                 const isPattern = isPatternProperties(this.pattern);
-                
 
                 if (isAdditional || isPattern) {
-
                     // One table with nested tables for each property
                     const data = getEditableItems(this.value, this.pattern, { name, schema: this.schema }).reduce(
                         (acc, { key, value }) => {
@@ -262,16 +259,14 @@ export class GuidedMetadataPage extends ManagedPage {
 
                     if (additionalPropertiesToRetitle.includes(this.form.base.join("."))) {
                         inputSchema.title = "";
-                        
-                        return Object.entries(data)
-                        .map(([name, value]) => {
 
+                        return Object.entries(data).map(([name, value]) => {
                             const mockInput = {
                                 schema: {
                                     type: "array",
                                     items: {
                                         type: "object",
-                                        additionalProperties: true
+                                        additionalProperties: true,
                                     },
                                 },
                                 renderTable: this.renderTable,
@@ -281,35 +276,31 @@ export class GuidedMetadataPage extends ManagedPage {
                                 },
                             };
 
-
                             const table = createTable.call(mockInput, [...localPath], {
                                 onUpdate: (localPath, value) => {
                                     onUpdate([name, ...localPath], value, true, {
                                         willTimeout: false,
                                         onError: (e) => e,
                                         onWarning: (e) => e,
-                                    })
+                                    });
                                 },
                                 onThrow: onThrow,
-                            })
+                            });
 
                             return html`
                                 <div style="width: 100%;">
-                                <h3>${header(name)}</h3>
+                                    <h3>${header(name)}</h3>
                                     ${table}
                                 </div>
                             `;
-
-                        })
+                        });
                     }
-                      
+
                     if (patternPropsToRetitle.includes(this.form.base.join("."))) {
-                        
                         inputSchema.title = "Plane Metadata<hr>";
 
                         return Object.entries(data)
                             .map(([name, value]) => {
-
                                 const createNestedTable = (value, pattern, schema) => {
                                     const mockInput = {
                                         schema: {
@@ -339,39 +330,35 @@ export class GuidedMetadataPage extends ManagedPage {
                                             })}
                                         </div>
                                     `;
-                                }
+                                };
 
                                 if (isAdditional) {
-                                    console.warn(value)
+                                    console.warn(value);
                                     const data = value.reduce((acc, item) => {
-                                        const name = item.name
+                                        const name = item.name;
                                         acc[name] = item;
                                         return acc;
-                                    }, {})
-                                    console.error(data)
+                                    }, {});
+                                    console.error(data);
                                     return createNestedTable(data, undefined, {
                                         type: "object",
                                         items: {
                                             type: "object",
-                                            additionalProperties: true
-                                        }
-                                    })
+                                            additionalProperties: true,
+                                        },
+                                    });
                                 }
 
-
                                 return Object.entries(schemaCopy.patternProperties).map(([pattern, schema]) => {
-                                    return createNestedTable(value, pattern, schema)
+                                    return createNestedTable(value, pattern, schema);
                                 });
                             })
                             .flat();
-
-
                     }
                 }
             },
 
             renderTable: function (name, metadata) {
-
                 const updatedSchema = structuredClone(metadata.schema);
 
                 if (updatedSchema.additionalProperties !== true) updatedSchema.additionalProperties = false; // Indicate all additional properties are false (if not true)

From e4d5972839f7d0f81f1e94de11044aad598a50f5 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 23 Jan 2024 15:06:48 -0800
Subject: [PATCH 105/133] Fix tests

---
 src/renderer/src/stories/JSONSchemaInput.js | 16 ++++++----------
 src/renderer/src/stories/SimpleTable.js     |  4 ++--
 src/renderer/src/stories/table/Cell.ts      |  1 +
 3 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 1f157782e..cccd3964d 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -30,7 +30,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         path,
         parent,
         newValue,
-        baseSchema = itemSchema,
+        itemPropSchema,
         skip = 0
     ) => {
         const warnings = [];
@@ -38,14 +38,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
         const name = path.slice(-1)[0];
         const completePath = [...tableBasePath, ...path.slice(0, -1)];
-
-        // const toIterate = path.slice(skip);
-        const toIterate = path.filter((value) => typeof value === "string");
-
-        const itemPropSchema = toIterate.reduce((acc, key) => {
-            return acc?.properties?.[key] ?? acc?.items?.properties?.[key];
-        }, baseSchema);
-
         const result = await (validateOnChange
             ? this.onValidate
                 ? this.onValidate()
@@ -230,7 +222,11 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
                     } else delete previousValidValues[rowIdx];
                 }
 
-                return commonValidationFunction([], updatedPath, parent, newValue, schemaCopy, 1);
+                const toIterate = updatedPath.filter((value) => typeof value === "string");
+                
+                const itemPropsSchema = toIterate.reduce((acc, key) => acc?.properties?.[key] ?? acc?.items?.properties?.[key], schemaCopy);
+
+                return commonValidationFunction([], updatedPath, parent, newValue, itemPropsSchema, 1);
             },
             ...commonTableMetadata,
         };
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 0d5da283e..f41a0b871 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -743,12 +743,12 @@ export class SimpleTable extends LitElement {
                 value,
                 path = [],
                 parent = { ...this.#data[fullInfo.row] }, // A copy of the parent
-                schema
+                innerSchema = schema
             ) => {
                 if (!value && !this.validateEmptyCells) return true; // Empty cells are valid
 
                 const res = this.validateOnChange
-                    ? await this.validateOnChange([row, fullInfo.col, ...path], parent, value, schema)
+                    ? await this.validateOnChange([row, fullInfo.col, ...path], parent, value, innerSchema)
                     : true;
 
                 return res;
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index a7a7fd58e..0fa2e5c39 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -21,6 +21,7 @@ type OnValidateFunction = (info: ValidationResult) => void
 type TableCellProps = {
     value: string,
     info: { col: string }
+    ignore: { [key: string]: boolean },
     schema: {[key: string]: any},
     validateOnChange?: ValidationFunction,
     onValidate?: OnValidateFunction,

From 04aaba51b74d136c941d5c5ab0aac3f14721ceff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 23:07:14 +0000
Subject: [PATCH 106/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f888c679d..9e87694c2 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -24,14 +24,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
     const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : {};
 
-    const commonValidationFunction = async (
-        tableBasePath,
-        path,
-        parent,
-        newValue,
-        itemPropSchema,
-        skip = 0
-    ) => {
+    const commonValidationFunction = async (tableBasePath, path, parent, newValue, itemPropSchema, skip = 0) => {
         const warnings = [];
         const errors = [];
 
@@ -222,8 +215,11 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
                 }
 
                 const toIterate = updatedPath.filter((value) => typeof value === "string");
-                
-                const itemPropsSchema = toIterate.reduce((acc, key) => acc?.properties?.[key] ?? acc?.items?.properties?.[key], schemaCopy);
+
+                const itemPropsSchema = toIterate.reduce(
+                    (acc, key) => acc?.properties?.[key] ?? acc?.items?.properties?.[key],
+                    schemaCopy
+                );
 
                 return commonValidationFunction([], updatedPath, parent, newValue, itemPropsSchema, 1);
             },

From 591a14094d6e90db7f4b2c83ad3b0b63d16374c1 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 23 Jan 2024 15:35:09 -0800
Subject: [PATCH 107/133] Fix validation and pressing enter on table cells

---
 src/renderer/src/stories/JSONSchemaInput.js      |  5 +++--
 src/renderer/src/stories/SimpleTable.js          |  4 ++++
 .../pages/guided-mode/data/GuidedMetadata.js     |  2 +-
 src/renderer/src/stories/table/Cell.ts           |  3 +++
 src/renderer/src/stories/table/cells/base.ts     | 16 +++++++++++++++-
 src/renderer/src/stories/table/cells/input.ts    |  2 +-
 6 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index f888c679d..c88cd9a8f 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -29,14 +29,15 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         path,
         parent,
         newValue,
-        itemPropSchema,
-        skip = 0
+        itemPropSchema
     ) => {
         const warnings = [];
         const errors = [];
 
+
         const name = path.slice(-1)[0];
         const completePath = [...tableBasePath, ...path.slice(0, -1)];
+
         const result = await (validateOnChange
             ? this.onValidate
                 ? this.onValidate()
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index f41a0b871..2f2be5d16 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -800,6 +800,10 @@ export class SimpleTable extends LitElement {
 
         td.ondblclick = () => cell.toggle(true);
 
+        cell.addEventListener('blur', () => {
+            this.#clearSelected(); // NOTE: May now make other clearSelected calls redundant
+        })
+
         td.appendChild(cell);
         return td;
     };
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 0427a23d8..709689274 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -41,7 +41,7 @@ const propsToIgnore = {
             control_description: true,
             comments: true,
             resolution: true,
-            dimension: true,
+            // dimension: true,
             device: true,
             unit: true,
             conversion: true,
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 0fa2e5c39..e8ca07918 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -228,6 +228,9 @@ export class TableCell extends LitElement {
                     ignore: this.ignore
                 }
             })
+
+            // Forward blur events
+            this.input.addEventListener('blur', () =>  this.dispatchEvent(new Event('blur')))
         }
 
         this.#cls = cls
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index e0c94fe80..0e18174c2 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -93,7 +93,9 @@ export class TableCellBase extends LitElement {
             if (ev.inputType.includes('history')) this.setText(this.#editable.innerText) // Catch undo / redo}
         })
 
-        this.#editable.addEventListener('blur', () => this.#editable.removeAttribute('contenteditable'))
+        this.#editable.addEventListener('blur', () => {
+            this.#editable.removeAttribute('contenteditable')
+        })
 
     }
 
@@ -112,6 +114,18 @@ export class TableCellBase extends LitElement {
 
             this.setAttribute('editing', '')
 
+            const listenForEnter = (ev: KeyboardEvent) => {
+                if (ev.key === 'Enter') {
+                    ev.preventDefault()
+                    ev.stopPropagation()
+                    this.#editable.blur()
+                    this.removeEventListener('keydown', listenForEnter)
+                    this.toggle(false)
+                }
+            }
+
+            this.addEventListener('keydown', listenForEnter)
+
             if (this.#editor === this.#editable) {
                 this.#editable.setAttribute('contenteditable', '')
                 this.#editable.style.pointerEvents = 'auto'
diff --git a/src/renderer/src/stories/table/cells/input.ts b/src/renderer/src/stories/table/cells/input.ts
index 18ffbdbd5..a67486c52 100644
--- a/src/renderer/src/stories/table/cells/input.ts
+++ b/src/renderer/src/stories/table/cells/input.ts
@@ -53,7 +53,7 @@ export class NestedEditor extends LitElement {
                 triggerValidation: (name, completePath, _, __, schema, parent) => {
                     const path = [ ...completePath, name ]
                     const value = parent[name]
-                    if (this.validateOnChange) return this.validateOnChange(value, path, parent) // NOTE: Flipped because usually only value is passed
+                    if (this.validateOnChange) return this.validateOnChange(value, path, parent, schema) // NOTE: Flipped because usually only value is passed
                 }
             },
             renderTable: (name, metadata, path) => new SimpleTable(metadata) // NOTE: Would be most ideal to have a reference to the containing input...

From ef24e34fd84a278a5df632276fabc210a55f2f26 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 23:35:54 +0000
Subject: [PATCH 108/133] [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 +--------
 src/renderer/src/stories/SimpleTable.js     | 4 ++--
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 75a47b857..b9a9a81bf 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -24,14 +24,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
     const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : {};
 
-    const commonValidationFunction = async (
-        tableBasePath,
-        path,
-        parent,
-        newValue,
-        itemPropSchema
-    ) => {
-        
+    const commonValidationFunction = async (tableBasePath, path, parent, newValue, itemPropSchema) => {
         const warnings = [];
         const errors = [];
 
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 2f2be5d16..6edaa50aa 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -800,9 +800,9 @@ export class SimpleTable extends LitElement {
 
         td.ondblclick = () => cell.toggle(true);
 
-        cell.addEventListener('blur', () => {
+        cell.addEventListener("blur", () => {
             this.#clearSelected(); // NOTE: May now make other clearSelected calls redundant
-        })
+        });
 
         td.appendChild(cell);
         return td;

From 949dcedb4e4bd77121ba7501fcf8c9b93a535065 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 23 Jan 2024 15:39:28 -0800
Subject: [PATCH 109/133] Update GuidedMetadata.js

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

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 709689274..0427a23d8 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -41,7 +41,7 @@ const propsToIgnore = {
             control_description: true,
             comments: true,
             resolution: true,
-            // dimension: true,
+            dimension: true,
             device: true,
             unit: true,
             conversion: true,

From 44c902527a017a74df18af9ee66ddb189d2c3671 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 11:47:24 -0800
Subject: [PATCH 110/133] Fix array autofill for tables

---
 src/renderer/src/stories/SimpleTable.js      |  4 +--
 src/renderer/src/stories/table/Cell.ts       |  9 ++++---
 src/renderer/src/stories/table/cells/base.ts | 28 +++++++-------------
 src/renderer/src/stories/table/convert.ts    |  4 +++
 4 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 6edaa50aa..514d5d903 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -238,8 +238,8 @@ export class SimpleTable extends LitElement {
                 const path = this.#getPath(ev);
                 if (path[0] === document.body)
                     Object.values(this.#selected).forEach((row) => {
-                        row.forEach((row) => {
-                            if (row.type !== "table") row.setInput("");
+                        row.forEach((cell) => {
+                            if (cell.type !== "table") cell.setInput("");
                         });
                     });
                 return;
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index e8ca07918..86fe647a1 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -110,6 +110,8 @@ export class TableCell extends LitElement {
     }
 
     set value(value) {
+        if (!value) value = []
+
         if (this.input) this.input.set(renderValue(value, this.schema)) // Allow null to be set directly
         this.#value = this.input
                             ? this.input.getValue() // Ensure all operations are undoable / value is coerced
@@ -166,9 +168,10 @@ export class TableCell extends LitElement {
 
     setInput(value: any) {
         this.interacted = persistentInteraction
-        this.value = value
-        // if (this.input) this.input.set(value)  // Ensure all operations are undoable
-        // else this.#value = value // Silently set value if not rendered yet
+        // this.value = value
+
+        if (this.input) this.input.set(value)  // Ensure all operations are undoable
+        else this.#value = value // Silently set value if not rendered yet
     }
 
     #value
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 0e18174c2..feca9ca0b 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -35,7 +35,7 @@ export class TableCellBase extends LitElement {
     static get styles() {
         return css`
 
-            #editable {
+            .editable {
                 padding: 5px 10px;
                 pointer-events: none;
             }
@@ -45,14 +45,15 @@ export class TableCellBase extends LitElement {
                 cursor: text;
             }
 
-             .editor, :host([editing]) .renderer {
+            #editor, :host([editing]) .renderer {
                 opacity: 0;
                 pointer-events: none;
-                position: absolute;
+                display: none;
             }
 
-            .renderer, :host([editing]) .editor {
+            .renderer, :host([editing]) #editor {
                 position: relative;
+                display: unset;
                 pointer-events: all;
                 opacity: 1;
             }
@@ -229,33 +230,22 @@ export class TableCellBase extends LitElement {
 
         this.interacted = false
 
-        this.#editable.id = 'editable'
+        this.#editable.classList.add('editable')
 
         const editor = this.#editor = this.#render('editor')
         const renderer = this.#renderer = this.#render('renderer')
+        
 
         this.addEventListener('blur', (ev) => {
             ev.stopPropagation()
             this.toggle(false)
         })
 
+        
 
         if (!editor || !renderer || renderer === editor) return editor || renderer
-        // else {
-        //     const container = document.createElement('div')
-        //     const rendererContainer = document.createElement('div')
-        //     rendererContainer.classList.add('renderer')
-        //     rendererContainer.append(renderer)
 
-        //     const editorContainer = document.createElement('div')
-        //     editorContainer.classList.add('renderer')
-        //     editorContainer.append(renderer)
-
-        //     container.append(renderer, editor)
-        //     return container
-        // }
-
-        return html`<div class="renderer">${renderer}</div><div class="editor">${editor}</div>`
+        return html`<div class="renderer">${renderer}</div><div id="editor">${editor}</div>`
     }
 }
 
diff --git a/src/renderer/src/stories/table/convert.ts b/src/renderer/src/stories/table/convert.ts
index 62b437483..794724882 100644
--- a/src/renderer/src/stories/table/convert.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -1,4 +1,5 @@
 export const renderValue = (value: any, schema: any) => {
+    
     if (schema.type === 'number' || schema.type === 'integer') {
         if (value === null) return ''
     }
@@ -7,6 +8,9 @@ export const renderValue = (value: any, schema: any) => {
 }
 
 export const getValue = (value: any, schema: any) => {
+
+    if (schema.type === 'array' && !value.length) return undefined
+
     if (schema.type === 'number' || schema.type === 'integer') {
 
         if (typeof value === 'number') return value

From 713cee61cdc3dd46d45445c1ab492e3cb9dfb537 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 19:49:11 +0000
Subject: [PATCH 111/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/table/cells/base.ts | 4 ++--
 src/renderer/src/stories/table/convert.ts    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index feca9ca0b..1dca267cb 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -234,14 +234,14 @@ export class TableCellBase extends LitElement {
 
         const editor = this.#editor = this.#render('editor')
         const renderer = this.#renderer = this.#render('renderer')
-        
+
 
         this.addEventListener('blur', (ev) => {
             ev.stopPropagation()
             this.toggle(false)
         })
 
-        
+
 
         if (!editor || !renderer || renderer === editor) return editor || renderer
 
diff --git a/src/renderer/src/stories/table/convert.ts b/src/renderer/src/stories/table/convert.ts
index 794724882..cef7a43a4 100644
--- a/src/renderer/src/stories/table/convert.ts
+++ b/src/renderer/src/stories/table/convert.ts
@@ -1,5 +1,5 @@
 export const renderValue = (value: any, schema: any) => {
-    
+
     if (schema.type === 'number' || schema.type === 'integer') {
         if (value === null) return ''
     }

From 2c51b409f5f74ffb167b0890cae07f0c60f90173 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 11:49:45 -0800
Subject: [PATCH 112/133] Fix pipeline generation button

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

diff --git a/src/renderer/src/stories/pages/settings/SettingsPage.js b/src/renderer/src/stories/pages/settings/SettingsPage.js
index 3cd3ae357..8ba75bcc3 100644
--- a/src/renderer/src/stories/pages/settings/SettingsPage.js
+++ b/src/renderer/src/stories/pages/settings/SettingsPage.js
@@ -180,8 +180,7 @@ export class SettingsPage extends Page {
         });
 
         setTimeout(() => {
-            const testFolderInput = this.form.getInput(["developer", "testing_data_folder"]);
-            console.log(testFolderInput);
+            const testFolderInput = this.form.getFormElement(["developer", "testing_data_folder"]);
             testFolderInput.after(generatePipelineButton);
         }, 100);
 

From 83f0043bec3db5be1dc0e3040245dfcf2a354713 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 11:59:20 -0800
Subject: [PATCH 113/133] Fix error headers and modal header

---
 src/renderer/src/stories/JSONSchemaForm.js | 6 ++++--
 src/renderer/src/stories/Modal.ts          | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 6574a466a..24affb49f 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -388,12 +388,14 @@ export class JSONSchemaForm extends LitElement {
                     else e.message = `${e.message}. ${provideNaNMessage}`;
                 }
 
+                const prevHeader = name ? header(name) : 'Row'
+
                 return {
                     type: "error",
                     message: `${
                         typeof propName === "string"
-                            ? `${header(propName)}${isRow ? ` on Row ${rowName}` : ""}`
-                            : `Row ${propName}`
+                            ? `${header(propName)}${isRow ? ` on ${prevHeader} ${rowName}` : ""}`
+                            : `${prevHeader} ${propName}`
                     } ${e.message}.`,
                 };
             })
diff --git a/src/renderer/src/stories/Modal.ts b/src/renderer/src/stories/Modal.ts
index 18f943603..e9832e92c 100644
--- a/src/renderer/src/stories/Modal.ts
+++ b/src/renderer/src/stories/Modal.ts
@@ -189,7 +189,7 @@ export class Modal extends LitElement {
       <nwb-overlay .open=${this.open}>
         <div class="modal-content ${this.open ? 'open' : ''}" style="${this.width ? `width: ${this.width};` : ''} ${this.height ? `height: ${this.height};` : ''}">
           <div class="modal-header">
-              ${(this.header && this.header instanceof HTMLElement) ? this.header : html`span title="${this.header}">${this.header}</span>`}
+              ${(this.header && this.header instanceof HTMLElement) ? this.header : html`<span title="${this.header}">${this.header}</span>`}
               <div class="modal-controls">
               ${ this.controls }
               ${ this.showCloseButton ? html`<nwb-button secondary @click="${this.toggle}">${this.closeText ?? 'Close'}</nwb-button>` : '' }

From 10e4d6fa689eb81708414dabd091610d2c36b182 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 19:59:37 +0000
Subject: [PATCH 114/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 24affb49f..7c2a0814e 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -388,7 +388,7 @@ export class JSONSchemaForm extends LitElement {
                     else e.message = `${e.message}. ${provideNaNMessage}`;
                 }
 
-                const prevHeader = name ? header(name) : 'Row'
+                const prevHeader = name ? header(name) : "Row";
 
                 return {
                     type: "error",

From 88cead93094dda1ece02952c0d8c1aaf6c837903 Mon Sep 17 00:00:00 2001
From: codycbakerphd <cbaker9@nd.edu>
Date: Wed, 24 Jan 2024 15:13:43 -0500
Subject: [PATCH 115/133] add more test cases

---
 guide_testing_suite.yml | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/guide_testing_suite.yml b/guide_testing_suite.yml
index 9239f4c35..81631fa6d 100644
--- a/guide_testing_suite.yml
+++ b/guide_testing_suite.yml
@@ -14,6 +14,18 @@ pipelines:
     PhySortingInterface:
       folder_path: ephy_testing_data/phy/phy_example_0
 
-  SpikeGLX-v1-SingleProbe-AP:
+  SpikeGLX_v1_SingleProbe_AP:
     SpikeGLXRecordingInterface:
       file_path: ephy_testing_data/spikeglx/Noise4Sam_g0/Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.ap.bin
+
+  Suite2P_SinglePlane_SingleChannel:
+    Suite2pSegmentationInterface:
+      folder_path: ophys_testing_data/segmentation_datasets/suite2p
+
+  Caiman_SinglePlane_SingleChannel:
+    CaimanSegmentationInterface:
+      file_path: ophys_testing_data/segmentation_datasets/caiman/caiman_analysis.hdf5
+
+  ScanImage_SinglePlane_SingleChannel:
+    ScanImageImagingInterface:
+      file_path: ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_single.tif
\ No newline at end of file

From 1660a94a5b5e06ea955e2b5063c73f72cdff700e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 20:14:49 +0000
Subject: [PATCH 116/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 guide_testing_suite.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guide_testing_suite.yml b/guide_testing_suite.yml
index 81631fa6d..c54846f1d 100644
--- a/guide_testing_suite.yml
+++ b/guide_testing_suite.yml
@@ -28,4 +28,4 @@ pipelines:
 
   ScanImage_SinglePlane_SingleChannel:
     ScanImageImagingInterface:
-      file_path: ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_single.tif
\ No newline at end of file
+      file_path: ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_single.tif

From d4b73a491c4703617dc0a56f5c4d1115b4234012 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 14:18:29 -0800
Subject: [PATCH 117/133] Limit table interactions based on min/maxItems

---
 src/renderer/src/progress/index.js            |  2 +-
 src/renderer/src/stories/BasicTable.js        | 37 +++++---
 src/renderer/src/stories/JSONSchemaInput.js   | 49 ++++------
 src/renderer/src/stories/SimpleTable.js       | 92 +++++++++++++++----
 src/renderer/src/stories/Table.js             | 34 +++++--
 src/renderer/src/stories/forms/utils.ts       |  4 +-
 .../pages/guided-mode/data/GuidedMetadata.js  | 38 +++++++-
 .../stories/pages/guided-mode/data/utils.js   | 45 +++++++++
 .../pages/guided-mode/setup/GuidedSubjects.js |  5 +-
 src/renderer/src/stories/table/ContextMenu.ts |  7 +-
 10 files changed, 236 insertions(+), 77 deletions(-)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index 190933eca..652d60c49 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -52,7 +52,7 @@ function decode(text) {
     }
 }
 
-function drill(object, callback) {
+export function drill(object, callback) {
     if (object && typeof object === "object") {
         const copy = Array.isArray(object) ? [...object] : { ...object };
         for (let k in copy) {
diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 976524ed7..ef70cd39a 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -131,6 +131,22 @@ export class BasicTable extends LitElement {
         if (onLoaded) this.onLoaded = onLoaded;
     }
 
+
+    #schema = {}
+    #itemSchema = {}
+    #itemProps = {}
+
+    get schema() {
+        return this.#schema
+    }
+
+    set schema(schema) {
+        this.#schema = schema
+        this.#itemSchema = schema.items
+        this.#itemProps = {...this.#itemSchema.properties}
+    }
+
+
     #rendered;
     #updateRendered = (force) =>
         force || this.rendered === true
@@ -139,7 +155,7 @@ export class BasicTable extends LitElement {
     rendered = this.#updateRendered(true);
 
     #renderHeaderContent = (str) => {
-        const required = this.schema.required ? this.schema.required.includes(str) : false;
+        const required = this.#itemSchema.required ? this.#itemSchema.required.includes(str) : false;
         if (required) return html`<div class="relative"><span required>${header(str)}</span></div>`;
         return html`<div class="relative"><span>${header(str)}</span></div>`;
     };
@@ -160,7 +176,7 @@ export class BasicTable extends LitElement {
                 value =
                     (hasRow ? this.data[row][col] : undefined) ??
                     // this.globals[col] ??
-                    this.schema.properties[col].default ??
+                    this.#itemSchema.properties[col].default ??
                     "";
             return value;
         });
@@ -202,7 +218,7 @@ export class BasicTable extends LitElement {
 
         let result;
 
-        const propInfo = this.schema.properties[col] ?? {};
+        const propInfo = this.#itemProps[col] ?? {};
         let thisTypeOf = typeof value;
         let ogType;
         let type = (ogType = propInfo.type || propInfo.data_type);
@@ -223,13 +239,13 @@ export class BasicTable extends LitElement {
         }
 
         // Check if required
-        if (!value && "required" in this.schema && this.schema.required.includes(col))
+        if (!value && "required" in this.#itemSchema.required.includes(col))
             result = [{ message: `${col} is a required property`, type: "error" }];
         // If not required, check matching types for values that are defined
         else if (value !== "" && thisTypeOf !== type)
             result = [{ message: `${col} is expected to be of type ${ogType}, not ${thisTypeOf}`, type: "error" }];
         // Otherwise validate using the specified onChange function
-        else result = this.validateOnChange([col], parent, value, this.schema.properties[col]);
+        else result = this.validateOnChange([col], parent, value, this.#itemProps[col]);
 
         // Will run synchronously if not a promise result
         return promises.resolve(result, () => {
@@ -343,7 +359,7 @@ export class BasicTable extends LitElement {
             const cols = structuredData[row];
             const latest = (this.data[this.keyColumn ? cols[this.keyColumn] : row] = {});
             Object.entries(cols).forEach(([key, value]) =>
-                key in this.schema.properties ? (latest[key] = value) : ""
+                key in this.#itemProps ? (latest[key] = value) : ""
             ); // Only include data from schema
         });
 
@@ -354,13 +370,12 @@ export class BasicTable extends LitElement {
     render() {
         this.#updateRendered();
 
-        const entries = { ...this.schema.properties };
-
+        const entries = this.#itemProps;
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional properties to the entries variable if necessary
-        if (this.schema.additionalProperties) {
+        if (this.#itemSchema.additionalProperties) {
             Object.values(this.data).reduce((acc, v) => {
                 Object.keys(v).forEach((k) =>
                     !(k in entries)
@@ -379,11 +394,11 @@ export class BasicTable extends LitElement {
             this.colHeaders =
                 sortTable(
                     {
-                        ...this.schema,
+                        ...this.#itemSchema,
                         properties: entries,
                     },
                     this.keyColumn,
-                    this.schema.order
+                    this.#itemSchema.order
                 ));
 
         // Try to guess the key column if unspecified
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index b9a9a81bf..a266c4748 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -73,51 +73,37 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
     };
 
     const addPropertyKeyToSchema = (schema) => {
-        const schemaCopy = structuredClone(schema);
-
-        const schemaRef = forceItems ? schemaCopy["items"] : schemaCopy;
-
-        if (!schemaRef.properties) schemaRef.properties = {};
-        if (!schemaRef.required) schemaRef.required = [];
-
-        schemaRef.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
-        if (!schemaRef.order) schemaRef.order = [];
-        schemaRef.order.unshift(tempPropertyKey);
-
-        schemaRef.required.push(tempPropertyKey);
 
-        if (!schema["items"]) {
-            const resolvedItemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
-            if (!resolvedItemSchema) return schemaRef;
+        const schemaCopy = structuredClone(schema);
 
-            delete schemaRef.patternProperties;
+        const schemaItemsRef = schemaCopy["items"]//forceItems ? schemaCopy["items"] : schemaCopy;
 
-            schemaRef.properties[tempPropertyValueKey] = {
-                type: "array",
-                items: resolvedItemSchema.properties ? addPropertyKeyToSchema(itemSchema) : itemSchema,
-                title: "Property Value",
-                __generated: true,
-            };
+        if (!schemaItemsRef.properties) schemaItemsRef.properties = {};
+        if (!schemaItemsRef.required) schemaItemsRef.required = [];
 
-            schemaRef.required.push(tempPropertyValueKey);
-        }
+        schemaItemsRef.properties[tempPropertyKey] = { title: "Property Key", type: "string", pattern: name };
+        if (!schemaItemsRef.order) schemaItemsRef.order = [];
+        schemaItemsRef.order.unshift(tempPropertyKey);
 
-        if (schemaRef.__generated) return schemaRef["items"]; // Only return the relevant items for tables in nested tables
+        schemaItemsRef.required.push(tempPropertyKey);
 
-        return schemaRef;
+        return schemaCopy;
     };
 
-    const createNestedTable = (id, value, { name: propName = id, schema = itemSchema } = {}) => {
-        const schemaCopy = addPropertyKeyToSchema(schema);
+    const createNestedTable = (id, value, { name: propName = id, nestedSchema = schema } = {}) => {
+
+        const schemaCopy = addPropertyKeyToSchema(nestedSchema);
 
         const resultPath = [...path];
 
         const schemaPath = [...fullPath];
 
+        // THIS IS AN ISSUE
         const rowData = Object.entries(value).map(([key, value]) => {
-            return !schema["items"]
+            return !schemaCopy["items"]
                 ? { [tempPropertyKey]: key, [tempPropertyValueKey]: value }
-                : { [tempPropertyKey]: key, ...value };
+                : 
+                { [tempPropertyKey]: key, ...value };
         });
 
         if (propName) {
@@ -170,6 +156,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
         const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
 
+
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,
@@ -247,7 +234,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
     // Normal table parsing
     const tableMetadata = {
-        schema: itemSchema,
+        schema,
         data: this.value,
 
         ignore: nestedIgnore, // According to schema
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 514d5d903..263bb6922 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -169,6 +169,12 @@ export class SimpleTable extends LitElement {
             : this.rendered;
     rendered = this.#updateRendered(true);
 
+
+    #onUpdate = (...args) => {
+        this.onUpdate(...args)
+        if (this.#context) this.#updateContextMenuRendering()
+    }
+
     constructor({
         schema,
         data,
@@ -288,7 +294,7 @@ export class SimpleTable extends LitElement {
     get data() {
         // Remove empty array entries
         if (Array.isArray(this.#data))
-            return this.#data; //.filter((o) => Object.keys(o).length);
+            return this.#data.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
@@ -380,7 +386,7 @@ export class SimpleTable extends LitElement {
             } else {
                 value = hasRow ? this.#data[row][col] : undefined;
                 if (this.#isUndefined(value)) value = this.globals[col];
-                if (this.#isUndefined(value)) value = this.schema.properties?.[col]?.default;
+                if (this.#isUndefined(value)) value = this.#itemSchema.properties?.[col]?.default;
                 if (this.#isUndefined(value)) value = "";
             }
             return value;
@@ -444,9 +450,28 @@ export class SimpleTable extends LitElement {
     addRow = (anchorRow = this.#cells.length - 1, n) => this.#updateRows(anchorRow, 1)[0];
     getRow = (i) => Object.values(this.#cells[i]);
 
+    #updateContextMenuRendering = () => {
+        const { minItems, maxItems } = this.schema
+
+        if ( minItems || maxItems ) {
+            const nRows = this.data.length
+            const addRowButton = this.#context.shadowRoot.querySelector('#add-row')
+            const removeRowButton = this.#context.shadowRoot.querySelector('#remove-row')
+
+            removeRowButton.removeAttribute('disabled')
+            addRowButton.removeAttribute('disabled')
+
+            if (nRows <= minItems) removeRowButton.setAttribute('disabled', '')
+            
+            if (nRows >= maxItems) addRowButton.setAttribute('disabled', '')
+        
+        }
+    }
+
     #menuOptions = {
         row: {
             add: {
+                id:"add-row",
                 label: "Add Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
@@ -456,6 +481,7 @@ export class SimpleTable extends LitElement {
                 },
             },
             remove: {
+                id:"remove-row",
                 label: "Remove Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
@@ -480,6 +506,7 @@ export class SimpleTable extends LitElement {
 
         column: {
             add: {
+                id:"add-column",
                 label: "Add Column",
                 onclick: (path) => {
                     console.log("add column");
@@ -487,6 +514,7 @@ export class SimpleTable extends LitElement {
                 },
             },
             remove: {
+                id:"remove-column",
                 label: "Remove Column",
                 onclick: (path) => {
                     console.log("remove column");
@@ -498,17 +526,32 @@ export class SimpleTable extends LitElement {
 
     generateContextMenu(options) {
         const items = [];
-        if (options.row?.add) items.push(this.#menuOptions.row.add);
-        if (options.row?.remove) items.push(this.#menuOptions.row.remove);
+
+
+        const { minItems, maxItems } = this.schema
+        const nRows = this.data.length
+        
+        const noRowEdits = minItems && maxItems && minItems === maxItems && nRows === minItems && nRows === maxItems
+
+        if (!noRowEdits) {
+            if (options.row?.add) items.push(this.#menuOptions.row.add);
+            if (options.row?.remove) items.push(this.#menuOptions.row.remove);
+        }
+
         if (options.column?.add) items.push(this.#menuOptions.column.add);
         if (options.column?.remove) items.push(this.#menuOptions.column.remove);
 
-        this.#context = new ContextMenu({
-            target: this.shadowRoot.querySelector("table"),
-            items,
-        });
+        if (items.length) {
+
+            this.#context = new ContextMenu({
+                target: this.shadowRoot.querySelector("table"),
+                items,
+            });
+
+            this.#context.updated = () => this.#updateContextMenuRendering() // Run when done rendering
 
-        document.body.append(this.#context); // Insert context menu
+            document.body.append(this.#context); // Insert context menu
+        }
     }
 
     #loaded = false;
@@ -633,11 +676,11 @@ export class SimpleTable extends LitElement {
                 return this.getRow(i);
             });
 
-            this.onUpdate([], this.data);
+            this.#onUpdate([], this.data);
             return mapped;
         }
 
-        this.onUpdate([], this.data);
+        this.#onUpdate([], this.data);
     }
 
     #renderHeader = (str, { title, description }) => {
@@ -708,7 +751,7 @@ export class SimpleTable extends LitElement {
             else target[rowName][header] = value;
         }
 
-        if (cell.interacted) this.onUpdate([rowName, header], value);
+        if (cell.interacted) this.#onUpdate([rowName, header], value);
     };
 
     #createCell = (value, info) => {
@@ -722,7 +765,7 @@ export class SimpleTable extends LitElement {
             row: `${row}`,
         };
 
-        const schema = this.#schema[fullInfo.col];
+        const schema = this.#itemProps[fullInfo.col];
 
         const ignore = getIgnore(this.ignore, [fullInfo.col]);
 
@@ -810,17 +853,30 @@ export class SimpleTable extends LitElement {
 
     #schema = {};
 
+    #itemSchema = {}
+    #itemProps = {}
+
+    get schema () {
+        return this.#schema
+    }
+
+    set schema(schema){
+        this.#schema = schema
+        this.#itemSchema = this.#schema.items
+        this.#itemProps = { ...this.#itemSchema.properties }
+    }
+
     render() {
+        
         this.#updateRendered();
         this.#resetLoadState();
 
-        const entries = (this.#schema = { ...this.schema.properties });
-
+        const entries = this.#itemProps
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional / pattern properties to the entries variable if necessary
-        if (this.schema.additionalProperties !== false || this.schema.patternProperties) {
+        if (this.#itemSchema.additionalProperties !== false || this.#itemSchema.patternProperties) {
             Object.values(this.#data).reduce((acc, v) => {
                 Object.keys(v).forEach((k) =>
                     !(k in entries)
@@ -836,11 +892,11 @@ export class SimpleTable extends LitElement {
         // Sort Columns by Key Column and Requirement
         this.colHeaders = sortTable(
             {
-                ...this.schema,
+                ...this.#itemSchema,
                 properties: entries,
             },
             this.keyColumn,
-            this.schema.order ?? ["name"] // Specify the order of the columns
+            this.#itemSchema.order ?? ["name"] // Specify the order of the columns
         );
 
         // Try to guess the key column if unspecified
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 0d56e0da6..ef5b50b7a 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -201,18 +201,32 @@ export class Table extends LitElement {
     onOverride = () => {};
     onThrow = () => {};
 
+
+    #schema = {}
+    #itemSchema = {}
+    #itemProps = {}
+
+    get schema() {
+        return this.#schema
+    }
+
+    set schema(schema) {
+        this.#schema = schema
+        this.#itemSchema = schema.items
+        this.#itemProps = {...this.#itemSchema.properties}
+    }
+
     updated() {
         const div = (this.shadowRoot ?? this).querySelector("div");
 
         const unresolved = (this.unresolved = {});
 
-        const entries = { ...this.schema.properties };
-
+        const entries = this.#itemProps;
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
         // Add existing additional properties to the entries variable if necessary
-        if (this.schema.additionalProperties) {
+        if (this.#itemSchema.additionalProperties) {
             Object.values(this.data).reduce((acc, v) => {
                 Object.keys(v).forEach((k) =>
                     !(k in entries)
@@ -229,11 +243,11 @@ export class Table extends LitElement {
 
         const colHeaders = (this.colHeaders = sortTable(
             {
-                ...this.schema,
+                ...this.#itemSchema,
                 properties: entries,
             },
             this.keyColumn,
-            this.schema.order
+            this.#itemSchema.order
         ));
 
         // Try to guess the key column if unspecified
@@ -296,7 +310,7 @@ export class Table extends LitElement {
             };
 
             let instanceThis = this;
-            const required = isRequired(k, this.schema);
+            const required = isRequired(k, this.#itemSchema);
 
             const validator = async function (value, callback) {
                 const validateEmptyCells = instanceThis.validateEmptyCells;
@@ -380,7 +394,7 @@ export class Table extends LitElement {
 
             const rel = TH.querySelector(".relative");
 
-            const required = isRequired(col, this.schema);
+            const required = isRequired(col, this.#itemSchema);
             if (required)
                 rel.setAttribute(
                     "data-required",
@@ -411,7 +425,7 @@ export class Table extends LitElement {
         let nRows = rowHeaders.length;
 
         let contextMenu = ["row_below", "remove_row"];
-        if (this.schema.additionalProperties) contextMenu.push("col_right", "remove_col");
+        if (this.#itemSchema.additionalProperties) contextMenu.push("col_right", "remove_col");
 
         contextMenu = contextMenu.filter((k) => !(this.contextMenu.ignore ?? []).includes(k));
 
@@ -563,7 +577,7 @@ export class Table extends LitElement {
 
     #getRenderedData = (data) => {
         return Object.values(data).map((row) =>
-            row.map((value, j) => this.#getRenderedValue(value, this.schema.properties[this.colHeaders[j]]))
+            row.map((value, j) => this.#getRenderedValue(value, this.#itemSchema.properties[this.colHeaders[j]]))
         );
     };
 
@@ -577,7 +591,7 @@ export class Table extends LitElement {
 
     #setRow(row, data) {
         data.forEach((value, j) => {
-            value = this.#getRenderedValue(value, this.schema.properties[this.colHeaders[j]]);
+            value = this.#getRenderedValue(value, this.#itemSchema.properties[this.colHeaders[j]]);
             this.table.setDataAtCell(row, j, value);
         });
     }
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 1fc2466e5..06400ccb2 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -21,7 +21,7 @@ export const textToArray = (value: string) => value.split("\n")
     export const replaceRefsWithValue = (
         schema: any,
         path: string[] = [],
-        parent: { [x:string]: any } = schema
+        parent: { [x:string]: any } = structuredClone(schema)
     ) => {
 
         if (schema && typeof schema === "object" && !Array.isArray(schema)) {
@@ -45,6 +45,8 @@ export const textToArray = (value: string) => value.split("\n")
                 }
             }
 
+            if (parent.properties) delete parent.properties.definitions // Delete definitions when complete
+
             return copy as { [x:string]: any }
         }
 
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 82defa808..9d5325ab9 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -5,7 +5,7 @@ import { ManagedPage } from "./ManagedPage.js";
 import { Modal } from "../../../Modal";
 
 import { validateOnChange } from "../../../../validation/index.js";
-import { resolveGlobalOverrides, resolveMetadata, getInfoFromId } from "./utils.js";
+import { resolveGlobalOverrides, resolveMetadata, getInfoFromId, drillSchemaProperties, resolveFromPath } from "./utils.js";
 
 import Swal from "sweetalert2";
 import { SimpleTable } from "../../../SimpleTable";
@@ -180,10 +180,37 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
 
+        const resolvedSchema = preprocessMetadataSchema(schema)
+        const ophys = resolvedSchema.properties.Ophys
+        if (ophys) {
+
+            // Set most Ophys tables to have minItems / maxItems equal (i.e. no editing possible)
+            drillSchemaProperties(resolvedSchema, (path, schema, target, isPatternProperties) => {
+                if (path[0] === 'Ophys') {
+                    const name = path.slice(-1)[0]
+                    
+                    if (isPatternProperties) {
+                        schema.minItems = schema.maxItems = Object.values(resolveFromPath(path, results)).length
+                        return
+                    }
+
+                    if (schema.type === 'array') {
+                        if (
+                            name !== 'Device' 
+                            && (target && name in target) // Skip unresolved deep in pattern properties
+                        ) {
+                            schema.minItems = schema.maxItems = target[name].length
+                        }
+                    }
+                }
+            }, results)
+
+        }
+
         // Create the form
         const form = new JSONSchemaForm({
             identifier: instanceId,
-            schema: preprocessMetadataSchema(schema),
+            schema: resolvedSchema,
             results,
             globals: aggregateGlobalMetadata,
 
@@ -295,11 +322,17 @@ export class GuidedMetadataPage extends ManagedPage {
                         return Object.entries(data)
                             .map(([name, value]) => {
                                 const createNestedTable = (value, pattern, schema) => {
+
                                     const mockInput = {
                                         schema: {
                                             type: "object",
                                             items: schema,
+
+                                            // Transfer a subset of item schema values
+                                            minItems: schema.minItems,
+                                            maxItems: schema.maxItems
                                         },
+
                                         renderTable: this.renderTable,
                                         value,
                                         pattern: pattern,
@@ -312,7 +345,6 @@ export class GuidedMetadataPage extends ManagedPage {
                                         <div style="width: 100%;">
                                             ${nProps > 1 ? html`<h3>${header(name)}</h3>` : ""}
                                             ${createTable.call(mockInput, [...localPath], {
-                                                forceItems: true,
                                                 onUpdate: (localPath, value) =>
                                                     onUpdate([name, ...localPath], value, true, {
                                                         willTimeout: false,
diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index 740fa4be6..30a0a65c6 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -1,3 +1,4 @@
+import { getEditableItems } from "../../../JSONSchemaInput.js";
 import { merge } from "../../utils.js";
 
 // Merge project-wide data into metadata
@@ -34,6 +35,50 @@ export function resolveGlobalOverrides(subject, globalState) {
     return overrides;
 }
 
+const isPatternResult = Symbol('ispatternresult')
+
+export function resolveFromPath (path, target) {
+    return path.reduce((acc, key) => {
+        if (!acc) return
+        if (acc[isPatternResult]) return acc
+        if (key in acc) return acc[key]
+        else {
+            const items = getEditableItems(acc, true, { name: key })
+            const object = items.reduce((acc, {key, value}) => acc[key] = value, {})
+            object[isPatternResult] = true
+            return object
+        }
+    }, target)
+
+}
+
+export function drillSchemaProperties(schema={}, callback, target, path = [], inPatternProperties = false) {
+
+    const properties = schema.properties ?? {}
+
+    const patternProperties = schema.patternProperties ?? {}
+
+    for (let regexp in patternProperties) {
+        const info = patternProperties[regexp];
+        const updatedPath = [...path, regexp]
+        callback(updatedPath, info, undefined, true)
+        drillSchemaProperties(info, callback, undefined, updatedPath, true);
+    }
+
+    for (let name in properties) {
+        const info = properties[name];
+
+        const updatedPath = [...path, name]
+
+        callback(updatedPath, info, target)
+
+        drillSchemaProperties(info, callback, target?.[name], updatedPath, inPatternProperties);
+    }
+
+    return schema;
+
+}
+
 export function resolveProperties(properties = {}, target, globals = {}) {
     if ("properties" in properties && "type" in properties) properties = properties.properties; // Correct for when a schema is passed instead
 
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
index 515cc32a9..0602eaa65 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -114,7 +114,10 @@ export class GuidedSubjectsPage extends Page {
         }
 
         this.table = new Table({
-            schema: getSubjectSchema(),
+            schema: {
+                type: "array",
+                items: getSubjectSchema()
+            },
             data: subjects,
             globals: this.info.globalState.project.Subject,
             keyColumn: "subject_id",
diff --git a/src/renderer/src/stories/table/ContextMenu.ts b/src/renderer/src/stories/table/ContextMenu.ts
index 456ec61cb..4f382b78b 100644
--- a/src/renderer/src/stories/table/ContextMenu.ts
+++ b/src/renderer/src/stories/table/ContextMenu.ts
@@ -56,6 +56,11 @@ export class ContextMenu extends LitElement{
           .menu > li.trash > a:hover {
             color: red;
           }
+
+          .menu > li[disabled]{
+            pointer-events: none;
+            opacity: 0.5;
+          }
         `
     }
 
@@ -92,7 +97,7 @@ export class ContextMenu extends LitElement{
     render () {
         return html`
         <ul class="menu">
-            ${this.items.map(({ onclick , icon, label }) => html`<li class="share" @click=${() => {
+            ${this.items.map(({ id, onclick , icon, label }) => html`<li class="share" id="${id}" @click=${() => {
                 if (onclick) onclick(this.#activePath)
             }}><a href="#">${icon ?? ''}${label}</a></li>`)}
         </ul>

From 6e61a00eeab6b56315fce0706b3615cb02efffcd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 22:18:47 +0000
Subject: [PATCH 118/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/BasicTable.js        | 20 +++---
 src/renderer/src/stories/JSONSchemaInput.js   |  8 +--
 src/renderer/src/stories/SimpleTable.js       | 70 +++++++++----------
 src/renderer/src/stories/Table.js             | 15 ++--
 .../pages/guided-mode/data/GuidedMetadata.js  | 54 ++++++++------
 .../stories/pages/guided-mode/data/utils.js   | 37 +++++-----
 .../pages/guided-mode/setup/GuidedSubjects.js |  2 +-
 7 files changed, 98 insertions(+), 108 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index ef70cd39a..e880cd146 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -131,22 +131,20 @@ export class BasicTable extends LitElement {
         if (onLoaded) this.onLoaded = onLoaded;
     }
 
-
-    #schema = {}
-    #itemSchema = {}
-    #itemProps = {}
+    #schema = {};
+    #itemSchema = {};
+    #itemProps = {};
 
     get schema() {
-        return this.#schema
+        return this.#schema;
     }
 
     set schema(schema) {
-        this.#schema = schema
-        this.#itemSchema = schema.items
-        this.#itemProps = {...this.#itemSchema.properties}
+        this.#schema = schema;
+        this.#itemSchema = schema.items;
+        this.#itemProps = { ...this.#itemSchema.properties };
     }
 
-
     #rendered;
     #updateRendered = (force) =>
         force || this.rendered === true
@@ -358,9 +356,7 @@ export class BasicTable extends LitElement {
         Object.keys(data).forEach((row) => {
             const cols = structuredData[row];
             const latest = (this.data[this.keyColumn ? cols[this.keyColumn] : row] = {});
-            Object.entries(cols).forEach(([key, value]) =>
-                key in this.#itemProps ? (latest[key] = value) : ""
-            ); // Only include data from schema
+            Object.entries(cols).forEach(([key, value]) => (key in this.#itemProps ? (latest[key] = value) : "")); // Only include data from schema
         });
 
         this.onUpdate(null, null, value); // Update the whole table
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index a266c4748..5d993438c 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -73,10 +73,9 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
     };
 
     const addPropertyKeyToSchema = (schema) => {
-
         const schemaCopy = structuredClone(schema);
 
-        const schemaItemsRef = schemaCopy["items"]//forceItems ? schemaCopy["items"] : schemaCopy;
+        const schemaItemsRef = schemaCopy["items"]; //forceItems ? schemaCopy["items"] : schemaCopy;
 
         if (!schemaItemsRef.properties) schemaItemsRef.properties = {};
         if (!schemaItemsRef.required) schemaItemsRef.required = [];
@@ -91,7 +90,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
     };
 
     const createNestedTable = (id, value, { name: propName = id, nestedSchema = schema } = {}) => {
-
         const schemaCopy = addPropertyKeyToSchema(nestedSchema);
 
         const resultPath = [...path];
@@ -102,8 +100,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         const rowData = Object.entries(value).map(([key, value]) => {
             return !schemaCopy["items"]
                 ? { [tempPropertyKey]: key, [tempPropertyValueKey]: value }
-                : 
-                { [tempPropertyKey]: key, ...value };
+                : { [tempPropertyKey]: key, ...value };
         });
 
         if (propName) {
@@ -156,7 +153,6 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
         const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
 
-
         const tableMetadata = {
             keyColumn: tempPropertyKey,
             schema: schemaCopy,
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 263bb6922..e4179dc26 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -169,11 +169,10 @@ export class SimpleTable extends LitElement {
             : this.rendered;
     rendered = this.#updateRendered(true);
 
-
     #onUpdate = (...args) => {
-        this.onUpdate(...args)
-        if (this.#context) this.#updateContextMenuRendering()
-    }
+        this.onUpdate(...args);
+        if (this.#context) this.#updateContextMenuRendering();
+    };
 
     constructor({
         schema,
@@ -293,8 +292,7 @@ export class SimpleTable extends LitElement {
     #data = [];
     get data() {
         // Remove empty array entries
-        if (Array.isArray(this.#data))
-            return this.#data.filter((o) => Object.keys(o).length);
+        if (Array.isArray(this.#data)) return this.#data.filter((o) => Object.keys(o).length);
         else return this.#data;
     }
 
@@ -451,27 +449,26 @@ export class SimpleTable extends LitElement {
     getRow = (i) => Object.values(this.#cells[i]);
 
     #updateContextMenuRendering = () => {
-        const { minItems, maxItems } = this.schema
+        const { minItems, maxItems } = this.schema;
+
+        if (minItems || maxItems) {
+            const nRows = this.data.length;
+            const addRowButton = this.#context.shadowRoot.querySelector("#add-row");
+            const removeRowButton = this.#context.shadowRoot.querySelector("#remove-row");
 
-        if ( minItems || maxItems ) {
-            const nRows = this.data.length
-            const addRowButton = this.#context.shadowRoot.querySelector('#add-row')
-            const removeRowButton = this.#context.shadowRoot.querySelector('#remove-row')
+            removeRowButton.removeAttribute("disabled");
+            addRowButton.removeAttribute("disabled");
 
-            removeRowButton.removeAttribute('disabled')
-            addRowButton.removeAttribute('disabled')
+            if (nRows <= minItems) removeRowButton.setAttribute("disabled", "");
 
-            if (nRows <= minItems) removeRowButton.setAttribute('disabled', '')
-            
-            if (nRows >= maxItems) addRowButton.setAttribute('disabled', '')
-        
+            if (nRows >= maxItems) addRowButton.setAttribute("disabled", "");
         }
-    }
+    };
 
     #menuOptions = {
         row: {
             add: {
-                id:"add-row",
+                id: "add-row",
                 label: "Add Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
@@ -481,7 +478,7 @@ export class SimpleTable extends LitElement {
                 },
             },
             remove: {
-                id:"remove-row",
+                id: "remove-row",
                 label: "Remove Row",
                 onclick: (path) => {
                     const cell = this.#getCellFromPath(path);
@@ -506,7 +503,7 @@ export class SimpleTable extends LitElement {
 
         column: {
             add: {
-                id:"add-column",
+                id: "add-column",
                 label: "Add Column",
                 onclick: (path) => {
                     console.log("add column");
@@ -514,7 +511,7 @@ export class SimpleTable extends LitElement {
                 },
             },
             remove: {
-                id:"remove-column",
+                id: "remove-column",
                 label: "Remove Column",
                 onclick: (path) => {
                     console.log("remove column");
@@ -527,11 +524,10 @@ export class SimpleTable extends LitElement {
     generateContextMenu(options) {
         const items = [];
 
+        const { minItems, maxItems } = this.schema;
+        const nRows = this.data.length;
 
-        const { minItems, maxItems } = this.schema
-        const nRows = this.data.length
-        
-        const noRowEdits = minItems && maxItems && minItems === maxItems && nRows === minItems && nRows === maxItems
+        const noRowEdits = minItems && maxItems && minItems === maxItems && nRows === minItems && nRows === maxItems;
 
         if (!noRowEdits) {
             if (options.row?.add) items.push(this.#menuOptions.row.add);
@@ -542,13 +538,12 @@ export class SimpleTable extends LitElement {
         if (options.column?.remove) items.push(this.#menuOptions.column.remove);
 
         if (items.length) {
-
             this.#context = new ContextMenu({
                 target: this.shadowRoot.querySelector("table"),
                 items,
             });
 
-            this.#context.updated = () => this.#updateContextMenuRendering() // Run when done rendering
+            this.#context.updated = () => this.#updateContextMenuRendering(); // Run when done rendering
 
             document.body.append(this.#context); // Insert context menu
         }
@@ -853,25 +848,24 @@ export class SimpleTable extends LitElement {
 
     #schema = {};
 
-    #itemSchema = {}
-    #itemProps = {}
+    #itemSchema = {};
+    #itemProps = {};
 
-    get schema () {
-        return this.#schema
+    get schema() {
+        return this.#schema;
     }
 
-    set schema(schema){
-        this.#schema = schema
-        this.#itemSchema = this.#schema.items
-        this.#itemProps = { ...this.#itemSchema.properties }
+    set schema(schema) {
+        this.#schema = schema;
+        this.#itemSchema = this.#schema.items;
+        this.#itemProps = { ...this.#itemSchema.properties };
     }
 
     render() {
-        
         this.#updateRendered();
         this.#resetLoadState();
 
-        const entries = this.#itemProps
+        const entries = this.#itemProps;
         for (let key in this.ignore) delete entries[key];
         for (let key in this.ignore["*"] ?? {}) delete entries[key];
 
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index ef5b50b7a..ccf4980c7 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -201,19 +201,18 @@ export class Table extends LitElement {
     onOverride = () => {};
     onThrow = () => {};
 
-
-    #schema = {}
-    #itemSchema = {}
-    #itemProps = {}
+    #schema = {};
+    #itemSchema = {};
+    #itemProps = {};
 
     get schema() {
-        return this.#schema
+        return this.#schema;
     }
 
     set schema(schema) {
-        this.#schema = schema
-        this.#itemSchema = schema.items
-        this.#itemProps = {...this.#itemSchema.properties}
+        this.#schema = schema;
+        this.#itemSchema = schema.items;
+        this.#itemProps = { ...this.#itemSchema.properties };
     }
 
     updated() {
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 9d5325ab9..2b8253822 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -5,7 +5,13 @@ import { ManagedPage } from "./ManagedPage.js";
 import { Modal } from "../../../Modal";
 
 import { validateOnChange } from "../../../../validation/index.js";
-import { resolveGlobalOverrides, resolveMetadata, getInfoFromId, drillSchemaProperties, resolveFromPath } from "./utils.js";
+import {
+    resolveGlobalOverrides,
+    resolveMetadata,
+    getInfoFromId,
+    drillSchemaProperties,
+    resolveFromPath,
+} from "./utils.js";
 
 import Swal from "sweetalert2";
 import { SimpleTable } from "../../../SimpleTable";
@@ -180,31 +186,34 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const patternPropsToRetitle = ["Ophys.Fluorescence", "Ophys.DfOverF", "Ophys.SegmentationImages"];
 
-        const resolvedSchema = preprocessMetadataSchema(schema)
-        const ophys = resolvedSchema.properties.Ophys
+        const resolvedSchema = preprocessMetadataSchema(schema);
+        const ophys = resolvedSchema.properties.Ophys;
         if (ophys) {
-
             // Set most Ophys tables to have minItems / maxItems equal (i.e. no editing possible)
-            drillSchemaProperties(resolvedSchema, (path, schema, target, isPatternProperties) => {
-                if (path[0] === 'Ophys') {
-                    const name = path.slice(-1)[0]
-                    
-                    if (isPatternProperties) {
-                        schema.minItems = schema.maxItems = Object.values(resolveFromPath(path, results)).length
-                        return
-                    }
+            drillSchemaProperties(
+                resolvedSchema,
+                (path, schema, target, isPatternProperties) => {
+                    if (path[0] === "Ophys") {
+                        const name = path.slice(-1)[0];
+
+                        if (isPatternProperties) {
+                            schema.minItems = schema.maxItems = Object.values(resolveFromPath(path, results)).length;
+                            return;
+                        }
 
-                    if (schema.type === 'array') {
-                        if (
-                            name !== 'Device' 
-                            && (target && name in target) // Skip unresolved deep in pattern properties
-                        ) {
-                            schema.minItems = schema.maxItems = target[name].length
+                        if (schema.type === "array") {
+                            if (
+                                name !== "Device" &&
+                                target &&
+                                name in target // Skip unresolved deep in pattern properties
+                            ) {
+                                schema.minItems = schema.maxItems = target[name].length;
+                            }
                         }
                     }
-                }
-            }, results)
-
+                },
+                results
+            );
         }
 
         // Create the form
@@ -322,7 +331,6 @@ export class GuidedMetadataPage extends ManagedPage {
                         return Object.entries(data)
                             .map(([name, value]) => {
                                 const createNestedTable = (value, pattern, schema) => {
-
                                     const mockInput = {
                                         schema: {
                                             type: "object",
@@ -330,7 +338,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
                                             // Transfer a subset of item schema values
                                             minItems: schema.minItems,
-                                            maxItems: schema.maxItems
+                                            maxItems: schema.maxItems,
                                         },
 
                                         renderTable: this.renderTable,
diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index 30a0a65c6..e8d741dfd 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -35,48 +35,45 @@ export function resolveGlobalOverrides(subject, globalState) {
     return overrides;
 }
 
-const isPatternResult = Symbol('ispatternresult')
+const isPatternResult = Symbol("ispatternresult");
 
-export function resolveFromPath (path, target) {
+export function resolveFromPath(path, target) {
     return path.reduce((acc, key) => {
-        if (!acc) return
-        if (acc[isPatternResult]) return acc
-        if (key in acc) return acc[key]
+        if (!acc) return;
+        if (acc[isPatternResult]) return acc;
+        if (key in acc) return acc[key];
         else {
-            const items = getEditableItems(acc, true, { name: key })
-            const object = items.reduce((acc, {key, value}) => acc[key] = value, {})
-            object[isPatternResult] = true
-            return object
+            const items = getEditableItems(acc, true, { name: key });
+            const object = items.reduce((acc, { key, value }) => (acc[key] = value), {});
+            object[isPatternResult] = true;
+            return object;
         }
-    }, target)
-
+    }, target);
 }
 
-export function drillSchemaProperties(schema={}, callback, target, path = [], inPatternProperties = false) {
-
-    const properties = schema.properties ?? {}
+export function drillSchemaProperties(schema = {}, callback, target, path = [], inPatternProperties = false) {
+    const properties = schema.properties ?? {};
 
-    const patternProperties = schema.patternProperties ?? {}
+    const patternProperties = schema.patternProperties ?? {};
 
     for (let regexp in patternProperties) {
         const info = patternProperties[regexp];
-        const updatedPath = [...path, regexp]
-        callback(updatedPath, info, undefined, true)
+        const updatedPath = [...path, regexp];
+        callback(updatedPath, info, undefined, true);
         drillSchemaProperties(info, callback, undefined, updatedPath, true);
     }
 
     for (let name in properties) {
         const info = properties[name];
 
-        const updatedPath = [...path, name]
+        const updatedPath = [...path, name];
 
-        callback(updatedPath, info, target)
+        callback(updatedPath, info, target);
 
         drillSchemaProperties(info, callback, target?.[name], updatedPath, inPatternProperties);
     }
 
     return schema;
-
 }
 
 export function resolveProperties(properties = {}, target, globals = {}) {
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
index 0602eaa65..6890f697e 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -116,7 +116,7 @@ export class GuidedSubjectsPage extends Page {
         this.table = new Table({
             schema: {
                 type: "array",
-                items: getSubjectSchema()
+                items: getSubjectSchema(),
             },
             data: subjects,
             globals: this.info.globalState.project.Subject,

From 362b7c28c6fbfc046a1c78dc42ddad7957dbe1aa Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 14:42:42 -0800
Subject: [PATCH 119/133] Hide property key on custom tables

---
 src/renderer/src/stories/JSONSchemaInput.js   | 25 +++++++++++++----
 src/renderer/src/stories/SimpleTable.js       | 10 ++++---
 .../pages/guided-mode/data/GuidedMetadata.js  | 27 ++++++++++++-------
 3 files changed, 44 insertions(+), 18 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index a266c4748..46463aa52 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -13,13 +13,13 @@ import { capitalize } from "./forms/utils";
 import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
+import { merge } from "./pages/utils";
 
-export function createTable(fullPath, { onUpdate, onThrow, forceItems = false }) {
+export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
     const name = fullPath.slice(-1)[0];
     const path = fullPath.slice(0, -1);
 
     const schema = this.schema;
-    const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
     const validateOnChange = this.validateOnChange;
 
     const ignore = this.form?.ignore ? getIgnore(this.form?.ignore, path) : {};
@@ -76,7 +76,7 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
         const schemaCopy = structuredClone(schema);
 
-        const schemaItemsRef = schemaCopy["items"]//forceItems ? schemaCopy["items"] : schemaCopy;
+        const schemaItemsRef = schemaCopy["items"]
 
         if (!schemaItemsRef.properties) schemaItemsRef.properties = {};
         if (!schemaItemsRef.required) schemaItemsRef.required = [];
@@ -156,6 +156,11 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
         const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
 
+        merge(overrides.ignore, nestedIgnore)
+
+        merge(overrides.schema, schemaCopy, { arrays: true })
+
+        console.log('Ignoring', this.path, nestedIgnore, this.value, overrides)
 
         const tableMetadata = {
             keyColumn: tempPropertyKey,
@@ -218,10 +223,13 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
         return table; // Try rendering as a nested table with a fake property key (otherwise use nested forms)
     };
 
+    const schemaCopy = structuredClone(schema)
+
+
     // Possibly multiple tables
     if (isEditableObject(schema, this.value)) {
         // One table with nested tables for each property
-        const data = getEditableItems(this.value, this.pattern, { name, schema }).reduce((acc, { key, value }) => {
+        const data = getEditableItems(this.value, this.pattern, { name, schema: schemaCopy }).reduce((acc, { key, value }) => {
             acc[key] = value;
             return acc;
         }, {});
@@ -232,9 +240,16 @@ export function createTable(fullPath, { onUpdate, onThrow, forceItems = false })
 
     const nestedIgnore = getIgnore(ignore, fullPath);
 
+    Object.assign(nestedIgnore, overrides.ignore ?? {})
+
+    merge(overrides.ignore, nestedIgnore)
+
+    merge(overrides.schema, schemaCopy, { arrays: true })
+
+
     // Normal table parsing
     const tableMetadata = {
-        schema,
+        schema: schemaCopy,
         data: this.value,
 
         ignore: nestedIgnore, // According to schema
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 263bb6922..c9d92842c 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -1,5 +1,5 @@
 import { LitElement, css, html, unsafeCSS } from "lit";
-import { header, tempPropertyKey, tempPropertyValueKey } from "./forms/utils";
+import { header, tempPropertyValueKey } from "./forms/utils";
 import { checkStatus } from "../validation";
 
 import { TableCell } from "./table/Cell";
@@ -872,8 +872,7 @@ export class SimpleTable extends LitElement {
         this.#resetLoadState();
 
         const entries = this.#itemProps
-        for (let key in this.ignore) delete entries[key];
-        for (let key in this.ignore["*"] ?? {}) delete entries[key];
+
 
         // Add existing additional / pattern properties to the entries variable if necessary
         if (this.#itemSchema.additionalProperties !== false || this.#itemSchema.patternProperties) {
@@ -889,6 +888,11 @@ export class SimpleTable extends LitElement {
             }, entries);
         }
 
+        for (let key in this.ignore) delete entries[key];
+        for (let key in this.ignore["*"] ?? {}) delete entries[key];
+
+        console.error('Items', entries, this.ignore, this.schema)
+
         // Sort Columns by Key Column and Requirement
         this.colHeaders = sortTable(
             {
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 9d5325ab9..b949c3837 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -12,7 +12,7 @@ import { SimpleTable } from "../../../SimpleTable";
 import { onThrow } from "../../../../errors";
 import { merge } from "../../utils.js";
 import { NWBFilePreview } from "../../../preview/NWBFilePreview.js";
-import { header } from "../../../forms/utils";
+import { header, tempPropertyKey } from "../../../forms/utils";
 
 import { createGlobalFormModal } from "../../../forms/GlobalFormModal";
 import { Button } from "../../../Button.js";
@@ -27,12 +27,14 @@ const propsToIgnore = {
         "*": {
             starting_time: true,
             rate: true,
+            conversion: true,
+            offset: true,
+            unit: true,
+
         },
         ImagingPlane: {
             [imagingPlaneKey]: true,
             manifold: true,
-            unit: true,
-            conversion: true,
         },
         TwoPhotonSeries: {
             [imagingPlaneKey]: true,
@@ -44,9 +46,6 @@ const propsToIgnore = {
             resolution: true,
             dimension: true,
             device: true,
-            unit: true,
-            conversion: true,
-            offset: true,
         },
     },
     Icephys: true, // Always ignore icephys metadata (for now)
@@ -345,6 +344,17 @@ export class GuidedMetadataPage extends ManagedPage {
                                         <div style="width: 100%;">
                                             ${nProps > 1 ? html`<h3>${header(name)}</h3>` : ""}
                                             ${createTable.call(mockInput, [...localPath], {
+                                                overrides: {
+                                                    schema: {
+                                                        items: {
+                                                            order: ['name', 'description'],
+                                                            additionalProperties: false,
+                                                        }
+                                                    },
+                                                    ignore: {
+                                                        [tempPropertyKey]: true
+                                                    }
+                                                },
                                                 onUpdate: (localPath, value) =>
                                                     onUpdate([name, ...localPath], value, true, {
                                                         willTimeout: false,
@@ -358,13 +368,12 @@ export class GuidedMetadataPage extends ManagedPage {
                                 };
 
                                 if (isAdditional) {
-                                    console.warn(value);
                                     const data = value.reduce((acc, item) => {
                                         const name = item.name;
                                         acc[name] = item;
                                         return acc;
                                     }, {});
-                                    console.error(data);
+
                                     return createNestedTable(data, undefined, {
                                         type: "object",
                                         items: {
@@ -386,8 +395,6 @@ export class GuidedMetadataPage extends ManagedPage {
             renderTable: function (name, metadata) {
                 const updatedSchema = structuredClone(metadata.schema);
 
-                if (updatedSchema.additionalProperties !== true) updatedSchema.additionalProperties = false; // Indicate all additional properties are false (if not true)
-
                 metadata.schema = updatedSchema;
 
                 // NOTE: Handsontable will occasionally have a context menu that doesn't actually trigger any behaviors

From eb0f0a494e72b83fcab60e08d26378db9d9aa8e3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 22:43:49 +0000
Subject: [PATCH 120/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js   | 27 ++++++++++---------
 src/renderer/src/stories/SimpleTable.js       |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |  9 +++----
 3 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 8821babc8..29e0cb870 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -75,7 +75,7 @@ export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
     const addPropertyKeyToSchema = (schema) => {
         const schemaCopy = structuredClone(schema);
 
-        const schemaItemsRef = schemaCopy["items"]
+        const schemaItemsRef = schemaCopy["items"];
 
         if (!schemaItemsRef.properties) schemaItemsRef.properties = {};
         if (!schemaItemsRef.required) schemaItemsRef.required = [];
@@ -153,9 +153,9 @@ export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
 
         const nestedIgnore = this.form?.ignore ? getIgnore(this.form?.ignore, schemaPath) : {};
 
-        merge(overrides.ignore, nestedIgnore)
+        merge(overrides.ignore, nestedIgnore);
 
-        merge(overrides.schema, schemaCopy, { arrays: true })
+        merge(overrides.schema, schemaCopy, { arrays: true });
 
         const tableMetadata = {
             keyColumn: tempPropertyKey,
@@ -218,16 +218,18 @@ export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
         return table; // Try rendering as a nested table with a fake property key (otherwise use nested forms)
     };
 
-    const schemaCopy = structuredClone(schema)
-
+    const schemaCopy = structuredClone(schema);
 
     // Possibly multiple tables
     if (isEditableObject(schema, this.value)) {
         // One table with nested tables for each property
-        const data = getEditableItems(this.value, this.pattern, { name, schema: schemaCopy }).reduce((acc, { key, value }) => {
-            acc[key] = value;
-            return acc;
-        }, {});
+        const data = getEditableItems(this.value, this.pattern, { name, schema: schemaCopy }).reduce(
+            (acc, { key, value }) => {
+                acc[key] = value;
+                return acc;
+            },
+            {}
+        );
 
         const table = createNestedTable(name, data, { schema });
         if (table) return table;
@@ -235,12 +237,11 @@ export function createTable(fullPath, { onUpdate, onThrow, overrides = {} }) {
 
     const nestedIgnore = getIgnore(ignore, fullPath);
 
-    Object.assign(nestedIgnore, overrides.ignore ?? {})
-
-    merge(overrides.ignore, nestedIgnore)
+    Object.assign(nestedIgnore, overrides.ignore ?? {});
 
-    merge(overrides.schema, schemaCopy, { arrays: true })
+    merge(overrides.ignore, nestedIgnore);
 
+    merge(overrides.schema, schemaCopy, { arrays: true });
 
     // Normal table parsing
     const tableMetadata = {
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index e5c8df3cf..9a457a9ba 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -865,7 +865,7 @@ export class SimpleTable extends LitElement {
         this.#updateRendered();
         this.#resetLoadState();
 
-        const entries = this.#itemProps
+        const entries = this.#itemProps;
 
         // Add existing additional / pattern properties to the entries variable if necessary
         if (this.#itemSchema.additionalProperties !== false || this.#itemSchema.patternProperties) {
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 94d761428..f6affa1ff 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -36,7 +36,6 @@ const propsToIgnore = {
             conversion: true,
             offset: true,
             unit: true,
-
         },
         ImagingPlane: {
             [imagingPlaneKey]: true,
@@ -355,13 +354,13 @@ export class GuidedMetadataPage extends ManagedPage {
                                                 overrides: {
                                                     schema: {
                                                         items: {
-                                                            order: ['name', 'description'],
+                                                            order: ["name", "description"],
                                                             additionalProperties: false,
-                                                        }
+                                                        },
                                                     },
                                                     ignore: {
-                                                        [tempPropertyKey]: true
-                                                    }
+                                                        [tempPropertyKey]: true,
+                                                    },
                                                 },
                                                 onUpdate: (localPath, value) =>
                                                     onUpdate([name, ...localPath], value, true, {

From f9be972020fcb3b3bfb7f7196a9ed3c43d171d2c Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 14:51:00 -0800
Subject: [PATCH 121/133] Update Table.js

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

diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index ccf4980c7..be6d98ee4 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -298,7 +298,7 @@ export class Table extends LitElement {
                               [k],
                               { ...this.data[rowHeaders[row]] }, // Validate on a copy of the parent
                               value,
-                              info.properties[k]
+                              info
                           )
                         : true; // Return true if validation errored out on the JavaScript side (e.g. server is down)
 

From 792b1832479f997e6ff46a280381eded7a01cef8 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 24 Jan 2024 14:57:13 -0800
Subject: [PATCH 122/133] Fix nested copy/paste

---
 src/renderer/src/stories/SimpleTable.js | 40 ++++++++++++++-----------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 9a457a9ba..4ab61ddd0 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -210,37 +210,39 @@ export class SimpleTable extends LitElement {
         if (onThrow) this.onThrow = onThrow;
         if (onUpdate) this.onUpdate = onUpdate;
 
-        this.onmousedown = (ev) => {
-            ev.stopPropagation();
+        this.onmousedown = (pointerDownEvent) => {
+            pointerDownEvent.stopPropagation();
             this.#clearSelected();
             this.#selecting = true;
-            const cell = this.#getCellFromEvent(ev);
+            const cell = this.#getCellFromEvent(pointerDownEvent);
             if (cell) this.#selectCells(cell);
         };
 
-        this.onmouseup = (ev) => (this.#selecting = false);
+        this.onmouseup = () => (this.#selecting = false);
 
         document.addEventListener("onmouseup", this.onmouseup);
 
-        document.addEventListener("mousedown", (ev) => {
-            const path = this.#getPath(ev);
+        document.addEventListener("mousedown", (pointerDownEvent) => {
+            const path = this.#getPath(pointerDownEvent);
             if (!path.includes(this)) this.#clearSelected();
         });
 
         // Handle Copy-Paste Commands
-        this.addEventListener("copy", (ev) => {
-            ev.preventDefault();
+        this.addEventListener("copy", (copyEvent) => {
+            copyEvent.stopPropagation();
+            copyEvent.preventDefault();
+
             const tsv = Object.values(this.#selected)
                 .map((arr) => arr.map((inputElement) => inputElement.value).join("\t"))
                 .join("\n");
 
-            ev.clipboardData.setData("text/plain", tsv);
+            copyEvent.clipboardData.setData("text/plain", tsv);
         });
 
-        document.addEventListener("keydown", (ev) => {
-            var key = ev.keyCode || ev.charCode;
+        document.addEventListener("keydown", (keyDownEvent) => {
+            var key = keyDownEvent.keyCode || keyDownEvent.charCode;
             if (key == 8 || key == 46) {
-                const path = this.#getPath(ev);
+                const path = this.#getPath(keyDownEvent);
                 if (path[0] === document.body)
                     Object.values(this.#selected).forEach((row) => {
                         row.forEach((cell) => {
@@ -251,13 +253,13 @@ export class SimpleTable extends LitElement {
             }
 
             // Avoid special key clicks
-            if ((ev.metaKey || ev.ctrlKey || ev.shiftKey) && !ev.key) return;
+            if ((keyDownEvent.metaKey || keyDownEvent.ctrlKey || keyDownEvent.shiftKey) && !keyDownEvent.key) return;
 
             // Undo / Redo
-            if ((isMac ? ev.metaKey : ev.ctrlKey) && ev.key === "z") return this.#clearSelected();
+            if ((isMac ? keyDownEvent.metaKey : keyDownEvent.ctrlKey) && keyDownEvent.key === "z") return this.#clearSelected();
 
             if (this.#firstSelected) {
-                const path = this.#getPath(ev);
+                const path = this.#getPath(keyDownEvent);
                 if (path[0] === document.body) {
                     this.#firstSelected.input.toggle(true); // Open editor
                     this.#firstSelected.input.execute("selectAll"); // redirect keydown to the hidden input
@@ -265,12 +267,14 @@ export class SimpleTable extends LitElement {
             }
         });
 
-        this.addEventListener("paste", (ev) => {
-            ev.preventDefault();
+        this.addEventListener("paste", (pasteEvent) => {
+            pasteEvent.stopPropagation();
+            pasteEvent.preventDefault();
+
             const topLeftCell = Object.values(this.#selected)[0]?.[0];
             if (!topLeftCell) return;
             const { i: firstI, j: firstJ } = topLeftCell.simpleTableInfo;
-            const tsv = ev.clipboardData.getData("text/plain");
+            const tsv = pasteEvent.clipboardData.getData("text/plain");
             let lastCell;
 
             tsv.split("\n").map((str, i) =>

From b3e9bf00ace274647011652bb92f169815c53a12 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jan 2024 22:57:29 +0000
Subject: [PATCH 123/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/SimpleTable.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 4ab61ddd0..621c36863 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -256,7 +256,8 @@ export class SimpleTable extends LitElement {
             if ((keyDownEvent.metaKey || keyDownEvent.ctrlKey || keyDownEvent.shiftKey) && !keyDownEvent.key) return;
 
             // Undo / Redo
-            if ((isMac ? keyDownEvent.metaKey : keyDownEvent.ctrlKey) && keyDownEvent.key === "z") return this.#clearSelected();
+            if ((isMac ? keyDownEvent.metaKey : keyDownEvent.ctrlKey) && keyDownEvent.key === "z")
+                return this.#clearSelected();
 
             if (this.#firstSelected) {
                 const path = this.#getPath(keyDownEvent);

From b432f098c6a4b333ac9a345cbb10105da0c7fc20 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 25 Jan 2024 09:46:39 -0800
Subject: [PATCH 124/133] Do not delete definitions

---
 schemas/base-metadata.schema.ts                         | 6 +++---
 src/renderer/src/stories/forms/utils.ts                 | 4 +---
 src/renderer/src/stories/pages/settings/SettingsPage.js | 2 +-
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index ab22bbb18..726ac1df2 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -104,8 +104,8 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
 
         if (getProp("ImagingPlane")) {
-            const imagingPlane = getProp("ImagingPlane")
-            imagingPlane.items.order = [
+            const imagingPlaneItems = getProp("ImagingPlane").items
+            imagingPlaneItems.order = [
                 "name",
                 "description",
                 "device",
@@ -121,7 +121,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
                 'origin_coords_unit'
             ]
 
-            imagingPlane.items.properties.optical_channel.items.order = ["name", "description"]
+            imagingPlaneItems.properties.optical_channel.items.order = ["name", "description"]
 
         }
     }
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 06400ccb2..83149af1e 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -44,9 +44,7 @@ export const textToArray = (value: string) => value.split("\n")
                     }
                 }
             }
-
-            if (parent.properties) delete parent.properties.definitions // Delete definitions when complete
-
+            
             return copy as { [x:string]: any }
         }
 
diff --git a/src/renderer/src/stories/pages/settings/SettingsPage.js b/src/renderer/src/stories/pages/settings/SettingsPage.js
index 8ba75bcc3..a601e2abe 100644
--- a/src/renderer/src/stories/pages/settings/SettingsPage.js
+++ b/src/renderer/src/stories/pages/settings/SettingsPage.js
@@ -96,7 +96,7 @@ const schema = merge(
                 ...developerGlobalSchema,
             },
         },
-        required: ["DANDI"],
+        required: ["DANDI", "developer"],
     },
     {
         arrays: true,

From dfa145abd49ec5f61fb055e89340c4bf9ba79529 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 25 Jan 2024 17:46:55 +0000
Subject: [PATCH 125/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/forms/utils.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 83149af1e..598c998be 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -44,7 +44,7 @@ export const textToArray = (value: string) => value.split("\n")
                     }
                 }
             }
-            
+
             return copy as { [x:string]: any }
         }
 

From a0191f81dc5a2dfc14f4d558ebe3a6cfe8353590 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 25 Jan 2024 09:47:12 -0800
Subject: [PATCH 126/133] Update utils.ts

---
 src/renderer/src/stories/forms/utils.ts | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 83149af1e..b1d2ded83 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -35,7 +35,8 @@ export const textToArray = (value: string) => value.split("\n")
                     if (internalCopy["$ref"]) {
                         const prevItem = path.slice(-1)[0];
                         const resolved = parent.properties.definitions?.[prevItem];
-                        copy[propName] = resolved;
+                        if (resolved) copy[propName] = resolved;
+                        else delete copy[propName]
                     } else {
                         for (let key in internalCopy) {
                             const fullPath = [...path, propName, key];
@@ -44,7 +45,7 @@ export const textToArray = (value: string) => value.split("\n")
                     }
                 }
             }
-            
+
             return copy as { [x:string]: any }
         }
 

From 79fe2441180411895430afe1e7bc4a5703f085c4 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 25 Jan 2024 09:56:11 -0800
Subject: [PATCH 127/133] Update JSONSchemaInput.js

---
 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 29e0cb870..3240e355c 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -810,7 +810,7 @@ export class JSONSchemaInput extends LitElement {
             const filesystemSelectorElement = new FilesystemSelector({
                 type: format,
                 value: this.value,
-                onSelect: (paths) => {
+                onSelect: (paths = []) => {
                     const value = paths.length ? paths : undefined;
                     this.#updateData(fullPath, value);
                 },

From e89a4e5a58e2549ac9f0873100e685e2468cb340 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 25 Jan 2024 10:03:19 -0800
Subject: [PATCH 128/133] Fix table validation

---
 src/renderer/src/stories/JSONSchemaForm.js | 6 +++++-
 src/renderer/src/validation/validation.ts  | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 7c2a0814e..55d80e90b 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -253,7 +253,11 @@ export class JSONSchemaForm extends LitElement {
     }
 
     // Get the form element defined by the path (stops before table cells)
-    getFormElement = (path, { forms = true, tables = true, inputs = true } = {}) => {
+    getFormElement = (path, { forms, tables, inputs } = {
+        forms: true, 
+        tables: true, 
+        inputs: true
+    }) => {
         if (typeof path === "string") path = path.split(".");
         if (!path.length) return this;
 
diff --git a/src/renderer/src/validation/validation.ts b/src/renderer/src/validation/validation.ts
index 8a9b0f20c..62426ffdd 100644
--- a/src/renderer/src/validation/validation.ts
+++ b/src/renderer/src/validation/validation.ts
@@ -192,7 +192,7 @@ schema.Ophys.Device = {
             ]
 
             dependencies.forEach(path => {
-                const table = this.getFormElement(path)
+                const table = this.getFormElement(path, { tables: true })
                 if (table) {
                     const data = table.data
                     data.forEach(row => {

From 8729bf27c8cc350f319b1e10fc5551abdd9fc67b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 25 Jan 2024 18:03:35 +0000
Subject: [PATCH 129/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 55d80e90b..168313932 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -253,11 +253,14 @@ export class JSONSchemaForm extends LitElement {
     }
 
     // Get the form element defined by the path (stops before table cells)
-    getFormElement = (path, { forms, tables, inputs } = {
-        forms: true, 
-        tables: true, 
-        inputs: true
-    }) => {
+    getFormElement = (
+        path,
+        { forms, tables, inputs } = {
+            forms: true,
+            tables: true,
+            inputs: true,
+        }
+    ) => {
         if (typeof path === "string") path = path.split(".");
         if (!path.length) return this;
 

From 6bd83dd0c0c7c31b6e09c9807d7fb1b5554b7818 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 25 Jan 2024 10:58:51 -0800
Subject: [PATCH 130/133] Fix validation

---
 src/renderer/src/stories/JSONSchemaForm.js               | 2 +-
 src/renderer/src/stories/pages/guided-mode/data/utils.js | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 55d80e90b..fb7517e2d 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -795,7 +795,7 @@ export class JSONSchemaForm extends LitElement {
         const undefinedPathToken = localPath.findIndex((str) => !str && typeof str !== "number") !== -1;
         if (undefinedPathToken) return true; // Will be unable to get schema anyways (additionalProperties)
 
-        if (!input) input = this.getFormElement(localPath, { forms: false, tables: false });
+        if (!input) input = this.getFormElement(localPath, { inputs: true });
         if (!parent) parent = this.#get(path, this.resolved);
         if (!schema) schema = this.getSchema(localPath);
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index e8d741dfd..f5a028578 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -65,6 +65,8 @@ export function drillSchemaProperties(schema = {}, callback, target, path = [],
 
     for (let name in properties) {
         const info = properties[name];
+        
+        if (name === 'definitions') continue;
 
         const updatedPath = [...path, name];
 

From 7b4024fcf24dd6b53b97c10ac1698b8bdbee54c4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 25 Jan 2024 19:00:04 +0000
Subject: [PATCH 131/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/pages/guided-mode/data/utils.js b/src/renderer/src/stories/pages/guided-mode/data/utils.js
index f5a028578..dafaa89ca 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -65,8 +65,8 @@ export function drillSchemaProperties(schema = {}, callback, target, path = [],
 
     for (let name in properties) {
         const info = properties[name];
-        
-        if (name === 'definitions') continue;
+
+        if (name === "definitions") continue;
 
         const updatedPath = [...path, name];
 

From 3297634c2b341d73325855377132f12f857e6287 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Fri, 26 Jan 2024 08:58:14 -0800
Subject: [PATCH 132/133] Coerce to float in pattern properties

---
 pyflask/manageNeuroconv/manage_neuroconv.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index bff04fed0..2e88b8e87 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -74,7 +74,16 @@ def replace_none_with_nan(json_object, json_schema):
     def coerce_schema_compliance_recursive(obj, schema):
         if isinstance(obj, dict):
             for key, value in obj.items():
-                if key in schema.get("properties", {}):
+
+                # Coerce on pattern properties as well
+                pattern_properties = schema.get('patternProperties')
+                if (pattern_properties):
+                    for pattern, pattern_schema in pattern_properties.items():
+                        regex = re.compile(pattern)
+                        if (regex.match(key)):
+                            coerce_schema_compliance_recursive(value, pattern_schema)
+  
+                elif key in schema.get("properties", {}):
                     prop_schema = schema["properties"][key]
                     if prop_schema.get("type") == "number" and (value is None or value == "NaN"):
                         obj[

From 3fad7fc5224d33443c258faa5127b118c0295e53 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 26 Jan 2024 16:58:29 +0000
Subject: [PATCH 133/133] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/manageNeuroconv/manage_neuroconv.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index 2e88b8e87..21fceb3aa 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -74,15 +74,14 @@ def replace_none_with_nan(json_object, json_schema):
     def coerce_schema_compliance_recursive(obj, schema):
         if isinstance(obj, dict):
             for key, value in obj.items():
-
                 # Coerce on pattern properties as well
-                pattern_properties = schema.get('patternProperties')
-                if (pattern_properties):
+                pattern_properties = schema.get("patternProperties")
+                if pattern_properties:
                     for pattern, pattern_schema in pattern_properties.items():
                         regex = re.compile(pattern)
-                        if (regex.match(key)):
+                        if regex.match(key):
                             coerce_schema_compliance_recursive(value, pattern_schema)
-  
+
                 elif key in schema.get("properties", {}):
                     prop_schema = schema["properties"][key]
                     if prop_schema.get("type") == "number" and (value is None or value == "NaN"):