Merge branch 'main' into alphaomega

docs/developer_guide.rst

@@ -75,7 +75,7 @@ This will automatically add the new page to the sidebar. The page itself can be
         constructor(...args) {
             super(...args);
 
-            console.log(this.info.globalState) // This will print the global state that is currently being passed between subpages (i.e. within guided mode)
+            console.log(this.info.globalState) // This will print the global state that is currently being passed between subpages
         }
 
         render() {

guideGlobalMetadata.json

@@ -27,6 +27,7 @@
         "PlexonRecordingInterface",
         "PlexonSortingInterface",
         "AxonaRecordingInterface",
+        "NeuralynxRecordingInterface"
         "AlphaOmegaRecordingInterface"
     ]
 }

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -341,11 +341,7 @@ def convert_to_nwb(info: dict) -> str:
     resolved_output_path = resolved_output_directory / nwbfile_path
 
     # Remove symlink placed at the default_output_directory if this will hold real data
-    if (
-        not run_stub_test
-        and resolved_output_directory == default_output_directory
-        and default_output_directory.is_symlink()
-    ):
+    if resolved_output_directory == default_output_directory and default_output_directory.is_symlink():
         default_output_directory.unlink()
 
     resolved_output_path.parent.mkdir(exist_ok=True, parents=True)  # Ensure all parent directories exist
@@ -401,7 +397,7 @@ def update_conversion_progress(**kwargs):
     )
 
     # Create a symlink between the fake data and custom data
-    if not run_stub_test and not resolved_output_directory == default_output_directory:
+    if not resolved_output_directory == default_output_directory:
         if default_output_directory.exists():
             # If default default_output_directory is not a symlink, delete all contents and create a symlink there
             if not default_output_directory.is_symlink():

schemas/json/dandi/global.json

@@ -14,7 +14,7 @@
                     "description": "From the <a href='https://gui-staging.dandiarchive.org' target='_blank'>staging (testing) server</a>"
                 }
             },
-            "required": ["main_api_key", "staging_api_key"]
+            "required": ["main_api_key"]
         }
     }
 }

schemas/json/generated/NeuralynxRecordingInterface.json

@@ -0,0 +1,36 @@
+{
+    "required": [],
+    "properties": {
+        "NeuralynxRecordingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "stream_name": {
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": false
+                },
+                "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"
+}

src/renderer/assets/css/global.css

@@ -10,7 +10,7 @@
 
 /*  Notfy */
 .notyf__toast {
-    max-width: clamp(300px, 40vw, min-content) !important;
+    max-width: 40vw !important;
 }
 
 .notyf__message {

src/renderer/assets/css/guided.css

@@ -27,7 +27,6 @@
     width: 100%;
     height: 100%;
     border-radius: 5px;
-    margin-top: 15px;
 }
 
 .guided--nav-bar-dropdown {
@@ -434,14 +433,6 @@
     margin: 6px;
 }
 
-.guided--main-tab,
-.guided--parent-tab {
-    height: 100%;
-    width: 100%;
-    display: flex;
-    flex-direction: column;
-}
-
 .guided--page,
 .guided--panel {
     width: 100%;
@@ -900,9 +891,10 @@ h1.guided--text-sub-step {
     background-color: var(--color-border);
     border: none;
     display: inline-block;
-    cursor: pointer;
     border-radius: 16px;
+    cursor: pointer;
 }
+
 .guided--capsule.active {
     background-color: var(--color-light-green);
 }
@@ -922,7 +914,6 @@ h1.guided--text-sub-step {
     background-color: #d5eaff;
     border: none;
     display: inline-block;
-    cursor: pointer;
     transform: skewx(-25deg);
 }
 .guided--capsule-sub-page.active {
@@ -1196,7 +1187,6 @@ h1.guided--text-sub-step {
     margin-bottom: 15px;
     border-bottom: 5px solid #b80d49;
     width: 100%;
-    margin-top: -0.5rem !important;
 }
 
 .guided--button-tab-container {

src/renderer/assets/css/main.css

@@ -1471,43 +1471,12 @@ details[open] > summary::before {
     box-shadow: var(--tw-ring-offset-shadow, 0 0 #0000), var(--tw-ring-shadow, 0 0 #0000), var(--tw-shadow);
 }
 
-.getting-started-overview {
-    padding-left: 0 !important;
-    padding-right: 0 !important;
-    height: 100%;
-    text-align: center;
-    display: flex;
-    flex-direction: column;
-    /* display: grid;
-  grid-template-rows: 68% 14% 15%; */
-}
-
-.getting-started-header {
-    width: auto;
-    height: 18rem;
+.standalone-section {
+    width: 100%;
     display: flex;
     flex-direction: column;
-    justify-content: center;
-    margin: 0 auto;
-    margin-top: 3rem;
     align-items: center;
-    margin-bottom: 0rem;
-}
-
-.front-page_logo {
-    margin-top: 0.5rem;
-    display: flex;
-    align-items: center;
-    flex-direction: row;
-    width: 63rem;
-    flex-direction: column;
-    justify-content: center;
-}
-
-.header-text {
-    font-size: 18px;
-    margin-top: 1rem;
-    font-weight: bold;
+    margin-bottom: 20px;
 }
 
 .overview-card-layout {

src/renderer/assets/css/section.css

@@ -1,22 +1,12 @@
 /* Section ------------------ */
 
 .section {
-    /* position: absolute; */
-    top: 0;
-    left: 210px;
-    right: 0;
-    bottom: 0;
     height: 100%;
     width: 100%;
     margin-right: 0;
     padding: 0px 50px 50px 50px;
     display: flex;
     flex-direction: column;
-    /* display: grid;
-    grid-template-rows: min-content auto;
-    grid-template-columns: 1fr; */
-    /* padding-top: 7px;
-  padding-left: 30px; */
     box-sizing: border-box;
     overflow-x: hidden;
     overflow-y: auto;

src/renderer/assets/css/variables.css

@@ -32,9 +32,7 @@
 .u-category-windows {
     --color-accent: hsl(190, 60%, 36%);
 }
-.u-category-menu {
-    --color-accent: hsl(190, 60%, 36%);
-}
+
 .u-category-native-ui {
     --color-accent: hsl(222, 53%, 50%);
 }

src/renderer/src/stories/FileSystemSelector.js

@@ -1,6 +1,6 @@
 import { LitElement, css, html } from "lit";
 
-import { remote } from "../electron/index";
+import { fs, remote } from "../electron/index";
 const { dialog } = remote;
 
 function getObjectTypeReferenceString(type, multiple, { nested, native } = {}) {
@@ -126,7 +126,7 @@ export class FilesystemSelector extends LitElement {
     };
 
     #checkType = (value) => {
-        const isLikelyFile = value.split(".").length !== 1;
+        const isLikelyFile = fs ? fs.lstatSync(value).isFile() : value.split(".").length;
         if ((this.type === "directory" && isLikelyFile) || (this.type === "file" && !isLikelyFile))
             this.#onThrow("Incorrect filesystem object", `Please provide a <b>${this.type}</b> instead.`);
     };
@@ -150,8 +150,6 @@ export class FilesystemSelector extends LitElement {
 
         if (this.multiple && !Array.isArray(resolvedValue)) resolvedValue = [];
 
-        console.log(resolvedValue);
-
         this.value = resolvedValue;
         this.onSelect(this.value);
         const event = new Event("change"); // Create a new change event

src/renderer/src/stories/JSONSchemaInput.js

@@ -282,7 +282,14 @@ export class JSONSchemaInput extends LitElement {
                 modal.toggle(false);
             });
 
-            return html` <div>${list} ${addButton}</div> `;
+            return html`
+                <div
+                    class="schema-input"
+                    @change=${() => validateOnChange && this.#triggerValidation(name, list, path)}
+                >
+                    ${list} ${addButton}
+                </div>
+            `;
         }
 
         // Basic enumeration of properties on a select element

src/renderer/src/stories/List.ts

@@ -28,6 +28,7 @@ export class List extends LitElement {
 
       #empty {
         padding: 20px 10px;
+        margin-left: -40px;
         color: gray;
       }
 

src/renderer/src/stories/Main.js

@@ -104,11 +104,16 @@ export class Main extends LitElement {
             if (section) {
                 if (capsules === true || !("capsules" in page)) {
                     let pages = Object.values(section.pages);
-                    if (pages.length > 1)
-                        capsules = {
+                    const pageIds = Object.keys(section.pages);
+                    if (pages.length > 1) {
+                        const capsulesProps = {
                             n: pages.length,
                             selected: pages.map((o) => o.pageLabel).indexOf(page.info.label),
                         };
+
+                        capsules = new GuidedCapsules(capsulesProps);
+                        capsules.onClick = (i) => this.toRender.page.to(pageIds[i]);
+                    }
                 }
 
                 if (header === true || !("header" in page) || !("sections" in page.header)) {
@@ -123,7 +128,6 @@ export class Main extends LitElement {
 
         const headerEl = header ? new GuidedHeader(header) : html`<div></div>`; // Render for grid
 
-        const capsuleEl = capsules ? new GuidedCapsules(capsules) : "";
         const footerEl = footer ? new GuidedFooter(footer) : html`<div></div>`; // Render for grid
 
         const title = header?.title ?? page.info?.title;
@@ -137,12 +141,14 @@ export class Main extends LitElement {
         return html`
             ${headerEl}
             ${capsules
-                ? html`<div style="width: 100%; text-align: center; padding-top: 15px;">${capsuleEl}</div>`
-                : html`<div style="height: 25px;"></div>`}
+                ? html`<div style="width: 100%; text-align: center; padding-top: 15px;">${capsules}</div>`
+                : html`<div style="height: 50px;"></div>`}
             <main id="content" class="js-content" style="overflow: hidden; display: flex;">
-                <section class="section js-section u-category-windows">
+                <section class="section">
                     ${title
-                        ? html`<div style="position: sticky; top: 0; left: 0; background: white; z-index: 1;">
+                        ? html`<div
+                              style="position: sticky; top: 0; left: 0; background: white; z-index: 1; margin-bottom: 20px;"
+                          >
                               <div
                                   style="display: flex; flex: 1 1 0px; justify-content: space-between; align-items: end;"
                               >
@@ -156,7 +162,7 @@ export class Main extends LitElement {
                           </div>`
                         : ""}
 
-                    <div style="padding-top: 10px; height: 100%; width: 100%;">${page}</div>
+                    <div style="height: 100%; width: 100%;">${page}</div>
                 </section>
             </main>
             ${footerEl}

src/renderer/src/stories/NavigationSidebar.js

@@ -94,8 +94,8 @@ export class NavigationSidebar extends LitElement {
     render() {
         return html`
             <nav id="guided-nav" class="guided--nav">
-                <h1 class="guided--text-sub-step mb-0 mt-0">Guided Mode</h1>
-
+                <h4>Sections</h4>
+                <hr />
                 <ul id="guided-nav-items" class="guided--container-nav-items">
                     ${Object.entries(this.sections)
                         .map(([sectionName, info]) => {

src/renderer/src/stories/Search.js

@@ -21,13 +21,16 @@ export class Search extends LitElement {
                 background: white;
                 border-radius: 5px;
                 width: 100%;
+                height: 100%;
+                overflow: auto;
             }
 
             .header {
                 padding: 25px;
                 background: white;
                 position: sticky;
                 top: 0;
+                z-index: 1;
             }
 
             input {
@@ -45,7 +48,6 @@ export class Search extends LitElement {
                 position: absolute;
                 left: 0;
                 right: 0;
-                z-index: 1;
                 background: white;
             }
 

src/renderer/src/stories/Table.js

@@ -240,6 +240,11 @@ export class Table extends LitElement {
             const validator = async function (value, callback) {
                 if (!value) {
                     if (!ogThis.validateEmptyCells) {
+                        ogThis.#handleValidationResult(
+                            [], // Clear errors
+                            this.row,
+                            this.col
+                        );
                         callback(true); // Allow empty value
                         return true;
                     }
@@ -288,7 +293,6 @@ export class Table extends LitElement {
         let contextMenu = ["row_below", "remove_row"];
         if (this.schema.additionalProperties) contextMenu.push("col_right", "remove_col");
 
-        console.log(this.contextMenu);
         contextMenu = contextMenu.filter((k) => !(this.contextMenu.ignore ?? []).includes(k));
 
         const descriptionEl = this.querySelector("#description");