From 433b624616c4c76263b9820a32f2e76b659af86e Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 13 Jul 2023 16:52:16 -0700
Subject: [PATCH 01/71] Fix Ecephys access and block Behavior validation

---
 pyflask/manageNeuroconv/manage_neuroconv.py | 2 +-
 src/renderer/src/validation/validation.json | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
index 79bd70a37..a82baa340 100644
--- a/pyflask/manageNeuroconv/manage_neuroconv.py
+++ b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -297,7 +297,7 @@ def update_conversion_progress(**kwargs):
     # Update the first recording interface with Ecephys table data
     recording_interface = get_first_recording_interface(converter)
 
-    ecephys_metadata = info["metadata"]["Ecephys"]
+    ecephys_metadata = info["metadata"].get("Ecephys", {})
 
     if recording_interface and is_supported_recording_interface(recording_interface, info["metadata"]):
         electrode_column_results = ecephys_metadata["ElectrodeColumns"]
diff --git a/src/renderer/src/validation/validation.json b/src/renderer/src/validation/validation.json
index 9e3a422dd..21092c1e1 100644
--- a/src/renderer/src/validation/validation.json
+++ b/src/renderer/src/validation/validation.json
@@ -35,6 +35,8 @@
         "ElectrodeColumns": { }
     },
 
+    "Behavior": false,
+
     "Subject": {
         "description": false,
         "genotype": false,

From ff987a93e6e51335e6355c47a0e59b74a3ee9dba Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 3 Aug 2023 13:24:46 -0700
Subject: [PATCH 02/71] Open a popup when the user jumps to a new page using
 the sidebar

---
 src/renderer/src/stories/Dashboard.js | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index c878e9d51..4ce2aecff 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -31,6 +31,7 @@ import "../../../../node_modules/@sweetalert2/theme-bulma/bulma.css";
 import "../../assets/css/guided.css";
 import isElectron from "../electron/check.js";
 import { isStorybook, reloadPageToHome } from "../dependencies/globals.js";
+import Swal from "sweetalert2";
 
 // import "https://jsuites.net/v4/jsuites.js"
 // import "https://bossanova.uk/jspreadsheet/v4/jexcel.js"
@@ -86,7 +87,20 @@ export class Dashboard extends LitElement {
         this.sidebar.onClick = (_, value) => this.setAttribute("activePage", value.info.id);
 
         this.subSidebar = new NavigationSidebar();
-        this.subSidebar.onClick = (id) => this.setAttribute("activePage", id);
+        this.subSidebar.onClick = async (id) => {
+
+            const result = await Swal.fire({
+                title: "You may have unsaved data on this page. Would you like to continue?",
+                text: "You won't be able to revert this!",
+                icon: 'warning',
+                showCancelButton: true,
+                confirmButtonColor: '#3085d6',
+                confirmButtonText: 'Keep Editing',
+                cancelButtonText: 'Jump to Selected Page'
+            });
+
+            if (!result.isConfirmed) this.setAttribute("activePage", id);
+        }
 
         this.pages = props.pages ?? {};
         this.name = props.name;

From da55922d36cd165f24e3e17a1998e0a78d214c07 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 3 Aug 2023 20:27:20 +0000
Subject: [PATCH 03/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/Dashboard.js | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 4ce2aecff..50cc6d973 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -88,19 +88,18 @@ export class Dashboard extends LitElement {
 
         this.subSidebar = new NavigationSidebar();
         this.subSidebar.onClick = async (id) => {
-
             const result = await Swal.fire({
                 title: "You may have unsaved data on this page. Would you like to continue?",
                 text: "You won't be able to revert this!",
-                icon: 'warning',
+                icon: "warning",
                 showCancelButton: true,
-                confirmButtonColor: '#3085d6',
-                confirmButtonText: 'Keep Editing',
-                cancelButtonText: 'Jump to Selected Page'
+                confirmButtonColor: "#3085d6",
+                confirmButtonText: "Keep Editing",
+                cancelButtonText: "Jump to Selected Page",
             });
 
             if (!result.isConfirmed) this.setAttribute("activePage", id);
-        }
+        };
 
         this.pages = props.pages ?? {};
         this.name = props.name;

From 5751907f6fd03b31dbef51eb58bad542184be8fc Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Fri, 4 Aug 2023 11:37:46 -0700
Subject: [PATCH 04/71] Track actual changes that need to be saved

---
 src/renderer/src/stories/BasicTable.js        |  2 ++
 src/renderer/src/stories/Dashboard.js         | 20 +++++++++++--------
 src/renderer/src/stories/JSONSchemaForm.js    | 11 ++++++++++
 src/renderer/src/stories/SimpleTable.js       |  5 +++++
 src/renderer/src/stories/Table.js             | 16 ++++++++++++++-
 src/renderer/src/stories/pages/FormPage.js    |  1 +
 src/renderer/src/stories/pages/Page.js        | 11 +++++++++-
 .../pages/guided-mode/data/GuidedMetadata.js  |  3 +++
 .../guided-mode/data/GuidedPathExpansion.js   |  6 +++++-
 .../guided-mode/data/GuidedSourceData.js      |  1 +
 .../options/GuidedConversionOptions.js        |  1 +
 .../pages/guided-mode/options/GuidedUpload.js |  1 +
 .../guided-mode/setup/GuidedNewDatasetInfo.js |  1 +
 .../pages/guided-mode/setup/GuidedSubjects.js |  4 +++-
 .../src/stories/pages/tutorial/Tutorial.js    |  4 +---
 src/renderer/src/stories/table/Cell.ts        | 10 +++++++++-
 src/renderer/src/stories/table/cells/base.ts  |  6 ++++++
 17 files changed, 87 insertions(+), 16 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 47f19082e..0478a4d5a 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -330,6 +330,8 @@ export class BasicTable extends LitElement {
                 key in this.schema.properties ? (latest[key] = value) : ""
             ); // Only include data from schema
         });
+
+        this.onUpdate(null, null, value) // Update the whole table
     }
 
     // Render Code
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 50cc6d973..2c03322e9 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -88,17 +88,20 @@ export class Dashboard extends LitElement {
 
         this.subSidebar = new NavigationSidebar();
         this.subSidebar.onClick = async (id) => {
-            const result = await Swal.fire({
-                title: "You may have unsaved data on this page. Would you like to continue?",
-                text: "You won't be able to revert this!",
+
+            const result = this.#active.unsavedUpdates ? await Swal.fire({
+                title: "You have unsaved data on this page.",
+                text: "Would you like to save your changes?",
                 icon: "warning",
                 showCancelButton: true,
                 confirmButtonColor: "#3085d6",
-                confirmButtonText: "Keep Editing",
-                cancelButtonText: "Jump to Selected Page",
-            });
+                confirmButtonText: "Save and Continue",
+                cancelButtonText: "Ignore Changes",
+            }) : undefined;
 
-            if (!result.isConfirmed) this.setAttribute("activePage", id);
+            if (result && result.isConfirmed) this.#active.save()
+            
+            this.setAttribute("activePage", id);
         };
 
         this.pages = props.pages ?? {};
@@ -141,7 +144,8 @@ export class Dashboard extends LitElement {
         else if (key === "renderNameInSidebar") this.sidebar.renderName = latest === "true" || latest === true;
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
-            if (this.#active && this.#active.info.parent && this.#active.info.section) this.#active.save(); // Always properly saves the page
+
+            // if (this.#active && this.#active.info.parent && this.#active.info.section) this.#active.save(); // Always properly saves the page
 
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index b90306482..6c99fbccb 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -245,10 +245,12 @@ export class JSONSchemaForm extends LitElement {
         this.conditionalRequirements = props.conditionalRequirements ?? []; // NOTE: We assume properties only belong to one conditional requirement group
 
         this.validateEmptyValues = props.validateEmptyValues ?? true;
+
         if (props.onInvalid) this.onInvalid = props.onInvalid;
         if (props.validateOnChange) this.validateOnChange = props.validateOnChange;
         if (props.onThrow) this.onThrow = props.onThrow;
         if (props.onLoaded) this.onLoaded = props.onLoaded;
+        if (props.onUpdate) this.onUpdate = props.onUpdate
         if (props.renderTable) this.renderTable = props.renderTable;
 
         if (props.onStatusChange) this.onStatusChange = props.onStatusChange;
@@ -283,6 +285,9 @@ export class JSONSchemaForm extends LitElement {
 
     // Track resolved values for the form
     #update(fullPath, value) {
+
+        this.onUpdate(fullPath, value)
+
         const path = [...fullPath];
         const name = path.pop();
         const resultParent = path.reduce((acc, key) => acc[key], this.results);
@@ -535,6 +540,10 @@ export class JSONSchemaForm extends LitElement {
                                 onStatusChange: () => this.#checkStatus(), // Check status on all elements
                                 validateEmptyCells: this.validateEmptyValues,
                                 deferLoading: this.deferLoading,
+                                onUpdate: (row, col, value) => {
+                                    console.log(fullPath, row, col, value)
+                                    this.onUpdate([...fullPath. row, col], value)
+                                },
                                 onLoaded: () => {
                                     this.#nLoaded++;
                                     this.#checkAllLoaded();
@@ -603,6 +612,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
     // Checks missing required properties and throws an error if any are found
     onInvalid = () => {};
     onLoaded = () => {};
+    onUpdate = () => {};
 
     #deleteExtraneousResults = (results, schema) => {
         for (let name in results) {
@@ -860,6 +870,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
                     schema: info,
                     results: results[name],
                     globals: this.globals?.[name],
+                    onUpdate: (internalPath, value) => this.onUpdate([...fullPath, ...internalPath], value),
 
                     required: required[name], // Scoped to the sub-schema
                     ignore: this.ignore,
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 30def2ca2..89e904dfb 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -21,6 +21,7 @@ const isVisible = function (ele, container) {
 
 export class SimpleTable extends LitElement {
     validateOnChange;
+    onUpdate = () => {}
 
     static get styles() {
         return css`
@@ -168,6 +169,7 @@ export class SimpleTable extends LitElement {
         validateEmptyCells,
         onStatusChange,
         onLoaded,
+        onUpdate,
         onThrow,
         deferLoading,
         maxHeight,
@@ -185,6 +187,7 @@ export class SimpleTable extends LitElement {
         if (onStatusChange) this.onStatusChange = onStatusChange;
         if (onLoaded) this.onLoaded = onLoaded;
         if (onThrow) this.onThrow = onThrow;
+        if (onUpdate) this.onUpdate = onUpdate
 
         this.onmousedown = (ev) => {
             this.#clearSelected();
@@ -631,6 +634,8 @@ export class SimpleTable extends LitElement {
             if (value == undefined || value === "") delete target[rowName][header];
             else target[rowName][header] = value;
         }
+
+        if (cell.interacted) this.onUpdate(rowName, header, value)
     };
 
     #createCell = (value, info) => {
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 179408fec..1998ecf55 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -56,7 +56,7 @@ const styleSymbol = Symbol("table-styles");
 export class Table extends LitElement {
     validateOnChange;
 
-    constructor({ schema, data, template, keyColumn, validateOnChange, validateEmptyCells, onStatusChange } = {}) {
+    constructor({ schema, data, template, keyColumn, validateOnChange, onUpdate, validateEmptyCells, onStatusChange } = {}) {
         super();
         this.schema = schema ?? {};
         this.data = data ?? [];
@@ -64,6 +64,7 @@ export class Table extends LitElement {
         this.template = template ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
 
+        if (onUpdate) this.onUpdate = onUpdate
         if (validateOnChange) this.validateOnChange = validateOnChange;
         if (onStatusChange) this.onStatusChange = onStatusChange;
 
@@ -134,8 +135,12 @@ export class Table extends LitElement {
 
     status;
     onStatusChange = () => {};
+    onUpdate = () => {}
 
     updated() {
+
+        let updateComplete = false
+
         const div = (this.shadowRoot ?? this).querySelector("div");
 
         const entries = { ...this.schema.properties };
@@ -298,6 +303,9 @@ export class Table extends LitElement {
 
         const unresolved = (this.unresolved = {});
 
+        let validated = 0
+        const initialCellsToUpdate = data.reduce((acc, v) => acc + v.length, 0)
+
         table.addHook("afterValidate", (isValid, value, row, prop) => {
             const header = typeof prop === "number" ? colHeaders[prop] : prop;
             let rowName = this.keyColumn ? rowHeaders[row] : row;
@@ -333,6 +341,10 @@ export class Table extends LitElement {
                 else target[rowName][header] = value;
             }
 
+            validated++
+
+            if (initialCellsToUpdate < validated) this.onUpdate(rowName, header, value)
+
             if (typeof isValid === "function") isValid();
             // }
         });
@@ -364,6 +376,8 @@ export class Table extends LitElement {
 
         // Trigger validation on all cells
         data.forEach((row, i) => this.#setRow(i, row));
+
+        updateComplete = true
     }
 
     #setRow(row, data) {
diff --git a/src/renderer/src/stories/pages/FormPage.js b/src/renderer/src/stories/pages/FormPage.js
index 8a21d0f46..f298db657 100644
--- a/src/renderer/src/stories/pages/FormPage.js
+++ b/src/renderer/src/stories/pages/FormPage.js
@@ -64,6 +64,7 @@ export class GuidedFormPage extends Page {
         const form = (this.form = new JSONSchemaForm({
             ...this.info.formOptions,
             results,
+            onUpdate: () => this.unsavedUpdates = true,
             validateOnChange,
             onThrow,
         }));
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 407d2390b..35e15f58e 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -62,7 +62,10 @@ export class Page extends LitElement {
     onTransition = () => {}; // User-defined function
     updatePages = () => {}; // User-defined function
 
-    save = (overrides) => save(this, overrides);
+    save = (overrides) => {
+        save(this, overrides);
+        this.unsavedUpdates = false
+    }
 
     load = (datasetNameToResume = new URLSearchParams(window.location.search).get("project")) =>
         (this.info.globalState = get(datasetNameToResume));
@@ -165,6 +168,12 @@ export class Page extends LitElement {
         this.updatePages();
     };
 
+    unsavedUpdates = false // Track unsaved updates
+
+    updated() {
+        this.unsavedUpdates = false
+    }
+
     render() {
         return html`<slot></slot>`;
     }
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 36759e09b..8492c91e0 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -101,6 +101,9 @@ export class GuidedMetadataPage extends ManagedPage {
                 this.#nLoaded++;
                 this.#checkAllLoaded();
             },
+
+            onUpdate: () => this.unsavedUpdates = true,
+
             validateOnChange,
             onlyRequired: false,
             onStatusChange: (state) => this.manager.updateState(`sub-${subject}/ses-${session}`, state),
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 9ab15cabb..be0d1fff1 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -152,7 +152,11 @@ export class GuidedPathExpansionPage extends Page {
 
         this.optional.requestUpdate();
 
-        const form = (this.form = new JSONSchemaForm({ ...structureGlobalState, onThrow }));
+        const form = (this.form = new JSONSchemaForm({ 
+            ...structureGlobalState, 
+            onThrow ,
+            onUpdate: () => this.unsavedUpdates = true,
+        }));
 
         const pathExpansionInfoBox = new InfoBox({
             header: "How do I use a Python format string for path expansion?",
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 c960041c6..1f0c9a652 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -96,6 +96,7 @@ export class GuidedSourceDataPage extends ManagedPage {
             results: info.source_data,
             ignore: ["verbose", "es_key", "exclude_shanks"],
             // onlyRequired: true,
+            onUpdate: () => this.unsavedUpdates = true,
             onStatusChange: (state) => this.manager.updateState(instanceId, state),
             onThrow,
         });
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
index f8bb85e00..b5f413f4f 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
@@ -48,6 +48,7 @@ export class GuidedConversionOptionsPage extends Page {
             dialogOptions: {
                 properties: ["openDirectory", "createDirectory"],
             },
+            onUpdate: () => this.unsavedUpdates = true,
             onThrow,
         });
 
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 cd4422cdc..b2372f8c9 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -64,6 +64,7 @@ export class GuidedUploadPage extends Page {
                 //   { name: 'NWB File', extensions: ['nwb'] }
                 // ]
             },
+            onUpdate: () => this.unsavedUpdates = true,
             onThrow,
         });
 
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
index 2d36f6391..b47749061 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -91,6 +91,7 @@ export class GuidedNewDatasetPage extends Page {
                 properties: ["createDirectory"],
             },
             validateOnChange,
+            onUpdate: () => this.unsavedUpdates = true,
             onThrow,
         });
 
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 9404c6ff9..7d19b2f05 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -5,6 +5,7 @@ import { validateOnChange } from "../../../../validation/index.js";
 import { Table } from "../../../Table.js";
 
 import { updateResultsFromSubjects } from "./utils";
+import { SimpleTable } from "../../../SimpleTable.js";
 
 export class GuidedSubjectsPage extends Page {
     constructor(...args) {
@@ -65,12 +66,13 @@ export class GuidedSubjectsPage extends Page {
             subjects[subject].sessions = sessions;
         }
 
-        this.table = new Table({
+        this.table = new SimpleTable({
             schema: subjectSchema,
             data: subjects,
             template: this.info.globalState.project.Subject,
             keyColumn: "subject_id",
             validateEmptyCells: false,
+            onUpdate: () => this.unsavedUpdates = true,
             validateOnChange: (key, parent, v) => {
                 if (key === "sessions") return true;
                 else {
diff --git a/src/renderer/src/stories/pages/tutorial/Tutorial.js b/src/renderer/src/stories/pages/tutorial/Tutorial.js
index 7845838f8..2b7d5dab9 100644
--- a/src/renderer/src/stories/pages/tutorial/Tutorial.js
+++ b/src/renderer/src/stories/pages/tutorial/Tutorial.js
@@ -34,9 +34,7 @@ export class TutorialPage extends Page {
                 properties: ["createDirectory"],
             },
             results: state,
-            validateOnChange: () => {
-                global.save();
-            },
+            onUpdate: () => global.save()
         });
 
         form.style.width = "100%";
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index 24fc87c93..d02766419 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -132,6 +132,7 @@ export class TableCell extends LitElement {
     };
 
     setInput(value: any) {
+        this.interacted = true
         this.input.set(value)  // Ensure all operations are undoable
     }
 
@@ -146,6 +147,8 @@ export class TableCell extends LitElement {
 
     #cls: any
 
+    interacted = false
+
     // input = new TableCellBase({ })
 
     input: TableCellBase
@@ -153,6 +156,8 @@ export class TableCell extends LitElement {
     render() {
 
         let cls = TableCellBase
+        
+        this.interacted = false
 
         if (this.schema.type === "array") cls = ArrayCell
         else if (this.schema.format === "date-time") cls =  DateTimeCell
@@ -160,7 +165,10 @@ export class TableCell extends LitElement {
         // Only actually rerender if new class type
         if (cls !== this.#cls) {
             this.input = new cls({
-                onChange: () => this.validate(),
+                onChange: () => {
+                    if (this.input.interacted) this.interacted = true
+                    this.validate()
+                },
                 schema: this.schema
             })
         }
diff --git a/src/renderer/src/stories/table/cells/base.ts b/src/renderer/src/stories/table/cells/base.ts
index 7d6c9b3a1..3a52c7774 100644
--- a/src/renderer/src/stories/table/cells/base.ts
+++ b/src/renderer/src/stories/table/cells/base.ts
@@ -49,6 +49,8 @@ export class TableCellBase extends LitElement {
 
     schema: any;
 
+    interacted = false
+
     constructor({
         schema,
         onOpen,
@@ -64,6 +66,7 @@ export class TableCellBase extends LitElement {
         if (onClose) this.onClose = onClose
 
         this.#editable.addEventListener('input', (ev: InputEvent) => {
+            this.interacted = true
             if (ev.inputType.includes('history')) this.setText(this.#editable.innerText) // Catch undo / redo}
         })
 
@@ -118,6 +121,7 @@ export class TableCellBase extends LitElement {
     }
 
     set(value: any) {
+
         if (document.execCommand) {
             this.#editable.setAttribute('contenteditable', '')
             this.#editable.focus();
@@ -158,6 +162,8 @@ export class TableCellBase extends LitElement {
 
     render() {
 
+        this.interacted = false
+
         this.#editable.id = 'editable'
 
         const editor = this.#editor = this.#render('editor')

From 225daf489be225a7bfd0a196ba541ab71b8b63e6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 4 Aug 2023 18:38:03 +0000
Subject: [PATCH 05/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/BasicTable.js        |  2 +-
 src/renderer/src/stories/Dashboard.js         | 26 ++++++++---------
 src/renderer/src/stories/JSONSchemaForm.js    |  9 +++---
 src/renderer/src/stories/SimpleTable.js       |  6 ++--
 src/renderer/src/stories/Table.js             | 28 ++++++++++++-------
 src/renderer/src/stories/pages/FormPage.js    |  2 +-
 src/renderer/src/stories/pages/Page.js        |  8 +++---
 .../pages/guided-mode/data/GuidedMetadata.js  |  2 +-
 .../guided-mode/data/GuidedPathExpansion.js   |  8 +++---
 .../guided-mode/data/GuidedSourceData.js      |  2 +-
 .../options/GuidedConversionOptions.js        |  2 +-
 .../pages/guided-mode/options/GuidedUpload.js |  2 +-
 .../guided-mode/setup/GuidedNewDatasetInfo.js |  2 +-
 .../pages/guided-mode/setup/GuidedSubjects.js |  2 +-
 .../src/stories/pages/tutorial/Tutorial.js    |  2 +-
 src/renderer/src/stories/table/Cell.ts        |  2 +-
 16 files changed, 56 insertions(+), 49 deletions(-)

diff --git a/src/renderer/src/stories/BasicTable.js b/src/renderer/src/stories/BasicTable.js
index 0478a4d5a..1cad4503d 100644
--- a/src/renderer/src/stories/BasicTable.js
+++ b/src/renderer/src/stories/BasicTable.js
@@ -331,7 +331,7 @@ export class BasicTable extends LitElement {
             ); // Only include data from schema
         });
 
-        this.onUpdate(null, null, value) // Update the whole table
+        this.onUpdate(null, null, value); // Update the whole table
     }
 
     // Render Code
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 2c03322e9..75d2d1817 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -88,19 +88,20 @@ export class Dashboard extends LitElement {
 
         this.subSidebar = new NavigationSidebar();
         this.subSidebar.onClick = async (id) => {
+            const result = this.#active.unsavedUpdates
+                ? await Swal.fire({
+                      title: "You have unsaved data on this page.",
+                      text: "Would you like to save your changes?",
+                      icon: "warning",
+                      showCancelButton: true,
+                      confirmButtonColor: "#3085d6",
+                      confirmButtonText: "Save and Continue",
+                      cancelButtonText: "Ignore Changes",
+                  })
+                : undefined;
+
+            if (result && result.isConfirmed) this.#active.save();
 
-            const result = this.#active.unsavedUpdates ? await Swal.fire({
-                title: "You have unsaved data on this page.",
-                text: "Would you like to save your changes?",
-                icon: "warning",
-                showCancelButton: true,
-                confirmButtonColor: "#3085d6",
-                confirmButtonText: "Save and Continue",
-                cancelButtonText: "Ignore Changes",
-            }) : undefined;
-
-            if (result && result.isConfirmed) this.#active.save()
-            
             this.setAttribute("activePage", id);
         };
 
@@ -144,7 +145,6 @@ export class Dashboard extends LitElement {
         else if (key === "renderNameInSidebar") this.sidebar.renderName = latest === "true" || latest === true;
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
-
             // if (this.#active && this.#active.info.parent && this.#active.info.section) this.#active.save(); // Always properly saves the page
 
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 6c99fbccb..21240d714 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -250,7 +250,7 @@ export class JSONSchemaForm extends LitElement {
         if (props.validateOnChange) this.validateOnChange = props.validateOnChange;
         if (props.onThrow) this.onThrow = props.onThrow;
         if (props.onLoaded) this.onLoaded = props.onLoaded;
-        if (props.onUpdate) this.onUpdate = props.onUpdate
+        if (props.onUpdate) this.onUpdate = props.onUpdate;
         if (props.renderTable) this.renderTable = props.renderTable;
 
         if (props.onStatusChange) this.onStatusChange = props.onStatusChange;
@@ -285,8 +285,7 @@ export class JSONSchemaForm extends LitElement {
 
     // Track resolved values for the form
     #update(fullPath, value) {
-
-        this.onUpdate(fullPath, value)
+        this.onUpdate(fullPath, value);
 
         const path = [...fullPath];
         const name = path.pop();
@@ -541,8 +540,8 @@ export class JSONSchemaForm extends LitElement {
                                 validateEmptyCells: this.validateEmptyValues,
                                 deferLoading: this.deferLoading,
                                 onUpdate: (row, col, value) => {
-                                    console.log(fullPath, row, col, value)
-                                    this.onUpdate([...fullPath. row, col], value)
+                                    console.log(fullPath, row, col, value);
+                                    this.onUpdate([...fullPath.row, col], value);
                                 },
                                 onLoaded: () => {
                                     this.#nLoaded++;
diff --git a/src/renderer/src/stories/SimpleTable.js b/src/renderer/src/stories/SimpleTable.js
index 89e904dfb..0f09c62b5 100644
--- a/src/renderer/src/stories/SimpleTable.js
+++ b/src/renderer/src/stories/SimpleTable.js
@@ -21,7 +21,7 @@ const isVisible = function (ele, container) {
 
 export class SimpleTable extends LitElement {
     validateOnChange;
-    onUpdate = () => {}
+    onUpdate = () => {};
 
     static get styles() {
         return css`
@@ -187,7 +187,7 @@ export class SimpleTable extends LitElement {
         if (onStatusChange) this.onStatusChange = onStatusChange;
         if (onLoaded) this.onLoaded = onLoaded;
         if (onThrow) this.onThrow = onThrow;
-        if (onUpdate) this.onUpdate = onUpdate
+        if (onUpdate) this.onUpdate = onUpdate;
 
         this.onmousedown = (ev) => {
             this.#clearSelected();
@@ -635,7 +635,7 @@ 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) => {
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 1998ecf55..4e0a4c478 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -56,7 +56,16 @@ const styleSymbol = Symbol("table-styles");
 export class Table extends LitElement {
     validateOnChange;
 
-    constructor({ schema, data, template, keyColumn, validateOnChange, onUpdate, validateEmptyCells, onStatusChange } = {}) {
+    constructor({
+        schema,
+        data,
+        template,
+        keyColumn,
+        validateOnChange,
+        onUpdate,
+        validateEmptyCells,
+        onStatusChange,
+    } = {}) {
         super();
         this.schema = schema ?? {};
         this.data = data ?? [];
@@ -64,7 +73,7 @@ export class Table extends LitElement {
         this.template = template ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
 
-        if (onUpdate) this.onUpdate = onUpdate
+        if (onUpdate) this.onUpdate = onUpdate;
         if (validateOnChange) this.validateOnChange = validateOnChange;
         if (onStatusChange) this.onStatusChange = onStatusChange;
 
@@ -135,11 +144,10 @@ export class Table extends LitElement {
 
     status;
     onStatusChange = () => {};
-    onUpdate = () => {}
+    onUpdate = () => {};
 
     updated() {
-
-        let updateComplete = false
+        let updateComplete = false;
 
         const div = (this.shadowRoot ?? this).querySelector("div");
 
@@ -303,8 +311,8 @@ export class Table extends LitElement {
 
         const unresolved = (this.unresolved = {});
 
-        let validated = 0
-        const initialCellsToUpdate = data.reduce((acc, v) => acc + v.length, 0)
+        let validated = 0;
+        const initialCellsToUpdate = data.reduce((acc, v) => acc + v.length, 0);
 
         table.addHook("afterValidate", (isValid, value, row, prop) => {
             const header = typeof prop === "number" ? colHeaders[prop] : prop;
@@ -341,9 +349,9 @@ export class Table extends LitElement {
                 else target[rowName][header] = value;
             }
 
-            validated++
+            validated++;
 
-            if (initialCellsToUpdate < validated) this.onUpdate(rowName, header, value)
+            if (initialCellsToUpdate < validated) this.onUpdate(rowName, header, value);
 
             if (typeof isValid === "function") isValid();
             // }
@@ -377,7 +385,7 @@ export class Table extends LitElement {
         // Trigger validation on all cells
         data.forEach((row, i) => this.#setRow(i, row));
 
-        updateComplete = true
+        updateComplete = true;
     }
 
     #setRow(row, data) {
diff --git a/src/renderer/src/stories/pages/FormPage.js b/src/renderer/src/stories/pages/FormPage.js
index f298db657..dc5281837 100644
--- a/src/renderer/src/stories/pages/FormPage.js
+++ b/src/renderer/src/stories/pages/FormPage.js
@@ -64,7 +64,7 @@ export class GuidedFormPage extends Page {
         const form = (this.form = new JSONSchemaForm({
             ...this.info.formOptions,
             results,
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             validateOnChange,
             onThrow,
         }));
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 35e15f58e..879343b61 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -64,8 +64,8 @@ export class Page extends LitElement {
 
     save = (overrides) => {
         save(this, overrides);
-        this.unsavedUpdates = false
-    }
+        this.unsavedUpdates = false;
+    };
 
     load = (datasetNameToResume = new URLSearchParams(window.location.search).get("project")) =>
         (this.info.globalState = get(datasetNameToResume));
@@ -168,10 +168,10 @@ export class Page extends LitElement {
         this.updatePages();
     };
 
-    unsavedUpdates = false // Track unsaved updates
+    unsavedUpdates = false; // Track unsaved updates
 
     updated() {
-        this.unsavedUpdates = false
+        this.unsavedUpdates = false;
     }
 
     render() {
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 8492c91e0..32b52c9d7 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -102,7 +102,7 @@ export class GuidedMetadataPage extends ManagedPage {
                 this.#checkAllLoaded();
             },
 
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
 
             validateOnChange,
             onlyRequired: false,
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 be0d1fff1..098e626e1 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -152,10 +152,10 @@ export class GuidedPathExpansionPage extends Page {
 
         this.optional.requestUpdate();
 
-        const form = (this.form = new JSONSchemaForm({ 
-            ...structureGlobalState, 
-            onThrow ,
-            onUpdate: () => this.unsavedUpdates = true,
+        const form = (this.form = new JSONSchemaForm({
+            ...structureGlobalState,
+            onThrow,
+            onUpdate: () => (this.unsavedUpdates = true),
         }));
 
         const pathExpansionInfoBox = new InfoBox({
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 1f0c9a652..04e76358f 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -96,7 +96,7 @@ export class GuidedSourceDataPage extends ManagedPage {
             results: info.source_data,
             ignore: ["verbose", "es_key", "exclude_shanks"],
             // onlyRequired: true,
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             onStatusChange: (state) => this.manager.updateState(instanceId, state),
             onThrow,
         });
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
index b5f413f4f..fbd66ec08 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
@@ -48,7 +48,7 @@ export class GuidedConversionOptionsPage extends Page {
             dialogOptions: {
                 properties: ["openDirectory", "createDirectory"],
             },
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             onThrow,
         });
 
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 b2372f8c9..1b1133c89 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -64,7 +64,7 @@ export class GuidedUploadPage extends Page {
                 //   { name: 'NWB File', extensions: ['nwb'] }
                 // ]
             },
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             onThrow,
         });
 
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
index b47749061..831b708fb 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -91,7 +91,7 @@ export class GuidedNewDatasetPage extends Page {
                 properties: ["createDirectory"],
             },
             validateOnChange,
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             onThrow,
         });
 
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 7d19b2f05..475cae9a4 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -72,7 +72,7 @@ export class GuidedSubjectsPage extends Page {
             template: this.info.globalState.project.Subject,
             keyColumn: "subject_id",
             validateEmptyCells: false,
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => (this.unsavedUpdates = true),
             validateOnChange: (key, parent, v) => {
                 if (key === "sessions") return true;
                 else {
diff --git a/src/renderer/src/stories/pages/tutorial/Tutorial.js b/src/renderer/src/stories/pages/tutorial/Tutorial.js
index 2b7d5dab9..9cc911642 100644
--- a/src/renderer/src/stories/pages/tutorial/Tutorial.js
+++ b/src/renderer/src/stories/pages/tutorial/Tutorial.js
@@ -34,7 +34,7 @@ export class TutorialPage extends Page {
                 properties: ["createDirectory"],
             },
             results: state,
-            onUpdate: () => global.save()
+            onUpdate: () => global.save(),
         });
 
         form.style.width = "100%";
diff --git a/src/renderer/src/stories/table/Cell.ts b/src/renderer/src/stories/table/Cell.ts
index d02766419..e258e218f 100644
--- a/src/renderer/src/stories/table/Cell.ts
+++ b/src/renderer/src/stories/table/Cell.ts
@@ -156,7 +156,7 @@ export class TableCell extends LitElement {
     render() {
 
         let cls = TableCellBase
-        
+
         this.interacted = false
 
         if (this.schema.type === "array") cls = ArrayCell

From 681219ded39a1b281ae11f7997689d78d7dc4b18 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Fri, 4 Aug 2023 16:03:27 -0700
Subject: [PATCH 06/71] Interrim progress that generalizes save progression

---
 src/renderer/src/progress.js                  | 68 ++++++++++++----
 src/renderer/src/stories/Dashboard.js         | 23 ++----
 src/renderer/src/stories/JSONSchemaForm.js    |  2 +-
 src/renderer/src/stories/Main.js              |  7 +-
 src/renderer/src/stories/pages/FormPage.js    | 20 ++++-
 src/renderer/src/stories/pages/Page.js        | 36 ++++++++-
 .../pages/getting-started/GettingStarted.js   |  2 +-
 .../stories/pages/guided-mode/GuidedFooter.js |  8 +-
 .../stories/pages/guided-mode/GuidedHome.js   |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  | 42 ++++++++--
 .../guided-mode/data/GuidedPathExpansion.js   |  8 +-
 .../guided-mode/data/GuidedSourceData.js      | 21 +++--
 .../pages/guided-mode/data/GuidedStructure.js | 41 +++++-----
 .../stories/pages/guided-mode/data/utils.js   |  9 ++-
 .../options/GuidedConversionOptions.js        |  4 +-
 .../guided-mode/options/GuidedStubPreview.js  |  7 +-
 .../pages/guided-mode/options/GuidedUpload.js |  4 +-
 .../guided-mode/setup/GuidedNewDatasetInfo.js |  2 +-
 .../pages/guided-mode/setup/GuidedSubjects.js | 77 +++++++++++--------
 .../src/stories/pages/tutorial/Tutorial.js    |  2 +-
 src/renderer/src/stories/pages/utils.js       | 29 +++----
 21 files changed, 268 insertions(+), 146 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index 6e9930b65..d20d095af 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -3,6 +3,7 @@ import Swal from "sweetalert2";
 import { guidedProgressFilePath, reloadPageToHome, isStorybook, appDirectory } from "./dependencies/globals.js";
 import { fs } from "./electron/index.js";
 import { joinPath, runOnLoad } from "./globals.js";
+import { merge } from "./stories/pages/utils.js";
 
 class GlobalAppConfig {
     path = `${appDirectory}/config.json`;
@@ -48,33 +49,70 @@ export const update = (newDatasetName, previousDatasetName) => {
     } else throw new Error("No previous dataset name provided");
 };
 
+export const getCurrentProjectName = () => {
+    const params = new URLSearchParams(location.search);
+    return params.get("project");
+}
+
+export const updateAppProgress = (pageId, dataOrProjectName = {}, projectName = typeof dataOrProjectName === 'string' ? dataOrProjectName : undefined) => {
+ 
+    if (projectName) {
+        const params = new URLSearchParams(location.search);
+        params.set("project", projectName);
+
+        // Update browser history state
+        const value = `${location.pathname}?${params}`;
+        if (history.state) history.state.project = dataOrProjectName;
+        window.history.pushState(history.state, null, value);
+    }
+
+    // Is a project name
+    if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => data["page-before-exit"] = pageId)
+
+    // Is a data object
+    else dataOrProjectName["page-before-exit"] = pageId
+        
+}
+
 export const save = (page, overrides = {}) => {
-    const globalState = page.info.globalState;
-    let guidedProgressFileName = overrides.globalState?.project?.name ?? globalState.project?.name;
+
+    const globalState = merge(overrides, page.info.globalState); // Merge the overrides into the actual global state
+
+    let guidedProgressFileName = globalState.project?.name;
 
     //return if guidedProgressFileName is not a string greater than 0
     if (typeof guidedProgressFileName !== "string" || guidedProgressFileName.length === 0) return;
-    const params = new URLSearchParams(location.search);
 
-    params.set("project", guidedProgressFileName);
+    updateFile(guidedProgressFileName, () => {
+        updateAppProgress(page.info.id, globalState, guidedProgressFileName) // Will automatically set last updated time
+        return globalState
+    })
+};
+
+//Destination: HOMEDIR/NWB_GUIDE/pipelines
+export const updateFile = (projectName, callback) => {
+
+    let data = get(projectName)
 
-    // Update browser history state
-    const value = `${location.pathname}?${params}`;
-    if (history.state) history.state.project = guidedProgressFileName;
-    window.history.pushState(history.state, null, value);
+    if (callback) {
+        const result = callback(data)
+        if (result && typeof result === 'object') data = result
+    }
+
+    data["last-modified"] = new Date(); // Always update the last modified time
 
-    //Destination: HOMEDIR/NWB_GUIDE/pipelines
-    globalState["last-modified"] = new Date();
-    globalState["page-before-exit"] = overrides.id ?? page.info.id;
+    const copy = merge(data, {})
+    console.error(copy)
 
-    var guidedFilePath = joinPath(guidedProgressFilePath, guidedProgressFileName + ".json");
+    var guidedFilePath = joinPath(guidedProgressFilePath, projectName + ".json");
 
     // Save the file through the available mechanisms
     if (fs) {
         if (!fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //create progress folder if one does not exist
-        fs.writeFileSync(guidedFilePath, JSON.stringify(globalState, null, 2));
-    } else localStorage.setItem(guidedFilePath, JSON.stringify(globalState));
-};
+        fs.writeFileSync(guidedFilePath, JSON.stringify(data, null, 2));
+    } else localStorage.setItem(guidedFilePath, JSON.stringify(data));
+
+}
 
 export const getEntries = () => {
     if (fs && !fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 2c03322e9..4f54cef57 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -31,7 +31,7 @@ import "../../../../node_modules/@sweetalert2/theme-bulma/bulma.css";
 import "../../assets/css/guided.css";
 import isElectron from "../electron/check.js";
 import { isStorybook, reloadPageToHome } from "../dependencies/globals.js";
-import Swal from "sweetalert2";
+import { getCurrentProjectName, updateAppProgress } from "../progress.js";
 
 // import "https://jsuites.net/v4/jsuites.js"
 // import "https://bossanova.uk/jspreadsheet/v4/jexcel.js"
@@ -89,19 +89,9 @@ export class Dashboard extends LitElement {
         this.subSidebar = new NavigationSidebar();
         this.subSidebar.onClick = async (id) => {
 
-            const result = this.#active.unsavedUpdates ? await Swal.fire({
-                title: "You have unsaved data on this page.",
-                text: "Would you like to save your changes?",
-                icon: "warning",
-                showCancelButton: true,
-                confirmButtonColor: "#3085d6",
-                confirmButtonText: "Save and Continue",
-                cancelButtonText: "Ignore Changes",
-            }) : undefined;
-
-            if (result && result.isConfirmed) this.#active.save()
+            this.#active.to(id)
             
-            this.setAttribute("activePage", id);
+            // this.setAttribute("activePage", id);
         };
 
         this.pages = props.pages ?? {};
@@ -145,8 +135,11 @@ export class Dashboard extends LitElement {
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
 
-            // if (this.#active && this.#active.info.parent && this.#active.info.section) this.#active.save(); // Always properly saves the page
-
+            if (this.#active && this.#active.info.parent && this.#active.info.section) {
+                const currentProject = getCurrentProjectName()
+                updateAppProgress(latest, currentProject)
+            }
+            
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
 
             this.sidebar.selectItem(latest); // Just highlight the item
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 6c99fbccb..7e7d5fb18 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -976,7 +976,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
 
         const schema = this.schema ?? {};
 
-        this.resolved = merge(undefined, this.results, {}); // Track resolved values as a copy of the user-specified results
+        this.resolved = merge(this.results, {}); // Track resolved values as a copy of the user-specified results
 
         // Register default properties
         resolveProperties(schema.properties, this.resolved, this.globals);
diff --git a/src/renderer/src/stories/Main.js b/src/renderer/src/stories/Main.js
index ae55db1a0..1c9a5dbc0 100644
--- a/src/renderer/src/stories/Main.js
+++ b/src/renderer/src/stories/Main.js
@@ -71,6 +71,7 @@ export class Main extends LitElement {
     }
 
     render() {
+
         let { page = "", sections = {} } = this.toRender ?? {};
 
         let footer = page?.footer; // Page-specific footer
@@ -78,16 +79,20 @@ export class Main extends LitElement {
         let capsules = page?.capsules; // Page-specific capsules
 
         if (page) {
+
+            this.to = page.to
+
             const info = page.info ?? {};
 
             // Default Footer Behavior
             if (footer === true || (!("footer" in page) && info.parent)) {
+
                 // Go to home screen if there is no next page
                 if (!info.next)
                     footer = {
                         next: "Back to Home Screen",
                         exit: "Exit",
-                        onNext: () => this.onTransition("/"),
+                        onNext: () => this.toRender.page.to("/"),
                     };
                 // Allow navigating laterally if there is a next page
                 else footer = true;
diff --git a/src/renderer/src/stories/pages/FormPage.js b/src/renderer/src/stories/pages/FormPage.js
index f298db657..adf37f04b 100644
--- a/src/renderer/src/stories/pages/FormPage.js
+++ b/src/renderer/src/stories/pages/FormPage.js
@@ -3,6 +3,7 @@ import { JSONSchemaForm } from "../JSONSchemaForm.js";
 import { Page } from "./Page.js";
 import { validateOnChange } from "../../validation/index.js";
 import { onThrow } from "../../errors";
+import { merge } from "./utils.js";
 
 export function schemaToPages(schema, globalStatePath, options, transformationCallback = (info) => info) {
     return Object.entries(schema.properties)
@@ -46,11 +47,21 @@ export class GuidedFormPage extends Page {
         if (!this.info.formOptions.results) this.info.formOptions.results = {};
     }
 
+    beforeSave = () => {
+
+        // Merge results before saving
+        if (this.info.globalStatePath) {
+            const parent = this.info.globalStatePath.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.info.globalState)
+            parent[this.info.key] = this.localState[this.info.key]
+        }
+
+    }
+
     footer = {
         onNext: async () => {
-            this.save();
-            await this.form.validate();
-            this.onTransition(1);
+            await this.save(); // Save in case validation fails
+            await this.form.validate(); // Validate the results of the form
+            this.to(1);
         },
     };
 
@@ -59,7 +70,8 @@ export class GuidedFormPage extends Page {
         const temp = this.info.globalStatePath
             ? this.info.globalStatePath.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.info.globalState)
             : {};
-        const results = { [key]: temp[key] ?? (temp[key] = {}) };
+
+        const results = this.localState = merge({ [key]: temp[key] ?? (temp[key] = {}) }, {}); // Keep a local copy of the results
 
         const form = (this.form = new JSONSchemaForm({
             ...this.info.formOptions,
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 35e15f58e..eae6b34a0 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -6,6 +6,7 @@ import { merge, randomizeElements, mapSessions } from "./utils.js";
 
 import { ProgressBar } from "../ProgressBar";
 import { resolveResults } from "./guided-mode/data/utils.js";
+import Swal from "sweetalert2";
 
 export class Page extends LitElement {
     // static get styles() {
@@ -59,10 +60,39 @@ export class Page extends LitElement {
         this.#notifications.push(note);
     };
 
+    
+    to = async (transition) => {
+
+        // Otherwise note unsaved updates if present
+        if (this.unsavedUpdates) {
+            if (transition === 1) await this.save() // Save before a single forward transition
+            else {
+                Swal.fire({
+                    title: "You have unsaved data on this page.",
+                    text: "Would you like to save your changes?",
+                    icon: "warning",
+                    showCancelButton: true,
+                    confirmButtonColor: "#3085d6",
+                    confirmButtonText: "Save and Continue",
+                    cancelButtonText: "Ignore Changes",
+                }).then(async result => {
+                    if (result && result.isConfirmed) await this.save()
+                    this.onTransition(transition)
+                }) 
+
+                return
+            }
+        }
+
+        this.onTransition(transition)
+    }
+
     onTransition = () => {}; // User-defined function
     updatePages = () => {}; // User-defined function
+    beforeSave = () => {} // User-defined function
 
-    save = (overrides) => {
+    save = async (overrides, runBeforeSave = true) => {
+        if (runBeforeSave) await this.beforeSave()
         save(this, overrides);
         this.unsavedUpdates = false
     }
@@ -70,7 +100,6 @@ export class Page extends LitElement {
     load = (datasetNameToResume = new URLSearchParams(window.location.search).get("project")) =>
         (this.info.globalState = get(datasetNameToResume));
 
-    merge = merge;
 
     addSession({ subject, session, info }) {
         if (!this.info.globalState.results[subject]) this.info.globalState.results[subject] = {};
@@ -86,7 +115,7 @@ export class Page extends LitElement {
         delete this.info.globalState.results[subject][session];
     }
 
-    mapSessions = (callback) => mapSessions(callback, this.info.globalState);
+    mapSessions = (callback, data = this.info.globalState) => mapSessions(callback, data);
 
     async runConversions(conversionOptions = {}, toRun, options = {}) {
         let original = toRun;
@@ -170,6 +199,7 @@ export class Page extends LitElement {
 
     unsavedUpdates = false // Track unsaved updates
 
+    // NOTE: Make sure you call this explicitly if a child class overwrites this AND data is updated
     updated() {
         this.unsavedUpdates = false
     }
diff --git a/src/renderer/src/stories/pages/getting-started/GettingStarted.js b/src/renderer/src/stories/pages/getting-started/GettingStarted.js
index e5f80cf89..ae6359fb2 100644
--- a/src/renderer/src/stories/pages/getting-started/GettingStarted.js
+++ b/src/renderer/src/stories/pages/getting-started/GettingStarted.js
@@ -65,7 +65,7 @@ export class GettingStartedPage extends Page {
                     <button
                         id="home-button-guided-mode-link"
                         class="getting-started-btn secondary-plain-button text-base"
-                        @click="${() => this.onTransition("conversion/start")}"
+                        @click="${() => this.to("conversion/start")}"
                     >
                         <p class="getting-started-btn-txt">Convert a new dataset</p>
                         <i class="el-icon icon-animate"
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedFooter.js b/src/renderer/src/stories/pages/guided-mode/GuidedFooter.js
index 40c2142ee..7268708df 100644
--- a/src/renderer/src/stories/pages/guided-mode/GuidedFooter.js
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedFooter.js
@@ -28,9 +28,9 @@ export class GuidedFooter extends LitElement {
         back = "Back",
         next = "Next",
         exit = "Exit",
-        onBack = () => this.onTransition(-1),
-        onNext = () => this.onTransition(1),
-        onExit = () => this.onTransition("/"),
+        onBack = () => this.to(-1),
+        onNext = () => this.to(1),
+        onExit = () => this.to("/"),
     } = {}) {
         super();
         this.back = back;
@@ -48,7 +48,7 @@ export class GuidedFooter extends LitElement {
     }
 
     updated() {
-        this.onTransition = this.parentElement.onTransition;
+        this.to = (transition) => this.parentElement.to(transition);
     }
 
     render() {
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedHome.js b/src/renderer/src/stories/pages/guided-mode/GuidedHome.js
index 3cdbf64ef..ee6dddbf0 100644
--- a/src/renderer/src/stories/pages/guided-mode/GuidedHome.js
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedHome.js
@@ -193,7 +193,7 @@ export class GuidedHomePage extends Page {
                             class="container--dashed"
                             id="guided-button-start-new-curate"
                             style="width: 320px; margin: 5px; width: 28rem; height: 16.5rem"
-                            @click="${() => this.onTransition(1)}"
+                            @click="${() => this.to(1)}"
                         >
                             <div id="new-dataset-lottie-container" style="height: 150px; width: 150px"></div>
                             <h2 class="guided--text-sub-step" style="width: 100%;">Convert a new dataset</h2>
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 8492c91e0..0c0e771da 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -10,17 +10,30 @@ import Swal from "sweetalert2";
 import { SimpleTable } from "../../../SimpleTable.js";
 import { onThrow } from "../../../../errors";
 import { UnsafeComponent } from "../../Unsafe.js";
+import { merge } from "../../utils.js";
+
+const getInfoFromId = (key) => {
+    let [subject, session] = key.split("/");
+    if (subject.startsWith("sub-")) subject = subject.slice(4);
+    if (session.startsWith("ses-")) session = session.slice(4);
+
+    return { subject, session }
+}
 
 export class GuidedMetadataPage extends ManagedPage {
     constructor(...args) {
         super(...args);
     }
 
+    beforeSave  = () => {
+        merge(this.localState, this.info.globalState)
+    }
+
     form;
     footer = {
         next: "Run Conversion Preview",
         onNext: async () => {
-            this.save(); // Save in case the conversion fails
+            await this.save(); // Save in case the conversion fails
             for (let { form } of this.forms) await form.validate(); // Will throw an error in the callback
 
             // Preview a single random conversion
@@ -31,7 +44,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
             this.info.globalState.preview = result; // Save the preview results
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
@@ -143,7 +156,9 @@ export class GuidedMetadataPage extends ManagedPage {
     render() {
         this.#resetLoadState(); // Reset on each render
 
-        this.forms = this.mapSessions(this.createForm);
+        this.localState = {results: merge(this.info.globalState.results, {})}
+
+        this.forms = this.mapSessions(this.createForm, this.localState);
 
         let instances = {};
         this.forms.forEach(({ subject, session, form }) => {
@@ -151,6 +166,7 @@ export class GuidedMetadataPage extends ManagedPage {
             instances[`sub-${subject}`][`ses-${session}`] = form;
         });
 
+
         this.manager = new InstanceManager({
             header: "Sessions",
             instanceType: "Session",
@@ -161,9 +177,8 @@ export class GuidedMetadataPage extends ManagedPage {
                     name: "Preview",
                     primary: true,
                     onClick: async (key, el) => {
-                        let [subject, session] = key.split("/");
-                        if (subject.startsWith("sub-")) subject = subject.slice(4);
-                        if (session.startsWith("ses-")) session = session.slice(4);
+
+                        const { subject, session } = getInfoFromId(key)
 
                         const [{ file, html }] = await this.runConversions(
                             { stub_test: true },
@@ -188,9 +203,20 @@ export class GuidedMetadataPage extends ManagedPage {
                         document.body.append(modal);
                     },
                 },
+
+                // Only save the currently selected session
                 {
-                    name: "Save All Sessions",
-                    onClick: this.save,
+                    name: "Save",
+                    onClick: async (id) => {
+                        const ogCallback = this.beforeSave
+                        this.beforeSave = () => {
+                            const { subject, session } = getInfoFromId(id)
+
+                            merge(this.localState.results[subject][session], this.info.globalState.results[subject][session])
+                        }
+                        await this.save()
+                        this.beforeSave = ogCallback
+                    },
                 },
             ],
         });
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 be0d1fff1..3e275c8f2 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -10,6 +10,7 @@ import { onThrow } from "../../../../errors";
 
 import pathExpansionSchema from "../../../../../../../schemas/json/path-expansion.schema.json" assert { type: "json" };
 import { InfoBox } from "../../../InfoBox.js";
+import { merge } from "../../utils.js";
 
 export class GuidedPathExpansionPage extends Page {
     constructor(...args) {
@@ -17,8 +18,9 @@ export class GuidedPathExpansionPage extends Page {
     }
 
     footer = {
+        next: 'Populate Subject Details',
         onNext: async () => {
-            this.save(); // Save in case the request fails
+            await this.save(); // Save in case the request fails
 
             const hidden = this.optional.hidden;
             this.info.globalState.structure.state = !hidden;
@@ -89,7 +91,7 @@ export class GuidedPathExpansionPage extends Page {
                 }
 
                 // Save an overall results object organized by subject and session
-                this.merge("results", results);
+                merge(results, this.globalState.results);
 
                 // // NOTE: Current behavior is to ONLY add new results, not remove old ones
                 // // If we'd like, we could label sessions as user-defined so they never clear
@@ -104,7 +106,7 @@ export class GuidedPathExpansionPage extends Page {
                 // }
             }
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
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 1f0c9a652..330ca2141 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -7,21 +7,26 @@ import { InstanceManager } from "../../../InstanceManager.js";
 import { ManagedPage } from "./ManagedPage.js";
 import { baseUrl } from "../../../../globals.js";
 import { onThrow } from "../../../../errors";
+import { merge } from "../../utils.js";
 
 export class GuidedSourceDataPage extends ManagedPage {
     constructor(...args) {
         super(...args);
     }
 
+    beforeSave  = () => {
+        merge(this.localState, this.info.globalState)
+    }
+
     footer = {
+        next: 'Request Metadata Schema',
         onNext: async () => {
-            this.save(); // Save in case the conversion fails
+            await this.save(); // Save in case the conversion fails
+
             for (let { form } of this.forms) await form.validate(); // Will throw an error in the callback
 
             // const previousResults = this.info.globalState.metadata.results
 
-            this.save(); // Save in case the metadata request fails
-
             let stillFireSwal = false;
             const fireSwal = () => {
                 Swal.fire({
@@ -44,6 +49,7 @@ export class GuidedSourceDataPage extends ManagedPage {
 
             await Promise.all(
                 this.mapSessions(async ({ subject, session, info }) => {
+
                     // NOTE: This clears all user-defined results
                     const result = await fetch(`${baseUrl}/neuroconv/metadata`, {
                         method: "POST",
@@ -72,7 +78,7 @@ export class GuidedSourceDataPage extends ManagedPage {
                     }
 
                     // Merge metadata results with the generated info
-                    this.merge("metadata", result.results, info);
+                    merge(result.results, info.metadata);
 
                     // Mirror structure with metadata schema
                     const schema = this.info.globalState.schema;
@@ -82,7 +88,7 @@ export class GuidedSourceDataPage extends ManagedPage {
                 })
             );
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
@@ -109,7 +115,10 @@ export class GuidedSourceDataPage extends ManagedPage {
     };
 
     render() {
-        this.forms = this.mapSessions(this.createForm);
+
+        this.localState = {results: merge(this.info.globalState.results, {})}
+
+        this.forms = this.mapSessions(this.createForm, this.localState);
 
         let instances = {};
         this.forms.forEach(({ subject, session, form }) => {
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 1afd92339..664fd53aa 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -82,6 +82,7 @@ export class GuidedStructurePage extends Page {
 
         const deleteListItem = () => {
             li.remove();
+            this.unsavedUpdates = true
             delete this.#selected[resolvedKey];
         };
 
@@ -96,6 +97,8 @@ export class GuidedStructurePage extends Page {
         });
 
         button.onClick = deleteListItem;
+
+        this.unsavedUpdates = true
     };
 
     search = new Search({
@@ -108,30 +111,26 @@ export class GuidedStructurePage extends Page {
 
     searchModal = new Modal();
 
-    footer = {
-        onNext: async () => {
-            this.save(); // Save in case the schema request fails
-
-            const interfaces = { ...this.#selected };
+    beforeSave = async () => {
+        const interfaces = { ...this.#selected };
+        this.info.globalState.interfaces = interfaces;
 
-            const schema =
-                Object.keys(interfaces).length === 0
-                    ? {}
-                    : await fetch(`${baseUrl}/neuroconv/schema`, {
-                          method: "POST",
-                          headers: { "Content-Type": "application/json" },
-                          body: JSON.stringify(interfaces),
-                      }).then((res) => res.json());
+        await this.save(undefined, false) // Interrim save, in case the schema request fails
 
-            let schemas = this.info.globalState.schema;
-            if (!schemas) schemas = this.info.globalState.schema = {};
+        const schema =
+        Object.keys(interfaces).length === 0
+            ? {}
+            : await fetch(`${baseUrl}/neuroconv/schema`, {
+                  method: "POST",
+                  headers: { "Content-Type": "application/json" },
+                  body: JSON.stringify(interfaces),
+              }).then((res) => res.json());
 
-            schemas.source_data = schema;
-            this.info.globalState.interfaces = interfaces;
+        let schemas = this.info.globalState.schema;
+        if (!schemas) schemas = this.info.globalState.schema = {};
 
-            this.onTransition(1);
-        },
-    };
+        schemas.source_data = schema;
+    }
 
     async updated() {
         const selected = this.info.globalState.interfaces;
@@ -164,6 +163,8 @@ export class GuidedStructurePage extends Page {
 
             this.#addListItem({ ...found, key }); // Add previously selected items
         }
+
+        super.updated() // Call if updating data
     }
 
     render() {
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 be4ab93f7..e5ab73f9d 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/utils.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/utils.js
@@ -18,8 +18,8 @@ export function resolveGlobalOverrides(subject, globalState) {
     const subjectMetadataCopy = { ...globalState.subjects[subject] };
     delete subjectMetadataCopy.sessions; // Remove extra key from metadata
 
-    const overrides = merge(undefined, globalState.project, {}); // Copy project-wide metadata
-    merge("Subject", subjectMetadataCopy, overrides);
+    const overrides = merge(globalState.project, {}); // Copy project-wide metadata
+    merge(subjectMetadataCopy, overrides.Subject);
 
     return overrides;
 }
@@ -49,16 +49,17 @@ export function resolveProperties(properties = {}, target, globals = {}) {
 export function resolveResults(subject, session, globalState) {
     const overrides = resolveGlobalOverrides(subject, globalState); // Unique per-subject (but not sessions)
     const metadata = globalState.results[subject][session].metadata;
-    const results = merge(undefined, metadata, {}); // Copy the metadata results from the form
+    const results = merge(metadata, {}); // Copy the metadata results from the form
     const schema = globalState.schema.metadata[subject][session];
     resolveProperties(schema, results, overrides);
     return results;
 }
 
+// NOTE: Remove this...
 export function createResults({ subject, info }, globalState) {
     const results = populateWithProjectMetadata(info.metadata, globalState);
     const metadataCopy = { ...globalState.subjects[subject] };
     delete metadataCopy.sessions; // Remove extra key from metadata
-    merge("Subject", metadataCopy, results);
+    merge(metadataCopy, results.Subject);
     return results;
 }
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
index b5f413f4f..67eab3290 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js
@@ -11,7 +11,7 @@ export class GuidedConversionOptionsPage extends Page {
     footer = {
         next: "Run Conversion Preview",
         onNext: async () => {
-            this.save(); // Save in case the conversion fails
+            await this.save(); // Save in case the conversion fails
             await this.form.validate(); // Will throw an error in the callback
 
             // Preview a random conversion
@@ -21,7 +21,7 @@ export class GuidedConversionOptionsPage extends Page {
             });
             this.info.globalState.preview = results[0]; // Save the preview results
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index 09acada21..6052f50e4 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -23,16 +23,17 @@ export class GuidedStubPreviewPage extends Page {
             >`,
     };
 
+
+    // NOTE: We may want to trigger this whenever (1) this page is visited AND (2) data has been changed.
     footer = {
         next: "Run Conversion",
         onNext: async () => {
-            this.save(); // Save in case the conversion fails
-
+            await this.save(); // Save in case the conversion fails
             delete this.info.globalState.conversion;
             this.info.globalState.conversion = await this.runConversions({}, true, {
                 title: "Running all conversions",
             });
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
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 b2372f8c9..4d455b4dc 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -15,7 +15,7 @@ export class GuidedUploadPage extends Page {
         onNext: async () => {
             delete this.info.globalState.upload.results; // Clear the preview results
 
-            this.save(); // Save in case the conversion fails
+            await this.save(); // Save in case the conversion fails
             await this.form.validate(); // Will throw an error in the callback
 
             const info = { ...this.info.globalState.upload.info };
@@ -29,7 +29,7 @@ export class GuidedUploadPage extends Page {
 
             this.info.globalState.upload.results = results; // Save the preview results
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
index b47749061..7e3c96485 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -62,7 +62,7 @@ export class GuidedNewDatasetPage extends Page {
             globalState.initialized = true;
             Object.assign(globalState, this.state);
 
-            this.onTransition(1);
+            this.to(1);
         },
     };
 
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 7d19b2f05..8f92e4039 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -5,7 +5,7 @@ import { validateOnChange } from "../../../../validation/index.js";
 import { Table } from "../../../Table.js";
 
 import { updateResultsFromSubjects } from "./utils";
-import { SimpleTable } from "../../../SimpleTable.js";
+import { merge } from "../../utils.js";
 
 export class GuidedSubjectsPage extends Page {
     constructor(...args) {
@@ -16,44 +16,55 @@ export class GuidedSubjectsPage extends Page {
         subtitle: "Cross-session metadata applied to the final file metadata",
     };
 
+    // Only save if the subject structure is valid
+    beforeSave = () => {
+        const subjects = merge(this.localState, this.info.globalState.subjects ) // Merge the local and global states
+
+        try {
+            this.table.validate();
+        } catch (e) {
+            this.notify(e.message, "error");
+            throw e;
+        }
+
+        const { results } = this.info.globalState;
+        
+        // Object.keys(subjects).forEach((sub) => {
+        //     if (!subjects[sub].sessions?.length) {
+        //         delete subjects[sub]
+        //     }
+        // });
+
+        const noSessions = Object.keys(subjects).filter((sub) => !subjects[sub].sessions?.length);
+        if (noSessions.length) {
+            const error = `${noSessions.length} subject${noSessions.length > 1 ? "s are" : " is"} missing Sessions entries`
+            this.notify(error, "error");
+            throw new Error(error)
+        }
+
+        const sourceDataObject = Object.keys(this.info.globalState.interfaces).reduce((acc, key) => {
+            acc[key] = {};
+            return acc;
+        }, {});
+
+        // Modify the results object to track new subjects / sessions
+        updateResultsFromSubjects(results, subjects, sourceDataObject); // NOTE: This directly mutates the results object
+
+    }
+
     footer = {
-        onNext: () => {
-            const { results, subjects } = this.info.globalState;
-
-            try {
-                this.table.validate();
-            } catch (e) {
-                this.notify(e.message, "error");
-                throw e;
-            }
-
-            const noSessions = Object.keys(subjects).filter((sub) => !subjects[sub].sessions?.length);
-            if (noSessions.length)
-                return this.notify(
-                    `${noSessions.length} subject${noSessions.length > 1 ? "s are" : " is"} missing Sessions entries`,
-                    "error"
-                );
-
-            const sourceDataObject = Object.keys(this.info.globalState.interfaces).reduce((acc, key) => {
-                acc[key] = {};
-                return acc;
-            }, {});
-
-            // Modify the results object to track new subjects / sessions
-            updateResultsFromSubjects(results, subjects, sourceDataObject); // NOTE: This directly mutates the results object
-
-            this.onTransition(1);
-        },
+        next: 'Generate Data Structure'
     };
 
     updated() {
         const add = this.query("#addButton");
         add.onclick = () => this.table.table.alter("insert_row_below");
+        super.updated() // Call if updating data
     }
 
     render() {
-        let subjects = this.info.globalState.subjects;
-        if (!subjects) subjects = this.info.globalState.subjects = {}; // Ensure global subjects tracking
+
+        const subjects = this.localState = merge(this.info.globalState.subjects ?? {}, {})        
 
         // Ensure all the proper subjects are in the global state
         const toHave = Object.keys(this.info.globalState.results);
@@ -66,13 +77,15 @@ export class GuidedSubjectsPage extends Page {
             subjects[subject].sessions = sessions;
         }
 
-        this.table = new SimpleTable({
+        this.table = new Table({
             schema: subjectSchema,
             data: subjects,
             template: this.info.globalState.project.Subject,
             keyColumn: "subject_id",
             validateEmptyCells: false,
-            onUpdate: () => this.unsavedUpdates = true,
+            onUpdate: () => {
+                this.unsavedUpdates = true
+            },
             validateOnChange: (key, parent, v) => {
                 if (key === "sessions") return true;
                 else {
diff --git a/src/renderer/src/stories/pages/tutorial/Tutorial.js b/src/renderer/src/stories/pages/tutorial/Tutorial.js
index 2b7d5dab9..fc732f051 100644
--- a/src/renderer/src/stories/pages/tutorial/Tutorial.js
+++ b/src/renderer/src/stories/pages/tutorial/Tutorial.js
@@ -78,7 +78,7 @@ export class TutorialPage extends Page {
             ${hasEntry(tutorialPipelineName)
                 ? html`<div>
                       Data has been preloaded into the <b>${tutorialPipelineName}</b> pipeline, which can be accessed
-                      via the <a @click=${() => this.onTransition("guided")}>Guided Mode</a> conversion list.
+                      via the <a @click=${() => this.to("guided")}>Guided Mode</a> conversion list.
 
                       <br /><br />
 
diff --git a/src/renderer/src/stories/pages/utils.js b/src/renderer/src/stories/pages/utils.js
index 383e89f60..10266d847 100644
--- a/src/renderer/src/stories/pages/utils.js
+++ b/src/renderer/src/stories/pages/utils.js
@@ -14,30 +14,21 @@ export const randomizeElements = (array, count) => {
     return result;
 };
 
-export function merge(path, toMerge = {}, target = this.info.globalState) {
-    // Provide a temporary data structure to merge into
-    const isTemp = !path || path.length === 0;
-    if (isTemp) {
-        path = ["temp"];
-        target = { temp: target };
-    }
 
-    if (!Array.isArray(path)) path = path.split(".");
+const isObject = (o) => {
+    return o && typeof o === 'object' && !Array.isArray(o)
+}
 
-    const key = path.pop(); // Focus on the last key in the path
-    path.forEach((key) => (target = target[key]));
+export function merge(toMerge = {}, target = {}) {
 
     // Deep merge objects
-    if (key in target) {
-        for (const [k, v] of Object.entries(toMerge)) {
-            if (typeof v === "object" && !Array.isArray(v)) {
-                if (!target[key][k]) target[key][k] = { ...v }; // Copy objects
-                else this.merge(`${k}`, v, target[key]);
-            } else target[key][k] = v;
-        }
-    } else target[key] = toMerge;
+    for (const [k, v] of Object.entries(toMerge)) {
+        const targetV = target[k]
+        if (isObject(v) || isObject(targetV)) target[k] = merge(v, target[k])
+        else target[k] = v;
+    }
 
-    return isTemp ? target.temp : target;
+    return target
 }
 
 export function mapSessions(callback = (v) => v, globalState) {

From 6ed7ac95ebeaefbf29e1567cd60df361a980860e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 4 Aug 2023 23:04:36 +0000
Subject: [PATCH 07/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/progress.js                  | 38 +++++++++----------
 src/renderer/src/stories/Dashboard.js         |  9 ++---
 src/renderer/src/stories/Main.js              |  5 +--
 src/renderer/src/stories/pages/FormPage.js    | 13 ++++---
 src/renderer/src/stories/pages/Page.js        | 23 +++++------
 .../pages/guided-mode/data/GuidedMetadata.js  | 33 ++++++++--------
 .../guided-mode/data/GuidedPathExpansion.js   |  2 +-
 .../guided-mode/data/GuidedSourceData.js      | 12 +++---
 .../pages/guided-mode/data/GuidedStructure.js | 24 ++++++------
 .../guided-mode/options/GuidedStubPreview.js  |  1 -
 .../pages/guided-mode/setup/GuidedSubjects.js | 22 +++++------
 src/renderer/src/stories/pages/utils.js       | 12 +++---
 12 files changed, 91 insertions(+), 103 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index d20d095af..2ccabf208 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -52,10 +52,13 @@ export const update = (newDatasetName, previousDatasetName) => {
 export const getCurrentProjectName = () => {
     const params = new URLSearchParams(location.search);
     return params.get("project");
-}
+};
 
-export const updateAppProgress = (pageId, dataOrProjectName = {}, projectName = typeof dataOrProjectName === 'string' ? dataOrProjectName : undefined) => {
- 
+export const updateAppProgress = (
+    pageId,
+    dataOrProjectName = {},
+    projectName = typeof dataOrProjectName === "string" ? dataOrProjectName : undefined
+) => {
     if (projectName) {
         const params = new URLSearchParams(location.search);
         params.set("project", projectName);
@@ -67,15 +70,12 @@ export const updateAppProgress = (pageId, dataOrProjectName = {}, projectName =
     }
 
     // Is a project name
-    if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => data["page-before-exit"] = pageId)
-
+    if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => (data["page-before-exit"] = pageId));
     // Is a data object
-    else dataOrProjectName["page-before-exit"] = pageId
-        
-}
+    else dataOrProjectName["page-before-exit"] = pageId;
+};
 
 export const save = (page, overrides = {}) => {
-
     const globalState = merge(overrides, page.info.globalState); // Merge the overrides into the actual global state
 
     let guidedProgressFileName = globalState.project?.name;
@@ -84,25 +84,24 @@ export const save = (page, overrides = {}) => {
     if (typeof guidedProgressFileName !== "string" || guidedProgressFileName.length === 0) return;
 
     updateFile(guidedProgressFileName, () => {
-        updateAppProgress(page.info.id, globalState, guidedProgressFileName) // Will automatically set last updated time
-        return globalState
-    })
+        updateAppProgress(page.info.id, globalState, guidedProgressFileName); // Will automatically set last updated time
+        return globalState;
+    });
 };
 
 //Destination: HOMEDIR/NWB_GUIDE/pipelines
 export const updateFile = (projectName, callback) => {
-
-    let data = get(projectName)
+    let data = get(projectName);
 
     if (callback) {
-        const result = callback(data)
-        if (result && typeof result === 'object') data = result
+        const result = callback(data);
+        if (result && typeof result === "object") data = result;
     }
 
     data["last-modified"] = new Date(); // Always update the last modified time
 
-    const copy = merge(data, {})
-    console.error(copy)
+    const copy = merge(data, {});
+    console.error(copy);
 
     var guidedFilePath = joinPath(guidedProgressFilePath, projectName + ".json");
 
@@ -111,8 +110,7 @@ export const updateFile = (projectName, callback) => {
         if (!fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //create progress folder if one does not exist
         fs.writeFileSync(guidedFilePath, JSON.stringify(data, null, 2));
     } else localStorage.setItem(guidedFilePath, JSON.stringify(data));
-
-}
+};
 
 export const getEntries = () => {
     if (fs && !fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 5a7a5f086..6db73248a 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -100,7 +100,7 @@ export class Dashboard extends LitElement {
                   })
                 : undefined;
 
-            this.#active.to(id)
+            this.#active.to(id);
         };
 
         this.pages = props.pages ?? {};
@@ -143,12 +143,11 @@ export class Dashboard extends LitElement {
         else if (key === "renderNameInSidebar") this.sidebar.renderName = latest === "true" || latest === true;
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
-
             if (this.#active && this.#active.info.parent && this.#active.info.section) {
-                const currentProject = getCurrentProjectName()
-                updateAppProgress(latest, currentProject)
+                const currentProject = getCurrentProjectName();
+                updateAppProgress(latest, currentProject);
             }
-            
+
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
 
             this.sidebar.selectItem(latest); // Just highlight the item
diff --git a/src/renderer/src/stories/Main.js b/src/renderer/src/stories/Main.js
index 1c9a5dbc0..aafb77fc7 100644
--- a/src/renderer/src/stories/Main.js
+++ b/src/renderer/src/stories/Main.js
@@ -71,7 +71,6 @@ export class Main extends LitElement {
     }
 
     render() {
-
         let { page = "", sections = {} } = this.toRender ?? {};
 
         let footer = page?.footer; // Page-specific footer
@@ -79,14 +78,12 @@ export class Main extends LitElement {
         let capsules = page?.capsules; // Page-specific capsules
 
         if (page) {
-
-            this.to = page.to
+            this.to = page.to;
 
             const info = page.info ?? {};
 
             // Default Footer Behavior
             if (footer === true || (!("footer" in page) && info.parent)) {
-
                 // Go to home screen if there is no next page
                 if (!info.next)
                     footer = {
diff --git a/src/renderer/src/stories/pages/FormPage.js b/src/renderer/src/stories/pages/FormPage.js
index abf232924..1cd9ddc28 100644
--- a/src/renderer/src/stories/pages/FormPage.js
+++ b/src/renderer/src/stories/pages/FormPage.js
@@ -48,14 +48,15 @@ export class GuidedFormPage extends Page {
     }
 
     beforeSave = () => {
-
         // Merge results before saving
         if (this.info.globalStatePath) {
-            const parent = this.info.globalStatePath.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.info.globalState)
-            parent[this.info.key] = this.localState[this.info.key]
+            const parent = this.info.globalStatePath.reduce(
+                (acc, key) => acc[key] ?? (acc[key] = {}),
+                this.info.globalState
+            );
+            parent[this.info.key] = this.localState[this.info.key];
         }
-
-    }
+    };
 
     footer = {
         onNext: async () => {
@@ -71,7 +72,7 @@ export class GuidedFormPage extends Page {
             ? this.info.globalStatePath.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.info.globalState)
             : {};
 
-        const results = this.localState = merge({ [key]: temp[key] ?? (temp[key] = {}) }, {}); // Keep a local copy of the results
+        const results = (this.localState = merge({ [key]: temp[key] ?? (temp[key] = {}) }, {})); // Keep a local copy of the results
 
         const form = (this.form = new JSONSchemaForm({
             ...this.info.formOptions,
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index e331441f8..96e026609 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -60,12 +60,10 @@ export class Page extends LitElement {
         this.#notifications.push(note);
     };
 
-    
     to = async (transition) => {
-
         // Otherwise note unsaved updates if present
         if (this.unsavedUpdates) {
-            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 {
                 Swal.fire({
                     title: "You have unsaved data on this page.",
@@ -75,24 +73,24 @@ export class Page extends LitElement {
                     confirmButtonColor: "#3085d6",
                     confirmButtonText: "Save and Continue",
                     cancelButtonText: "Ignore Changes",
-                }).then(async result => {
-                    if (result && result.isConfirmed) await this.save()
-                    this.onTransition(transition)
-                }) 
+                }).then(async (result) => {
+                    if (result && result.isConfirmed) await this.save();
+                    this.onTransition(transition);
+                });
 
-                return
+                return;
             }
         }
 
-        this.onTransition(transition)
-    }
+        this.onTransition(transition);
+    };
 
     onTransition = () => {}; // User-defined function
     updatePages = () => {}; // User-defined function
-    beforeSave = () => {} // User-defined function
+    beforeSave = () => {}; // User-defined function
 
     save = async (overrides, runBeforeSave = true) => {
-        if (runBeforeSave) await this.beforeSave()
+        if (runBeforeSave) await this.beforeSave();
         save(this, overrides);
         this.unsavedUpdates = false;
     };
@@ -100,7 +98,6 @@ export class Page extends LitElement {
     load = (datasetNameToResume = new URLSearchParams(window.location.search).get("project")) =>
         (this.info.globalState = get(datasetNameToResume));
 
-
     addSession({ subject, session, info }) {
         if (!this.info.globalState.results[subject]) this.info.globalState.results[subject] = {};
         if (this.info.globalState.results[subject][session])
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 1a258c989..d95f53f71 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -17,17 +17,17 @@ const getInfoFromId = (key) => {
     if (subject.startsWith("sub-")) subject = subject.slice(4);
     if (session.startsWith("ses-")) session = session.slice(4);
 
-    return { subject, session }
-}
+    return { subject, session };
+};
 
 export class GuidedMetadataPage extends ManagedPage {
     constructor(...args) {
         super(...args);
     }
 
-    beforeSave  = () => {
-        merge(this.localState, this.info.globalState)
-    }
+    beforeSave = () => {
+        merge(this.localState, this.info.globalState);
+    };
 
     form;
     footer = {
@@ -156,7 +156,7 @@ export class GuidedMetadataPage extends ManagedPage {
     render() {
         this.#resetLoadState(); // Reset on each render
 
-        this.localState = {results: merge(this.info.globalState.results, {})}
+        this.localState = { results: merge(this.info.globalState.results, {}) };
 
         this.forms = this.mapSessions(this.createForm, this.localState);
 
@@ -166,7 +166,6 @@ export class GuidedMetadataPage extends ManagedPage {
             instances[`sub-${subject}`][`ses-${session}`] = form;
         });
 
-
         this.manager = new InstanceManager({
             header: "Sessions",
             instanceType: "Session",
@@ -177,8 +176,7 @@ export class GuidedMetadataPage extends ManagedPage {
                     name: "Preview",
                     primary: true,
                     onClick: async (key, el) => {
-
-                        const { subject, session } = getInfoFromId(key)
+                        const { subject, session } = getInfoFromId(key);
 
                         const [{ file, html }] = await this.runConversions(
                             { stub_test: true },
@@ -208,14 +206,17 @@ export class GuidedMetadataPage extends ManagedPage {
                 {
                     name: "Save",
                     onClick: async (id) => {
-                        const ogCallback = this.beforeSave
+                        const ogCallback = this.beforeSave;
                         this.beforeSave = () => {
-                            const { subject, session } = getInfoFromId(id)
-
-                            merge(this.localState.results[subject][session], this.info.globalState.results[subject][session])
-                        }
-                        await this.save()
-                        this.beforeSave = ogCallback
+                            const { subject, session } = getInfoFromId(id);
+
+                            merge(
+                                this.localState.results[subject][session],
+                                this.info.globalState.results[subject][session]
+                            );
+                        };
+                        await this.save();
+                        this.beforeSave = ogCallback;
                     },
                 },
             ],
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 490d23a4c..cb9545424 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -18,7 +18,7 @@ export class GuidedPathExpansionPage extends Page {
     }
 
     footer = {
-        next: 'Populate Subject Details',
+        next: "Populate Subject Details",
         onNext: async () => {
             await this.save(); // Save in case the request fails
 
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 978d4064f..014ab593b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -14,12 +14,12 @@ export class GuidedSourceDataPage extends ManagedPage {
         super(...args);
     }
 
-    beforeSave  = () => {
-        merge(this.localState, this.info.globalState)
-    }
+    beforeSave = () => {
+        merge(this.localState, this.info.globalState);
+    };
 
     footer = {
-        next: 'Request Metadata Schema',
+        next: "Request Metadata Schema",
         onNext: async () => {
             await this.save(); // Save in case the conversion fails
 
@@ -49,7 +49,6 @@ export class GuidedSourceDataPage extends ManagedPage {
 
             await Promise.all(
                 this.mapSessions(async ({ subject, session, info }) => {
-
                     // NOTE: This clears all user-defined results
                     const result = await fetch(`${baseUrl}/neuroconv/metadata`, {
                         method: "POST",
@@ -115,8 +114,7 @@ export class GuidedSourceDataPage extends ManagedPage {
     };
 
     render() {
-
-        this.localState = {results: merge(this.info.globalState.results, {})}
+        this.localState = { results: merge(this.info.globalState.results, {}) };
 
         this.forms = this.mapSessions(this.createForm, this.localState);
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 664fd53aa..01064c9f6 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -82,7 +82,7 @@ export class GuidedStructurePage extends Page {
 
         const deleteListItem = () => {
             li.remove();
-            this.unsavedUpdates = true
+            this.unsavedUpdates = true;
             delete this.#selected[resolvedKey];
         };
 
@@ -98,7 +98,7 @@ export class GuidedStructurePage extends Page {
 
         button.onClick = deleteListItem;
 
-        this.unsavedUpdates = true
+        this.unsavedUpdates = true;
     };
 
     search = new Search({
@@ -115,22 +115,22 @@ export class GuidedStructurePage extends Page {
         const interfaces = { ...this.#selected };
         this.info.globalState.interfaces = interfaces;
 
-        await this.save(undefined, false) // Interrim save, in case the schema request fails
+        await this.save(undefined, false); // Interrim save, in case the schema request fails
 
         const schema =
-        Object.keys(interfaces).length === 0
-            ? {}
-            : await fetch(`${baseUrl}/neuroconv/schema`, {
-                  method: "POST",
-                  headers: { "Content-Type": "application/json" },
-                  body: JSON.stringify(interfaces),
-              }).then((res) => res.json());
+            Object.keys(interfaces).length === 0
+                ? {}
+                : await fetch(`${baseUrl}/neuroconv/schema`, {
+                      method: "POST",
+                      headers: { "Content-Type": "application/json" },
+                      body: JSON.stringify(interfaces),
+                  }).then((res) => res.json());
 
         let schemas = this.info.globalState.schema;
         if (!schemas) schemas = this.info.globalState.schema = {};
 
         schemas.source_data = schema;
-    }
+    };
 
     async updated() {
         const selected = this.info.globalState.interfaces;
@@ -164,7 +164,7 @@ export class GuidedStructurePage extends Page {
             this.#addListItem({ ...found, key }); // Add previously selected items
         }
 
-        super.updated() // Call if updating data
+        super.updated(); // Call if updating data
     }
 
     render() {
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index 6052f50e4..efc491f2a 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -23,7 +23,6 @@ export class GuidedStubPreviewPage extends Page {
             >`,
     };
 
-
     // NOTE: We may want to trigger this whenever (1) this page is visited AND (2) data has been changed.
     footer = {
         next: "Run Conversion",
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 8f92e4039..ebdbd5188 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -18,7 +18,7 @@ export class GuidedSubjectsPage extends Page {
 
     // Only save if the subject structure is valid
     beforeSave = () => {
-        const subjects = merge(this.localState, this.info.globalState.subjects ) // Merge the local and global states
+        const subjects = merge(this.localState, this.info.globalState.subjects); // Merge the local and global states
 
         try {
             this.table.validate();
@@ -28,7 +28,7 @@ export class GuidedSubjectsPage extends Page {
         }
 
         const { results } = this.info.globalState;
-        
+
         // Object.keys(subjects).forEach((sub) => {
         //     if (!subjects[sub].sessions?.length) {
         //         delete subjects[sub]
@@ -37,9 +37,11 @@ export class GuidedSubjectsPage extends Page {
 
         const noSessions = Object.keys(subjects).filter((sub) => !subjects[sub].sessions?.length);
         if (noSessions.length) {
-            const error = `${noSessions.length} subject${noSessions.length > 1 ? "s are" : " is"} missing Sessions entries`
+            const error = `${noSessions.length} subject${
+                noSessions.length > 1 ? "s are" : " is"
+            } missing Sessions entries`;
             this.notify(error, "error");
-            throw new Error(error)
+            throw new Error(error);
         }
 
         const sourceDataObject = Object.keys(this.info.globalState.interfaces).reduce((acc, key) => {
@@ -49,22 +51,20 @@ export class GuidedSubjectsPage extends Page {
 
         // Modify the results object to track new subjects / sessions
         updateResultsFromSubjects(results, subjects, sourceDataObject); // NOTE: This directly mutates the results object
-
-    }
+    };
 
     footer = {
-        next: 'Generate Data Structure'
+        next: "Generate Data Structure",
     };
 
     updated() {
         const add = this.query("#addButton");
         add.onclick = () => this.table.table.alter("insert_row_below");
-        super.updated() // Call if updating data
+        super.updated(); // Call if updating data
     }
 
     render() {
-
-        const subjects = this.localState = merge(this.info.globalState.subjects ?? {}, {})        
+        const subjects = (this.localState = merge(this.info.globalState.subjects ?? {}, {}));
 
         // Ensure all the proper subjects are in the global state
         const toHave = Object.keys(this.info.globalState.results);
@@ -84,7 +84,7 @@ export class GuidedSubjectsPage extends Page {
             keyColumn: "subject_id",
             validateEmptyCells: false,
             onUpdate: () => {
-                this.unsavedUpdates = true
+                this.unsavedUpdates = true;
             },
             validateOnChange: (key, parent, v) => {
                 if (key === "sessions") return true;
diff --git a/src/renderer/src/stories/pages/utils.js b/src/renderer/src/stories/pages/utils.js
index 10266d847..732b06f5b 100644
--- a/src/renderer/src/stories/pages/utils.js
+++ b/src/renderer/src/stories/pages/utils.js
@@ -14,21 +14,19 @@ export const randomizeElements = (array, count) => {
     return result;
 };
 
-
 const isObject = (o) => {
-    return o && typeof o === 'object' && !Array.isArray(o)
-}
+    return o && typeof o === "object" && !Array.isArray(o);
+};
 
 export function merge(toMerge = {}, target = {}) {
-
     // Deep merge objects
     for (const [k, v] of Object.entries(toMerge)) {
-        const targetV = target[k]
-        if (isObject(v) || isObject(targetV)) target[k] = merge(v, target[k])
+        const targetV = target[k];
+        if (isObject(v) || isObject(targetV)) target[k] = merge(v, target[k]);
         else target[k] = v;
     }
 
-    return target
+    return target;
 }
 
 export function mapSessions(callback = (v) => v, globalState) {

From f33b82e7e7f99c3d153c10ca8130f484faca8cf3 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 07:28:16 -0700
Subject: [PATCH 08/71] Ensure complete save flow is working properly

---
 src/renderer/src/progress.js                  | 29 ++++++++++---------
 src/renderer/src/stories/Dashboard.js         |  4 +--
 .../pages/guided-mode/options/GuidedUpload.js | 25 +++++++++++-----
 .../pages/guided-mode/setup/GuidedSubjects.js |  2 +-
 4 files changed, 35 insertions(+), 25 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index 2ccabf208..5372acea6 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -63,17 +63,19 @@ export const updateAppProgress = (
         const params = new URLSearchParams(location.search);
         params.set("project", projectName);
 
-        // Update browser history state
-        const value = `${location.pathname}?${params}`;
-        if (history.state) history.state.project = dataOrProjectName;
-        window.history.pushState(history.state, null, value);
-    }
+            // Update browser history state
+            const value = `${location.pathname}?${params}`;
+            if (history.state) history.state.project = dataOrProjectName;
+            window.history.pushState(history.state, null, value);
+        }
 
-    // Is a project name
-    if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => (data["page-before-exit"] = pageId));
-    // Is a data object
-    else dataOrProjectName["page-before-exit"] = pageId;
-};
+        // Is a project name
+        if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => data["page-before-exit"] = pageId)
+
+        // Is a data object
+        else dataOrProjectName["page-before-exit"] = pageId
+        
+}
 
 export const save = (page, overrides = {}) => {
     const globalState = merge(overrides, page.info.globalState); // Merge the overrides into the actual global state
@@ -100,9 +102,6 @@ export const updateFile = (projectName, callback) => {
 
     data["last-modified"] = new Date(); // Always update the last modified time
 
-    const copy = merge(data, {});
-    console.error(copy);
-
     var guidedFilePath = joinPath(guidedProgressFilePath, projectName + ".json");
 
     // Save the file through the available mechanisms
@@ -146,7 +145,9 @@ export const get = (name) => {
     }
 
     let progressFilePath = joinPath(guidedProgressFilePath, name + ".json");
-    return JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath));
+
+    const exists = fs ? fs.existsSync(progressFilePath) : (localStorage.getItem(progressFilePath) !== null);
+    return exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {};
 };
 
 export function resume(name) {
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 6db73248a..695641233 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -144,8 +144,8 @@ export class Dashboard extends LitElement {
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
             if (this.#active && this.#active.info.parent && this.#active.info.section) {
-                const currentProject = getCurrentProjectName();
-                updateAppProgress(latest, currentProject);
+                const currentProject = getCurrentProjectName()
+                if (currentProject) updateAppProgress(latest, currentProject)
             }
 
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
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 849747053..3a86f9e7b 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -3,6 +3,7 @@ import { JSONSchemaForm } from "../../../JSONSchemaForm.js";
 import { Page } from "../../Page.js";
 import { run } from "./utils.js";
 import { onThrow } from "../../../../errors";
+import { merge } from "../../utils.js";
 
 export class GuidedUploadPage extends Page {
     constructor(...args) {
@@ -11,29 +12,40 @@ export class GuidedUploadPage extends Page {
 
     form;
 
+    beforeSave = () => {
+        merge(this.localState, this.info.globalState.upload) // Merge the local and global states
+        delete globalUploadInfo.results; // Clear the preview results
+    }
+
     footer = {
         onNext: async () => {
-            delete this.info.globalState.upload.results; // Clear the preview results
 
             await this.save(); // Save in case the conversion fails
+
             await this.form.validate(); // Will throw an error in the callback
 
-            const info = { ...this.info.globalState.upload.info };
+            const info = { ...globalUploadInfo.info };
             info.project = this.info.globalState.project.name;
-            info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs
+            info.staging = globalUploadInfo.info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs
 
             const results = await run("upload", info, { title: "Uploading to DANDI" }).catch((e) => {
                 this.notify(e.message, "error");
                 throw e;
             });
 
-            this.info.globalState.upload.results = results; // Save the preview results
+            globalUploadInfo.results = results; // Save the preview results
+
+            this.unsavedUpdates = true // Ensure that this saves automatically
 
             this.to(1);
         },
     };
 
     render() {
+
+
+        const state = this.localState = merge(this.info.globalState.upload ?? { info: {}, results: null }, {})
+
         const schema = {
             properties: {
                 api_key: {
@@ -51,12 +63,9 @@ export class GuidedUploadPage extends Page {
             required: ["api_key", "dandiset_id"],
         };
 
-        let uploadGlobalState = this.info.globalState.upload;
-        if (!uploadGlobalState) uploadGlobalState = this.info.globalState.upload = { info: {}, results: null };
-
         this.form = new JSONSchemaForm({
             schema,
-            results: uploadGlobalState.info,
+            results: state.info,
             // dialogType: 'showSaveDialog',
             dialogOptions: {
                 properties: ["createDirectory"],
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 ebdbd5188..4fc00e6f7 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -18,7 +18,7 @@ export class GuidedSubjectsPage extends Page {
 
     // Only save if the subject structure is valid
     beforeSave = () => {
-        const subjects = merge(this.localState, this.info.globalState.subjects); // Merge the local and global states
+        const subjects = this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects ) // Merge the local and global states
 
         try {
             this.table.validate();

From acd92f11b560a548d53e4fd91ce1f28ab210d9d6 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 07:28:37 -0700
Subject: [PATCH 09/71] Update GuidedUpload.js

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

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 3a86f9e7b..43986f9f9 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -24,6 +24,8 @@ export class GuidedUploadPage extends Page {
 
             await this.form.validate(); // Will throw an error in the callback
 
+            const globalUploadInfo = this.info.globalState.upload
+
             const info = { ...globalUploadInfo.info };
             info.project = this.info.globalState.project.name;
             info.staging = globalUploadInfo.info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs

From e2c54a777de3ddfd99fca5533bfd0787780f3e41 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 07:29:10 -0700
Subject: [PATCH 10/71] Update GuidedUpload.js

---
 .../src/stories/pages/guided-mode/options/GuidedUpload.js    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
index 43986f9f9..95ffc36b7 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -24,10 +24,11 @@ export class GuidedUploadPage extends Page {
 
             await this.form.validate(); // Will throw an error in the callback
 
-            const globalUploadInfo = this.info.globalState.upload
+            const globalState = this.info.globalState
+            const globalUploadInfo = globalState.upload
 
             const info = { ...globalUploadInfo.info };
-            info.project = this.info.globalState.project.name;
+            info.project = globalState.project.name;
             info.staging = globalUploadInfo.info.staging = parseInt(info.dandiset_id) >= 100000; // Automatically detect staging IDs
 
             const results = await run("upload", info, { title: "Uploading to DANDI" }).catch((e) => {

From ae2a0370e256576a4ad13460c1752e4a810da1d6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Aug 2023 14:31:53 +0000
Subject: [PATCH 11/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/progress.js                  | 24 +++++++++----------
 src/renderer/src/stories/Dashboard.js         |  4 ++--
 .../pages/guided-mode/options/GuidedUpload.js | 15 +++++-------
 .../pages/guided-mode/setup/GuidedSubjects.js |  2 +-
 4 files changed, 20 insertions(+), 25 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index 5372acea6..40717fa7b 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -63,19 +63,17 @@ export const updateAppProgress = (
         const params = new URLSearchParams(location.search);
         params.set("project", projectName);
 
-            // Update browser history state
-            const value = `${location.pathname}?${params}`;
-            if (history.state) history.state.project = dataOrProjectName;
-            window.history.pushState(history.state, null, value);
-        }
-
-        // Is a project name
-        if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => data["page-before-exit"] = pageId)
+        // Update browser history state
+        const value = `${location.pathname}?${params}`;
+        if (history.state) history.state.project = dataOrProjectName;
+        window.history.pushState(history.state, null, value);
+    }
 
-        // Is a data object
-        else dataOrProjectName["page-before-exit"] = pageId
-        
-}
+    // Is a project name
+    if (dataOrProjectName === projectName) updateFile(dataOrProjectName, (data) => (data["page-before-exit"] = pageId));
+    // Is a data object
+    else dataOrProjectName["page-before-exit"] = pageId;
+};
 
 export const save = (page, overrides = {}) => {
     const globalState = merge(overrides, page.info.globalState); // Merge the overrides into the actual global state
@@ -146,7 +144,7 @@ export const get = (name) => {
 
     let progressFilePath = joinPath(guidedProgressFilePath, name + ".json");
 
-    const exists = fs ? fs.existsSync(progressFilePath) : (localStorage.getItem(progressFilePath) !== null);
+    const exists = fs ? fs.existsSync(progressFilePath) : localStorage.getItem(progressFilePath) !== null;
     return exists ? JSON.parse(fs ? fs.readFileSync(progressFilePath) : localStorage.getItem(progressFilePath)) : {};
 };
 
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 695641233..5c3d2c9e0 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -144,8 +144,8 @@ export class Dashboard extends LitElement {
         else if (key === "pages") this.#updated(latest);
         else if (key.toLowerCase() === "activepage") {
             if (this.#active && this.#active.info.parent && this.#active.info.section) {
-                const currentProject = getCurrentProjectName()
-                if (currentProject) updateAppProgress(latest, currentProject)
+                const currentProject = getCurrentProjectName();
+                if (currentProject) updateAppProgress(latest, currentProject);
             }
 
             while (latest && !this.pagesById[latest]) latest = latest.split("/").slice(0, -1).join("/"); // Trim off last character until you find a page
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 95ffc36b7..7a2d3d04f 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -13,19 +13,18 @@ export class GuidedUploadPage extends Page {
     form;
 
     beforeSave = () => {
-        merge(this.localState, this.info.globalState.upload) // Merge the local and global states
+        merge(this.localState, this.info.globalState.upload); // Merge the local and global states
         delete globalUploadInfo.results; // Clear the preview results
-    }
+    };
 
     footer = {
         onNext: async () => {
-
             await this.save(); // Save in case the conversion fails
 
             await this.form.validate(); // Will throw an error in the callback
 
-            const globalState = this.info.globalState
-            const globalUploadInfo = globalState.upload
+            const globalState = this.info.globalState;
+            const globalUploadInfo = globalState.upload;
 
             const info = { ...globalUploadInfo.info };
             info.project = globalState.project.name;
@@ -38,16 +37,14 @@ export class GuidedUploadPage extends Page {
 
             globalUploadInfo.results = results; // Save the preview results
 
-            this.unsavedUpdates = true // Ensure that this saves automatically
+            this.unsavedUpdates = true; // Ensure that this saves automatically
 
             this.to(1);
         },
     };
 
     render() {
-
-
-        const state = this.localState = merge(this.info.globalState.upload ?? { info: {}, results: null }, {})
+        const state = (this.localState = merge(this.info.globalState.upload ?? { info: {}, results: null }, {}));
 
         const schema = {
             properties: {
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 4fc00e6f7..7b64bdbe5 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -18,7 +18,7 @@ export class GuidedSubjectsPage extends Page {
 
     // Only save if the subject structure is valid
     beforeSave = () => {
-        const subjects = this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects ) // Merge the local and global states
+        const subjects = (this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects)); // Merge the local and global states
 
         try {
             this.table.validate();

From e6bef685fe2d9db1eb7120e0911e0db4ba93cf62 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 11:51:16 -0700
Subject: [PATCH 12/71] Log when a file is opened with the app

---
 package.json                       | 7 +++++++
 src/main/main.ts                   | 9 +++++++++
 src/renderer/src/electron/index.js | 4 ++++
 3 files changed, 20 insertions(+)

diff --git a/package.json b/package.json
index ce9b3859e..0c8136f2e 100644
--- a/package.json
+++ b/package.json
@@ -45,6 +45,13 @@
     "appId": "com.catalystneuro.nwbguide",
     "generateUpdatesFilesForAllChannels": true,
     "afterSign": "./notarize.js",
+    "fileAssociations": [
+      {
+        "ext": "nwb",
+        "name": "NWB File",
+        "role": "Editor"
+      }
+    ],
     "files": [
       "**/*",
       "!pysoda/",
diff --git a/src/main/main.ts b/src/main/main.ts
index e8706ef64..664147fb8 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -307,8 +307,17 @@ function initialize() {
   app.on("will-quit", () => {
     app.quit();
   });
+
+  app.on("open-file", onFileOpened)
+}
+
+function onFileOpened(...args) {
+    console.log('File opened!', ...args)
+    mainWindow.webContents.send('fileOpened', ...args)
 }
 
+if (process.argv[2]) onFileOpened(process.argv[2])
+
 // function run_pre_flight_checks() {
 //   console.log("Running pre-checks");
 //   mainWindow.webContents.send("run_pre_flight_checks");
diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 277c31632..bbfd5e50b 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -27,6 +27,10 @@ if (isElectron) {
             console.log(...args);
         });
 
+        electron.ipcRenderer.on("fileOpened", (info, ...args) => {
+            console.log("File opened!", ...args);
+        });
+
         port = electron.ipcRenderer.sendSync("get-port");
         console.log("User OS:", os.type(), os.platform(), "version:", os.release());
 

From 22eab31a337020ad0ec6f6826c7bb17805fb4235 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 14:37:01 -0700
Subject: [PATCH 13/71] Properly pass file path to the browser

---
 src/main/main.ts                   | 49 +++++++++++++++++++-----------
 src/renderer/src/electron/index.js |  2 +-
 2 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index c48087ae1..f30178394 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -40,6 +40,8 @@ let PORT: number | string | null = 4242;
 let selectedPort: number | string | null = null;
 const portRange = 100;
 
+const isWindows = process.platform === 'win32'
+
 
 /**
  * Determine if the application is running from a packaged version or from a dev version.
@@ -47,15 +49,8 @@ const portRange = 100;
  * @returns {boolean} True if the app is packaged, false if it is running from a dev version.
  */
 const getPackagedPath = () => {
-
-  const windowsPath = path.join(__dirname, PY_FLASK_DIST_FOLDER, PY_FLASK_MODULE + ".exe");
-  const unixPath = path.join(process.resourcesPath, PY_FLASK_MODULE);
-
-  debugLog.unixPath = unixPath
-  debugLog.windowsPath = windowsPath
-
-  if ((process.platform === "darwin" || process.platform === "linux") && fs.existsSync(unixPath)) return unixPath;
-  if (process.platform === "win32" && fs.existsSync(windowsPath)) return windowsPath;
+  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PY_FLASK_MODULE + ".exe") : path.join(process.resourcesPath, PY_FLASK_MODULE)
+  if (fs.existsSync(scriptPath)) return path;
 };
 
 /**
@@ -172,7 +167,24 @@ const killAllPreviousProcesses = async () => {
  * Main app window
  *************************************************************/
 
+let isReady = false
 let mainWindow: BrowserWindow;
+let isReadyQueue: Function[] = []
+
+
+function onReady (fn: Function) {
+  if (!isReady) isReadyQueue.push(fn)
+  else fn()
+}
+
+function setReady(state = true) {
+  isReady = state
+  if (isReady) {
+    isReadyQueue.forEach(onReady)
+    isReadyQueue = []
+  }
+}
+
 let user_restart_confirmed = false;
 let updatechecked = false;
 
@@ -302,7 +314,8 @@ function initialize() {
         autoUpdater.checkForUpdatesAndNotify();
         updatechecked = true;
 
-        mainWindow.webContents.send('logOnBrowser', debugLog)
+        setReady() // Ensure window is ready to show before sending anything through it
+        onReady(() => mainWindow.webContents.send('logOnBrowser', debugLog))
 
       }, 1000);
     });
@@ -320,16 +333,18 @@ function initialize() {
   app.on("open-file", onFileOpened)
 }
 
-function onFileOpened(...args) {
-    console.log('File opened!', ...args)
-    mainWindow.webContents.send('fileOpened', ...args)
+function onFileOpened(_, path) {
+    onReady(() => mainWindow.webContents.send('fileOpened', path))
 }
 
-if (process.argv[2]) onFileOpened(process.argv[2])
+if (isWindows && process.argv.length >= 2) {
+  const openFilePath = process.argv[1];
+  if (openFilePath !== "") onFileOpened(null, openFilePath)
+}
 
 // function run_pre_flight_checks() {
 //   console.log("Running pre-checks");
-//   mainWindow.webContents.send("run_pre_flight_checks");
+//   sendToMainWindow("run_pre_flight_checks");
 // }
 
 // Make this app a single instance app.
@@ -367,11 +382,11 @@ ipcMain.on("resize-window", (event, dir) => {
 });
 
 autoUpdater.on("update-available", () => {
-  mainWindow.webContents.send("update_available");
+  sendToMainWindow("update_available");
 });
 
 autoUpdater.on("update-downloaded", () => {
-  mainWindow.webContents.send("update_downloaded");
+  sendToMainWindow("update_downloaded");
 });
 
 ipcMain.on("restart_app", async () => {
diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index bbfd5e50b..9b54c311c 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -24,7 +24,7 @@ if (isElectron) {
         app = remote.app;
 
         electron.ipcRenderer.on("logOnBrowser", (info, ...args) => {
-            console.log(...args);
+            console.log("From Main Process", ...args);
         });
 
         electron.ipcRenderer.on("fileOpened", (info, ...args) => {

From 3f42f9ba856a250deb1f86feb04325fdbea77a06 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 14:37:09 -0700
Subject: [PATCH 14/71] Update main.ts

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

diff --git a/src/main/main.ts b/src/main/main.ts
index f30178394..6e0c287ff 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -333,7 +333,7 @@ function initialize() {
   app.on("open-file", onFileOpened)
 }
 
-function onFileOpened(_, path) {
+function onFileOpened(_, path: string) {
     onReady(() => mainWindow.webContents.send('fileOpened', path))
 }
 

From aa2dee30d63b9b8eb14681f514928d385a481552 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 16:39:46 -0700
Subject: [PATCH 15/71] Nicely handle the open and closing of the Mac
 application for both files and dock interactions

---
 src/main/main.ts | 134 ++++++++++++++++++++++-------------------------
 1 file changed, 62 insertions(+), 72 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 6e0c287ff..8b58c53b6 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -23,7 +23,9 @@ import splashHTML from './splash-screen.html?asset'
 
 autoUpdater.channel = "latest";
 
-const debugLog: any = {}
+import { homedir}  from 'os'
+const homeDir = homedir(); // See: https://www.npmjs.com/package/os
+const desktopDir = `${homeDir}/Desktop`;
 
 /*************************************************************
  * Python Process
@@ -66,8 +68,6 @@ const getScriptPath = () => {
 const createPyProc = async () => {
   let script = getScriptPath();
 
-  debugLog.script = script
-
   await killAllPreviousProcesses();
 
   const defaultPort = PORT as number
@@ -90,16 +90,12 @@ const createPyProc = async () => {
       if (pyflaskProcess != null) {
         console.log("child process success on port " + port);
 
-        debugLog.errors = []
-
         // Listen for errors from Python process
         pyflaskProcess.stderr.on("data", function (data: any) {
-          debugLog.errors.push(data)
           console.log("[python]:", data.toString());
         });
       } else console.error("child process failed to start on port" + port);
 
-      debugLog.port = selectedPort = port;
     })
     .catch((err: Error) => {
       console.log(err);
@@ -111,31 +107,19 @@ const createPyProc = async () => {
  */
 const exitPyProc = async () => {
 
-  // Windows does not properly shut off the python server process. This ensures it is killed.
-  const killPythonProcess = () => {
-    // kill pyproc with command line
-    const cmd = child_process.spawnSync("taskkill", [
-      "/pid",
-      pyflaskProcess.pid,
-      "/f",
-      "/t",
-    ]);
-  };
-
   await killAllPreviousProcesses();
 
-  // check if the platform is Windows
-  if (process.platform === "win32") {
-    killPythonProcess();
-    pyflaskProcess = null;
-    // PORT = null;
-    return;
-  }
+  // Kill signal to pyproc
+  if (isWindows) child_process.spawnSync("taskkill", [
+    "/pid",
+    pyflaskProcess.pid,
+    "/f",
+    "/t",
+  ])  // Windows does not properly shut off the python server process. This ensures it is killed.
+
+  else pyflaskProcess.kill()
 
-  // kill signal to pyProc
-  pyflaskProcess.kill();
   pyflaskProcess = null;
-  // PORT = null;
 };
 
 const killAllPreviousProcesses = async () => {
@@ -188,12 +172,13 @@ function setReady(state = true) {
 let user_restart_confirmed = false;
 let updatechecked = false;
 
+let hasBeenOpened = false;
+
 function initialize() {
 
   makeSingleInstance();
 
   function createWindow() {
-    mainWindow.webContents.openDevTools();
 
     mainWindow.webContents.setWindowOpenHandler(({ url }) => {
       shell.openExternal(url);
@@ -206,7 +191,7 @@ function initialize() {
       }
     });
 
-    mainWindow.on("close", async (e) => {
+    mainWindow.once("close", async (e) => {
       if (!user_restart_confirmed) {
         if (showExitPrompt) {
           e.preventDefault(); // Prevents the window from closing
@@ -219,10 +204,7 @@ function initialize() {
             })
             .then((responseObject) => {
               let { response } = responseObject;
-              if (response === 0) {
-                // Runs the following if 'Yes' is clicked
-                quit_app();
-              }
+              if (response === 0) quit_app()
             });
         }
       } else {
@@ -233,17 +215,13 @@ function initialize() {
   }
 
   const quit_app = () => {
-    console.log("Quit app called");
-    showExitPrompt = false;
+    // showExitPrompt = false;
     mainWindow.close();
-    /// feedback form iframe prevents closing gracefully
-    /// so force close
-    if (!mainWindow.closed) {
-      mainWindow.destroy();
-    }
+    if (!mainWindow.closed) mainWindow.destroy()
   };
 
-  app.on("ready", () => {
+  function onAppReady () {
+
     const promise = createPyProc();
 
     // Listen after first load
@@ -289,7 +267,10 @@ function initialize() {
   if (is.dev && process.env['ELECTRON_RENDERER_URL']) mainWindow.loadURL(process.env['ELECTRON_RENDERER_URL'])
   else mainWindow.loadFile(path.join(__dirname, '../renderer/index.html'))
 
-
+    mainWindow.once("closed", () => {
+      isReady = false
+      mainWindow = undefined
+    })
 
     const splash = new BrowserWindow({
       width: 340,
@@ -299,41 +280,36 @@ function initialize() {
       alwaysOnTop: true,
       transparent: true,
     });
-
+    
     splash.loadFile(splashHTML)
 
-
     //  if main window is ready to show, then destroy the splash window and show up the main window
     mainWindow.once("ready-to-show", () => {
+
       setTimeout(function () {
+
+        hasBeenOpened = true
+
         splash.close();
-        //mainWindow.maximize();
         mainWindow.show();
         createWindow();
-        // run_pre_flight_checks();
+
         autoUpdater.checkForUpdatesAndNotify();
         updatechecked = true;
 
         setReady() // Ensure window is ready to show before sending anything through it
-        onReady(() => mainWindow.webContents.send('logOnBrowser', debugLog))
 
-      }, 1000);
+      }, hasBeenOpened ? 100 : 1000);
     });
-  });
-
-  app.on("window-all-closed", async () => {
-    await exitPyProc();
-    app.quit();
-  });
+  }
 
-  app.on("will-quit", () => {
-    app.quit();
-  });
 
-  app.on("open-file", onFileOpened)
+  if (app.isReady()) onAppReady()
+  else app.on("ready", onAppReady)
 }
 
 function onFileOpened(_, path: string) {
+    restoreWindow() || initialize(); // Ensure the application is properly visible
     onReady(() => mainWindow.webContents.send('fileOpened', path))
 }
 
@@ -344,30 +320,44 @@ if (isWindows && process.argv.length >= 2) {
 
 // function run_pre_flight_checks() {
 //   console.log("Running pre-checks");
-//   sendToMainWindow("run_pre_flight_checks");
+//   mainWindow.webContents.send("run_pre_flight_checks");
 // }
 
 // Make this app a single instance app.
 const gotTheLock = app.requestSingleInstanceLock();
 
+function restoreWindow(){
+  if (mainWindow) {
+    if (mainWindow.isMinimized()) mainWindow.restore();
+    mainWindow.focus();
+  }
+
+  return mainWindow
+}
+
 function makeSingleInstance() {
   if (process.mas) return;
 
-  if (!gotTheLock) {
-    app.quit();
-  } else {
-    app.on("second-instance", () => {
-      if (mainWindow) {
-        if (mainWindow.isMinimized()) mainWindow.restore();
-        mainWindow.focus();
-      }
-    });
+  if (!gotTheLock) app.quit();
+  else {
+    app.on("second-instance", () => restoreWindow());
   }
 }
 
-
 initialize();
 
+app.on('activate', () => {
+  if (BrowserWindow.getAllWindows().length === 0) initialize()
+})
+
+app.on("window-all-closed", async () => {
+  await exitPyProc();
+  app.quit();
+});
+
+app.on("will-quit", () => app.quit());
+app.on("open-file", onFileOpened)
+
 ipcMain.on("resize-window", (event, dir) => {
   var x = mainWindow.getSize()[0];
   var y = mainWindow.getSize()[1];
@@ -382,11 +372,11 @@ ipcMain.on("resize-window", (event, dir) => {
 });
 
 autoUpdater.on("update-available", () => {
-  sendToMainWindow("update_available");
+  mainWindow.webContents.send("update_available");
 });
 
 autoUpdater.on("update-downloaded", () => {
-  sendToMainWindow("update_downloaded");
+  mainWindow.webContents.send("update_downloaded");
 });
 
 ipcMain.on("restart_app", async () => {

From d868080297b177a33095d4acf21712c80988477d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Aug 2023 23:45:14 +0000
Subject: [PATCH 16/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/main/main.ts b/src/main/main.ts
index 8b58c53b6..aad7d801a 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -280,7 +280,7 @@ function initialize() {
       alwaysOnTop: true,
       transparent: true,
     });
-    
+
     splash.loadFile(splashHTML)
 
     //  if main window is ready to show, then destroy the splash window and show up the main window

From be22cbb89a2c68b8feb5aaab579aea1e26b452ba Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 7 Aug 2023 16:54:06 -0700
Subject: [PATCH 17/71] Update GuidedPathExpansion.js

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

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 cb9545424..59b7f784e 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -91,7 +91,7 @@ export class GuidedPathExpansionPage extends Page {
                 }
 
                 // Save an overall results object organized by subject and session
-                merge(results, this.globalState.results);
+                merge(results, this.info.globalState.results);
 
                 // // NOTE: Current behavior is to ONLY add new results, not remove old ones
                 // // If we'd like, we could label sessions as user-defined so they never clear

From a5e39eeac187a7cff66193266d9a1fe0748318b8 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 8 Aug 2023 10:21:33 -0700
Subject: [PATCH 18/71] Fix updates to the subject and metadata forms

---
 src/renderer/src/stories/JSONSchemaForm.js    | 29 +++++++++++--------
 src/renderer/src/stories/Table.js             | 13 ++++-----
 src/renderer/src/stories/pages/Page.js        | 15 +++++-----
 .../pages/guided-mode/data/GuidedMetadata.js  | 10 +++++--
 .../pages/guided-mode/setup/GuidedSubjects.js | 17 +++++++----
 5 files changed, 50 insertions(+), 34 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index fbf131bc1..5c47f97ca 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -345,7 +345,7 @@ export class JSONSchemaForm extends LitElement {
 
     validate = async () => {
         // Check if any required inputs are missing
-        const invalidInputs = await this.#validateRequirements(this.resolved, this.#requirements); // get missing required paths
+        const invalidInputs = await this.#validateRequirements(); // get missing required paths
         const isValid = !invalidInputs.length;
 
         // Print out a detailed error message if any inputs are missing
@@ -423,7 +423,7 @@ export class JSONSchemaForm extends LitElement {
         return resolved;
     }
 
-    #renderInteractiveElement = (name, info, parent, required, path = []) => {
+    #renderInteractiveElement = (name, info, required, path = []) => {
         let isRequired = required[name];
 
         const isArray = info.type === "array"; // Handle string (and related) formats / types
@@ -557,9 +557,10 @@ export class JSONSchemaForm extends LitElement {
                                 validateEmptyCells: this.validateEmptyValues,
                                 deferLoading: this.deferLoading,
                                 onUpdate: (row, col, value) => {
-                                    console.log(fullPath, row, col, value);
-                                    this.onUpdate([...fullPath.row, col], value);
-                                },
+                                    const path = [...fullPath, row, col]
+                                    console.error('Updating JSON Schema Form Table', path, value) // NOTE: Not sure if this works
+                                    this.#update(path, value)
+                               },
                                 onLoaded: () => {
                                     this.#nLoaded++;
                                     this.#checkAllLoaded();
@@ -608,17 +609,18 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
 
     #filesystemQueries = ["file", "directory"];
 
-    #validateRequirements = async (results, requirements, parent) => {
+    #validateRequirements = async (resolved = this.resolved, requirements = this.#requirements, parentPath) => {
         let invalid = [];
 
         for (let name in requirements) {
             let isRequired = requirements[name];
             if (typeof isRequired === "function") isRequired = await isRequired.call(this.resolved);
             if (isRequired) {
-                let path = parent ? `${parent}-${name}` : name;
+                let path = parentPath ? `${parentPath}-${name}` : name;
+
                 if (typeof isRequired === "object" && !Array.isArray(isRequired))
-                    invalid.push(...(await this.#validateRequirements(results[name], isRequired, path)));
-                else if (!results[name]) invalid.push(path);
+                    invalid.push(...(await this.#validateRequirements(resolved[name], isRequired, path)));
+                else if (!resolved[name]) invalid.push(path);
             }
         }
 
@@ -862,7 +864,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
                 const linkedProperties = info.properties.map((path) => {
                     const pathCopy = [...path].slice((this.#base ?? []).length);
                     const name = pathCopy.pop();
-                    return this.#renderInteractiveElement(name, schema.properties[name], results, required, pathCopy);
+                    return this.#renderInteractiveElement(name, schema.properties[name], required, pathCopy);
                 });
                 return html`
                     <div class="link" data-name="${info.name}">
@@ -872,7 +874,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
             }
 
             // Directly render the interactive property element
-            if (!info.properties) return this.#renderInteractiveElement(name, info, results, required, path);
+            if (!info.properties) return this.#renderInteractiveElement(name, info, required, path);
 
             const hasMany = renderable.length > 1; // How many siblings?
 
@@ -886,7 +888,10 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
                     schema: info,
                     results: results[name],
                     globals: this.globals?.[name],
-                    onUpdate: (internalPath, value) => this.onUpdate([...fullPath, ...internalPath], value),
+                    onUpdate: (internalPath, value) => {
+                        const path = [...fullPath, ...internalPath]
+                        this.#update(path, value)
+                    },
 
                     required: required[name], // Scoped to the sub-schema
                     ignore: this.ignore,
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 4e0a4c478..b18ee3fb1 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -147,7 +147,6 @@ export class Table extends LitElement {
     onUpdate = () => {};
 
     updated() {
-        let updateComplete = false;
 
         const div = (this.shadowRoot ?? this).querySelector("div");
 
@@ -239,6 +238,12 @@ export class Table extends LitElement {
 
             const validator = async function (value, callback) {
                 if (!value) {
+                    
+                    if (!ogThis.validateEmptyCells) {
+                        callback(true); // Allow empty value
+                        return true;
+                    }
+
                     if (isRequired) {
                         ogThis.#handleValidationResult(
                             [{ message: `${k} is a required property.`, type: "error" }],
@@ -248,10 +253,6 @@ export class Table extends LitElement {
                         callback(false);
                         return true;
                     }
-                    if (!ogThis.validateEmptyCells) {
-                        callback(true); // Allow empty value
-                        return true;
-                    }
                 }
 
                 if (!(await runThisValidator(value, this.row, this.col))) {
@@ -384,8 +385,6 @@ export class Table extends LitElement {
 
         // Trigger validation on all cells
         data.forEach((row, i) => this.#setRow(i, row));
-
-        updateComplete = true;
     }
 
     #setRow(row, data) {
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 96e026609..0b678afed 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -61,6 +61,9 @@ export class Page extends LitElement {
     };
 
     to = async (transition) => {
+
+        this.beforeTransition()
+
         // Otherwise note unsaved updates if present
         if (this.unsavedUpdates) {
             if (transition === 1) await this.save(); // Save before a single forward transition
@@ -88,6 +91,7 @@ export class Page extends LitElement {
     onTransition = () => {}; // User-defined function
     updatePages = () => {}; // User-defined function
     beforeSave = () => {}; // User-defined function
+    beforeTransition = () => {}; // User-defined function
 
     save = async (overrides, runBeforeSave = true) => {
         if (runBeforeSave) await this.beforeSave();
@@ -144,16 +148,13 @@ export class Page extends LitElement {
         elements.progress.value = { b: completed, tsize: toRun.length };
 
         for (let info of toRun) {
-            const { subject, session } = info;
+            const { subject, session, globalState = this.info.globalState } = info;
             const file = `sub-${subject}/sub-${subject}_ses-${session}.nwb`;
 
-            const { conversion_output_folder, stub_output_folder, name } = this.info.globalState.project;
+            const { conversion_output_folder, stub_output_folder, name } = globalState.project;
 
             // Resolve the correct session info from all of the metadata for this conversion
-            const sessionInfo = {
-                ...this.info.globalState.results[subject][session],
-                metadata: resolveResults(subject, session, this.info.globalState),
-            };
+            const sessionInfo = { ...globalState.results[subject][session], metadata: resolveResults(subject, session, globalState) };
 
             const result = await runConversion(
                 {
@@ -164,7 +165,7 @@ export class Page extends LitElement {
                     ...sessionInfo, // source_data and metadata are passed in here
                     ...conversionOptions, // Any additional conversion options override the defaults
 
-                    interfaces: this.info.globalState.interfaces,
+                    interfaces: globalState.interfaces,
                 },
                 { swal: popup, ...options }
             ).catch((e) => {
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 d95f53f71..0dc6f1432 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -26,7 +26,7 @@ export class GuidedMetadataPage extends ManagedPage {
     }
 
     beforeSave = () => {
-        merge(this.localState, this.info.globalState);
+        merge( this.localState.results, this.info.globalState.results )
     };
 
     form;
@@ -34,6 +34,7 @@ export class GuidedMetadataPage extends ManagedPage {
         next: "Run Conversion Preview",
         onNext: async () => {
             await this.save(); // Save in case the conversion fails
+
             for (let { form } of this.forms) await form.validate(); // Will throw an error in the callback
 
             // Preview a single random conversion
@@ -42,7 +43,9 @@ export class GuidedMetadataPage extends ManagedPage {
                 title: "Testing conversion on a random session",
             });
 
-            this.info.globalState.preview = result; // Save the preview results
+            // Save the preview results
+            this.info.globalState.preview = result;
+            this.unsavedUpdates = true
 
             this.to(1);
         },
@@ -178,9 +181,10 @@ export class GuidedMetadataPage extends ManagedPage {
                     onClick: async (key, el) => {
                         const { subject, session } = getInfoFromId(key);
 
+
                         const [{ file, html }] = await this.runConversions(
                             { stub_test: true },
-                            [{ subject, session }],
+                            [{ subject, session, globalState: merge(this.localState, merge(this.info.globalState, {})) }],
                             { title: "Running conversion preview" }
                         ).catch((e) => {
                             this.notify(e.message, "error");
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 7b64bdbe5..acb0787ec 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -13,12 +13,12 @@ export class GuidedSubjectsPage extends Page {
     }
 
     header = {
-        subtitle: "Cross-session metadata applied to the final file metadata",
+        subtitle: "Cross-session metadata applied to the final file metadata"
     };
 
-    // Only save if the subject structure is valid
     beforeSave = () => {
-        const subjects = (this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects)); // Merge the local and global states
+
+        this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects); // Merge the local and global states
 
         try {
             this.table.validate();
@@ -27,7 +27,14 @@ export class GuidedSubjectsPage extends Page {
             throw e;
         }
 
-        const { results } = this.info.globalState;
+    }
+
+    // Only save if the subject structure is valid
+    beforeTransition = () => {
+
+        this.save() // Save on each transition
+
+        const { results, subjects } = this.info.globalState;
 
         // Object.keys(subjects).forEach((sub) => {
         //     if (!subjects[sub].sessions?.length) {
@@ -54,7 +61,7 @@ export class GuidedSubjectsPage extends Page {
     };
 
     footer = {
-        next: "Generate Data Structure",
+        next: "Generate Data Structure"
     };
 
     updated() {

From a52f11fe39e5eaeb5cf78cb92b9ec760d71de51b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Aug 2023 17:21:51 +0000
Subject: [PATCH 19/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js          | 12 ++++++------
 src/renderer/src/stories/Table.js                   |  2 --
 src/renderer/src/stories/pages/Page.js              |  8 +++++---
 .../pages/guided-mode/data/GuidedMetadata.js        | 13 +++++++++----
 .../pages/guided-mode/setup/GuidedSubjects.js       | 11 ++++-------
 5 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 5c47f97ca..e8c9ea65e 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -557,10 +557,10 @@ export class JSONSchemaForm extends LitElement {
                                 validateEmptyCells: this.validateEmptyValues,
                                 deferLoading: this.deferLoading,
                                 onUpdate: (row, col, value) => {
-                                    const path = [...fullPath, row, col]
-                                    console.error('Updating JSON Schema Form Table', path, value) // NOTE: Not sure if this works
-                                    this.#update(path, value)
-                               },
+                                    const path = [...fullPath, row, col];
+                                    console.error("Updating JSON Schema Form Table", path, value); // NOTE: Not sure if this works
+                                    this.#update(path, value);
+                                },
                                 onLoaded: () => {
                                     this.#nLoaded++;
                                     this.#checkAllLoaded();
@@ -889,8 +889,8 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
                     results: results[name],
                     globals: this.globals?.[name],
                     onUpdate: (internalPath, value) => {
-                        const path = [...fullPath, ...internalPath]
-                        this.#update(path, value)
+                        const path = [...fullPath, ...internalPath];
+                        this.#update(path, value);
                     },
 
                     required: required[name], // Scoped to the sub-schema
diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index b18ee3fb1..79211c08e 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -147,7 +147,6 @@ export class Table extends LitElement {
     onUpdate = () => {};
 
     updated() {
-
         const div = (this.shadowRoot ?? this).querySelector("div");
 
         const entries = { ...this.schema.properties };
@@ -238,7 +237,6 @@ export class Table extends LitElement {
 
             const validator = async function (value, callback) {
                 if (!value) {
-                    
                     if (!ogThis.validateEmptyCells) {
                         callback(true); // Allow empty value
                         return true;
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 0b678afed..1e7515a02 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -61,8 +61,7 @@ export class Page extends LitElement {
     };
 
     to = async (transition) => {
-
-        this.beforeTransition()
+        this.beforeTransition();
 
         // Otherwise note unsaved updates if present
         if (this.unsavedUpdates) {
@@ -154,7 +153,10 @@ export class Page extends LitElement {
             const { conversion_output_folder, stub_output_folder, name } = globalState.project;
 
             // Resolve the correct session info from all of the metadata for this conversion
-            const sessionInfo = { ...globalState.results[subject][session], metadata: resolveResults(subject, session, globalState) };
+            const sessionInfo = {
+                ...globalState.results[subject][session],
+                metadata: resolveResults(subject, session, globalState),
+            };
 
             const result = await runConversion(
                 {
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 0dc6f1432..f71b2ebba 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -26,7 +26,7 @@ export class GuidedMetadataPage extends ManagedPage {
     }
 
     beforeSave = () => {
-        merge( this.localState.results, this.info.globalState.results )
+        merge(this.localState.results, this.info.globalState.results);
     };
 
     form;
@@ -45,7 +45,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
             // Save the preview results
             this.info.globalState.preview = result;
-            this.unsavedUpdates = true
+            this.unsavedUpdates = true;
 
             this.to(1);
         },
@@ -181,10 +181,15 @@ export class GuidedMetadataPage extends ManagedPage {
                     onClick: async (key, el) => {
                         const { subject, session } = getInfoFromId(key);
 
-
                         const [{ file, html }] = await this.runConversions(
                             { stub_test: true },
-                            [{ subject, session, globalState: merge(this.localState, merge(this.info.globalState, {})) }],
+                            [
+                                {
+                                    subject,
+                                    session,
+                                    globalState: merge(this.localState, merge(this.info.globalState, {})),
+                                },
+                            ],
                             { title: "Running conversion preview" }
                         ).catch((e) => {
                             this.notify(e.message, "error");
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 acb0787ec..e9052bc4f 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -13,11 +13,10 @@ export class GuidedSubjectsPage extends Page {
     }
 
     header = {
-        subtitle: "Cross-session metadata applied to the final file metadata"
+        subtitle: "Cross-session metadata applied to the final file metadata",
     };
 
     beforeSave = () => {
-
         this.info.globalState.subjects = merge(this.localState, this.info.globalState.subjects); // Merge the local and global states
 
         try {
@@ -26,13 +25,11 @@ export class GuidedSubjectsPage extends Page {
             this.notify(e.message, "error");
             throw e;
         }
-
-    }
+    };
 
     // Only save if the subject structure is valid
     beforeTransition = () => {
-
-        this.save() // Save on each transition
+        this.save(); // Save on each transition
 
         const { results, subjects } = this.info.globalState;
 
@@ -61,7 +58,7 @@ export class GuidedSubjectsPage extends Page {
     };
 
     footer = {
-        next: "Generate Data Structure"
+        next: "Generate Data Structure",
     };
 
     updated() {

From f5fc37756e8d014bf64c9c4aa572bb5e7f8b64ed Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 8 Aug 2023 11:35:01 -0700
Subject: [PATCH 20/71] Fix updates on PathExpansion page

---
 src/renderer/src/progress.js                  |   7 +
 src/renderer/src/stories/OptionalSection.js   |  16 +-
 .../guided-mode/data/GuidedPathExpansion.js   | 172 ++++++++++--------
 3 files changed, 113 insertions(+), 82 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index 40717fa7b..abdde7c48 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -59,6 +59,13 @@ export const updateAppProgress = (
     dataOrProjectName = {},
     projectName = typeof dataOrProjectName === "string" ? dataOrProjectName : undefined
 ) => {
+
+    const transitionOffPipeline = pageId && pageId.split('/')[0] !== 'conversion'
+
+    if (transitionOffPipeline) {
+        return // Only save last page if within the conversion workflow
+    }
+
     if (projectName) {
         const params = new URLSearchParams(location.search);
         params.set("project", projectName);
diff --git a/src/renderer/src/stories/OptionalSection.js b/src/renderer/src/stories/OptionalSection.js
index e867a759f..d4ccdacff 100644
--- a/src/renderer/src/stories/OptionalSection.js
+++ b/src/renderer/src/stories/OptionalSection.js
@@ -34,6 +34,8 @@ export class OptionalSection extends LitElement {
         if (args[0] === "state") this.requestUpdate();
     }
 
+    changed;
+
     constructor(props) {
         super();
         this.header = props.header ?? "";
@@ -41,21 +43,29 @@ export class OptionalSection extends LitElement {
         this.content = props.content ?? "";
         this.altContent = props.altContent ?? "";
         this.state = props.state;
+
+        if (props.onChange) this.onChange = props.onChange
     }
 
+    onChange = () => {} // User-defined function
+
     show(state) {
         this.toggled = true;
         const content = this.shadowRoot.querySelector(".optional-section__content");
         const altContent = this.shadowRoot.querySelector("#altContent");
 
+        if (this.changed === undefined) this.changed = false
+        else this.changed = true
+
         if (state === undefined) state = !content.classList.contains("hidden");
+        else if (this.changed && this.hidden === state) this.onChange()
 
         if (state) {
             content.removeAttribute("hidden");
             altContent.setAttribute("hidden", true);
         } else {
             content.setAttribute("hidden", true);
-            altContent.removeAttribute("hidden", "");
+            altContent.removeAttribute("hidden");
         }
     }
 
@@ -80,8 +90,8 @@ export class OptionalSection extends LitElement {
     });
 
     updated() {
-        if (this.state === undefined) return;
-        if (this.state) this.yes.onClick();
+        if (this.state === undefined) this.shadowRoot.querySelector(".optional-section__content").hidden = true
+        else if (this.state) this.yes.onClick();
         else this.no.onClick();
     }
 
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 59b7f784e..f1330b1a1 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -17,13 +17,94 @@ export class GuidedPathExpansionPage extends Page {
         super(...args);
     }
 
+     beforeSave = async () => {
+
+        const globalState = this.info.globalState
+        merge({ structure: this.localState }, globalState) // Merge the actual entries into the structure
+
+        const hidden = this.optional.hidden;
+        globalState.structure.state = !hidden;
+
+        // Force single subject/session
+        if (hidden) {
+            const source_data = {};
+            for (let key in globalState.interfaces) source_data[key] = {};
+
+            const existingMetadata =
+                globalState.results?.[this.altInfo.subject_id]?.[this.altInfo.session_id]?.metadata;
+
+            globalState.results = {
+                [this.altInfo.subject_id]: {
+                    [this.altInfo.session_id]: {
+                        source_data,
+                        metadata: {
+                            NWBFile: {
+                                session_id: this.altInfo.session_id,
+                                ...(existingMetadata?.NWBFile ?? {}),
+                            },
+                            Subject: {
+                                subject_id: this.altInfo.subject_id,
+                                ...(existingMetadata?.Subject ?? {}),
+                            },
+                        },
+                    },
+                },
+            };
+        }
+
+        // Otherwise use path expansion to merge into existing subjects
+        else if (!hidden && hidden !== undefined) {
+            const structure = globalState.structure.results;
+
+            const finalStructure = {};
+            for (let key in structure) {
+                const entry = { ...structure[key] };
+                const fstring = entry.format_string_path;
+                if (fstring.split(".").length > 1) entry.file_path = fstring;
+                else entry.folder_path = fstring;
+                delete entry.format_string_path;
+                finalStructure[key] = entry;
+            }
+
+            const results = await run(`locate`, finalStructure, { title: "Locating Data" }).catch((e) => {
+                this.notify(e.message, "error");
+                throw e;
+            });
+
+            const subjects = Object.keys(results);
+            if (subjects.length === 0) {
+                const message = "No subjects found with the current configuration. Please try again.";
+                notyf.open({
+                    type: "error",
+                    message,
+                });
+                throw message;
+            }
+
+            // Save an overall results object organized by subject and session
+            merge({ results }, globalState);
+
+            // // NOTE: Current behavior is to ONLY add new results, not remove old ones
+            // // If we'd like, we could label sessions as user-defined so they never clear
+
+            // // Remove previous results that are no longer present
+            // const globalResults = this.info.globalState.results
+            // for (let sub in globalResults) {
+            //   for (let ses in globalResults[sub]) {
+            //     if (!results[sub]?.[ses]) delete globalResults[sub]?.[ses]
+            //   }
+            //   if (Object.keys(globalResults[sub]).length === 0) delete globalResults[sub]
+            // }
+        }
+
+    }
+
     footer = {
         next: "Populate Subject Details",
         onNext: async () => {
-            await this.save(); // Save in case the request fails
 
-            const hidden = this.optional.hidden;
-            this.info.globalState.structure.state = !hidden;
+
+            await this.save(); // Save in case the request fails
 
             if (!this.optional.toggled) {
                 const message = "Please select a path expansion option.";
@@ -34,77 +115,6 @@ export class GuidedPathExpansionPage extends Page {
                 throw new Error(message);
             }
 
-            // Force single subject/session
-            if (hidden) {
-                const source_data = {};
-                for (let key in this.info.globalState.interfaces) source_data[key] = {};
-
-                const existingMetadata =
-                    this.info.globalState.results?.[this.altInfo.subject_id]?.[this.altInfo.session_id]?.metadata;
-
-                this.info.globalState.results = {
-                    [this.altInfo.subject_id]: {
-                        [this.altInfo.session_id]: {
-                            source_data,
-                            metadata: {
-                                NWBFile: {
-                                    session_id: this.altInfo.session_id,
-                                    ...(existingMetadata?.NWBFile ?? {}),
-                                },
-                                Subject: {
-                                    subject_id: this.altInfo.subject_id,
-                                    ...(existingMetadata?.Subject ?? {}),
-                                },
-                            },
-                        },
-                    },
-                };
-            }
-
-            // Otherwise use path expansion to merge into existing subjects
-            else if (!hidden && hidden !== undefined) {
-                const structure = this.info.globalState.structure.results;
-
-                const finalStructure = {};
-                for (let key in structure) {
-                    const entry = { ...structure[key] };
-                    const fstring = entry.format_string_path;
-                    if (fstring.split(".").length > 1) entry.file_path = fstring;
-                    else entry.folder_path = fstring;
-                    delete entry.format_string_path;
-                    finalStructure[key] = entry;
-                }
-
-                const results = await run(`locate`, finalStructure, { title: "Locating Data" }).catch((e) => {
-                    this.notify(e.message, "error");
-                    throw e;
-                });
-
-                const subjects = Object.keys(results);
-                if (subjects.length === 0) {
-                    const message = "No subjects found with the current configuration. Please try again.";
-                    notyf.open({
-                        type: "error",
-                        message,
-                    });
-                    throw message;
-                }
-
-                // Save an overall results object organized by subject and session
-                merge(results, this.info.globalState.results);
-
-                // // NOTE: Current behavior is to ONLY add new results, not remove old ones
-                // // If we'd like, we could label sessions as user-defined so they never clear
-
-                // // Remove previous results that are no longer present
-                // const globalResults = this.info.globalState.results
-                // for (let sub in globalResults) {
-                //   for (let ses in globalResults[sub]) {
-                //     if (!results[sub]?.[ses]) delete globalResults[sub]?.[ses]
-                //   }
-                //   if (Object.keys(globalResults[sub]).length === 0) delete globalResults[sub]
-                // }
-            }
 
             this.to(1);
         },
@@ -136,26 +146,30 @@ export class GuidedPathExpansionPage extends Page {
     optional = new OptionalSection({
         header: "Would you like to locate data programmatically?",
         description: html`<p>Automatically detect source data for multiple subjects and sessions.</p>`,
+        onChange: () => this.unsavedUpdates = true
         // altContent: this.altForm,
     });
 
+    localState = {}
+
     render() {
-        let structureGlobalState = this.info.globalState.structure;
-        if (!structureGlobalState) structureGlobalState = this.info.globalState.structure = { results: {} };
 
-        const state = this.info.globalState.structure.state;
+
+        const structureState = this.localState = merge(this.info.globalState.structure, {results: {}})
+
+        const state = structureState.state;
         if (state !== undefined) this.optional.state = state;
 
         // Require properties for all sources
         const generatedSchema = { type: "object", properties: {} };
         for (let key in this.info.globalState.interfaces)
             generatedSchema.properties[key] = { type: "object", ...pathExpansionSchema };
-        structureGlobalState.schema = generatedSchema;
+            structureState.schema = generatedSchema;
 
         this.optional.requestUpdate();
 
         const form = (this.form = new JSONSchemaForm({
-            ...structureGlobalState,
+            ...structureState,
             onThrow,
             onUpdate: () => (this.unsavedUpdates = true),
         }));

From 0719a1fc2e1851dae24695eef830e133f0e9fd82 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Aug 2023 18:35:28 +0000
Subject: [PATCH 21/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/progress.js                  |  5 ++--
 src/renderer/src/stories/OptionalSection.js   | 12 +++++-----
 .../guided-mode/data/GuidedPathExpansion.js   | 23 +++++++------------
 3 files changed, 16 insertions(+), 24 deletions(-)

diff --git a/src/renderer/src/progress.js b/src/renderer/src/progress.js
index abdde7c48..5b5f27223 100644
--- a/src/renderer/src/progress.js
+++ b/src/renderer/src/progress.js
@@ -59,11 +59,10 @@ export const updateAppProgress = (
     dataOrProjectName = {},
     projectName = typeof dataOrProjectName === "string" ? dataOrProjectName : undefined
 ) => {
-
-    const transitionOffPipeline = pageId && pageId.split('/')[0] !== 'conversion'
+    const transitionOffPipeline = pageId && pageId.split("/")[0] !== "conversion";
 
     if (transitionOffPipeline) {
-        return // Only save last page if within the conversion workflow
+        return; // Only save last page if within the conversion workflow
     }
 
     if (projectName) {
diff --git a/src/renderer/src/stories/OptionalSection.js b/src/renderer/src/stories/OptionalSection.js
index d4ccdacff..aa46e45d2 100644
--- a/src/renderer/src/stories/OptionalSection.js
+++ b/src/renderer/src/stories/OptionalSection.js
@@ -44,21 +44,21 @@ export class OptionalSection extends LitElement {
         this.altContent = props.altContent ?? "";
         this.state = props.state;
 
-        if (props.onChange) this.onChange = props.onChange
+        if (props.onChange) this.onChange = props.onChange;
     }
 
-    onChange = () => {} // User-defined function
+    onChange = () => {}; // User-defined function
 
     show(state) {
         this.toggled = true;
         const content = this.shadowRoot.querySelector(".optional-section__content");
         const altContent = this.shadowRoot.querySelector("#altContent");
 
-        if (this.changed === undefined) this.changed = false
-        else this.changed = true
+        if (this.changed === undefined) this.changed = false;
+        else this.changed = true;
 
         if (state === undefined) state = !content.classList.contains("hidden");
-        else if (this.changed && this.hidden === state) this.onChange()
+        else if (this.changed && this.hidden === state) this.onChange();
 
         if (state) {
             content.removeAttribute("hidden");
@@ -90,7 +90,7 @@ export class OptionalSection extends LitElement {
     });
 
     updated() {
-        if (this.state === undefined) this.shadowRoot.querySelector(".optional-section__content").hidden = true
+        if (this.state === undefined) this.shadowRoot.querySelector(".optional-section__content").hidden = true;
         else if (this.state) this.yes.onClick();
         else this.no.onClick();
     }
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 f1330b1a1..3b1705405 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -17,10 +17,9 @@ export class GuidedPathExpansionPage extends Page {
         super(...args);
     }
 
-     beforeSave = async () => {
-
-        const globalState = this.info.globalState
-        merge({ structure: this.localState }, globalState) // Merge the actual entries into the structure
+    beforeSave = async () => {
+        const globalState = this.info.globalState;
+        merge({ structure: this.localState }, globalState); // Merge the actual entries into the structure
 
         const hidden = this.optional.hidden;
         globalState.structure.state = !hidden;
@@ -96,14 +95,11 @@ export class GuidedPathExpansionPage extends Page {
             //   if (Object.keys(globalResults[sub]).length === 0) delete globalResults[sub]
             // }
         }
-
-    }
+    };
 
     footer = {
         next: "Populate Subject Details",
         onNext: async () => {
-
-
             await this.save(); // Save in case the request fails
 
             if (!this.optional.toggled) {
@@ -115,7 +111,6 @@ export class GuidedPathExpansionPage extends Page {
                 throw new Error(message);
             }
 
-
             this.to(1);
         },
     };
@@ -146,16 +141,14 @@ export class GuidedPathExpansionPage extends Page {
     optional = new OptionalSection({
         header: "Would you like to locate data programmatically?",
         description: html`<p>Automatically detect source data for multiple subjects and sessions.</p>`,
-        onChange: () => this.unsavedUpdates = true
+        onChange: () => (this.unsavedUpdates = true),
         // altContent: this.altForm,
     });
 
-    localState = {}
+    localState = {};
 
     render() {
-
-
-        const structureState = this.localState = merge(this.info.globalState.structure, {results: {}})
+        const structureState = (this.localState = merge(this.info.globalState.structure, { results: {} }));
 
         const state = structureState.state;
         if (state !== undefined) this.optional.state = state;
@@ -164,7 +157,7 @@ export class GuidedPathExpansionPage extends Page {
         const generatedSchema = { type: "object", properties: {} };
         for (let key in this.info.globalState.interfaces)
             generatedSchema.properties[key] = { type: "object", ...pathExpansionSchema };
-            structureState.schema = generatedSchema;
+        structureState.schema = generatedSchema;
 
         this.optional.requestUpdate();
 

From 1ebb4ac6f2dc7159aef9f2efb4b2202baa8224c6 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 8 Aug 2023 13:42:10 -0700
Subject: [PATCH 22/71] Fixed schema request

---
 .../pages/guided-mode/data/GuidedStructure.js | 35 +++++++++++++------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 01064c9f6..98ab4f13c 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -111,27 +111,40 @@ export class GuidedStructurePage extends Page {
 
     searchModal = new Modal();
 
-    beforeSave = async () => {
-        const interfaces = { ...this.#selected };
-        this.info.globalState.interfaces = interfaces;
 
-        await this.save(undefined, false); // Interrim save, in case the schema request fails
+    getSchema = async () => {
+
+        const interfaces = { ...this.#selected };
 
         const schema =
-            Object.keys(interfaces).length === 0
-                ? {}
-                : await fetch(`${baseUrl}/neuroconv/schema`, {
-                      method: "POST",
-                      headers: { "Content-Type": "application/json" },
-                      body: JSON.stringify(interfaces),
-                  }).then((res) => res.json());
+        Object.keys(interfaces).length === 0
+            ? {}
+            : await fetch(`${baseUrl}/neuroconv/schema`, {
+                  method: "POST",
+                  headers: { "Content-Type": "application/json" },
+                  body: JSON.stringify(interfaces),
+              }).then((res) => res.json());
 
         let schemas = this.info.globalState.schema;
         if (!schemas) schemas = this.info.globalState.schema = {};
 
         schemas.source_data = schema;
+        this.unsavedUpdates = true
+    }
+
+    beforeSave = async () => {
+        this.info.globalState.interfaces = { ...this.#selected };;
+        await this.save(undefined, false); // Interrim save, in case the schema request fails
+        await this.getSchema()
     };
 
+    footer = {
+        onNext: async () => {
+            if (!this.info.globalState.schema) await this.getSchema() // Initialize schema
+            this.to(1)
+        }
+    }
+
     async updated() {
         const selected = this.info.globalState.interfaces;
 

From 21b8dd718bc0cdc49c003dedb375470d210ddbfb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Aug 2023 20:42:26 +0000
Subject: [PATCH 23/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../pages/guided-mode/data/GuidedStructure.js | 32 +++++++++----------
 1 file changed, 15 insertions(+), 17 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 98ab4f13c..28e2a7b3a 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -111,39 +111,37 @@ export class GuidedStructurePage extends Page {
 
     searchModal = new Modal();
 
-
     getSchema = async () => {
-
         const interfaces = { ...this.#selected };
 
         const schema =
-        Object.keys(interfaces).length === 0
-            ? {}
-            : await fetch(`${baseUrl}/neuroconv/schema`, {
-                  method: "POST",
-                  headers: { "Content-Type": "application/json" },
-                  body: JSON.stringify(interfaces),
-              }).then((res) => res.json());
+            Object.keys(interfaces).length === 0
+                ? {}
+                : await fetch(`${baseUrl}/neuroconv/schema`, {
+                      method: "POST",
+                      headers: { "Content-Type": "application/json" },
+                      body: JSON.stringify(interfaces),
+                  }).then((res) => res.json());
 
         let schemas = this.info.globalState.schema;
         if (!schemas) schemas = this.info.globalState.schema = {};
 
         schemas.source_data = schema;
-        this.unsavedUpdates = true
-    }
+        this.unsavedUpdates = true;
+    };
 
     beforeSave = async () => {
-        this.info.globalState.interfaces = { ...this.#selected };;
+        this.info.globalState.interfaces = { ...this.#selected };
         await this.save(undefined, false); // Interrim save, in case the schema request fails
-        await this.getSchema()
+        await this.getSchema();
     };
 
     footer = {
         onNext: async () => {
-            if (!this.info.globalState.schema) await this.getSchema() // Initialize schema
-            this.to(1)
-        }
-    }
+            if (!this.info.globalState.schema) await this.getSchema(); // Initialize schema
+            this.to(1);
+        },
+    };
 
     async updated() {
         const selected = this.info.globalState.interfaces;

From 26b1a9b43920d3b052b743b027f31f531d9c677a Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 8 Aug 2023 14:01:45 -0700
Subject: [PATCH 24/71] Fix DANDI upload page

---
 .../src/stories/pages/guided-mode/data/GuidedSourceData.js   | 2 +-
 .../src/stories/pages/guided-mode/options/GuidedUpload.js    | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

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 cb3e4a924..0bc48db84 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -28,7 +28,7 @@ export class GuidedSourceDataPage extends ManagedPage {
 
             // const previousResults = this.info.globalState.metadata.results
 
-            let stillFireSwal = false;
+            let stillFireSwal = true;
             const fireSwal = () => {
                 Swal.fire({
                     title: "Getting metadata for source data",
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 7a2d3d04f..a58dfdde2 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -13,8 +13,9 @@ export class GuidedUploadPage extends Page {
     form;
 
     beforeSave = () => {
-        merge(this.localState, this.info.globalState.upload); // Merge the local and global states
-        delete globalUploadInfo.results; // Clear the preview results
+        const globalState = this.info.globalState;
+        merge({ upload: this.localState}, globalState); // Merge the local and global states
+        delete globalState.upload.results; // Clear the preview results
     };
 
     footer = {

From 0bcbb6d5ea1775ba5d94623cab1cb3dc106de1ab Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Aug 2023 21:02:43 +0000
Subject: [PATCH 25/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
index a58dfdde2..55077069a 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js
@@ -14,7 +14,7 @@ export class GuidedUploadPage extends Page {
 
     beforeSave = () => {
         const globalState = this.info.globalState;
-        merge({ upload: this.localState}, globalState); // Merge the local and global states
+        merge({ upload: this.localState }, globalState); // Merge the local and global states
         delete globalState.upload.results; // Clear the preview results
     };
 

From 3e0ef8558449d8f4102c049640de5f4e95a5a219 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 8 Aug 2023 14:13:45 -0700
Subject: [PATCH 26/71] Update Table.js

---
 src/renderer/src/stories/Table.js | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 179408fec..610784169 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -399,18 +399,32 @@ export class Table extends LitElement {
 
     #root;
 
-    render() {
+
+    // Clean up after the injected stylesheet, which may affect the rendering of other elements (e.g. the main sidebar list items)
+    disconnectedCallback() {
+        super.disconnectedCallback()
+        this.stylesheet[styleSymbol]--
+        if (this.stylesheet[styleSymbol] === 0) this.stylesheet.remove()
+    }
+
+    connectedCallback() {
+
+        super.connectedCallback()
         const root = this.getRootNode().body ?? this.getRootNode();
         this.#root = root;
         const stylesheets = Array.from(root.querySelectorAll("style"));
-        const exists = stylesheets.find((el) => el[styleSymbol]);
+        const exists = this.stylesheet = stylesheets.find((el) => styleSymbol in el);
 
-        if (!exists) {
-            const stylesheet = document.createElement("style");
+        if (exists) exists[styleSymbol]++
+        else {
+            const stylesheet = this.stylesheet = document.createElement("style");
             stylesheet.innerHTML = styles;
-            stylesheet[styleSymbol] = true;
+            stylesheet[styleSymbol] = true //1;
             root.append(stylesheet);
-        }
+        } 
+    }
+
+    render() {
 
         return html`
             <div></div>

From 6bafa29a548830967882ac892e549aa85333d02e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Aug 2023 21:16:23 +0000
Subject: [PATCH 27/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/Table.js | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/src/renderer/src/stories/Table.js b/src/renderer/src/stories/Table.js
index 610784169..51a188ae0 100644
--- a/src/renderer/src/stories/Table.js
+++ b/src/renderer/src/stories/Table.js
@@ -399,33 +399,30 @@ export class Table extends LitElement {
 
     #root;
 
-
     // Clean up after the injected stylesheet, which may affect the rendering of other elements (e.g. the main sidebar list items)
     disconnectedCallback() {
-        super.disconnectedCallback()
-        this.stylesheet[styleSymbol]--
-        if (this.stylesheet[styleSymbol] === 0) this.stylesheet.remove()
+        super.disconnectedCallback();
+        this.stylesheet[styleSymbol]--;
+        if (this.stylesheet[styleSymbol] === 0) this.stylesheet.remove();
     }
 
     connectedCallback() {
-
-        super.connectedCallback()
+        super.connectedCallback();
         const root = this.getRootNode().body ?? this.getRootNode();
         this.#root = root;
         const stylesheets = Array.from(root.querySelectorAll("style"));
-        const exists = this.stylesheet = stylesheets.find((el) => styleSymbol in el);
+        const exists = (this.stylesheet = stylesheets.find((el) => styleSymbol in el));
 
-        if (exists) exists[styleSymbol]++
+        if (exists) exists[styleSymbol]++;
         else {
-            const stylesheet = this.stylesheet = document.createElement("style");
+            const stylesheet = (this.stylesheet = document.createElement("style"));
             stylesheet.innerHTML = styles;
-            stylesheet[styleSymbol] = true //1;
+            stylesheet[styleSymbol] = true; //1;
             root.append(stylesheet);
-        } 
+        }
     }
 
     render() {
-
         return html`
             <div></div>
             <p style="width: 100%; margin: 10px 0px">

From a8416587d3b54b753c598cd2fdbafa3b56601d3a Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Wed, 9 Aug 2023 10:53:17 -0700
Subject: [PATCH 28/71] Generate source data schema and update the stories to
 use them properly.

---
 generateInterfaceSchema.py                    |  60 +++++++
 .../generated/BiocamRecordingInterface.json   |  33 ++++
 .../generated/IntanRecordingInterface.json    |  37 +++++
 .../generated/NeuroScopeLFPInterface.json     |  32 ++++
 .../NeuroScopeRecordingInterface.json         |  40 +++++
 .../generated/NeuroScopeSortingInterface.json |  40 +++++
 .../OpenEphysRecordingInterface.json          |  32 ++++
 .../json/generated/PhySortingInterface.json   |  32 ++++
 .../json/generated/SpikeGLXNIDQInterface.json |  38 +++++
 .../generated/SpikeGLXRecordingInterface.json |  33 ++++
 src/renderer/src/stories/Dashboard.js         |   5 +-
 src/renderer/src/stories/JSONSchemaForm.js    |   9 +-
 .../src/stories/pages/GuidedMode.stories.js   | 150 ------------------
 .../pages/guided-mode/GuidedHome.stories.js   |  15 ++
 .../pages/guided-mode/GuidedStart.stories.js  |  15 ++
 .../pages/guided-mode/Locate.stories.js       |  15 ++
 .../pages/guided-mode/Metadata.stories.js     |  15 ++
 .../pages/guided-mode/NewDataset.stories.js   |  15 ++
 .../pages/guided-mode/Preview.stories.js      |  15 ++
 .../pages/guided-mode/Review.stories.js       |  15 ++
 .../pages/guided-mode/SourceData.stories.js   |  78 +++++++++
 .../pages/guided-mode/Structure.stories.js    |  15 ++
 .../pages/guided-mode/Subjects.stories.js     |  15 ++
 .../pages/guided-mode/Upload.stories.js       |  15 ++
 .../guided-mode/options/GuidedStubPreview.js  |  12 +-
 .../guided-mode/results/GuidedResults.js      |   5 +-
 .../stories/pages/guided-mode/storyStates.ts  |  63 ++++++++
 27 files changed, 688 insertions(+), 161 deletions(-)
 create mode 100644 generateInterfaceSchema.py
 create mode 100644 schemas/json/generated/BiocamRecordingInterface.json
 create mode 100644 schemas/json/generated/IntanRecordingInterface.json
 create mode 100644 schemas/json/generated/NeuroScopeLFPInterface.json
 create mode 100644 schemas/json/generated/NeuroScopeRecordingInterface.json
 create mode 100644 schemas/json/generated/NeuroScopeSortingInterface.json
 create mode 100644 schemas/json/generated/OpenEphysRecordingInterface.json
 create mode 100644 schemas/json/generated/PhySortingInterface.json
 create mode 100644 schemas/json/generated/SpikeGLXNIDQInterface.json
 create mode 100644 schemas/json/generated/SpikeGLXRecordingInterface.json
 delete mode 100644 src/renderer/src/stories/pages/GuidedMode.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Locate.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Preview.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Review.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Structure.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/Upload.stories.js
 create mode 100644 src/renderer/src/stories/pages/guided-mode/storyStates.ts

diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
new file mode 100644
index 000000000..1c0348d38
--- /dev/null
+++ b/generateInterfaceSchema.py
@@ -0,0 +1,60 @@
+
+from pathlib import Path
+import json
+from neuroconv import datainterfaces, NWBConverter
+
+filepath = Path('guideGlobalMetadata.json')
+generatedJSONSchemaPath = Path('schemas', 'json', 'generated')
+generatedJSONSchemaPath.mkdir(exist_ok=True, parents=True)
+
+f = filepath.open()
+data = json.load(f)
+
+# Create JSON for the Schema
+paths = {}
+for interface in data["supported_interfaces"]:
+    interface_class_dict = {interface: interface}
+
+    class CustomNWBConverter(NWBConverter):
+        data_interface_classes = {
+            custom_name: getattr(datainterfaces, interface_name)
+            for custom_name, interface_name in interface_class_dict.items()
+        }
+
+    schema = CustomNWBConverter.get_source_schema()
+
+    json_object = json.dumps(schema, indent=4)
+    paths[interface] = filepath = generatedJSONSchemaPath / f"{interface}.json"
+    with open(filepath, "w") as outfile:
+        outfile.write(json.dumps(schema, indent=4))
+
+
+sourceDataStoryPath = Path('src/renderer/src/stories/pages/guided-mode/SourceData.stories.js')
+
+importCode = "\n".join(map(lambda arr: f"import {arr[0]}Schema from '../../../../../../{arr[1]}'", paths.items()))
+storyCode = "\n".join(map(lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});
+const {arr[0]}GlobalCopy = JSON.parse(JSON.stringify(globalState))
+{arr[0]}GlobalCopy.interfaces.interface = {arr[0]}
+{arr[0]}GlobalCopy.schema.source_data.properties.interface = {arr[0]}Schema
+{arr[0]}.args = {{ activePage, globalState: {arr[0]}GlobalCopy }};
+""", paths.items()))
+
+with open(sourceDataStoryPath, "w") as outfile:
+    outfile.write(f"""import {{ globalState, PageTemplate }} from "./storyStates";
+{importCode}
+
+export default {{
+    title: "Pages/Guided Mode/Source Data",
+    parameters: {{
+        chromatic: {{ disableSnapshot: false }},
+    }}
+}};
+
+const activePage = "conversion/sourcedata"
+
+
+export const Example = PageTemplate.bind({{}});
+Example.args = {{ activePage, globalState }};
+
+{storyCode}
+""")
diff --git a/schemas/json/generated/BiocamRecordingInterface.json b/schemas/json/generated/BiocamRecordingInterface.json
new file mode 100644
index 000000000..3265fe263
--- /dev/null
+++ b/schemas/json/generated/BiocamRecordingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "BiocamRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/IntanRecordingInterface.json b/schemas/json/generated/IntanRecordingInterface.json
new file mode 100644
index 000000000..b75b39eda
--- /dev/null
+++ b/schemas/json/generated/IntanRecordingInterface.json
@@ -0,0 +1,37 @@
+{
+    "required": [],
+    "properties": {
+        "IntanRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "stream_id": {
+                    "type": "string",
+                    "default": "0"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeLFPInterface.json b/schemas/json/generated/NeuroScopeLFPInterface.json
new file mode 100644
index 000000000..3c6224cf0
--- /dev/null
+++ b/schemas/json/generated/NeuroScopeLFPInterface.json
@@ -0,0 +1,32 @@
+{
+    "required": [],
+    "properties": {
+        "NeuroScopeLFPInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "gain": {
+                    "type": "number"
+                },
+                "xml_file_path": {
+                    "format": "file",
+                    "type": "string"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeRecordingInterface.json b/schemas/json/generated/NeuroScopeRecordingInterface.json
new file mode 100644
index 000000000..2077b287a
--- /dev/null
+++ b/schemas/json/generated/NeuroScopeRecordingInterface.json
@@ -0,0 +1,40 @@
+{
+    "required": [],
+    "properties": {
+        "NeuroScopeRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "gain": {
+                    "type": "number"
+                },
+                "xml_file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeSortingInterface.json b/schemas/json/generated/NeuroScopeSortingInterface.json
new file mode 100644
index 000000000..fe3d76fe6
--- /dev/null
+++ b/schemas/json/generated/NeuroScopeSortingInterface.json
@@ -0,0 +1,40 @@
+{
+    "required": [],
+    "properties": {
+        "NeuroScopeSortingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "keep_mua_units": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "exclude_shanks": {
+                    "type": "array"
+                },
+                "xml_file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/OpenEphysRecordingInterface.json b/schemas/json/generated/OpenEphysRecordingInterface.json
new file mode 100644
index 000000000..73d9c1dbb
--- /dev/null
+++ b/schemas/json/generated/OpenEphysRecordingInterface.json
@@ -0,0 +1,32 @@
+{
+    "required": [],
+    "properties": {
+        "OpenEphysRecordingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "stream_name": {
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/PhySortingInterface.json b/schemas/json/generated/PhySortingInterface.json
new file mode 100644
index 000000000..182494ca2
--- /dev/null
+++ b/schemas/json/generated/PhySortingInterface.json
@@ -0,0 +1,32 @@
+{
+    "required": [],
+    "properties": {
+        "PhySortingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "exclude_cluster_groups": {
+                    "type": "array"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/SpikeGLXNIDQInterface.json b/schemas/json/generated/SpikeGLXNIDQInterface.json
new file mode 100644
index 000000000..8a38f1387
--- /dev/null
+++ b/schemas/json/generated/SpikeGLXNIDQInterface.json
@@ -0,0 +1,38 @@
+{
+    "required": [],
+    "properties": {
+        "SpikeGLXNIDQInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string",
+                    "description": "Path to SpikeGLX .nidq file."
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "load_sync_channel": {
+                    "type": "boolean",
+                    "default": false
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeriesNIDQ"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/SpikeGLXRecordingInterface.json b/schemas/json/generated/SpikeGLXRecordingInterface.json
new file mode 100644
index 000000000..603158605
--- /dev/null
+++ b/schemas/json/generated/SpikeGLXRecordingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "SpikeGLXRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string",
+                    "description": "Path to SpikeGLX ap.bin or lf.bin file."
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index c878e9d51..39311bc5b 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -65,7 +65,7 @@ export class Dashboard extends LitElement {
             logo: { type: String, reflect: true },
             subtitle: { type: String, reflect: true },
             activePage: { type: String, reflect: true },
-            globalState: { type: Object },
+            globalState: { type: Object, reflect: true },
         };
     }
 
@@ -136,6 +136,9 @@ export class Dashboard extends LitElement {
             this.sidebar.initialize = false;
             this.#activatePage(latest);
             return;
+        } else if (key.toLowerCase() === 'globalstate' && this.#active) {
+            this.#active.info.globalState = JSON.parse(latest)
+            this.#active.requestUpdate()
         }
     }
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bec2ed225..9fb210918 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -296,8 +296,11 @@ export class JSONSchemaForm extends LitElement {
     #update(fullPath, value) {
         const path = [...fullPath];
         const name = path.pop();
-        const resultParent = path.reduce((acc, key) => acc[key], this.results);
-        const resolvedParent = path.reduce((acc, key) => acc[key], this.resolved);
+
+        const reducer = (acc, key) => key in acc ? acc[key] : (acc[key] = {}) // NOTE: Create nested objects if required to set a new path
+
+        const resultParent = path.reduce(reducer, this.results);
+        const resolvedParent = path.reduce(reducer, this.resolved);
 
         if (!value) {
             delete resultParent[name];
@@ -917,7 +920,7 @@ ${info.default ? JSON.stringify(info.default, null, 2) : "No default value"}</pr
             }
 
             // Render properties in the sub-schema
-            const rendered = this.#render(info, results[name], required[name], fullPath);
+            const rendered = this.#render(info, results?.[name], required[name], fullPath);
             return hasMany || path.length > 1
                 ? html`
                       <div style="margin-top: 40px;">
diff --git a/src/renderer/src/stories/pages/GuidedMode.stories.js b/src/renderer/src/stories/pages/GuidedMode.stories.js
deleted file mode 100644
index 4ee9acf89..000000000
--- a/src/renderer/src/stories/pages/GuidedMode.stories.js
+++ /dev/null
@@ -1,150 +0,0 @@
-import { dashboard } from "../../pages.js";
-import nwbBaseSchema from "../../../../../schemas/base-metadata.schema";
-import exephysExampleSchema from "../../../../../schemas/json/ecephys_metadata_schema_example.json";
-
-const options = Object.keys(dashboard.pagesById).filter((k) => k.includes("conversion"));
-
-export default {
-    title: "Pages/Guided Mode",
-    parameters: {
-        chromatic: { disableSnapshot: false },
-    },
-    argTypes: {
-        activePage: {
-            options,
-            control: { type: "select" },
-        },
-    },
-};
-
-nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
-
-const globalState = {
-    project: {
-        name: "test",
-        NWBFile: {
-            lab: "My Lab",
-        },
-        Subject: {
-            species: "Mus musculus",
-        },
-    },
-    subjects: {
-        subject_id: {},
-    },
-    results: {
-        subject_id: {
-            session_id: {
-                metadata: {},
-                source_data: {},
-            },
-        },
-    },
-    interfaces: {
-        neuropixel: "SpikeGLXRecordingInterface",
-    },
-    schema: {
-        source_data: {
-            properties: {
-                neuropixel: {
-                    type: "object",
-                    properties: {
-                        file_path: {
-                            type: "string",
-                            description: "Enter the path to the source data file.",
-                            format: "file",
-                        },
-                    },
-                    required: ["file_path"],
-                },
-            },
-        },
-        metadata: {
-            subject_id: {
-                session_id: nwbBaseSchema,
-            },
-        },
-    },
-};
-
-const Template = (args = {}) => {
-    for (let k in args) dashboard[k] = args[k];
-    return dashboard;
-};
-
-export const Home = Template.bind({});
-Home.args = {
-    activePage: "conversion",
-};
-
-export const Start = Template.bind({});
-Start.args = {
-    activePage: "conversion/start",
-};
-
-export const NewDataset = Template.bind({});
-NewDataset.args = {
-    activePage: "conversion/details",
-};
-
-export const Structure = Template.bind({});
-Structure.args = {
-    activePage: "conversion/structure",
-};
-
-export const Locate = Template.bind({});
-Locate.args = {
-    activePage: "conversion/locate",
-};
-
-export const Subjects = Template.bind({});
-Subjects.args = {
-    activePage: "conversion/subjects",
-};
-
-export const SourceData = Template.bind({});
-SourceData.args = {
-    activePage: "conversion/sourcedata",
-};
-
-export const Metadata = Template.bind({});
-Metadata.args = {
-    activePage: "conversion/metadata",
-};
-
-export const ConversionOptions = Template.bind({});
-ConversionOptions.args = {
-    activePage: "conversion/options",
-};
-
-export const StubPreview = Template.bind({});
-StubPreview.args = {
-    activePage: "conversion/preview",
-};
-
-export const Upload = Template.bind({});
-Upload.args = {
-    activePage: "conversion/upload",
-};
-
-export const Results = Template.bind({});
-Results.args = {
-    activePage: "conversion/review",
-};
-
-const statefulPages = [
-    Home,
-    Start,
-    NewDataset,
-    Structure,
-    Locate,
-    Subjects,
-    SourceData,
-    Metadata,
-    ConversionOptions,
-    StubPreview,
-    Upload,
-    Results,
-];
-
-statefulPages.forEach((page) => (page.args.globalState = globalState));
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js b/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
new file mode 100644
index 000000000..817c862b2
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Home",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js b/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
new file mode 100644
index 000000000..f0ff538ed
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Start",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/start",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
new file mode 100644
index 000000000..1b5172835
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Locate",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/locate",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js b/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
new file mode 100644
index 000000000..c3270b65c
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Metadata",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/metadata",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js b/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
new file mode 100644
index 000000000..e70509b5c
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/New Dataset",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/details",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Preview.stories.js b/src/renderer/src/stories/pages/guided-mode/Preview.stories.js
new file mode 100644
index 000000000..3399da59f
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Preview.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Preview",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/preview",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Review.stories.js b/src/renderer/src/stories/pages/guided-mode/Review.stories.js
new file mode 100644
index 000000000..c876076ab
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Review.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Review",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/review",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
new file mode 100644
index 000000000..996c102ce
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -0,0 +1,78 @@
+import { globalState, PageTemplate } from "./storyStates";
+import SpikeGLXRecordingInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json'
+import SpikeGLXNIDQInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json'
+import PhySortingInterfaceSchema from '../../../../../../schemas/json/generated/PhySortingInterface.json'
+import NeuroScopeRecordingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json'
+import NeuroScopeLFPInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json'
+import NeuroScopeSortingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json'
+import BiocamRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BiocamRecordingInterface.json'
+import IntanRecordingInterfaceSchema from '../../../../../../schemas/json/generated/IntanRecordingInterface.json'
+import OpenEphysRecordingInterfaceSchema from '../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json'
+
+export default {
+    title: "Pages/Guided Mode/Source Data",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+const activePage = "conversion/sourcedata"
+
+
+export const Example = PageTemplate.bind({});
+Example.args = { activePage, globalState };
+
+export const SpikeGLXRecordingInterface = PageTemplate.bind({});
+const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface
+SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXRecordingInterfaceSchema
+SpikeGLXRecordingInterface.args = { activePage, globalState: SpikeGLXRecordingInterfaceGlobalCopy };
+
+export const SpikeGLXNIDQInterface = PageTemplate.bind({});
+const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface
+SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXNIDQInterfaceSchema
+SpikeGLXNIDQInterface.args = { activePage, globalState: SpikeGLXNIDQInterfaceGlobalCopy };
+
+export const PhySortingInterface = PageTemplate.bind({});
+const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface
+PhySortingInterfaceGlobalCopy.schema.source_data.properties.interface = PhySortingInterfaceSchema
+PhySortingInterface.args = { activePage, globalState: PhySortingInterfaceGlobalCopy };
+
+export const NeuroScopeRecordingInterface = PageTemplate.bind({});
+const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface
+NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeRecordingInterfaceSchema
+NeuroScopeRecordingInterface.args = { activePage, globalState: NeuroScopeRecordingInterfaceGlobalCopy };
+
+export const NeuroScopeLFPInterface = PageTemplate.bind({});
+const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface
+NeuroScopeLFPInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeLFPInterfaceSchema
+NeuroScopeLFPInterface.args = { activePage, globalState: NeuroScopeLFPInterfaceGlobalCopy };
+
+export const NeuroScopeSortingInterface = PageTemplate.bind({});
+const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface
+NeuroScopeSortingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeSortingInterfaceSchema
+NeuroScopeSortingInterface.args = { activePage, globalState: NeuroScopeSortingInterfaceGlobalCopy };
+
+export const BiocamRecordingInterface = PageTemplate.bind({});
+const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface
+BiocamRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = BiocamRecordingInterfaceSchema
+BiocamRecordingInterface.args = { activePage, globalState: BiocamRecordingInterfaceGlobalCopy };
+
+export const IntanRecordingInterface = PageTemplate.bind({});
+const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface
+IntanRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = IntanRecordingInterfaceSchema
+IntanRecordingInterface.args = { activePage, globalState: IntanRecordingInterfaceGlobalCopy };
+
+export const OpenEphysRecordingInterface = PageTemplate.bind({});
+const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface
+OpenEphysRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = OpenEphysRecordingInterfaceSchema
+OpenEphysRecordingInterface.args = { activePage, globalState: OpenEphysRecordingInterfaceGlobalCopy };
+
diff --git a/src/renderer/src/stories/pages/guided-mode/Structure.stories.js b/src/renderer/src/stories/pages/guided-mode/Structure.stories.js
new file mode 100644
index 000000000..5a411eb96
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Structure.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Structure",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/structure",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js b/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
new file mode 100644
index 000000000..6c24f6837
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Subjects",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/subjects",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/Upload.stories.js b/src/renderer/src/stories/pages/guided-mode/Upload.stories.js
new file mode 100644
index 000000000..90244b864
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/Upload.stories.js
@@ -0,0 +1,15 @@
+import { globalState, PageTemplate } from "./storyStates";
+
+export default {
+    title: "Pages/Guided Mode/Upload",
+    parameters: {
+        chromatic: { disableSnapshot: false },
+    }
+};
+
+
+export const Default = PageTemplate.bind({});
+Default.args = {
+    activePage: "conversion/upload",
+    globalState
+};
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index 09acada21..bed49b260 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -14,13 +14,15 @@ export class GuidedStubPreviewPage extends Page {
     }
 
     header = {
-        subtitle: () => this.info.globalState.preview.file,
-        controls: () =>
-            html`<nwb-button
+        subtitle: () => this.info.globalState.preview?.file,
+        controls: () => {
+            const { preview } = this.info.globalState
+            preview ? html`<nwb-button
                 size="small"
-                @click=${() => (shell ? shell.showItemInFolder(this.info.globalState.preview.file) : "")}
+                @click=${() => (shell ? shell.showItemInFolder(preview.file) : "")}
                 >${unsafeSVG(folderOpenSVG)}</nwb-button
-            >`,
+            >` : ''
+        },
     };
 
     footer = {
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 4fdf7782a..d6e22e514 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -23,7 +23,7 @@ export class GuidedResultsPage extends Page {
             }
         };
 
-        const { dandiset_id, staging } = this.info.globalState.upload.info;
+        const { dandiset_id, staging } = this.info.globalState.upload?.info ?? {};
 
         const elIds = ["name", "modified"];
 
@@ -66,12 +66,13 @@ export class GuidedResultsPage extends Page {
     }
 
     render() {
-        const { dandiset_id } = this.info.globalState.upload.info;
         const results = this.info.globalState.conversion;
 
         if (!results)
             return html`<div style="text-align: center;"><p>Your conversion failed. Please try again.</p></div>`;
 
+        const { dandiset_id } = this.info.globalState.upload?.info ?? {};
+
         return html`
             <div style="text-align: center;">
                 <div style="display: inline-block; width: 100%; text-align: left;">
diff --git a/src/renderer/src/stories/pages/guided-mode/storyStates.ts b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
new file mode 100644
index 000000000..3d8f39c60
--- /dev/null
+++ b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
@@ -0,0 +1,63 @@
+import nwbBaseSchema from "../../../../../../schemas/base-metadata.schema";
+import exephysExampleSchema from "../../../../../../schemas/json/ecephys_metadata_schema_example.json";
+
+import { dashboard } from "../../../pages.js";
+export const PageTemplate = (args = {}) => {
+    for (let k in args) dashboard[k] = args[k];
+    return dashboard;
+};
+
+
+nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
+
+export const globalState = {
+    project: {
+        name: "test",
+        NWBFile: {
+            lab: "My Lab",
+        },
+        Subject: {
+            species: "Mus musculus",
+        },
+    },
+    subjects: {
+        subject_id: {},
+    },
+    results: {
+        subject_id: {
+            session_id: {
+                metadata: {},
+                source_data: {},
+            },
+        },
+    },
+    interfaces: {
+        interface: "SpikeGLXRecordingInterface",
+    },
+    schema: {
+
+        // Default source data schema
+        source_data: {
+            properties: {
+                interface: {
+                    type: "object",
+                    properties: {
+                        file_path: {
+                            type: "string",
+                            description: "Enter the path to the source data file.",
+                            format: "file",
+                        },
+                    },
+                    required: ["file_path"],
+                },
+            },
+        },
+
+        // Base metadata schema for one session
+        metadata: {
+            subject_id: {
+                session_id: nwbBaseSchema,
+            },
+        },
+    },
+};
\ No newline at end of file

From dbba901d06d8ef134d1b4e882fed895372c42b01 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 9 Aug 2023 17:56:37 +0000
Subject: [PATCH 29/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 generateInterfaceSchema.py                    | 22 ++++--
 .../generated/BiocamRecordingInterface.json   |  2 +-
 .../generated/IntanRecordingInterface.json    |  2 +-
 .../generated/NeuroScopeLFPInterface.json     |  2 +-
 .../NeuroScopeRecordingInterface.json         |  2 +-
 .../generated/NeuroScopeSortingInterface.json |  2 +-
 .../OpenEphysRecordingInterface.json          |  2 +-
 .../json/generated/PhySortingInterface.json   |  2 +-
 .../json/generated/SpikeGLXNIDQInterface.json |  2 +-
 .../generated/SpikeGLXRecordingInterface.json |  2 +-
 src/renderer/src/stories/Dashboard.js         |  6 +-
 src/renderer/src/stories/JSONSchemaForm.js    |  2 +-
 .../pages/guided-mode/GuidedHome.stories.js   |  5 +-
 .../pages/guided-mode/GuidedStart.stories.js  |  5 +-
 .../pages/guided-mode/Locate.stories.js       |  5 +-
 .../pages/guided-mode/Metadata.stories.js     |  5 +-
 .../pages/guided-mode/NewDataset.stories.js   |  5 +-
 .../pages/guided-mode/Preview.stories.js      |  5 +-
 .../pages/guided-mode/Review.stories.js       |  5 +-
 .../pages/guided-mode/SourceData.stories.js   | 78 +++++++++----------
 .../pages/guided-mode/Structure.stories.js    |  5 +-
 .../pages/guided-mode/Subjects.stories.js     |  5 +-
 .../pages/guided-mode/Upload.stories.js       |  5 +-
 .../guided-mode/options/GuidedStubPreview.js  | 12 +--
 .../stories/pages/guided-mode/storyStates.ts  |  2 +-
 25 files changed, 92 insertions(+), 98 deletions(-)

diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
index 1c0348d38..00b27812b 100644
--- a/generateInterfaceSchema.py
+++ b/generateInterfaceSchema.py
@@ -1,10 +1,9 @@
-
 from pathlib import Path
 import json
 from neuroconv import datainterfaces, NWBConverter
 
-filepath = Path('guideGlobalMetadata.json')
-generatedJSONSchemaPath = Path('schemas', 'json', 'generated')
+filepath = Path("guideGlobalMetadata.json")
+generatedJSONSchemaPath = Path("schemas", "json", "generated")
 generatedJSONSchemaPath.mkdir(exist_ok=True, parents=True)
 
 f = filepath.open()
@@ -29,18 +28,24 @@ class CustomNWBConverter(NWBConverter):
         outfile.write(json.dumps(schema, indent=4))
 
 
-sourceDataStoryPath = Path('src/renderer/src/stories/pages/guided-mode/SourceData.stories.js')
+sourceDataStoryPath = Path("src/renderer/src/stories/pages/guided-mode/SourceData.stories.js")
 
 importCode = "\n".join(map(lambda arr: f"import {arr[0]}Schema from '../../../../../../{arr[1]}'", paths.items()))
-storyCode = "\n".join(map(lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});
+storyCode = "\n".join(
+    map(
+        lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});
 const {arr[0]}GlobalCopy = JSON.parse(JSON.stringify(globalState))
 {arr[0]}GlobalCopy.interfaces.interface = {arr[0]}
 {arr[0]}GlobalCopy.schema.source_data.properties.interface = {arr[0]}Schema
 {arr[0]}.args = {{ activePage, globalState: {arr[0]}GlobalCopy }};
-""", paths.items()))
+""",
+        paths.items(),
+    )
+)
 
 with open(sourceDataStoryPath, "w") as outfile:
-    outfile.write(f"""import {{ globalState, PageTemplate }} from "./storyStates";
+    outfile.write(
+        f"""import {{ globalState, PageTemplate }} from "./storyStates";
 {importCode}
 
 export default {{
@@ -57,4 +62,5 @@ class CustomNWBConverter(NWBConverter):
 Example.args = {{ activePage, globalState }};
 
 {storyCode}
-""")
+"""
+    )
diff --git a/schemas/json/generated/BiocamRecordingInterface.json b/schemas/json/generated/BiocamRecordingInterface.json
index 3265fe263..8d51c7b06 100644
--- a/schemas/json/generated/BiocamRecordingInterface.json
+++ b/schemas/json/generated/BiocamRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/IntanRecordingInterface.json b/schemas/json/generated/IntanRecordingInterface.json
index b75b39eda..07904ada2 100644
--- a/schemas/json/generated/IntanRecordingInterface.json
+++ b/schemas/json/generated/IntanRecordingInterface.json
@@ -34,4 +34,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeLFPInterface.json b/schemas/json/generated/NeuroScopeLFPInterface.json
index 3c6224cf0..d42a885ab 100644
--- a/schemas/json/generated/NeuroScopeLFPInterface.json
+++ b/schemas/json/generated/NeuroScopeLFPInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeRecordingInterface.json b/schemas/json/generated/NeuroScopeRecordingInterface.json
index 2077b287a..3e95a33d0 100644
--- a/schemas/json/generated/NeuroScopeRecordingInterface.json
+++ b/schemas/json/generated/NeuroScopeRecordingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeSortingInterface.json b/schemas/json/generated/NeuroScopeSortingInterface.json
index fe3d76fe6..680fcbce9 100644
--- a/schemas/json/generated/NeuroScopeSortingInterface.json
+++ b/schemas/json/generated/NeuroScopeSortingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/OpenEphysRecordingInterface.json b/schemas/json/generated/OpenEphysRecordingInterface.json
index 73d9c1dbb..9accfcf55 100644
--- a/schemas/json/generated/OpenEphysRecordingInterface.json
+++ b/schemas/json/generated/OpenEphysRecordingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/PhySortingInterface.json b/schemas/json/generated/PhySortingInterface.json
index 182494ca2..edcc2183d 100644
--- a/schemas/json/generated/PhySortingInterface.json
+++ b/schemas/json/generated/PhySortingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/SpikeGLXNIDQInterface.json b/schemas/json/generated/SpikeGLXNIDQInterface.json
index 8a38f1387..14ad82eb8 100644
--- a/schemas/json/generated/SpikeGLXNIDQInterface.json
+++ b/schemas/json/generated/SpikeGLXNIDQInterface.json
@@ -35,4 +35,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/SpikeGLXRecordingInterface.json b/schemas/json/generated/SpikeGLXRecordingInterface.json
index 603158605..4b2034df8 100644
--- a/schemas/json/generated/SpikeGLXRecordingInterface.json
+++ b/schemas/json/generated/SpikeGLXRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index 39311bc5b..5b6aa36f7 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -136,9 +136,9 @@ export class Dashboard extends LitElement {
             this.sidebar.initialize = false;
             this.#activatePage(latest);
             return;
-        } else if (key.toLowerCase() === 'globalstate' && this.#active) {
-            this.#active.info.globalState = JSON.parse(latest)
-            this.#active.requestUpdate()
+        } else if (key.toLowerCase() === "globalstate" && this.#active) {
+            this.#active.info.globalState = JSON.parse(latest);
+            this.#active.requestUpdate();
         }
     }
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 9fb210918..bdcda8a3e 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -297,7 +297,7 @@ export class JSONSchemaForm extends LitElement {
         const path = [...fullPath];
         const name = path.pop();
 
-        const reducer = (acc, key) => key in acc ? acc[key] : (acc[key] = {}) // NOTE: Create nested objects if required to set a new path
+        const reducer = (acc, key) => (key in acc ? acc[key] : (acc[key] = {})); // NOTE: Create nested objects if required to set a new path
 
         const resultParent = path.reduce(reducer, this.results);
         const resolvedParent = path.reduce(reducer, this.resolved);
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js b/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
index 817c862b2..ddbd278eb 100644
--- a/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedHome.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Home",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js b/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
index f0ff538ed..0453a2854 100644
--- a/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/GuidedStart.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Start",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/start",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
index 1b5172835..c8f3855c1 100644
--- a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Locate",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/locate",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js b/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
index c3270b65c..54f0cafba 100644
--- a/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Metadata.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Metadata",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/metadata",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js b/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
index e70509b5c..dcbc8cda7 100644
--- a/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/NewDataset.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/New Dataset",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/details",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Preview.stories.js b/src/renderer/src/stories/pages/guided-mode/Preview.stories.js
index 3399da59f..e04431df1 100644
--- a/src/renderer/src/stories/pages/guided-mode/Preview.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Preview.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Preview",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/preview",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Review.stories.js b/src/renderer/src/stories/pages/guided-mode/Review.stories.js
index c876076ab..28ec3a26d 100644
--- a/src/renderer/src/stories/pages/guided-mode/Review.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Review.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Review",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/review",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
index 996c102ce..cab7bae33 100644
--- a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -1,78 +1,76 @@
 import { globalState, PageTemplate } from "./storyStates";
-import SpikeGLXRecordingInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json'
-import SpikeGLXNIDQInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json'
-import PhySortingInterfaceSchema from '../../../../../../schemas/json/generated/PhySortingInterface.json'
-import NeuroScopeRecordingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json'
-import NeuroScopeLFPInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json'
-import NeuroScopeSortingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json'
-import BiocamRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BiocamRecordingInterface.json'
-import IntanRecordingInterfaceSchema from '../../../../../../schemas/json/generated/IntanRecordingInterface.json'
-import OpenEphysRecordingInterfaceSchema from '../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json'
+import SpikeGLXRecordingInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json";
+import SpikeGLXNIDQInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json";
+import PhySortingInterfaceSchema from "../../../../../../schemas/json/generated/PhySortingInterface.json";
+import NeuroScopeRecordingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json";
+import NeuroScopeLFPInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json";
+import NeuroScopeSortingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json";
+import BiocamRecordingInterfaceSchema from "../../../../../../schemas/json/generated/BiocamRecordingInterface.json";
+import IntanRecordingInterfaceSchema from "../../../../../../schemas/json/generated/IntanRecordingInterface.json";
+import OpenEphysRecordingInterfaceSchema from "../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json";
 
 export default {
     title: "Pages/Guided Mode/Source Data",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-const activePage = "conversion/sourcedata"
-
+const activePage = "conversion/sourcedata";
 
 export const Example = PageTemplate.bind({});
 Example.args = { activePage, globalState };
 
 export const SpikeGLXRecordingInterface = PageTemplate.bind({});
-const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface
-SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXRecordingInterfaceSchema
+const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface;
+SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXRecordingInterfaceSchema;
 SpikeGLXRecordingInterface.args = { activePage, globalState: SpikeGLXRecordingInterfaceGlobalCopy };
 
 export const SpikeGLXNIDQInterface = PageTemplate.bind({});
-const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface
-SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXNIDQInterfaceSchema
+const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface;
+SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXNIDQInterfaceSchema;
 SpikeGLXNIDQInterface.args = { activePage, globalState: SpikeGLXNIDQInterfaceGlobalCopy };
 
 export const PhySortingInterface = PageTemplate.bind({});
-const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface
-PhySortingInterfaceGlobalCopy.schema.source_data.properties.interface = PhySortingInterfaceSchema
+const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface;
+PhySortingInterfaceGlobalCopy.schema.source_data.properties.interface = PhySortingInterfaceSchema;
 PhySortingInterface.args = { activePage, globalState: PhySortingInterfaceGlobalCopy };
 
 export const NeuroScopeRecordingInterface = PageTemplate.bind({});
-const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface
-NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeRecordingInterfaceSchema
+const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface;
+NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeRecordingInterfaceSchema;
 NeuroScopeRecordingInterface.args = { activePage, globalState: NeuroScopeRecordingInterfaceGlobalCopy };
 
 export const NeuroScopeLFPInterface = PageTemplate.bind({});
-const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface
-NeuroScopeLFPInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeLFPInterfaceSchema
+const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface;
+NeuroScopeLFPInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeLFPInterfaceSchema;
 NeuroScopeLFPInterface.args = { activePage, globalState: NeuroScopeLFPInterfaceGlobalCopy };
 
 export const NeuroScopeSortingInterface = PageTemplate.bind({});
-const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface
-NeuroScopeSortingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeSortingInterfaceSchema
+const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface;
+NeuroScopeSortingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeSortingInterfaceSchema;
 NeuroScopeSortingInterface.args = { activePage, globalState: NeuroScopeSortingInterfaceGlobalCopy };
 
 export const BiocamRecordingInterface = PageTemplate.bind({});
-const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface
-BiocamRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = BiocamRecordingInterfaceSchema
+const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface;
+BiocamRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = BiocamRecordingInterfaceSchema;
 BiocamRecordingInterface.args = { activePage, globalState: BiocamRecordingInterfaceGlobalCopy };
 
 export const IntanRecordingInterface = PageTemplate.bind({});
-const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface
-IntanRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = IntanRecordingInterfaceSchema
+const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface;
+IntanRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = IntanRecordingInterfaceSchema;
 IntanRecordingInterface.args = { activePage, globalState: IntanRecordingInterfaceGlobalCopy };
 
 export const OpenEphysRecordingInterface = PageTemplate.bind({});
-const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface
-OpenEphysRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = OpenEphysRecordingInterfaceSchema
+const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface;
+OpenEphysRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = OpenEphysRecordingInterfaceSchema;
 OpenEphysRecordingInterface.args = { activePage, globalState: OpenEphysRecordingInterfaceGlobalCopy };
-
diff --git a/src/renderer/src/stories/pages/guided-mode/Structure.stories.js b/src/renderer/src/stories/pages/guided-mode/Structure.stories.js
index 5a411eb96..f7426c335 100644
--- a/src/renderer/src/stories/pages/guided-mode/Structure.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Structure.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Structure",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/structure",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js b/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
index 6c24f6837..a14a1f199 100644
--- a/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Subjects.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Subjects",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/subjects",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/Upload.stories.js b/src/renderer/src/stories/pages/guided-mode/Upload.stories.js
index 90244b864..3c4e40377 100644
--- a/src/renderer/src/stories/pages/guided-mode/Upload.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Upload.stories.js
@@ -4,12 +4,11 @@ export default {
     title: "Pages/Guided Mode/Upload",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-
 export const Default = PageTemplate.bind({});
 Default.args = {
     activePage: "conversion/upload",
-    globalState
+    globalState,
 };
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index bed49b260..3af424a3c 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -16,12 +16,12 @@ export class GuidedStubPreviewPage extends Page {
     header = {
         subtitle: () => this.info.globalState.preview?.file,
         controls: () => {
-            const { preview } = this.info.globalState
-            preview ? html`<nwb-button
-                size="small"
-                @click=${() => (shell ? shell.showItemInFolder(preview.file) : "")}
-                >${unsafeSVG(folderOpenSVG)}</nwb-button
-            >` : ''
+            const { preview } = this.info.globalState;
+            preview
+                ? html`<nwb-button size="small" @click=${() => (shell ? shell.showItemInFolder(preview.file) : "")}
+                      >${unsafeSVG(folderOpenSVG)}</nwb-button
+                  >`
+                : "";
         },
     };
 
diff --git a/src/renderer/src/stories/pages/guided-mode/storyStates.ts b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
index 3d8f39c60..b25023ca8 100644
--- a/src/renderer/src/stories/pages/guided-mode/storyStates.ts
+++ b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
@@ -60,4 +60,4 @@ export const globalState = {
             },
         },
     },
-};
\ No newline at end of file
+};

From b86de5edc297e299e176db941bd0e2ca06ec9654 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 17:26:01 +0000
Subject: [PATCH 30/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/src/renderer/src/electron/index.js b/src/renderer/src/electron/index.js
index 554673153..4f9b30865 100644
--- a/src/renderer/src/electron/index.js
+++ b/src/renderer/src/electron/index.js
@@ -24,7 +24,7 @@ if (isElectron) {
         electron.ipcRenderer.on("fileOpened", (info, ...args) => {
             console.log("File opened!", ...args);
         });
-        
+
         ["log", "warn", "error"].forEach((method) =>
             electron.ipcRenderer.on(`console.${method}`, (_, ...args) => console[method](`[main-process]:`, ...args))
         );

From 6a00ff8c6bd7be2517c353effdfadcb02d6123ab Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 17:44:01 +0000
Subject: [PATCH 31/71] [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         | 1 -
 1 file changed, 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 c0fac8478..49939f0eb 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 +20,6 @@ const getInfoFromId = (key) => {
     return { subject, session };
 };
 
-
 export class GuidedMetadataPage extends ManagedPage {
     constructor(...args) {
         super(...args);

From dfc9cc38ae6817a360b53a36205e70c6050e49c4 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 10:48:29 -0700
Subject: [PATCH 32/71] Fix merge

---
 src/renderer/src/stories/JSONSchemaForm.js                    | 4 ----
 .../src/stories/pages/guided-mode/data/GuidedStructure.js     | 4 ++--
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 3c07fb654..8dd73b32a 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -761,10 +761,6 @@ export class JSONSchemaForm extends LitElement {
                     schema: info,
                     results: results[name],
                     globals: this.globals?.[name],
-                    onUpdate: (internalPath, value) => {
-                        const path = [...fullPath, ...internalPath];
-                        this.#update(path, value);
-                    },
 
                     onUpdate: (internalPath, value) => {
                         const path = [...fullPath, ...internalPath];
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
index 28563af0e..5ef34442c 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -43,7 +43,7 @@ export class GuidedStructurePage extends Page {
     });
 
     getSchema = async () => {
-        const interfaces = { ...this.#selected };
+        const interfaces = { ...this.list.object };
 
         const schema =
             Object.keys(interfaces).length === 0
@@ -62,7 +62,7 @@ export class GuidedStructurePage extends Page {
     };
 
     beforeSave = async () => {
-        this.info.globalState.interfaces = { ...this.#selected };
+        this.info.globalState.interfaces = { ...this.list.object };
         await this.save(undefined, false); // Interrim save, in case the schema request fails
         await this.getSchema();
     };

From c2ca3f3e6879d8bbfaf65d790f47c2393f227d96 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 11:08:19 -0700
Subject: [PATCH 33/71] Rename global object variable and run all stubs

---
 .../stories/pages/guided-mode/data/GuidedMetadata.js   |  8 +++-----
 .../pages/guided-mode/options/GuidedStubPreview.js     | 10 +++++-----
 2 files changed, 8 insertions(+), 10 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 4205819c3..225d04cb0 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -25,12 +25,10 @@ export class GuidedMetadataPage extends ManagedPage {
             for (let { form } of this.forms) await form.validate(); // Will throw an error in the callback
 
             // Preview a single random conversion
-            delete this.info.globalState.preview; // Clear the preview results
-            const [result] = await this.runConversions({ stub_test: true }, 1, {
-                title: "Testing conversion on a random session",
-            });
+            delete this.info.globalState.stubs; // Clear the preview results
+            const results = await this.runConversions({ stub_test: true }, undefined, { title: "Running stub conversion on all sessions..." });
 
-            this.info.globalState.preview = result; // Save the preview results
+            this.info.globalState.stubs = results; // Save the preview results
 
             this.onTransition(1);
         },
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index eae26b3c6..234994cd1 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -14,11 +14,11 @@ export class GuidedStubPreviewPage extends Page {
     }
 
     header = {
-        subtitle: () => this.info.globalState.preview,
+        subtitle: () => this.info.globalState.stubs[0],
         controls: () =>
             html`<nwb-button
                 size="small"
-                @click=${() => (shell ? shell.showItemInFolder(this.info.globalState.preview) : "")}
+                @click=${() => (shell ? shell.showItemInFolder(this.info.globalState.stubs[0]) : "")}
                 >${unsafeSVG(folderOpenSVG)}</nwb-button
             >`,
     };
@@ -37,10 +37,10 @@ export class GuidedStubPreviewPage extends Page {
     };
 
     render() {
-        const { project, preview } = this.info.globalState;
+        const { project, stubs } = this.info.globalState;
 
-        return preview
-            ? new Neurosift({ url: getURLFromFilePath(preview, project.name) })
+        return stubs
+            ? new Neurosift({ url: getURLFromFilePath(stubs[0], project.name) })
             : html`<p style="text-align: center;">Your conversion preview failed. Please try again.</p>`;
     }
 }

From a4b899e5aca9d1ef55427ac8627bb503a6bb11f3 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 11:14:40 -0700
Subject: [PATCH 34/71] Fix bad merge and ensure onUpdate only calls when the
 value changes

---
 src/renderer/src/stories/Dashboard.js                | 12 ------------
 src/renderer/src/stories/JSONSchemaForm.js           |  4 +++-
 .../stories/pages/guided-mode/data/GuidedMetadata.js |  6 +++++-
 3 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/src/renderer/src/stories/Dashboard.js b/src/renderer/src/stories/Dashboard.js
index ad553baa1..c8859d295 100644
--- a/src/renderer/src/stories/Dashboard.js
+++ b/src/renderer/src/stories/Dashboard.js
@@ -98,18 +98,6 @@ export class Dashboard extends LitElement {
 
         this.subSidebar = new NavigationSidebar();
         this.subSidebar.onClick = async (id) => {
-            const result = this.#active.unsavedUpdates
-                ? await Swal.fire({
-                      title: "You have unsaved data on this page.",
-                      text: "Would you like to save your changes?",
-                      icon: "warning",
-                      showCancelButton: true,
-                      confirmButtonColor: "#3085d6",
-                      confirmButtonText: "Save and Continue",
-                      cancelButtonText: "Ignore Changes",
-                  })
-                : undefined;
-
             this.#active.to(id);
         };
 
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 8dd73b32a..b1bff8ecd 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -259,12 +259,14 @@ export class JSONSchemaForm extends LitElement {
 
     // Track resolved values for the form (data only)
     updateData(fullPath, value) {
-        this.onUpdate(fullPath, value);
         const path = [...fullPath];
         const name = path.pop();
         const resultParent = path.reduce((acc, key) => acc[key], this.results);
         const resolvedParent = path.reduce((acc, key) => acc[key], this.resolved);
 
+        if (resolvedParent[name] !== value) this.onUpdate(fullPath, value); // Ensure the value has actually changed
+
+
         if (!value) {
             delete resultParent[name];
             delete resolvedParent[name];
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 49939f0eb..0ae15aeb8 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -45,6 +45,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
             // Save the preview results
             this.info.globalState.preview = result;
+            
             this.unsavedUpdates = true;
 
             this.to(1);
@@ -118,7 +119,10 @@ export class GuidedMetadataPage extends ManagedPage {
                 this.#checkAllLoaded();
             },
 
-            onUpdate: () => (this.unsavedUpdates = true),
+            onUpdate: (...args) => {
+                console.log(...args);
+                (this.unsavedUpdates = true)
+            },
 
             validateOnChange,
             onlyRequired: false,

From 090adb9acd2fcfaddf7e20aac6274806c60b2a55 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 18:14:56 +0000
Subject: [PATCH 35/71] [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/stories/pages/guided-mode/data/GuidedMetadata.js      | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index b1bff8ecd..9930c8393 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -266,7 +266,6 @@ export class JSONSchemaForm extends LitElement {
 
         if (resolvedParent[name] !== value) this.onUpdate(fullPath, value); // Ensure the value has actually changed
 
-
         if (!value) {
             delete resultParent[name];
             delete resolvedParent[name];
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 0ae15aeb8..26da77c09 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -45,7 +45,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
             // Save the preview results
             this.info.globalState.preview = result;
-            
+
             this.unsavedUpdates = true;
 
             this.to(1);
@@ -121,7 +121,7 @@ export class GuidedMetadataPage extends ManagedPage {
 
             onUpdate: (...args) => {
                 console.log(...args);
-                (this.unsavedUpdates = true)
+                this.unsavedUpdates = true;
             },
 
             validateOnChange,

From 46fb1c5d2afb72a083bd21d8b4b42bf4390e0a8a Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 11:17:29 -0700
Subject: [PATCH 36/71] Update main.ts

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

diff --git a/src/main/main.ts b/src/main/main.ts
index 2da4f295d..718de1b84 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -358,7 +358,6 @@ if (isWindows && process.argv.length >= 2) {
 }
 
 // Make this app a single instance app.
-const gotTheLock = app.requestSingleInstanceLock();
 
 function restoreWindow(){
   if (globals.mainWindow) {
@@ -372,7 +371,7 @@ function restoreWindow(){
 function makeSingleInstance() {
   if (process.mas) return;
 
-  if (!gotTheLock) app.quit();
+  if (!app.requestSingleInstanceLock()) app.quit();
   else app.on("second-instance", () => restoreWindow());
 }
 

From 685456e77aa0f98a32394b65fbbb46bc184fc4c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 18:23:27 +0000
Subject: [PATCH 37/71] [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      | 4 +++-
 1 file changed, 3 insertions(+), 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 225d04cb0..35d03f068 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -26,7 +26,9 @@ export class GuidedMetadataPage extends ManagedPage {
 
             // Preview a single random conversion
             delete this.info.globalState.stubs; // Clear the preview results
-            const results = await this.runConversions({ stub_test: true }, undefined, { title: "Running stub conversion on all sessions..." });
+            const results = await this.runConversions({ stub_test: true }, undefined, {
+                title: "Running stub conversion on all sessions...",
+            });
 
             this.info.globalState.stubs = results; // Save the preview results
 

From 7d8cf6f1230f99d1e873f62e8fce82763d917314 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 11:48:31 -0700
Subject: [PATCH 38/71] Add conditionals for restart condition

---
 src/main/main.ts          | 68 ++++++++++++++++++++++-----------------
 src/renderer/src/index.ts | 13 +++++++-
 2 files changed, 50 insertions(+), 31 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 035436381..d188fd8e6 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -48,6 +48,7 @@ let globals =  {
   python: {
     status: false,
     sent: false,
+    restart: false,
     latestError: ''
   },
 
@@ -98,7 +99,7 @@ const pythonIsOpen = (force = false) => {
 const pythonIsClosed = (err = globals.python.latestError) => {
 
     onWindowReady(win => {
-      send.call(win, "python.closed", err)
+      send.call(win, globals.python.restart ? "python.restart" : "python.closed", err)
       globals.python.sent = true
     })
 
@@ -120,41 +121,49 @@ const getPackagedPath = () => {
 };
 
 const createPyProc = async () => {
-  let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
-  await killAllPreviousProcesses();
 
-  const defaultPort = PORT as number
+  return new Promise(async (resolve, reject) => {
 
+    let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
+    await killAllPreviousProcesses();
 
-  fp(defaultPort, defaultPort + portRange)
-    .then(([freePort]: string[]) => {
-      selectedPort = freePort;
+    const defaultPort = PORT as number
 
-      pyflaskProcess = (script.slice(-3) === '.py') ? child_process.spawn("python", [script, freePort], {}) : child_process.spawn(`${script}`, [freePort], {});
 
-      if (pyflaskProcess != null) {
+    fp(defaultPort, defaultPort + portRange)
+      .then(([freePort]: string[]) => {
+        selectedPort = freePort;
 
-        // Listen for errors from Python process
-        pyflaskProcess.stderr.on("data", (data: string) => {
-          console.error(`${data}`)
-          globals.python.latestError = data.toString()
-        });
+        pyflaskProcess = (script.slice(-3) === '.py') ? child_process.spawn("python", [script, freePort], {}) : child_process.spawn(`${script}`, [freePort], {});
 
-        pyflaskProcess.stdout.on('data', (data: string) => {
-          pythonIsOpen();
-          console.log(`${data}`)
-        });
+        if (pyflaskProcess != null) {
 
-        pyflaskProcess.on('close', (code: number) => {
-          console.error(`exit code ${code}`)
-          pythonIsClosed()
-        });
+          // Listen for errors from Python process
+          pyflaskProcess.stderr.on("data", (data: string) => {
+            console.error(`${data}`)
+            globals.python.latestError = data.toString()
+          });
 
-      }
+          pyflaskProcess.stdout.on('data', (data: string) => {
+            const isRestarting = globals.python.restart
+            setTimeout(() => pythonIsOpen(isRestarting), 100); // Wait just a bit to give the server some time to come online
+            console.log(`${data}`)
+            resolve(true)
+          });
+
+          pyflaskProcess.on('close', (code: number) => {
+            console.error(`exit code ${code}`)
+            pythonIsClosed()
+            reject()
+          });
+
+        }
+      })
+      .catch((err: Error) => {
+        console.log(err);
+        reject(err)
+      });
     })
-    .catch((err: Error) => {
-      console.log(err);
-    });
 };
 
 /**
@@ -283,16 +292,15 @@ function initialize() {
     // Listen after first load
     promise.then(() => {
       const chokidar = require('chokidar');
-      let done = true
       chokidar.watch(path.join(__dirname, "../../pyflask"), {
         ignored:  ['**/__pycache__/**']
       }).on('all', async (event: string) => {
-        if (event === 'change' && done) {
-          done = false
+        if (event === 'change' && !globals.python.restart) {
+          globals.python.restart = true
           await exitPyProc();
           setTimeout(async () => {
             await createPyProc();
-            done = true
+            globals.python.restart = false
           }, 1000)
         }
       });
diff --git a/src/renderer/src/index.ts b/src/renderer/src/index.ts
index 1ce8be251..f00643058 100644
--- a/src/renderer/src/index.ts
+++ b/src/renderer/src/index.ts
@@ -100,6 +100,7 @@ const serverIsLiveStartup = async () => {
   return echoResponse === "server ready" ? true : false;
 };
 
+let openPythonStatusNotyf: undefined | any;
 
 async function pythonServerOpened() {
 
@@ -109,7 +110,9 @@ async function pythonServerOpened() {
 
   // Update server status and throw a notification
   statusBar.items[2].status = true
-  notyf.open({
+
+  if (openPythonStatusNotyf) notyf.dismiss(openPythonStatusNotyf)
+  openPythonStatusNotyf = notyf.open({
     type: "success",
     message: "Backend services are available",
   });
@@ -145,6 +148,14 @@ if (isElectron) {
     ipcRenderer.on("python.open", pythonServerOpened);
 
     ipcRenderer.on("python.closed", (_, message) => pythonServerClosed(message));
+    ipcRenderer.on("python.restart", () => {
+      statusBar.items[2].status = undefined
+      if (openPythonStatusNotyf) notyf.dismiss(openPythonStatusNotyf)
+      openPythonStatusNotyf = notyf.open({
+        type: "warning",
+        message: "Backend services are restarting...",
+      })
+    });
 
     // Check for update and show the pop up box
     ipcRenderer.on("update_available", () => {

From 74cc9a44663ec7c548a67579e20177d79ad69c25 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 12:05:54 -0700
Subject: [PATCH 39/71] Update JSONSchemaForm.js

---
 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 d44c065b7..a4e742fd0 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -260,8 +260,8 @@ export class JSONSchemaForm extends LitElement {
         this.onUpdate(fullPath, value);
         const path = [...fullPath];
         const name = path.pop();
-        const resultParent = path.reduce((acc, key) => acc[key], this.results);
-        const resolvedParent = path.reduce((acc, key) => acc[key], this.resolved);
+        const resultParent = path.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.results);
+        const resolvedParent = path.reduce((acc, key) => acc[key] ?? (acc[key] = {}), this.resolved);
 
         if (!value) {
             delete resultParent[name];

From c0ac40afdc07fd29527eb8532b5d86fbfc2c35ff Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 12:34:34 -0700
Subject: [PATCH 40/71] Fix value derivation after merge

---
 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 9930c8393..fa0714343 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -419,7 +419,7 @@ export class JSONSchemaForm extends LitElement {
             info,
             parent,
             path: fullPath,
-            value: parent[name],
+            value,
             form: this,
             required: isRequired,
         });

From 9d13e49662fd3ac222c72117ce1053ecfbffd287 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 21:18:36 +0000
Subject: [PATCH 41/71] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/mirrors-prettier: v3.0.1 → v3.0.2](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.1...v3.0.2)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e572233f0..8387c3882 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
     -   id: black
         exclude: ^docs/
 -   repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.1"
+    rev: "v3.0.2"
     hooks:
     -   id: prettier
         types_or: [css, javascript]

From 37b71035f2e2e7362acf383cf770934cfcfe0f63 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 15:30:23 -0700
Subject: [PATCH 42/71] Create a new script to run tests on the executable

---
 package.json                    |  1 +
 pyflask/tests/conftest.py       | 61 ++++++++++++++++++++++++++-------
 pyflask/tests/test_neuroconv.py | 35 +++----------------
 pyflask/tests/utils.py          | 34 ++++++++++++++++++
 4 files changed, 88 insertions(+), 43 deletions(-)
 create mode 100644 pyflask/tests/utils.py

diff --git a/package.json b/package.json
index c3fb8587a..8c385c209 100644
--- a/package.json
+++ b/package.json
@@ -24,6 +24,7 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
+    "test:executable": "pytest pyflask/tests/ -s --executable",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",
diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index 0de8193d9..c98c1b2da 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -1,23 +1,60 @@
 import pytest
 import app as flask
+import sys
+import subprocess
+from pathlib import Path
+from multiprocessing import Process
+import multiprocessing as mp
+import os
+import time
 
+executable_flag = '--executable'
+use_executable = executable_flag in sys.argv
+is_windows = os.name == 'nt'
 
-@pytest.fixture()
-def app():
-    app = flask.app
-    app.config.update(
-        {
-            "TESTING": True,
-        }
-    )
+args = list(sys.argv)
 
-    yield app
+PORT = 1234
+exe_process = None
 
+def pytest_addoption(parser):
+    parser.addoption("--executable", action="store_true", help='Run the executable instead of the standard Flask app')
 
-@pytest.fixture()
-def client(app):
-    return app.test_client()
+@pytest.fixture(scope="session")
+def client(request):
+    exe_path = Path("build/flask/nwb-guide", 'nwb-guide.exe' if is_windows else 'nwb-guide' ) 
+    if (use_executable and exe_path.is_file()):
+
+        if (not is_windows):
+            mp.set_start_method('fork')
+
+        def runExecutable(port):
+            subprocess.run([exe_path, str(port)])
+
+        exe_process = Process(target=runExecutable, args=(PORT,))
+        exe_process.start()
+        time.sleep(1) # Give time to start
+
+        def stop():
+            exe_process.kill()
+
+        request.addfinalizer(stop)
+
+        return PORT
+
+
+    else: 
+        if (use_executable):
+            print("The executable could not be found. Using the standard Flask test server instead...")
+
+        app = flask.app
+        app.config.update(
+            {
+                "TESTING": True,
+            }
+        )
 
+        return app.test_client()
 
 @pytest.fixture()
 def runner(app):
diff --git a/pyflask/tests/test_neuroconv.py b/pyflask/tests/test_neuroconv.py
index 693b51e8d..2330aeeb9 100644
--- a/pyflask/tests/test_neuroconv.py
+++ b/pyflask/tests/test_neuroconv.py
@@ -1,37 +1,11 @@
 from jsonschema import validate
-
-
-def get_converter_output_schema(interfaces: dict):
-    return {
-        "type": "object",
-        "properties": {
-            "title": {"type": "string"},
-            "description": {"type": "string"},
-            "version": {"type": "string"},
-            "properties": {
-                "type": "object",
-                "properties": {
-                    interface: {
-                        "type": "object",
-                        "properties": {
-                            "properties": {"type": "object"},
-                            "required": {"type": "array"},
-                        },
-                    }
-                    for interface in interfaces.keys()
-                },
-                "additionalProperties": False,
-            },
-        },
-    }
-
+from utils import get, post, get_converter_output_schema
 
 # --------------------- Tests ---------------------
 # Accesses the dictionary of all interfaces and their metadata
 def test_get_all_interfaces(client):
-    all_interfaces = client.get("/neuroconv", follow_redirects=True).json
     validate(
-        all_interfaces,
+        get('neuroconv', client),
         schema={
             "type": "object",
             "patternProperties": {
@@ -51,12 +25,11 @@ def test_get_all_interfaces(client):
 # Test single interface schema request
 def test_single_schema_request(client):
     interfaces = {"myname": "SpikeGLXRecordingInterface"}
-    data = client.post("/neuroconv/schema", json=interfaces, follow_redirects=True).json
-    validate(data, schema=get_converter_output_schema(interfaces))
+    validate(post('neuroconv/schema', interfaces, client), schema=get_converter_output_schema(interfaces))
 
 
 # Uses the NWBConverter Class to combine multiple interfaces
 def test_multiple_schema_request(client):
     interfaces = {"myname": "SpikeGLXRecordingInterface", "myphyinterface": "PhySortingInterface"}
-    data = client.post("/neuroconv/schema", json=interfaces, follow_redirects=True).json
+    data = post("/neuroconv/schema", interfaces, client)
     validate(data, schema=get_converter_output_schema(interfaces))
diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
new file mode 100644
index 000000000..1cc91e511
--- /dev/null
+++ b/pyflask/tests/utils.py
@@ -0,0 +1,34 @@
+import requests
+
+def get(path, client):
+    return (requests.get(f'http://localhost:{client}/{path}')).json() if isinstance(client, int) else client.get(f"/{path}", follow_redirects=True).json
+
+
+def post(path, json, client):
+    return (requests.post(f'http://localhost:{client}/{path}', json=json)).json() if isinstance(client, int) else client.post(path, json=json, follow_redirects=True).json
+
+
+def get_converter_output_schema(interfaces: dict):
+    return {
+        "type": "object",
+        "properties": {
+            "title": {"type": "string"},
+            "description": {"type": "string"},
+            "version": {"type": "string"},
+            "properties": {
+                "type": "object",
+                "properties": {
+                    interface: {
+                        "type": "object",
+                        "properties": {
+                            "properties": {"type": "object"},
+                            "required": {"type": "array"},
+                        },
+                    }
+                    for interface in interfaces.keys()
+                },
+                "additionalProperties": False,
+            },
+        },
+    }
+

From 9eedfac70b8afef2b1819bfb5ba76bc1eda4eb2a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 22:31:12 +0000
Subject: [PATCH 43/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/tests/conftest.py       | 25 +++++++++++++------------
 pyflask/tests/test_neuroconv.py |  5 +++--
 pyflask/tests/utils.py          | 14 +++++++++++---
 3 files changed, 27 insertions(+), 17 deletions(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index c98c1b2da..be789d6d0 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -8,32 +8,33 @@
 import os
 import time
 
-executable_flag = '--executable'
+executable_flag = "--executable"
 use_executable = executable_flag in sys.argv
-is_windows = os.name == 'nt'
+is_windows = os.name == "nt"
 
 args = list(sys.argv)
 
 PORT = 1234
 exe_process = None
 
+
 def pytest_addoption(parser):
-    parser.addoption("--executable", action="store_true", help='Run the executable instead of the standard Flask app')
+    parser.addoption("--executable", action="store_true", help="Run the executable instead of the standard Flask app")
+
 
 @pytest.fixture(scope="session")
 def client(request):
-    exe_path = Path("build/flask/nwb-guide", 'nwb-guide.exe' if is_windows else 'nwb-guide' ) 
-    if (use_executable and exe_path.is_file()):
-
-        if (not is_windows):
-            mp.set_start_method('fork')
+    exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
+    if use_executable and exe_path.is_file():
+        if not is_windows:
+            mp.set_start_method("fork")
 
         def runExecutable(port):
             subprocess.run([exe_path, str(port)])
 
         exe_process = Process(target=runExecutable, args=(PORT,))
         exe_process.start()
-        time.sleep(1) # Give time to start
+        time.sleep(1)  # Give time to start
 
         def stop():
             exe_process.kill()
@@ -42,9 +43,8 @@ def stop():
 
         return PORT
 
-
-    else: 
-        if (use_executable):
+    else:
+        if use_executable:
             print("The executable could not be found. Using the standard Flask test server instead...")
 
         app = flask.app
@@ -56,6 +56,7 @@ def stop():
 
         return app.test_client()
 
+
 @pytest.fixture()
 def runner(app):
     return app.test_cli_runner()
diff --git a/pyflask/tests/test_neuroconv.py b/pyflask/tests/test_neuroconv.py
index 2330aeeb9..8c363c004 100644
--- a/pyflask/tests/test_neuroconv.py
+++ b/pyflask/tests/test_neuroconv.py
@@ -1,11 +1,12 @@
 from jsonschema import validate
 from utils import get, post, get_converter_output_schema
 
+
 # --------------------- Tests ---------------------
 # Accesses the dictionary of all interfaces and their metadata
 def test_get_all_interfaces(client):
     validate(
-        get('neuroconv', client),
+        get("neuroconv", client),
         schema={
             "type": "object",
             "patternProperties": {
@@ -25,7 +26,7 @@ def test_get_all_interfaces(client):
 # Test single interface schema request
 def test_single_schema_request(client):
     interfaces = {"myname": "SpikeGLXRecordingInterface"}
-    validate(post('neuroconv/schema', interfaces, client), schema=get_converter_output_schema(interfaces))
+    validate(post("neuroconv/schema", interfaces, client), schema=get_converter_output_schema(interfaces))
 
 
 # Uses the NWBConverter Class to combine multiple interfaces
diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index 1cc91e511..88dc185d2 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -1,11 +1,20 @@
 import requests
 
+
 def get(path, client):
-    return (requests.get(f'http://localhost:{client}/{path}')).json() if isinstance(client, int) else client.get(f"/{path}", follow_redirects=True).json
+    return (
+        (requests.get(f"http://localhost:{client}/{path}")).json()
+        if isinstance(client, int)
+        else client.get(f"/{path}", follow_redirects=True).json
+    )
 
 
 def post(path, json, client):
-    return (requests.post(f'http://localhost:{client}/{path}', json=json)).json() if isinstance(client, int) else client.post(path, json=json, follow_redirects=True).json
+    return (
+        (requests.post(f"http://localhost:{client}/{path}", json=json)).json()
+        if isinstance(client, int)
+        else client.post(path, json=json, follow_redirects=True).json
+    )
 
 
 def get_converter_output_schema(interfaces: dict):
@@ -31,4 +40,3 @@ def get_converter_output_schema(interfaces: dict):
             },
         },
     }
-

From f7df15c3429a291a15aa9525bc42422a11ed054c Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 15:32:19 -0700
Subject: [PATCH 44/71] Update pyflask-build-and-dist-tests.yml

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 15a222b25..7f0be94dc 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -95,3 +95,6 @@ jobs:
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js
+
+      - name: Run Python tests on distributed executable
+        run: npm run test:executable

From 3cb6ffdb49528e828e816676be2e5b976e7f85e4 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 15:59:32 -0700
Subject: [PATCH 45/71] Update package.json

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 8c385c209..9de2bec4b 100644
--- a/package.json
+++ b/package.json
@@ -15,9 +15,9 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-data jsonschema_specifications --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From cf1873b67488c818e77a01c591a3cb593eedd084 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 16:18:23 -0700
Subject: [PATCH 46/71] Update conftest.py

---
 pyflask/tests/conftest.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index be789d6d0..1246ea177 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -8,15 +8,14 @@
 import os
 import time
 
+PORT = 1234
 executable_flag = "--executable"
 use_executable = executable_flag in sys.argv
 is_windows = os.name == "nt"
 
-args = list(sys.argv)
-
-PORT = 1234
-exe_process = None
-
+exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
+def runExecutable(port):
+    subprocess.run([exe_path, str(port)])
 
 def pytest_addoption(parser):
     parser.addoption("--executable", action="store_true", help="Run the executable instead of the standard Flask app")
@@ -24,13 +23,10 @@ def pytest_addoption(parser):
 
 @pytest.fixture(scope="session")
 def client(request):
-    exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
     if use_executable and exe_path.is_file():
         if not is_windows:
             mp.set_start_method("fork")
 
-        def runExecutable(port):
-            subprocess.run([exe_path, str(port)])
 
         exe_process = Process(target=runExecutable, args=(PORT,))
         exe_process.start()

From cfad480fb6f8b493ca973d2aa3690c32f280b71c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Aug 2023 23:19:25 +0000
Subject: [PATCH 47/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/tests/conftest.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index 1246ea177..d4e3ab9cd 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -14,9 +14,12 @@
 is_windows = os.name == "nt"
 
 exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
+
+
 def runExecutable(port):
     subprocess.run([exe_path, str(port)])
 
+
 def pytest_addoption(parser):
     parser.addoption("--executable", action="store_true", help="Run the executable instead of the standard Flask app")
 
@@ -27,7 +30,6 @@ def client(request):
         if not is_windows:
             mp.set_start_method("fork")
 
-
         exe_process = Process(target=runExecutable, args=(PORT,))
         exe_process.start()
         time.sleep(1)  # Give time to start

From 78afc697cafdfbc0fac3de6551d65afbf2b7d977 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 21 Aug 2023 16:55:52 -0700
Subject: [PATCH 48/71] Fix windows build

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index c3fb8587a..60010f4f4 100644
--- a/package.json
+++ b/package.json
@@ -15,9 +15,9 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-data jsonschema_specifications --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From df2d930b5ce1c7f647ca08f8fd7899f58d5c6f1a Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 08:47:27 -0700
Subject: [PATCH 49/71] Create a test for valid parent creation

---
 .../src/stories/FileSystemSelector.js         |  2 +-
 src/renderer/src/stories/JSONSchemaForm.js    | 11 +++-
 src/renderer/src/stories/JSONSchemaInput.js   | 17 ++++-
 tests/metadata.test.ts                        | 63 ++++++++++++++++++-
 4 files changed, 88 insertions(+), 5 deletions(-)

diff --git a/src/renderer/src/stories/FileSystemSelector.js b/src/renderer/src/stories/FileSystemSelector.js
index cc0e2b4c3..06d397672 100644
--- a/src/renderer/src/stories/FileSystemSelector.js
+++ b/src/renderer/src/stories/FileSystemSelector.js
@@ -137,4 +137,4 @@ export class FilesystemSelector extends LitElement {
     }
 }
 
-customElements.get("nwb-filesystem-selector") || customElements.define("nwb-filesystem-selector", FilesystemSelector);
+customElements.get("filesystem-selector") || customElements.define("filesystem-selector", FilesystemSelector);
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 03164a463..37fee5830 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -250,6 +250,13 @@ export class JSONSchemaForm extends LitElement {
         return form.getForm(path.slice(1));
     };
 
+    getInput = (path) => {
+        if (typeof path === "string") path = path.split(".");
+        const container = this.shadowRoot.querySelector(`#${path.join('-')}`)
+        if (!container) return
+        return container.querySelector('jsonschema-input')
+    };
+
     #requirements = {};
 
     attributeChangedCallback(changedProperties, oldValue, newValue) {
@@ -426,7 +433,7 @@ export class JSONSchemaForm extends LitElement {
 
         interactiveInput.updated = () => {
             let input = interactiveInput.shadowRoot.querySelector(".schema-input");
-            if (!input) input = interactiveInput.shadowRoot.querySelector("nwb-filesystem-selector");
+            if (!input) input = interactiveInput.shadowRoot.querySelector("filesystem-selector");
 
             if (input) {
                 if (this.validateEmptyValues || (input.value ?? input.checked) !== "")
@@ -438,7 +445,7 @@ export class JSONSchemaForm extends LitElement {
 
         // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("nwb-jsonschema-input")).map(input => input.children)
         // const inputs = possibleInputs.filter(el => el instanceof HTMLElement);
-        // const fileInputs = Array.from(this.shadowRoot.querySelectorAll("nwb-filesystem-selector") ?? []);
+        // const fileInputs = Array.from(this.shadowRoot.querySelectorAll("filesystem-selector") ?? []);
         // const allInputs = [...inputs, ...fileInputs];
         // const filtered = filter ? allInputs.filter(filter) : allInputs;
         // filtered.forEach((input) => input.dispatchEvent(new Event("change")));
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index bb32865b2..6cbbfdc22 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -76,6 +76,21 @@ export class JSONSchemaInput extends LitElement {
     // onUpdate = () => {}
     // onValidate = () => {}
 
+    getElement = () => {
+        const el = this.shadowRoot.querySelector('input, select, textarea')
+        if (el) return el
+        return this.shadowRoot.querySelector('filesystem-selector')
+    }
+
+    updateData = (value) => {
+        const { path: fullPath } = this;
+        const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
+        const name = path.splice(-1)[0];
+        this.#triggerValidation(name, this.getElement(), path)
+        this.#updateData(fullPath, value)
+        return true
+    }
+
     #updateData = (path, value) => {
         this.onUpdate ? this.onUpdate(value) : this.form.updateData(path, value);
     };
@@ -268,4 +283,4 @@ export class JSONSchemaInput extends LitElement {
     }
 }
 
-customElements.get("nwb-jsonschema-input") || customElements.define("nwb-jsonschema-input", JSONSchemaInput);
+customElements.get("jsonschema-input") || customElements.define("jsonschema-input", JSONSchemaInput);
diff --git a/tests/metadata.test.ts b/tests/metadata.test.ts
index 55d5eb53c..f87c95870 100644
--- a/tests/metadata.test.ts
+++ b/tests/metadata.test.ts
@@ -126,7 +126,68 @@ test('inter-table updates are triggered', async () => {
         else cell.value = baseRow[i].value // Otherwise carry over info
     })
 
-    // Valalidate that the new structure is correct
+    // Validate that the new structure is correct
+    await form.validate().then(res => errors = false).catch(e => errors = true)
+    expect(errors).toBe(false) // Is valid
+})
+
+
+// TODO: Convert an integration
+test('changes are resolved correctly', async () => {
+
+    const results = {}
+
+    const schema = {
+        properties: {
+            v0: {
+                type: 'string'
+            },
+            l1: {
+                type: "object",
+                properties: {
+                    l2: {
+                        type: "object",
+                        properties: {
+                            v2: {
+                                type: 'string'
+                            }
+                        },
+                        required: ['v2']
+                    },
+                    v1: {
+                        type: 'string'
+                    }
+                },
+                required: ['v1']
+            }
+        },
+        required: ['v0']
+    }
+
+    // Create the form
+    const form = new JSONSchemaForm({
+        schema,
+        results
+    })
+
+    document.body.append(form)
+
+    await form.rendered
+
+    // Validate that the results are incorrect
+    let errors = false
+    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', 'v2'])
+
+    input1.updateData('test')
+    input2.updateData('test')
+    input3.updateData('test')
+
+    // Validate that the new structure is correct
     await form.validate().then(res => errors = false).catch(e => errors = true)
     expect(errors).toBe(false) // Is valid
 })

From 7c4b4e4db24ca70c364103bf8786a7289f7f71a6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 15:47:44 +0000
Subject: [PATCH 50/71] [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 +++---
 src/renderer/src/stories/JSONSchemaInput.js | 16 ++++++++--------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index 37fee5830..5f41f0b42 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -252,9 +252,9 @@ export class JSONSchemaForm extends LitElement {
 
     getInput = (path) => {
         if (typeof path === "string") path = path.split(".");
-        const container = this.shadowRoot.querySelector(`#${path.join('-')}`)
-        if (!container) return
-        return container.querySelector('jsonschema-input')
+        const container = this.shadowRoot.querySelector(`#${path.join("-")}`);
+        if (!container) return;
+        return container.querySelector("jsonschema-input");
     };
 
     #requirements = {};
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 6cbbfdc22..6b9575cb3 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -77,19 +77,19 @@ export class JSONSchemaInput extends LitElement {
     // onValidate = () => {}
 
     getElement = () => {
-        const el = this.shadowRoot.querySelector('input, select, textarea')
-        if (el) return el
-        return this.shadowRoot.querySelector('filesystem-selector')
-    }
+        const el = this.shadowRoot.querySelector("input, select, textarea");
+        if (el) return el;
+        return this.shadowRoot.querySelector("filesystem-selector");
+    };
 
     updateData = (value) => {
         const { path: fullPath } = this;
         const path = typeof fullPath === "string" ? fullPath.split("-") : [...fullPath];
         const name = path.splice(-1)[0];
-        this.#triggerValidation(name, this.getElement(), path)
-        this.#updateData(fullPath, value)
-        return true
-    }
+        this.#triggerValidation(name, this.getElement(), path);
+        this.#updateData(fullPath, value);
+        return true;
+    };
 
     #updateData = (path, value) => {
         this.onUpdate ? this.onUpdate(value) : this.form.updateData(path, value);

From 87da2831066ac55435cb8947022b90f5e7d68ed5 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 09:10:08 -0700
Subject: [PATCH 51/71] Attempt to catch exceptions from subprocess

---
 pyflask/tests/conftest.py | 25 ++++++++++++++++++++++++-
 pyflask/tests/utils.py    |  4 ++--
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index d4e3ab9cd..ca9008e5f 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -3,10 +3,10 @@
 import sys
 import subprocess
 from pathlib import Path
-from multiprocessing import Process
 import multiprocessing as mp
 import os
 import time
+import traceback
 
 PORT = 1234
 executable_flag = "--executable"
@@ -16,6 +16,29 @@
 exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
 
 
+class Process(mp.Process):
+    def __init__(self, *args, **kwargs):
+        mp.Process.__init__(self, *args, **kwargs)
+        self._pconn, self._cconn = mp.Pipe()
+        self._exception = None
+
+    def run(self):
+        try:
+            mp.Process.run(self)
+            self._cconn.send(None)
+        except Exception as e:
+            tb = traceback.format_exc()
+            self._cconn.send((e, tb))
+            raise e  # You can still rise this exception if you need to
+
+    @property
+    def exception(self):
+        if self._pconn.poll():
+            self._exception = self._pconn.recv()
+
+        return self._exception
+
+
 def runExecutable(port):
     subprocess.run([exe_path, str(port)])
 
diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index 88dc185d2..8ca714a03 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -3,7 +3,7 @@
 
 def get(path, client):
     return (
-        (requests.get(f"http://localhost:{client}/{path}")).json()
+        (requests.get(f"http://localhost:{client}/{path}", allow_redirects=True)).json()
         if isinstance(client, int)
         else client.get(f"/{path}", follow_redirects=True).json
     )
@@ -11,7 +11,7 @@ def get(path, client):
 
 def post(path, json, client):
     return (
-        (requests.post(f"http://localhost:{client}/{path}", json=json)).json()
+        (requests.post(f"http://localhost:{client}/{path}", json=json, allow_redirects=True)).json()
         if isinstance(client, int)
         else client.post(path, json=json, follow_redirects=True).json
     )

From 4f15f27276ed44549b06a3ef2e72c60740c2c7d0 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 09:29:42 -0700
Subject: [PATCH 52/71] Fix gain rendering

---
 generateInterfaceSchema.py                    |   2 +-
 .../generated/BiocamRecordingInterface.json   |   2 +-
 .../BlackrockRecordingInterface.json          |  38 +++++++
 .../generated/BlackrockSortingInterface.json  |  33 ++++++
 .../CellExplorerSortingInterface.json         |  29 +++++
 .../generated/IntanRecordingInterface.json    |   2 +-
 .../generated/KiloSortSortingInterface.json   |  33 ++++++
 .../generated/NeuroScopeLFPInterface.json     |   2 +-
 .../NeuroScopeRecordingInterface.json         |   2 +-
 .../generated/NeuroScopeSortingInterface.json |   2 +-
 .../OpenEphysRecordingInterface.json          |   2 +-
 .../json/generated/PhySortingInterface.json   |   2 +-
 .../json/generated/SpikeGLXNIDQInterface.json |   2 +-
 .../generated/SpikeGLXRecordingInterface.json |   2 +-
 src/renderer/src/stories/JSONSchemaForm.js    |  11 --
 src/renderer/src/stories/JSONSchemaInput.js   |  12 ++
 .../pages/guided-mode/SourceData.stories.js   | 106 +++++++++++-------
 .../guided-mode/data/GuidedSourceData.js      |   2 +
 18 files changed, 225 insertions(+), 59 deletions(-)
 create mode 100644 schemas/json/generated/BlackrockRecordingInterface.json
 create mode 100644 schemas/json/generated/BlackrockSortingInterface.json
 create mode 100644 schemas/json/generated/CellExplorerSortingInterface.json
 create mode 100644 schemas/json/generated/KiloSortSortingInterface.json

diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
index 00b27812b..ada04314e 100644
--- a/generateInterfaceSchema.py
+++ b/generateInterfaceSchema.py
@@ -36,7 +36,7 @@ class CustomNWBConverter(NWBConverter):
         lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});
 const {arr[0]}GlobalCopy = JSON.parse(JSON.stringify(globalState))
 {arr[0]}GlobalCopy.interfaces.interface = {arr[0]}
-{arr[0]}GlobalCopy.schema.source_data.properties.interface = {arr[0]}Schema
+{arr[0]}GlobalCopy.schema.source_data = {arr[0]}Schema
 {arr[0]}.args = {{ activePage, globalState: {arr[0]}GlobalCopy }};
 """,
         paths.items(),
diff --git a/schemas/json/generated/BiocamRecordingInterface.json b/schemas/json/generated/BiocamRecordingInterface.json
index 8d51c7b06..3265fe263 100644
--- a/schemas/json/generated/BiocamRecordingInterface.json
+++ b/schemas/json/generated/BiocamRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/BlackrockRecordingInterface.json b/schemas/json/generated/BlackrockRecordingInterface.json
new file mode 100644
index 000000000..32de2a224
--- /dev/null
+++ b/schemas/json/generated/BlackrockRecordingInterface.json
@@ -0,0 +1,38 @@
+{
+    "required": [],
+    "properties": {
+        "BlackrockRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string",
+                    "description": "Path to Blackrock file."
+                },
+                "nsx_override": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/BlackrockSortingInterface.json b/schemas/json/generated/BlackrockSortingInterface.json
new file mode 100644
index 000000000..1b0b34068
--- /dev/null
+++ b/schemas/json/generated/BlackrockSortingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "BlackrockSortingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string",
+                    "description": "Path to Blackrock file."
+                },
+                "sampling_frequency": {
+                    "type": "number"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": true
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/CellExplorerSortingInterface.json b/schemas/json/generated/CellExplorerSortingInterface.json
new file mode 100644
index 000000000..e2cc689b1
--- /dev/null
+++ b/schemas/json/generated/CellExplorerSortingInterface.json
@@ -0,0 +1,29 @@
+{
+    "required": [],
+    "properties": {
+        "CellExplorerSortingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/IntanRecordingInterface.json b/schemas/json/generated/IntanRecordingInterface.json
index 07904ada2..b75b39eda 100644
--- a/schemas/json/generated/IntanRecordingInterface.json
+++ b/schemas/json/generated/IntanRecordingInterface.json
@@ -34,4 +34,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/KiloSortSortingInterface.json b/schemas/json/generated/KiloSortSortingInterface.json
new file mode 100644
index 000000000..5ef66d490
--- /dev/null
+++ b/schemas/json/generated/KiloSortSortingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "KiloSortSortingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "keep_good_only": {
+                    "type": "boolean",
+                    "default": false
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeLFPInterface.json b/schemas/json/generated/NeuroScopeLFPInterface.json
index d42a885ab..3c6224cf0 100644
--- a/schemas/json/generated/NeuroScopeLFPInterface.json
+++ b/schemas/json/generated/NeuroScopeLFPInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeRecordingInterface.json b/schemas/json/generated/NeuroScopeRecordingInterface.json
index 3e95a33d0..2077b287a 100644
--- a/schemas/json/generated/NeuroScopeRecordingInterface.json
+++ b/schemas/json/generated/NeuroScopeRecordingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/NeuroScopeSortingInterface.json b/schemas/json/generated/NeuroScopeSortingInterface.json
index 680fcbce9..fe3d76fe6 100644
--- a/schemas/json/generated/NeuroScopeSortingInterface.json
+++ b/schemas/json/generated/NeuroScopeSortingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/OpenEphysRecordingInterface.json b/schemas/json/generated/OpenEphysRecordingInterface.json
index 9accfcf55..73d9c1dbb 100644
--- a/schemas/json/generated/OpenEphysRecordingInterface.json
+++ b/schemas/json/generated/OpenEphysRecordingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/PhySortingInterface.json b/schemas/json/generated/PhySortingInterface.json
index edcc2183d..182494ca2 100644
--- a/schemas/json/generated/PhySortingInterface.json
+++ b/schemas/json/generated/PhySortingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/SpikeGLXNIDQInterface.json b/schemas/json/generated/SpikeGLXNIDQInterface.json
index 14ad82eb8..8a38f1387 100644
--- a/schemas/json/generated/SpikeGLXNIDQInterface.json
+++ b/schemas/json/generated/SpikeGLXNIDQInterface.json
@@ -35,4 +35,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/schemas/json/generated/SpikeGLXRecordingInterface.json b/schemas/json/generated/SpikeGLXRecordingInterface.json
index 4b2034df8..603158605 100644
--- a/schemas/json/generated/SpikeGLXRecordingInterface.json
+++ b/schemas/json/generated/SpikeGLXRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
+}
\ No newline at end of file
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bca774e6d..091b50eb9 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -143,17 +143,6 @@ pre {
     padding-top: 4px;
     color: dimgray !important;
   }
-
-  input[type=number].hideStep::-webkit-outer-spin-button,
-  input[type=number].hideStep::-webkit-inner-spin-button {
-    -webkit-appearance: none;
-    margin: 0;
-  }
-
-    /* Firefox */
-    input[type=number].hideStep {
-        -moz-appearance: textfield;
-    }
 `;
 
 document.addEventListener("dragover", (e) => {
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index bb32865b2..d0c7e3cd8 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -58,6 +58,18 @@ export class JSONSchemaInput extends LitElement {
                 outline: 0;
                 box-shadow: var(--color-light-green) 0px 0px 0px 1px;
             }
+
+
+            input[type=number].hideStep::-webkit-outer-spin-button,
+            input[type=number].hideStep::-webkit-inner-spin-button {
+                -webkit-appearance: none;
+                margin: 0;
+            }
+
+            /* Firefox */
+            input[type=number].hideStep {
+                -moz-appearance: textfield;
+            }
         `;
     }
 
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
index cab7bae33..981b7df72 100644
--- a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -1,76 +1,106 @@
 import { globalState, PageTemplate } from "./storyStates";
-import SpikeGLXRecordingInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json";
-import SpikeGLXNIDQInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json";
-import PhySortingInterfaceSchema from "../../../../../../schemas/json/generated/PhySortingInterface.json";
-import NeuroScopeRecordingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json";
-import NeuroScopeLFPInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json";
-import NeuroScopeSortingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json";
-import BiocamRecordingInterfaceSchema from "../../../../../../schemas/json/generated/BiocamRecordingInterface.json";
-import IntanRecordingInterfaceSchema from "../../../../../../schemas/json/generated/IntanRecordingInterface.json";
-import OpenEphysRecordingInterfaceSchema from "../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json";
+import SpikeGLXRecordingInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json'
+import SpikeGLXNIDQInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json'
+import PhySortingInterfaceSchema from '../../../../../../schemas/json/generated/PhySortingInterface.json'
+import NeuroScopeRecordingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json'
+import NeuroScopeLFPInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json'
+import NeuroScopeSortingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json'
+import BiocamRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BiocamRecordingInterface.json'
+import IntanRecordingInterfaceSchema from '../../../../../../schemas/json/generated/IntanRecordingInterface.json'
+import OpenEphysRecordingInterfaceSchema from '../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json'
+import BlackrockRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BlackrockRecordingInterface.json'
+import BlackrockSortingInterfaceSchema from '../../../../../../schemas/json/generated/BlackrockSortingInterface.json'
+import CellExplorerSortingInterfaceSchema from '../../../../../../schemas/json/generated/CellExplorerSortingInterface.json'
+import KiloSortSortingInterfaceSchema from '../../../../../../schemas/json/generated/KiloSortSortingInterface.json'
 
 export default {
     title: "Pages/Guided Mode/Source Data",
     parameters: {
         chromatic: { disableSnapshot: false },
-    },
+    }
 };
 
-const activePage = "conversion/sourcedata";
+const activePage = "conversion/sourcedata"
+
 
 export const Example = PageTemplate.bind({});
 Example.args = { activePage, globalState };
 
 export const SpikeGLXRecordingInterface = PageTemplate.bind({});
-const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface;
-SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXRecordingInterfaceSchema;
+const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface
+SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data = SpikeGLXRecordingInterfaceSchema
 SpikeGLXRecordingInterface.args = { activePage, globalState: SpikeGLXRecordingInterfaceGlobalCopy };
 
 export const SpikeGLXNIDQInterface = PageTemplate.bind({});
-const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface;
-SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data.properties.interface = SpikeGLXNIDQInterfaceSchema;
+const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface
+SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data = SpikeGLXNIDQInterfaceSchema
 SpikeGLXNIDQInterface.args = { activePage, globalState: SpikeGLXNIDQInterfaceGlobalCopy };
 
 export const PhySortingInterface = PageTemplate.bind({});
-const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface;
-PhySortingInterfaceGlobalCopy.schema.source_data.properties.interface = PhySortingInterfaceSchema;
+const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface
+PhySortingInterfaceGlobalCopy.schema.source_data = PhySortingInterfaceSchema
 PhySortingInterface.args = { activePage, globalState: PhySortingInterfaceGlobalCopy };
 
 export const NeuroScopeRecordingInterface = PageTemplate.bind({});
-const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface;
-NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeRecordingInterfaceSchema;
+const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface
+NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data = NeuroScopeRecordingInterfaceSchema
 NeuroScopeRecordingInterface.args = { activePage, globalState: NeuroScopeRecordingInterfaceGlobalCopy };
 
 export const NeuroScopeLFPInterface = PageTemplate.bind({});
-const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface;
-NeuroScopeLFPInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeLFPInterfaceSchema;
+const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface
+NeuroScopeLFPInterfaceGlobalCopy.schema.source_data = NeuroScopeLFPInterfaceSchema
 NeuroScopeLFPInterface.args = { activePage, globalState: NeuroScopeLFPInterfaceGlobalCopy };
 
 export const NeuroScopeSortingInterface = PageTemplate.bind({});
-const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface;
-NeuroScopeSortingInterfaceGlobalCopy.schema.source_data.properties.interface = NeuroScopeSortingInterfaceSchema;
+const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface
+NeuroScopeSortingInterfaceGlobalCopy.schema.source_data = NeuroScopeSortingInterfaceSchema
 NeuroScopeSortingInterface.args = { activePage, globalState: NeuroScopeSortingInterfaceGlobalCopy };
 
 export const BiocamRecordingInterface = PageTemplate.bind({});
-const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface;
-BiocamRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = BiocamRecordingInterfaceSchema;
+const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface
+BiocamRecordingInterfaceGlobalCopy.schema.source_data = BiocamRecordingInterfaceSchema
 BiocamRecordingInterface.args = { activePage, globalState: BiocamRecordingInterfaceGlobalCopy };
 
 export const IntanRecordingInterface = PageTemplate.bind({});
-const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface;
-IntanRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = IntanRecordingInterfaceSchema;
+const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface
+IntanRecordingInterfaceGlobalCopy.schema.source_data = IntanRecordingInterfaceSchema
 IntanRecordingInterface.args = { activePage, globalState: IntanRecordingInterfaceGlobalCopy };
 
 export const OpenEphysRecordingInterface = PageTemplate.bind({});
-const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
-OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface;
-OpenEphysRecordingInterfaceGlobalCopy.schema.source_data.properties.interface = OpenEphysRecordingInterfaceSchema;
+const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface
+OpenEphysRecordingInterfaceGlobalCopy.schema.source_data = OpenEphysRecordingInterfaceSchema
 OpenEphysRecordingInterface.args = { activePage, globalState: OpenEphysRecordingInterfaceGlobalCopy };
+
+export const BlackrockRecordingInterface = PageTemplate.bind({});
+const BlackrockRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+BlackrockRecordingInterfaceGlobalCopy.interfaces.interface = BlackrockRecordingInterface
+BlackrockRecordingInterfaceGlobalCopy.schema.source_data = BlackrockRecordingInterfaceSchema
+BlackrockRecordingInterface.args = { activePage, globalState: BlackrockRecordingInterfaceGlobalCopy };
+
+export const BlackrockSortingInterface = PageTemplate.bind({});
+const BlackrockSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+BlackrockSortingInterfaceGlobalCopy.interfaces.interface = BlackrockSortingInterface
+BlackrockSortingInterfaceGlobalCopy.schema.source_data = BlackrockSortingInterfaceSchema
+BlackrockSortingInterface.args = { activePage, globalState: BlackrockSortingInterfaceGlobalCopy };
+
+export const CellExplorerSortingInterface = PageTemplate.bind({});
+const CellExplorerSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+CellExplorerSortingInterfaceGlobalCopy.interfaces.interface = CellExplorerSortingInterface
+CellExplorerSortingInterfaceGlobalCopy.schema.source_data = CellExplorerSortingInterfaceSchema
+CellExplorerSortingInterface.args = { activePage, globalState: CellExplorerSortingInterfaceGlobalCopy };
+
+export const KiloSortSortingInterface = PageTemplate.bind({});
+const KiloSortSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
+KiloSortSortingInterfaceGlobalCopy.interfaces.interface = KiloSortSortingInterface
+KiloSortSortingInterfaceGlobalCopy.schema.source_data = KiloSortSortingInterfaceSchema
+KiloSortSortingInterface.args = { activePage, globalState: KiloSortSortingInterfaceGlobalCopy };
+
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
index 5abb23272..76e793ea9 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -105,6 +105,8 @@ export class GuidedSourceDataPage extends ManagedPage {
 
         const schema = this.info.globalState.schema.source_data;
 
+        console.log('Show schema', schema)
+
         const form = new JSONSchemaForm({
             identifier: instanceId,
             mode: "accordion",

From 8ffb5755fece3b402a811208ce90e05b8e9c2398 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 16:30:58 +0000
Subject: [PATCH 53/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../generated/BiocamRecordingInterface.json   |   2 +-
 .../BlackrockRecordingInterface.json          |   2 +-
 .../generated/BlackrockSortingInterface.json  |   2 +-
 .../CellExplorerSortingInterface.json         |   2 +-
 .../generated/IntanRecordingInterface.json    |   2 +-
 .../generated/KiloSortSortingInterface.json   |   2 +-
 .../generated/NeuroScopeLFPInterface.json     |   2 +-
 .../NeuroScopeRecordingInterface.json         |   2 +-
 .../generated/NeuroScopeSortingInterface.json |   2 +-
 .../OpenEphysRecordingInterface.json          |   2 +-
 .../json/generated/PhySortingInterface.json   |   2 +-
 .../json/generated/SpikeGLXNIDQInterface.json |   2 +-
 .../generated/SpikeGLXRecordingInterface.json |   2 +-
 src/renderer/src/stories/JSONSchemaInput.js   |   7 +-
 .../pages/guided-mode/SourceData.stories.js   | 110 +++++++++---------
 .../guided-mode/data/GuidedSourceData.js      |   2 +-
 16 files changed, 71 insertions(+), 74 deletions(-)

diff --git a/schemas/json/generated/BiocamRecordingInterface.json b/schemas/json/generated/BiocamRecordingInterface.json
index 3265fe263..8d51c7b06 100644
--- a/schemas/json/generated/BiocamRecordingInterface.json
+++ b/schemas/json/generated/BiocamRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/BlackrockRecordingInterface.json b/schemas/json/generated/BlackrockRecordingInterface.json
index 32de2a224..25190ebf2 100644
--- a/schemas/json/generated/BlackrockRecordingInterface.json
+++ b/schemas/json/generated/BlackrockRecordingInterface.json
@@ -35,4 +35,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/BlackrockSortingInterface.json b/schemas/json/generated/BlackrockSortingInterface.json
index 1b0b34068..02661e794 100644
--- a/schemas/json/generated/BlackrockSortingInterface.json
+++ b/schemas/json/generated/BlackrockSortingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/CellExplorerSortingInterface.json b/schemas/json/generated/CellExplorerSortingInterface.json
index e2cc689b1..c51a65d4e 100644
--- a/schemas/json/generated/CellExplorerSortingInterface.json
+++ b/schemas/json/generated/CellExplorerSortingInterface.json
@@ -26,4 +26,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/IntanRecordingInterface.json b/schemas/json/generated/IntanRecordingInterface.json
index b75b39eda..07904ada2 100644
--- a/schemas/json/generated/IntanRecordingInterface.json
+++ b/schemas/json/generated/IntanRecordingInterface.json
@@ -34,4 +34,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/KiloSortSortingInterface.json b/schemas/json/generated/KiloSortSortingInterface.json
index 5ef66d490..a31d22b75 100644
--- a/schemas/json/generated/KiloSortSortingInterface.json
+++ b/schemas/json/generated/KiloSortSortingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeLFPInterface.json b/schemas/json/generated/NeuroScopeLFPInterface.json
index 3c6224cf0..d42a885ab 100644
--- a/schemas/json/generated/NeuroScopeLFPInterface.json
+++ b/schemas/json/generated/NeuroScopeLFPInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeRecordingInterface.json b/schemas/json/generated/NeuroScopeRecordingInterface.json
index 2077b287a..3e95a33d0 100644
--- a/schemas/json/generated/NeuroScopeRecordingInterface.json
+++ b/schemas/json/generated/NeuroScopeRecordingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/NeuroScopeSortingInterface.json b/schemas/json/generated/NeuroScopeSortingInterface.json
index fe3d76fe6..680fcbce9 100644
--- a/schemas/json/generated/NeuroScopeSortingInterface.json
+++ b/schemas/json/generated/NeuroScopeSortingInterface.json
@@ -37,4 +37,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/OpenEphysRecordingInterface.json b/schemas/json/generated/OpenEphysRecordingInterface.json
index 73d9c1dbb..9accfcf55 100644
--- a/schemas/json/generated/OpenEphysRecordingInterface.json
+++ b/schemas/json/generated/OpenEphysRecordingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/PhySortingInterface.json b/schemas/json/generated/PhySortingInterface.json
index 182494ca2..edcc2183d 100644
--- a/schemas/json/generated/PhySortingInterface.json
+++ b/schemas/json/generated/PhySortingInterface.json
@@ -29,4 +29,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/SpikeGLXNIDQInterface.json b/schemas/json/generated/SpikeGLXNIDQInterface.json
index 8a38f1387..14ad82eb8 100644
--- a/schemas/json/generated/SpikeGLXNIDQInterface.json
+++ b/schemas/json/generated/SpikeGLXNIDQInterface.json
@@ -35,4 +35,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/schemas/json/generated/SpikeGLXRecordingInterface.json b/schemas/json/generated/SpikeGLXRecordingInterface.json
index 603158605..4b2034df8 100644
--- a/schemas/json/generated/SpikeGLXRecordingInterface.json
+++ b/schemas/json/generated/SpikeGLXRecordingInterface.json
@@ -30,4 +30,4 @@
     "title": "Source data schema",
     "description": "Schema for the source data, files and directories",
     "version": "0.1.0"
-}
\ No newline at end of file
+}
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index e9bd65ed4..b67a0bc72 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -59,15 +59,14 @@ export class JSONSchemaInput extends LitElement {
                 box-shadow: var(--color-light-green) 0px 0px 0px 1px;
             }
 
-
-            input[type=number].hideStep::-webkit-outer-spin-button,
-            input[type=number].hideStep::-webkit-inner-spin-button {
+            input[type="number"].hideStep::-webkit-outer-spin-button,
+            input[type="number"].hideStep::-webkit-inner-spin-button {
                 -webkit-appearance: none;
                 margin: 0;
             }
 
             /* Firefox */
-            input[type=number].hideStep {
+            input[type="number"].hideStep {
                 -moz-appearance: textfield;
             }
         `;
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
index 981b7df72..d1a7ab8e1 100644
--- a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -1,106 +1,104 @@
 import { globalState, PageTemplate } from "./storyStates";
-import SpikeGLXRecordingInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json'
-import SpikeGLXNIDQInterfaceSchema from '../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json'
-import PhySortingInterfaceSchema from '../../../../../../schemas/json/generated/PhySortingInterface.json'
-import NeuroScopeRecordingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json'
-import NeuroScopeLFPInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json'
-import NeuroScopeSortingInterfaceSchema from '../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json'
-import BiocamRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BiocamRecordingInterface.json'
-import IntanRecordingInterfaceSchema from '../../../../../../schemas/json/generated/IntanRecordingInterface.json'
-import OpenEphysRecordingInterfaceSchema from '../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json'
-import BlackrockRecordingInterfaceSchema from '../../../../../../schemas/json/generated/BlackrockRecordingInterface.json'
-import BlackrockSortingInterfaceSchema from '../../../../../../schemas/json/generated/BlackrockSortingInterface.json'
-import CellExplorerSortingInterfaceSchema from '../../../../../../schemas/json/generated/CellExplorerSortingInterface.json'
-import KiloSortSortingInterfaceSchema from '../../../../../../schemas/json/generated/KiloSortSortingInterface.json'
+import SpikeGLXRecordingInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXRecordingInterface.json";
+import SpikeGLXNIDQInterfaceSchema from "../../../../../../schemas/json/generated/SpikeGLXNIDQInterface.json";
+import PhySortingInterfaceSchema from "../../../../../../schemas/json/generated/PhySortingInterface.json";
+import NeuroScopeRecordingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeRecordingInterface.json";
+import NeuroScopeLFPInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeLFPInterface.json";
+import NeuroScopeSortingInterfaceSchema from "../../../../../../schemas/json/generated/NeuroScopeSortingInterface.json";
+import BiocamRecordingInterfaceSchema from "../../../../../../schemas/json/generated/BiocamRecordingInterface.json";
+import IntanRecordingInterfaceSchema from "../../../../../../schemas/json/generated/IntanRecordingInterface.json";
+import OpenEphysRecordingInterfaceSchema from "../../../../../../schemas/json/generated/OpenEphysRecordingInterface.json";
+import BlackrockRecordingInterfaceSchema from "../../../../../../schemas/json/generated/BlackrockRecordingInterface.json";
+import BlackrockSortingInterfaceSchema from "../../../../../../schemas/json/generated/BlackrockSortingInterface.json";
+import CellExplorerSortingInterfaceSchema from "../../../../../../schemas/json/generated/CellExplorerSortingInterface.json";
+import KiloSortSortingInterfaceSchema from "../../../../../../schemas/json/generated/KiloSortSortingInterface.json";
 
 export default {
     title: "Pages/Guided Mode/Source Data",
     parameters: {
         chromatic: { disableSnapshot: false },
-    }
+    },
 };
 
-const activePage = "conversion/sourcedata"
-
+const activePage = "conversion/sourcedata";
 
 export const Example = PageTemplate.bind({});
 Example.args = { activePage, globalState };
 
 export const SpikeGLXRecordingInterface = PageTemplate.bind({});
-const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface
-SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data = SpikeGLXRecordingInterfaceSchema
+const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+SpikeGLXRecordingInterfaceGlobalCopy.interfaces.interface = SpikeGLXRecordingInterface;
+SpikeGLXRecordingInterfaceGlobalCopy.schema.source_data = SpikeGLXRecordingInterfaceSchema;
 SpikeGLXRecordingInterface.args = { activePage, globalState: SpikeGLXRecordingInterfaceGlobalCopy };
 
 export const SpikeGLXNIDQInterface = PageTemplate.bind({});
-const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface
-SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data = SpikeGLXNIDQInterfaceSchema
+const SpikeGLXNIDQInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+SpikeGLXNIDQInterfaceGlobalCopy.interfaces.interface = SpikeGLXNIDQInterface;
+SpikeGLXNIDQInterfaceGlobalCopy.schema.source_data = SpikeGLXNIDQInterfaceSchema;
 SpikeGLXNIDQInterface.args = { activePage, globalState: SpikeGLXNIDQInterfaceGlobalCopy };
 
 export const PhySortingInterface = PageTemplate.bind({});
-const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface
-PhySortingInterfaceGlobalCopy.schema.source_data = PhySortingInterfaceSchema
+const PhySortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+PhySortingInterfaceGlobalCopy.interfaces.interface = PhySortingInterface;
+PhySortingInterfaceGlobalCopy.schema.source_data = PhySortingInterfaceSchema;
 PhySortingInterface.args = { activePage, globalState: PhySortingInterfaceGlobalCopy };
 
 export const NeuroScopeRecordingInterface = PageTemplate.bind({});
-const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface
-NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data = NeuroScopeRecordingInterfaceSchema
+const NeuroScopeRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeRecordingInterfaceGlobalCopy.interfaces.interface = NeuroScopeRecordingInterface;
+NeuroScopeRecordingInterfaceGlobalCopy.schema.source_data = NeuroScopeRecordingInterfaceSchema;
 NeuroScopeRecordingInterface.args = { activePage, globalState: NeuroScopeRecordingInterfaceGlobalCopy };
 
 export const NeuroScopeLFPInterface = PageTemplate.bind({});
-const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface
-NeuroScopeLFPInterfaceGlobalCopy.schema.source_data = NeuroScopeLFPInterfaceSchema
+const NeuroScopeLFPInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeLFPInterfaceGlobalCopy.interfaces.interface = NeuroScopeLFPInterface;
+NeuroScopeLFPInterfaceGlobalCopy.schema.source_data = NeuroScopeLFPInterfaceSchema;
 NeuroScopeLFPInterface.args = { activePage, globalState: NeuroScopeLFPInterfaceGlobalCopy };
 
 export const NeuroScopeSortingInterface = PageTemplate.bind({});
-const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface
-NeuroScopeSortingInterfaceGlobalCopy.schema.source_data = NeuroScopeSortingInterfaceSchema
+const NeuroScopeSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+NeuroScopeSortingInterfaceGlobalCopy.interfaces.interface = NeuroScopeSortingInterface;
+NeuroScopeSortingInterfaceGlobalCopy.schema.source_data = NeuroScopeSortingInterfaceSchema;
 NeuroScopeSortingInterface.args = { activePage, globalState: NeuroScopeSortingInterfaceGlobalCopy };
 
 export const BiocamRecordingInterface = PageTemplate.bind({});
-const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface
-BiocamRecordingInterfaceGlobalCopy.schema.source_data = BiocamRecordingInterfaceSchema
+const BiocamRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BiocamRecordingInterfaceGlobalCopy.interfaces.interface = BiocamRecordingInterface;
+BiocamRecordingInterfaceGlobalCopy.schema.source_data = BiocamRecordingInterfaceSchema;
 BiocamRecordingInterface.args = { activePage, globalState: BiocamRecordingInterfaceGlobalCopy };
 
 export const IntanRecordingInterface = PageTemplate.bind({});
-const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface
-IntanRecordingInterfaceGlobalCopy.schema.source_data = IntanRecordingInterfaceSchema
+const IntanRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+IntanRecordingInterfaceGlobalCopy.interfaces.interface = IntanRecordingInterface;
+IntanRecordingInterfaceGlobalCopy.schema.source_data = IntanRecordingInterfaceSchema;
 IntanRecordingInterface.args = { activePage, globalState: IntanRecordingInterfaceGlobalCopy };
 
 export const OpenEphysRecordingInterface = PageTemplate.bind({});
-const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface
-OpenEphysRecordingInterfaceGlobalCopy.schema.source_data = OpenEphysRecordingInterfaceSchema
+const OpenEphysRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+OpenEphysRecordingInterfaceGlobalCopy.interfaces.interface = OpenEphysRecordingInterface;
+OpenEphysRecordingInterfaceGlobalCopy.schema.source_data = OpenEphysRecordingInterfaceSchema;
 OpenEphysRecordingInterface.args = { activePage, globalState: OpenEphysRecordingInterfaceGlobalCopy };
 
 export const BlackrockRecordingInterface = PageTemplate.bind({});
-const BlackrockRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-BlackrockRecordingInterfaceGlobalCopy.interfaces.interface = BlackrockRecordingInterface
-BlackrockRecordingInterfaceGlobalCopy.schema.source_data = BlackrockRecordingInterfaceSchema
+const BlackrockRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BlackrockRecordingInterfaceGlobalCopy.interfaces.interface = BlackrockRecordingInterface;
+BlackrockRecordingInterfaceGlobalCopy.schema.source_data = BlackrockRecordingInterfaceSchema;
 BlackrockRecordingInterface.args = { activePage, globalState: BlackrockRecordingInterfaceGlobalCopy };
 
 export const BlackrockSortingInterface = PageTemplate.bind({});
-const BlackrockSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-BlackrockSortingInterfaceGlobalCopy.interfaces.interface = BlackrockSortingInterface
-BlackrockSortingInterfaceGlobalCopy.schema.source_data = BlackrockSortingInterfaceSchema
+const BlackrockSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BlackrockSortingInterfaceGlobalCopy.interfaces.interface = BlackrockSortingInterface;
+BlackrockSortingInterfaceGlobalCopy.schema.source_data = BlackrockSortingInterfaceSchema;
 BlackrockSortingInterface.args = { activePage, globalState: BlackrockSortingInterfaceGlobalCopy };
 
 export const CellExplorerSortingInterface = PageTemplate.bind({});
-const CellExplorerSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-CellExplorerSortingInterfaceGlobalCopy.interfaces.interface = CellExplorerSortingInterface
-CellExplorerSortingInterfaceGlobalCopy.schema.source_data = CellExplorerSortingInterfaceSchema
+const CellExplorerSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+CellExplorerSortingInterfaceGlobalCopy.interfaces.interface = CellExplorerSortingInterface;
+CellExplorerSortingInterfaceGlobalCopy.schema.source_data = CellExplorerSortingInterfaceSchema;
 CellExplorerSortingInterface.args = { activePage, globalState: CellExplorerSortingInterfaceGlobalCopy };
 
 export const KiloSortSortingInterface = PageTemplate.bind({});
-const KiloSortSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
-KiloSortSortingInterfaceGlobalCopy.interfaces.interface = KiloSortSortingInterface
-KiloSortSortingInterfaceGlobalCopy.schema.source_data = KiloSortSortingInterfaceSchema
+const KiloSortSortingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+KiloSortSortingInterfaceGlobalCopy.interfaces.interface = KiloSortSortingInterface;
+KiloSortSortingInterfaceGlobalCopy.schema.source_data = KiloSortSortingInterfaceSchema;
 KiloSortSortingInterface.args = { activePage, globalState: KiloSortSortingInterfaceGlobalCopy };
-
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 76e793ea9..8cb6f7a40 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -105,7 +105,7 @@ export class GuidedSourceDataPage extends ManagedPage {
 
         const schema = this.info.globalState.schema.source_data;
 
-        console.log('Show schema', schema)
+        console.log("Show schema", schema);
 
         const form = new JSONSchemaForm({
             identifier: instanceId,

From 60c9315d5183a9d18a741ce428df37476e3e866a Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 22 Aug 2023 09:34:03 -0700
Subject: [PATCH 54/71] Update pyflask/tests/conftest.py

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 pyflask/tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index ca9008e5f..94f2a54e6 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -11,7 +11,7 @@
 PORT = 1234
 executable_flag = "--executable"
 use_executable = executable_flag in sys.argv
-is_windows = os.name == "nt"
+is_windows = sys.platform.startswith("win32")
 
 exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
 

From 4764d9b1b5157492ef899cf48ca5687a62ac18f0 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 09:55:20 -0700
Subject: [PATCH 55/71] Fill in the results for the second interface

---
 generateInterfaceSchema.py                    | 18 +++++++++++--
 .../pages/guided-mode/SourceData.stories.js   | 25 +++++++++++++++++--
 .../guided-mode/data/GuidedSourceData.js      |  3 +--
 3 files changed, 40 insertions(+), 6 deletions(-)

diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
index ada04314e..070a20fe0 100644
--- a/generateInterfaceSchema.py
+++ b/generateInterfaceSchema.py
@@ -43,6 +43,16 @@ class CustomNWBConverter(NWBConverter):
     )
 )
 
+
+allInterfaceCode = "\n".join(map(lambda arr: f"globalStateCopy.schema.source_data.properties.{arr[0]} = {arr[0]}Schema.properties.{arr[0]}", paths.items()))
+
+setDummyPathCode = f"""
+const results = globalStateCopy.results
+for (let sub in results){{
+    for (let ses in results[sub]) results[sub][ses].source_data = {{{list(paths.keys())[1]}: {{file_path: '/dummy/file/path'}}}}
+}}
+"""
+
 with open(sourceDataStoryPath, "w") as outfile:
     outfile.write(
         f"""import {{ globalState, PageTemplate }} from "./storyStates";
@@ -58,8 +68,12 @@ class CustomNWBConverter(NWBConverter):
 const activePage = "conversion/sourcedata"
 
 
-export const Example = PageTemplate.bind({{}});
-Example.args = {{ activePage, globalState }};
+const globalStateCopy = JSON.parse(JSON.stringify(globalState))
+{allInterfaceCode}
+{setDummyPathCode}
+
+export const All = PageTemplate.bind({{}});
+All.args = {{ activePage, globalState: globalStateCopy }};
 
 {storyCode}
 """
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
index 981b7df72..1b5c9d90a 100644
--- a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -23,8 +23,29 @@ export default {
 const activePage = "conversion/sourcedata"
 
 
-export const Example = PageTemplate.bind({});
-Example.args = { activePage, globalState };
+const globalStateCopy = JSON.parse(JSON.stringify(globalState))
+globalStateCopy.schema.source_data.properties.SpikeGLXRecordingInterface = SpikeGLXRecordingInterfaceSchema.properties.SpikeGLXRecordingInterface
+globalStateCopy.schema.source_data.properties.SpikeGLXNIDQInterface = SpikeGLXNIDQInterfaceSchema.properties.SpikeGLXNIDQInterface
+globalStateCopy.schema.source_data.properties.PhySortingInterface = PhySortingInterfaceSchema.properties.PhySortingInterface
+globalStateCopy.schema.source_data.properties.NeuroScopeRecordingInterface = NeuroScopeRecordingInterfaceSchema.properties.NeuroScopeRecordingInterface
+globalStateCopy.schema.source_data.properties.NeuroScopeLFPInterface = NeuroScopeLFPInterfaceSchema.properties.NeuroScopeLFPInterface
+globalStateCopy.schema.source_data.properties.NeuroScopeSortingInterface = NeuroScopeSortingInterfaceSchema.properties.NeuroScopeSortingInterface
+globalStateCopy.schema.source_data.properties.BiocamRecordingInterface = BiocamRecordingInterfaceSchema.properties.BiocamRecordingInterface
+globalStateCopy.schema.source_data.properties.IntanRecordingInterface = IntanRecordingInterfaceSchema.properties.IntanRecordingInterface
+globalStateCopy.schema.source_data.properties.OpenEphysRecordingInterface = OpenEphysRecordingInterfaceSchema.properties.OpenEphysRecordingInterface
+globalStateCopy.schema.source_data.properties.BlackrockRecordingInterface = BlackrockRecordingInterfaceSchema.properties.BlackrockRecordingInterface
+globalStateCopy.schema.source_data.properties.BlackrockSortingInterface = BlackrockSortingInterfaceSchema.properties.BlackrockSortingInterface
+globalStateCopy.schema.source_data.properties.CellExplorerSortingInterface = CellExplorerSortingInterfaceSchema.properties.CellExplorerSortingInterface
+globalStateCopy.schema.source_data.properties.KiloSortSortingInterface = KiloSortSortingInterfaceSchema.properties.KiloSortSortingInterface
+
+const results = globalStateCopy.results
+for (let sub in results){
+    for (let ses in results[sub]) results[sub][ses].source_data = {SpikeGLXNIDQInterface: {file_path: '/dummy/file/path'}}
+}
+
+
+export const All = PageTemplate.bind({});
+All.args = { activePage, globalState: globalStateCopy };
 
 export const SpikeGLXRecordingInterface = PageTemplate.bind({});
 const SpikeGLXRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState))
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 76e793ea9..5de73934d 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -104,8 +104,7 @@ export class GuidedSourceDataPage extends ManagedPage {
         const instanceId = `sub-${subject}/ses-${session}`;
 
         const schema = this.info.globalState.schema.source_data;
-
-        console.log('Show schema', schema)
+        console.log(info)
 
         const form = new JSONSchemaForm({
             identifier: instanceId,

From 88633642fb62d9615eebef18f7b707b274163534 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 10:00:01 -0700
Subject: [PATCH 56/71] Remove ecephys

---
 src/renderer/src/stories/pages/guided-mode/storyStates.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/storyStates.ts b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
index b25023ca8..9b7ce576b 100644
--- a/src/renderer/src/stories/pages/guided-mode/storyStates.ts
+++ b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
@@ -1,5 +1,5 @@
 import nwbBaseSchema from "../../../../../../schemas/base-metadata.schema";
-import exephysExampleSchema from "../../../../../../schemas/json/ecephys_metadata_schema_example.json";
+// import exephysExampleSchema from "../../../../../../schemas/json/ecephys_metadata_schema_example.json";
 
 import { dashboard } from "../../../pages.js";
 export const PageTemplate = (args = {}) => {
@@ -8,7 +8,7 @@ export const PageTemplate = (args = {}) => {
 };
 
 
-nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
+// nwbBaseSchema.properties.Ecephys = exephysExampleSchema;
 
 export const globalState = {
     project: {

From cfa237be2aa5a99627646a6adda10ad07799816f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 17:00:17 +0000
Subject: [PATCH 57/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 generateInterfaceSchema.py                    |  7 ++-
 .../pages/guided-mode/SourceData.stories.js   | 51 ++++++++++++-------
 2 files changed, 38 insertions(+), 20 deletions(-)

diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
index 070a20fe0..87a35155f 100644
--- a/generateInterfaceSchema.py
+++ b/generateInterfaceSchema.py
@@ -44,7 +44,12 @@ class CustomNWBConverter(NWBConverter):
 )
 
 
-allInterfaceCode = "\n".join(map(lambda arr: f"globalStateCopy.schema.source_data.properties.{arr[0]} = {arr[0]}Schema.properties.{arr[0]}", paths.items()))
+allInterfaceCode = "\n".join(
+    map(
+        lambda arr: f"globalStateCopy.schema.source_data.properties.{arr[0]} = {arr[0]}Schema.properties.{arr[0]}",
+        paths.items(),
+    )
+)
 
 setDummyPathCode = f"""
 const results = globalStateCopy.results
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
index 1cb01eceb..950a4ebf8 100644
--- a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -22,27 +22,40 @@ export default {
 
 const activePage = "conversion/sourcedata";
 
-const globalStateCopy = JSON.parse(JSON.stringify(globalState))
-globalStateCopy.schema.source_data.properties.SpikeGLXRecordingInterface = SpikeGLXRecordingInterfaceSchema.properties.SpikeGLXRecordingInterface
-globalStateCopy.schema.source_data.properties.SpikeGLXNIDQInterface = SpikeGLXNIDQInterfaceSchema.properties.SpikeGLXNIDQInterface
-globalStateCopy.schema.source_data.properties.PhySortingInterface = PhySortingInterfaceSchema.properties.PhySortingInterface
-globalStateCopy.schema.source_data.properties.NeuroScopeRecordingInterface = NeuroScopeRecordingInterfaceSchema.properties.NeuroScopeRecordingInterface
-globalStateCopy.schema.source_data.properties.NeuroScopeLFPInterface = NeuroScopeLFPInterfaceSchema.properties.NeuroScopeLFPInterface
-globalStateCopy.schema.source_data.properties.NeuroScopeSortingInterface = NeuroScopeSortingInterfaceSchema.properties.NeuroScopeSortingInterface
-globalStateCopy.schema.source_data.properties.BiocamRecordingInterface = BiocamRecordingInterfaceSchema.properties.BiocamRecordingInterface
-globalStateCopy.schema.source_data.properties.IntanRecordingInterface = IntanRecordingInterfaceSchema.properties.IntanRecordingInterface
-globalStateCopy.schema.source_data.properties.OpenEphysRecordingInterface = OpenEphysRecordingInterfaceSchema.properties.OpenEphysRecordingInterface
-globalStateCopy.schema.source_data.properties.BlackrockRecordingInterface = BlackrockRecordingInterfaceSchema.properties.BlackrockRecordingInterface
-globalStateCopy.schema.source_data.properties.BlackrockSortingInterface = BlackrockSortingInterfaceSchema.properties.BlackrockSortingInterface
-globalStateCopy.schema.source_data.properties.CellExplorerSortingInterface = CellExplorerSortingInterfaceSchema.properties.CellExplorerSortingInterface
-globalStateCopy.schema.source_data.properties.KiloSortSortingInterface = KiloSortSortingInterfaceSchema.properties.KiloSortSortingInterface
-
-const results = globalStateCopy.results
-for (let sub in results){
-    for (let ses in results[sub]) results[sub][ses].source_data = {SpikeGLXNIDQInterface: {file_path: '/dummy/file/path'}}
+const globalStateCopy = JSON.parse(JSON.stringify(globalState));
+globalStateCopy.schema.source_data.properties.SpikeGLXRecordingInterface =
+    SpikeGLXRecordingInterfaceSchema.properties.SpikeGLXRecordingInterface;
+globalStateCopy.schema.source_data.properties.SpikeGLXNIDQInterface =
+    SpikeGLXNIDQInterfaceSchema.properties.SpikeGLXNIDQInterface;
+globalStateCopy.schema.source_data.properties.PhySortingInterface =
+    PhySortingInterfaceSchema.properties.PhySortingInterface;
+globalStateCopy.schema.source_data.properties.NeuroScopeRecordingInterface =
+    NeuroScopeRecordingInterfaceSchema.properties.NeuroScopeRecordingInterface;
+globalStateCopy.schema.source_data.properties.NeuroScopeLFPInterface =
+    NeuroScopeLFPInterfaceSchema.properties.NeuroScopeLFPInterface;
+globalStateCopy.schema.source_data.properties.NeuroScopeSortingInterface =
+    NeuroScopeSortingInterfaceSchema.properties.NeuroScopeSortingInterface;
+globalStateCopy.schema.source_data.properties.BiocamRecordingInterface =
+    BiocamRecordingInterfaceSchema.properties.BiocamRecordingInterface;
+globalStateCopy.schema.source_data.properties.IntanRecordingInterface =
+    IntanRecordingInterfaceSchema.properties.IntanRecordingInterface;
+globalStateCopy.schema.source_data.properties.OpenEphysRecordingInterface =
+    OpenEphysRecordingInterfaceSchema.properties.OpenEphysRecordingInterface;
+globalStateCopy.schema.source_data.properties.BlackrockRecordingInterface =
+    BlackrockRecordingInterfaceSchema.properties.BlackrockRecordingInterface;
+globalStateCopy.schema.source_data.properties.BlackrockSortingInterface =
+    BlackrockSortingInterfaceSchema.properties.BlackrockSortingInterface;
+globalStateCopy.schema.source_data.properties.CellExplorerSortingInterface =
+    CellExplorerSortingInterfaceSchema.properties.CellExplorerSortingInterface;
+globalStateCopy.schema.source_data.properties.KiloSortSortingInterface =
+    KiloSortSortingInterfaceSchema.properties.KiloSortSortingInterface;
+
+const results = globalStateCopy.results;
+for (let sub in results) {
+    for (let ses in results[sub])
+        results[sub][ses].source_data = { SpikeGLXNIDQInterface: { file_path: "/dummy/file/path" } };
 }
 
-
 export const All = PageTemplate.bind({});
 All.args = { activePage, globalState: globalStateCopy };
 

From c9a3b561c1a8d8b67d5ed449cbed560ebcb26e55 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 10:10:49 -0700
Subject: [PATCH 58/71] Update locate data page

---
 .../pages/guided-mode/Locate.stories.js       | 21 +++++++++++++++++--
 .../stories/pages/guided-mode/storyStates.ts  |  4 ++++
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
index c8f3855c1..fc4ec4653 100644
--- a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
@@ -7,8 +7,25 @@ export default {
     },
 };
 
-export const Default = PageTemplate.bind({});
-Default.args = {
+export const Invalid = PageTemplate.bind({});
+Invalid.args = {
     activePage: "conversion/locate",
     globalState,
 };
+
+
+export const Valid = PageTemplate.bind({});
+
+const validGlobalState = structuredClone(globalState)
+validGlobalState.structure.results = {
+    interface: {
+        "base_directory": "/Users/garrettflynn/NWB_GUIDE/tutorial/Dataset",
+        "format_string_path": "{subject_id}/{subject_id}_{session_id}/{subject_id}_{session_id}_phy"
+      }
+}
+
+Valid.args = {
+    activePage: "conversion/locate",
+    globalState: validGlobalState,
+};
+
diff --git a/src/renderer/src/stories/pages/guided-mode/storyStates.ts b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
index 9b7ce576b..72257d829 100644
--- a/src/renderer/src/stories/pages/guided-mode/storyStates.ts
+++ b/src/renderer/src/stories/pages/guided-mode/storyStates.ts
@@ -20,6 +20,10 @@ export const globalState = {
             species: "Mus musculus",
         },
     },
+    structure: {
+        results: {},
+        state: true
+    },
     subjects: {
         subject_id: {},
     },

From bf0a8ac8a8dfdfddee829d5e83d4de2e24d54e33 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 17:11:29 +0000
Subject: [PATCH 59/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../src/stories/pages/guided-mode/Locate.stories.js  | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
index fc4ec4653..af533c5ec 100644
--- a/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
+++ b/src/renderer/src/stories/pages/guided-mode/Locate.stories.js
@@ -13,19 +13,17 @@ Invalid.args = {
     globalState,
 };
 
-
 export const Valid = PageTemplate.bind({});
 
-const validGlobalState = structuredClone(globalState)
+const validGlobalState = structuredClone(globalState);
 validGlobalState.structure.results = {
     interface: {
-        "base_directory": "/Users/garrettflynn/NWB_GUIDE/tutorial/Dataset",
-        "format_string_path": "{subject_id}/{subject_id}_{session_id}/{subject_id}_{session_id}_phy"
-      }
-}
+        base_directory: "/Users/garrettflynn/NWB_GUIDE/tutorial/Dataset",
+        format_string_path: "{subject_id}/{subject_id}_{session_id}/{subject_id}_{session_id}_phy",
+    },
+};
 
 Valid.args = {
     activePage: "conversion/locate",
     globalState: validGlobalState,
 };
-

From ef6df034823a9720fb2773e2b3dd60c210e4fa46 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 22 Aug 2023 13:21:02 -0400
Subject: [PATCH 60/71] trying to fix RTD

---
 docs/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 9db89e050..188bbc260 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -22,7 +22,7 @@
 templates_path = ["_templates"]
 master_doc = "index"
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-# html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_rtd_theme"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

From 1506dd71139cb5f3ba7774ea98064c6727d088b2 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 10:25:29 -0700
Subject: [PATCH 61/71] Raise status errors

---
 pyflask/tests/utils.py | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index 8ca714a03..a4c6709c0 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -2,19 +2,21 @@
 
 
 def get(path, client):
-    return (
-        (requests.get(f"http://localhost:{client}/{path}", allow_redirects=True)).json()
-        if isinstance(client, int)
-        else client.get(f"/{path}", follow_redirects=True).json
-    )
+    if isinstance(client,int):
+        r = (requests.get(f"http://localhost:{client}/{path}", allow_redirects=True))
+        r.raise_for_status()
+        return r.json()
+    else:
+        return client.get(f"/{path}", follow_redirects=True).json
 
 
 def post(path, json, client):
-    return (
-        (requests.post(f"http://localhost:{client}/{path}", json=json, allow_redirects=True)).json()
-        if isinstance(client, int)
-        else client.post(path, json=json, follow_redirects=True).json
-    )
+    if isinstance(client,int):
+        r = requests.post(f"http://localhost:{client}/{path}", json=json, allow_redirects=True)
+        r.raise_for_status()
+        return r.json()
+    else:
+        return client.post(path, json=json, follow_redirects=True).json
 
 
 def get_converter_output_schema(interfaces: dict):

From 274ef2a3871b4d522a4ddff9d8984ef70c8233c5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 17:25:46 +0000
Subject: [PATCH 62/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/tests/utils.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index a4c6709c0..bcb346ffc 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -2,8 +2,8 @@
 
 
 def get(path, client):
-    if isinstance(client,int):
-        r = (requests.get(f"http://localhost:{client}/{path}", allow_redirects=True))
+    if isinstance(client, int):
+        r = requests.get(f"http://localhost:{client}/{path}", allow_redirects=True)
         r.raise_for_status()
         return r.json()
     else:
@@ -11,7 +11,7 @@ def get(path, client):
 
 
 def post(path, json, client):
-    if isinstance(client,int):
+    if isinstance(client, int):
         r = requests.post(f"http://localhost:{client}/{path}", json=json, allow_redirects=True)
         r.raise_for_status()
         return r.json()

From d922ca27e34e9b589b9fe9d52ab6fbb57c61506e Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 10:39:54 -0700
Subject: [PATCH 63/71] Improved test and pyinstaller test configurations

---
 .../pyflask-build-and-dist-tests.yml          | 15 ++---
 package.json                                  |  2 +-
 pyflask/tests/conftest.py                     | 66 ++-----------------
 pyflask/tests/utils.py                        |  8 +--
 tests/testPyinstallerExecutable.js            | 20 ++++--
 5 files changed, 29 insertions(+), 82 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 7f0be94dc..b4db951db 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -84,14 +84,13 @@ jobs:
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}
 
-      # encountering parsing issue for second arg
-      #- if: matrix.os == 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide.exe
-
-      #- if: matrix.os != 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide
+      - if: matrix.os == 'windows-latest'
+       name: Run test on build executable
+       run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
+
+      - if: matrix.os != 'windows-latest'
+       name: Run test on build executable
+       run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js
diff --git a/package.json b/package.json
index 9de2bec4b..892e7af8a 100644
--- a/package.json
+++ b/package.json
@@ -24,7 +24,7 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
-    "test:executable": "pytest pyflask/tests/ -s --executable",
+    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 1234 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:1234\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",
diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index 94f2a54e6..2a92b80b9 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -1,73 +1,15 @@
 import pytest
 import app as flask
-import sys
-import subprocess
-from pathlib import Path
-import multiprocessing as mp
-import os
-import time
-import traceback
-
-PORT = 1234
-executable_flag = "--executable"
-use_executable = executable_flag in sys.argv
-is_windows = sys.platform.startswith("win32")
-
-exe_path = Path("build/flask/nwb-guide", "nwb-guide.exe" if is_windows else "nwb-guide")
-
-
-class Process(mp.Process):
-    def __init__(self, *args, **kwargs):
-        mp.Process.__init__(self, *args, **kwargs)
-        self._pconn, self._cconn = mp.Pipe()
-        self._exception = None
-
-    def run(self):
-        try:
-            mp.Process.run(self)
-            self._cconn.send(None)
-        except Exception as e:
-            tb = traceback.format_exc()
-            self._cconn.send((e, tb))
-            raise e  # You can still rise this exception if you need to
-
-    @property
-    def exception(self):
-        if self._pconn.poll():
-            self._exception = self._pconn.recv()
-
-        return self._exception
-
-
-def runExecutable(port):
-    subprocess.run([exe_path, str(port)])
-
 
 def pytest_addoption(parser):
-    parser.addoption("--executable", action="store_true", help="Run the executable instead of the standard Flask app")
-
+    parser.addoption("--target", action="store", help="Run the executable instead of the standard Flask app")
 
 @pytest.fixture(scope="session")
 def client(request):
-    if use_executable and exe_path.is_file():
-        if not is_windows:
-            mp.set_start_method("fork")
-
-        exe_process = Process(target=runExecutable, args=(PORT,))
-        exe_process.start()
-        time.sleep(1)  # Give time to start
-
-        def stop():
-            exe_process.kill()
-
-        request.addfinalizer(stop)
-
-        return PORT
-
+    target = request.config.getoption("--target")
+    if target:
+        return target
     else:
-        if use_executable:
-            print("The executable could not be found. Using the standard Flask test server instead...")
-
         app = flask.app
         app.config.update(
             {
diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index a4c6709c0..ee33affc9 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -2,8 +2,8 @@
 
 
 def get(path, client):
-    if isinstance(client,int):
-        r = (requests.get(f"http://localhost:{client}/{path}", allow_redirects=True))
+    if isinstance(client, str):
+        r = (requests.get(f"{client}/{path}", allow_redirects=True))
         r.raise_for_status()
         return r.json()
     else:
@@ -11,8 +11,8 @@ def get(path, client):
 
 
 def post(path, json, client):
-    if isinstance(client,int):
-        r = requests.post(f"http://localhost:{client}/{path}", json=json, allow_redirects=True)
+    if isinstance(client, str):
+        r = requests.post(f"{client}/{path}", json=json, allow_redirects=True)
         r.raise_for_status()
         return r.json()
     else:
diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index 3ee379952..3d71a88c9 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -2,14 +2,20 @@ const path = require("path");
 const child_process = require("child_process");
 const fs = require("fs");
 
-const port = 1234;
-const script =
-    process.argv[2] ||
-    path.resolve(__dirname, `../build/flask/nwb-guide/nwb-guide${process.platform === "win32" ? ".exe" : ""}`);
+const cmds = {
+    port: 1234,
+    script: path.resolve(__dirname, `../build/flask/nwb-guide/nwb-guide${process.platform === "win32" ? ".exe" : ""}`)
+}
+
+process.argv.forEach((v, i) => {
+    if (v === '--script') cmds.script = process.argv[i + 1]
+    if (v === '--port') cmds.port = parseInt(process.argv[i + 1])
+    if (v === '--forever') cmds.forever = true
+})
 
-console.log("Found file", fs.existsSync(script));
+console.log("Found file", fs.existsSync(cmds.script));
 
-const proc2 = child_process.spawn(`${script}`, [port + 1]);
+const proc2 = child_process.spawn(`${cmds.script}`, [cmds.port]);
 handleProcess(proc2, "spawn");
 
 let now = Date.now();
@@ -30,7 +36,7 @@ function handleProcess(proc, id = "process") {
 
         proc.stdout.on("data", function (data) {
             console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
-            process.exit();
+            if (!cmds.forever) process.exit();
         });
 
         const error = () => () => {

From 45458c38072424d117260b8ab0e3714d88c5236c Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 10:43:09 -0700
Subject: [PATCH 64/71] Update pyflask-build-and-dist-tests.yml

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index b4db951db..5e44c3c20 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -84,13 +84,13 @@ jobs:
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}
 
-      - if: matrix.os == 'windows-latest'
-       name: Run test on build executable
-       run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
+      #- if: matrix.os == 'windows-latest'
+      #  name: Run test on build executable
+      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
 
-      - if: matrix.os != 'windows-latest'
-       name: Run test on build executable
-       run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
+      #- if: matrix.os != 'windows-latest'
+      #  name: Run test on build executable
+      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js

From 2ec3388e8a93eb0b421c76d786a1604660f0ee76 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 17:43:25 +0000
Subject: [PATCH 65/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyflask/tests/conftest.py          |  2 ++
 pyflask/tests/utils.py             |  2 +-
 tests/testPyinstallerExecutable.js | 12 ++++++------
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/pyflask/tests/conftest.py b/pyflask/tests/conftest.py
index 2a92b80b9..4ecf00e8b 100644
--- a/pyflask/tests/conftest.py
+++ b/pyflask/tests/conftest.py
@@ -1,9 +1,11 @@
 import pytest
 import app as flask
 
+
 def pytest_addoption(parser):
     parser.addoption("--target", action="store", help="Run the executable instead of the standard Flask app")
 
+
 @pytest.fixture(scope="session")
 def client(request):
     target = request.config.getoption("--target")
diff --git a/pyflask/tests/utils.py b/pyflask/tests/utils.py
index ee33affc9..5e74d9eac 100644
--- a/pyflask/tests/utils.py
+++ b/pyflask/tests/utils.py
@@ -3,7 +3,7 @@
 
 def get(path, client):
     if isinstance(client, str):
-        r = (requests.get(f"{client}/{path}", allow_redirects=True))
+        r = requests.get(f"{client}/{path}", allow_redirects=True)
         r.raise_for_status()
         return r.json()
     else:
diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index 3d71a88c9..4611dba7a 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -4,14 +4,14 @@ const fs = require("fs");
 
 const cmds = {
     port: 1234,
-    script: path.resolve(__dirname, `../build/flask/nwb-guide/nwb-guide${process.platform === "win32" ? ".exe" : ""}`)
-}
+    script: path.resolve(__dirname, `../build/flask/nwb-guide/nwb-guide${process.platform === "win32" ? ".exe" : ""}`),
+};
 
 process.argv.forEach((v, i) => {
-    if (v === '--script') cmds.script = process.argv[i + 1]
-    if (v === '--port') cmds.port = parseInt(process.argv[i + 1])
-    if (v === '--forever') cmds.forever = true
-})
+    if (v === "--script") cmds.script = process.argv[i + 1];
+    if (v === "--port") cmds.port = parseInt(process.argv[i + 1]);
+    if (v === "--forever") cmds.forever = true;
+});
 
 console.log("Found file", fs.existsSync(cmds.script));
 

From 938116e8c830cb2be66556aa483e3216f618acd7 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 11:15:54 -0700
Subject: [PATCH 66/71] Use instance manager to show stub preview through
 Neurosift

---
 src/renderer/src/stories/InstanceManager.js   |  4 +++
 src/renderer/src/stories/JSONSchemaForm.js    |  4 +--
 src/renderer/src/stories/Neurosift.js         |  2 +-
 src/renderer/src/stories/pages/Page.js        |  5 +--
 .../pages/guided-mode/data/GuidedMetadata.js  | 10 ++++--
 .../guided-mode/options/GuidedStubPreview.js  | 31 +++++++++++++++++--
 .../guided-mode/results/GuidedResults.js      |  2 +-
 7 files changed, 48 insertions(+), 10 deletions(-)

diff --git a/src/renderer/src/stories/InstanceManager.js b/src/renderer/src/stories/InstanceManager.js
index c54a5f6f9..328882416 100644
--- a/src/renderer/src/stories/InstanceManager.js
+++ b/src/renderer/src/stories/InstanceManager.js
@@ -75,6 +75,10 @@ export class InstanceManager extends LitElement {
                 height: 100%;
             }
 
+            #instance-display > div {
+                height: 100%;
+            }
+
             #content {
                 overflow: hidden;
                 display: flex;
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index d4b68320c..4ecd4447f 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -368,7 +368,7 @@ export class JSONSchemaForm extends LitElement {
         const name = path.pop();
         const element = this.shadowRoot
             .querySelector(`#${fullPath.join("-")}`)
-            .querySelector("nwb-jsonschema-input")
+            .querySelector("jsonschema-input")
             .shadowRoot.querySelector(".guided--input");
         const isValid = await this.triggerValidation(name, element, path, false);
         if (!isValid) return true;
@@ -435,7 +435,7 @@ export class JSONSchemaForm extends LitElement {
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
 
-        // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("nwb-jsonschema-input")).map(input => input.children)
+        // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("jsonschema-input")).map(input => input.children)
         // const inputs = possibleInputs.filter(el => el instanceof HTMLElement);
         // const fileInputs = Array.from(this.shadowRoot.querySelectorAll("filesystem-selector") ?? []);
         // const allInputs = [...inputs, ...fileInputs];
diff --git a/src/renderer/src/stories/Neurosift.js b/src/renderer/src/stories/Neurosift.js
index 7fb3e9029..c505beba8 100644
--- a/src/renderer/src/stories/Neurosift.js
+++ b/src/renderer/src/stories/Neurosift.js
@@ -23,7 +23,7 @@ export class Neurosift extends LitElement {
     }
 
     render() {
-        return html`<iframe src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"></iframe>`;
+        return html`<iframe class="iframe-placeholder" src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"></iframe>`;
     }
 }
 
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 1e7515a02..2c6a97cbf 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -126,7 +126,7 @@ export class Page extends LitElement {
         else if (typeof original === "string") toRun = toRun.filter(({ subject }) => subject === original);
         else if (typeof original === "function") toRun = toRun.filter(original);
 
-        let results = [];
+        const results = {};
 
         const popup = await openProgressSwal({ title: `Running conversion`, ...options });
 
@@ -182,7 +182,8 @@ export class Page extends LitElement {
                 elements.progress.value = progressInfo;
             }
 
-            results.push(result);
+            const subRef = results[subject] ?? (results[subject] = {})
+            subRef[session] = result
         }
 
         popup.close();
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 e9982db5d..5aa26bf80 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -184,7 +184,8 @@ export class GuidedMetadataPage extends ManagedPage {
                     onClick: async (key, el) => {
                         const { subject, session } = getInfoFromId(key);
 
-                        const [{ file, html }] = await this.runConversions(
+
+                        const results = await this.runConversions(
                             { stub_test: true },
                             [
                                 {
@@ -199,6 +200,11 @@ export class GuidedMetadataPage extends ManagedPage {
                             throw e;
                         });
 
+                        const firstSubject = Object.values(results)[0]
+                        const file = Object.values(firstSubject)[0] // Get the information from the first subject
+
+                        console.log(firstSubject, file, results)
+
                         const modal = new Modal({
                             header: `Conversion Preview: ${key}`,
                             open: true,
@@ -207,7 +213,7 @@ export class GuidedMetadataPage extends ManagedPage {
                             height: "100%",
                         });
 
-                        modal.append(new Neurosift({ url: getURLFromFilePath(file, project.name) }));
+                        modal.append(new Neurosift({ url: getURLFromFilePath(file, this.info.globalState.project.name) }));
                         document.body.append(modal);
                     },
                 },
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index 7ae926f19..111bcd183 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -6,6 +6,8 @@ import folderOpenSVG from "../../../assets/folder_open.svg?raw";
 
 import { electron } from "../../../../electron/index.js";
 import { Neurosift, getURLFromFilePath } from "../../../Neurosift.js";
+import { InstanceManager } from "../../../InstanceManager.js";
+
 const { shell } = electron;
 
 export class GuidedStubPreviewPage extends Page {
@@ -36,11 +38,36 @@ export class GuidedStubPreviewPage extends Page {
         },
     };
 
-    render() {
+
+    createInstance = ({ subject, session, info }) => {
+
         const { project, stubs } = this.info.globalState;
 
+        return {
+            subject,
+            session,
+            display: new Neurosift({ url: getURLFromFilePath(stubs[subject][session], project.name) })
+        }
+    }
+
+    render() {
+        const { stubs } = this.info.globalState;
+
+        const _instances = this.mapSessions(this.createInstance);
+
+        const instances = _instances.reduce((acc, { subject, session, display }) => {
+            if (!acc[`sub-${subject}`]) acc[`sub-${subject}`] = {};
+            acc[`sub-${subject}`][`ses-${session}`] = display;
+            return acc
+        }, {});
+
+
         return stubs
-            ? new Neurosift({ url: getURLFromFilePath(stubs[0], project.name) })
+            ? this.manager = new InstanceManager({
+                header: "Sessions",
+                instanceType: "Session",
+                instances,
+            })
             : html`<p style="text-align: center;">Your conversion preview failed. Please try again.</p>`;
     }
 }
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 e57aae259..50d300d99 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -92,7 +92,7 @@ export class GuidedResultsPage extends Page {
                     <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
                     <hr />
                     <ol>
-                        ${results.map((o) => html`<li>${o.file}</li>`)}
+                        ${Object.values(results).flat(v => Object.values(v)).map((o) => html`<li>${o.file}</li>`)}
                     </ol>
                 </div>
             </div>

From 739ff13bde634e1b589382494219f288dac3f666 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 18:17:09 +0000
Subject: [PATCH 67/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/Neurosift.js         |  5 ++++-
 src/renderer/src/stories/pages/Page.js        |  4 ++--
 .../pages/guided-mode/data/GuidedMetadata.js  | 11 +++++-----
 .../guided-mode/options/GuidedStubPreview.js  | 21 ++++++++-----------
 .../guided-mode/results/GuidedResults.js      |  4 +++-
 5 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/src/renderer/src/stories/Neurosift.js b/src/renderer/src/stories/Neurosift.js
index c505beba8..1080a04e9 100644
--- a/src/renderer/src/stories/Neurosift.js
+++ b/src/renderer/src/stories/Neurosift.js
@@ -23,7 +23,10 @@ export class Neurosift extends LitElement {
     }
 
     render() {
-        return html`<iframe class="iframe-placeholder" src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"></iframe>`;
+        return html`<iframe
+            class="iframe-placeholder"
+            src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"
+        ></iframe>`;
     }
 }
 
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index 2c6a97cbf..d5376f502 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -182,8 +182,8 @@ export class Page extends LitElement {
                 elements.progress.value = progressInfo;
             }
 
-            const subRef = results[subject] ?? (results[subject] = {})
-            subRef[session] = result
+            const subRef = results[subject] ?? (results[subject] = {});
+            subRef[session] = result;
         }
 
         popup.close();
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 5aa26bf80..4cda34c94 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -184,7 +184,6 @@ export class GuidedMetadataPage extends ManagedPage {
                     onClick: async (key, el) => {
                         const { subject, session } = getInfoFromId(key);
 
-
                         const results = await this.runConversions(
                             { stub_test: true },
                             [
@@ -200,10 +199,10 @@ export class GuidedMetadataPage extends ManagedPage {
                             throw e;
                         });
 
-                        const firstSubject = Object.values(results)[0]
-                        const file = Object.values(firstSubject)[0] // Get the information from the first subject
+                        const firstSubject = Object.values(results)[0];
+                        const file = Object.values(firstSubject)[0]; // Get the information from the first subject
 
-                        console.log(firstSubject, file, results)
+                        console.log(firstSubject, file, results);
 
                         const modal = new Modal({
                             header: `Conversion Preview: ${key}`,
@@ -213,7 +212,9 @@ export class GuidedMetadataPage extends ManagedPage {
                             height: "100%",
                         });
 
-                        modal.append(new Neurosift({ url: getURLFromFilePath(file, this.info.globalState.project.name) }));
+                        modal.append(
+                            new Neurosift({ url: getURLFromFilePath(file, this.info.globalState.project.name) })
+                        );
                         document.body.append(modal);
                     },
                 },
diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
index 111bcd183..55780c2d2 100644
--- a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
+++ b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -38,17 +38,15 @@ export class GuidedStubPreviewPage extends Page {
         },
     };
 
-
     createInstance = ({ subject, session, info }) => {
-
         const { project, stubs } = this.info.globalState;
 
         return {
             subject,
             session,
-            display: new Neurosift({ url: getURLFromFilePath(stubs[subject][session], project.name) })
-        }
-    }
+            display: new Neurosift({ url: getURLFromFilePath(stubs[subject][session], project.name) }),
+        };
+    };
 
     render() {
         const { stubs } = this.info.globalState;
@@ -58,16 +56,15 @@ export class GuidedStubPreviewPage extends Page {
         const instances = _instances.reduce((acc, { subject, session, display }) => {
             if (!acc[`sub-${subject}`]) acc[`sub-${subject}`] = {};
             acc[`sub-${subject}`][`ses-${session}`] = display;
-            return acc
+            return acc;
         }, {});
 
-
         return stubs
-            ? this.manager = new InstanceManager({
-                header: "Sessions",
-                instanceType: "Session",
-                instances,
-            })
+            ? (this.manager = new InstanceManager({
+                  header: "Sessions",
+                  instanceType: "Session",
+                  instances,
+              }))
             : html`<p style="text-align: center;">Your conversion preview failed. Please try again.</p>`;
     }
 }
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 50d300d99..f0a97aed5 100644
--- a/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
+++ b/src/renderer/src/stories/pages/guided-mode/results/GuidedResults.js
@@ -92,7 +92,9 @@ export class GuidedResultsPage extends Page {
                     <h3 style="padding: 0;">Files Uploaded with this Conversion</h3>
                     <hr />
                     <ol>
-                        ${Object.values(results).flat(v => Object.values(v)).map((o) => html`<li>${o.file}</li>`)}
+                        ${Object.values(results)
+                            .flat((v) => Object.values(v))
+                            .map((o) => html`<li>${o.file}</li>`)}
                     </ol>
                 </div>
             </div>

From ad8fd63869e9e3c9d7cc3cc78d6f35e7200826e5 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Tue, 22 Aug 2023 11:21:31 -0700
Subject: [PATCH 68/71] Update pyflask-build-and-dist-tests.yml

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 5e44c3c20..900e93556 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -80,6 +80,8 @@ jobs:
         uses: actions/setup-node@v3
         with:
           node-version: "18"
+          
+      - run: npm ci
 
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}

From aed6cc1bf8b6418e734ed6736d8659a7c7c9c871 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 18:21:49 +0000
Subject: [PATCH 69/71] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 900e93556..e2e983010 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -80,7 +80,7 @@ jobs:
         uses: actions/setup-node@v3
         with:
           node-version: "18"
-          
+
       - run: npm ci
 
       - name: Build PyFlask distribution

From b0952703f09245c24e5b262a2c750f5edf85b736 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 11:32:24 -0700
Subject: [PATCH 70/71] Update package.json

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

diff --git a/package.json b/package.json
index 892e7af8a..bad2cfe3e 100644
--- a/package.json
+++ b/package.json
@@ -24,7 +24,7 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
-    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 1234 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:1234\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",

From a3dee5cd2ba85c10e761a7be8f6fa5fd40dbcf42 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 22 Aug 2023 12:16:25 -0700
Subject: [PATCH 71/71] Update JSONSchemaForm.js

---
 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 d4b68320c..4ecd4447f 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -368,7 +368,7 @@ export class JSONSchemaForm extends LitElement {
         const name = path.pop();
         const element = this.shadowRoot
             .querySelector(`#${fullPath.join("-")}`)
-            .querySelector("nwb-jsonschema-input")
+            .querySelector("jsonschema-input")
             .shadowRoot.querySelector(".guided--input");
         const isValid = await this.triggerValidation(name, element, path, false);
         if (!isValid) return true;
@@ -435,7 +435,7 @@ export class JSONSchemaForm extends LitElement {
 
         // this.validateEmptyValues ? undefined : (el) => (el.value ?? el.checked) !== ""
 
-        // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("nwb-jsonschema-input")).map(input => input.children)
+        // const possibleInputs = Array.from(this.shadowRoot.querySelectorAll("jsonschema-input")).map(input => input.children)
         // const inputs = possibleInputs.filter(el => el instanceof HTMLElement);
         // const fileInputs = Array.from(this.shadowRoot.querySelectorAll("filesystem-selector") ?? []);
         // const allInputs = [...inputs, ...fileInputs];