Merge branch 'main' into conversion-events

src/renderer/src/stories/JSONSchemaForm.js

@@ -3,7 +3,7 @@ import { notify } from "../globals";
 import { FilesystemSelector } from "./FileSystemSelector";
 import { Accordion } from "./Accordion";
 
-import { capitalize, header } from "./forms/utils";
+import { capitalize, header, textToArray } from "./forms/utils";
 
 const componentCSS = `
 
@@ -425,9 +425,7 @@ export class JSONSchemaForm extends LitElement {
                                 @input=${(ev) => {
                                     this.#updateParent(
                                         name,
-                                        isStringArray
-                                            ? ev.target.value.split("\n").map((str) => str.trim())
-                                            : ev.target.value,
+                                        isStringArray ? textToArray(ev.target.value) : ev.target.value,
                                         parent
                                     );
                                 }}

src/renderer/src/stories/ProgressBar.stories.js

@@ -0,0 +1,32 @@
+import { ProgressBar } from "./ProgressBar";
+
+export default {
+    title: "Components/Progress Bar",
+};
+
+const Template = (args) => new ProgressBar(args);
+
+const b = 0;
+const tsize = 50;
+const bsize = 1;
+
+export const Default = Template.bind({});
+Default.args = {
+    value: {
+        b,
+        bsize,
+        tsize,
+    },
+};
+
+function sleep(ms) {
+    return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+Default.play = async ({ canvasElement }) => {
+    const progressBar = canvasElement.querySelector("nwb-progress");
+    for (let i = 1; i <= tsize; i++) {
+        await sleep(1000);
+        progressBar.value = { b: i, tsize };
+    }
+};

src/renderer/src/stories/ProgressBar.ts

@@ -0,0 +1,69 @@
+
+
+import { LitElement, html, css } from 'lit';
+
+export type ProgressProps = {
+    value?: {
+        b: number,
+        bsize?: number,
+        tsize: number
+    },
+}
+
+export class ProgressBar extends LitElement {
+
+    static get styles() {
+    return css`
+
+        :host {
+            display: flex;
+            align-items: center;
+        }
+
+        :host > div {
+            width: 100%;
+            height: 10px;
+            border: 1px solid lightgray;
+            overflow: hidden;
+        }
+
+        :host > div > div {
+            width: 0%;
+            height: 100%;
+            background-color: #029CFD;
+            transition: width 0.5s;
+        }
+
+        small {
+            white-space: nowrap;
+            margin-left: 10px;
+        }
+
+    `;
+    }
+
+    static get properties() {
+        return {
+            value: {
+                type: Object,
+                reflect: true,
+            }
+        };
+    }
+
+    declare value: any
+
+    constructor(props: ProgressProps = {}) {
+        super();
+
+        this.value = props.value ?? {}
+    }
+
+    render() {
+
+        const value = this.value.b / this.value.tsize * 100
+        return html`<div><div style="width: ${value}%"></div></div><small>${this.value.b}/${this.value.tsize} (${value.toFixed(0)}%)</small>`
+    }
+}
+
+customElements.get('nwb-progress') || customElements.define('nwb-progress',  ProgressBar);

src/renderer/src/stories/forms/utils.ts

@@ -4,3 +4,7 @@ export const capitalize = (str: string) => str[0].toUpperCase() + str.slice(1)
 export const header = (headerStr: string) => {
     return headerStr.split('_').filter(str => !!str).map(capitalize).join(' ')
 }
+
+export const textToArray = (value: string) => value.split("\n")
+                                            .map((str) => str.trim())
+                                            .filter((str) => str) // Only keep strings that are not empty

src/renderer/src/stories/pages/Page.js

@@ -1,6 +1,6 @@
 import { LitElement, html } from "lit";
 import useGlobalStyles from "../utils/useGlobalStyles.js";
-import { runConversion } from "./guided-mode/options/utils.js";
+import { openProgressSwal, runConversion } from "./guided-mode/options/utils.js";
 import { get, save } from "../../progress.js";
 import { dismissNotification, notify } from "../../globals.js";
 import { merge, randomizeElements, mapSessions } from "./utils.js";
@@ -83,7 +83,7 @@ export class Page extends LitElement {
 
     mapSessions = (callback) => mapSessions(callback, this.info.globalState);
 
-    async runConversions(conversionOptions = {}, toRun) {
+    async runConversions(conversionOptions = {}, toRun, options = {}) {
         let original = toRun;
         if (!Array.isArray(toRun)) toRun = this.mapSessions();
 
@@ -95,26 +95,55 @@ export class Page extends LitElement {
         const folder = this.info.globalState.conversion?.info?.output_folder; // Do not require output_folder on the frontend
         let results = [];
 
-        for (let { subject, session } of toRun) {
+        const popup = await openProgressSwal({ title: `Running conversion`, ...options });
+
+        const isMultiple = toRun.length > 1;
+
+        let elements = {};
+        if (isMultiple) {
+            popup.hideLoading();
+            const element = popup.getHtmlContainer();
+            element.innerText = "";
+
+            const progressBar = new ProgressBar();
+            elements.progress = progressBar;
+            element.append(progressBar);
+        }
+
+        let completed = 0;
+        for (let info of toRun) {
+            const { subject, session } = info;
             const basePath = `sub-${subject}/sub-${subject}_ses-${session}.nwb`;
             const file = folder ? `${folder}/${basePath}` : basePath;
 
-            const result = await runConversion({
-                folder,
-                nwbfile_path: file,
-                overwrite: true, // We assume override is true because the native NWB file dialog will not allow the user to select an existing file (unless they approve the overwrite)
-                ...this.info.globalState.results[subject][session], // source_data and metadata are passed in here
-                ...conversionOptions, // Any additional conversion options override the defaults
-
-                interfaces: this.info.globalState.interfaces,
-            }).catch((e) => {
+            const result = await runConversion(
+                {
+                    folder,
+                    nwbfile_path: file,
+                    overwrite: true, // We assume override is true because the native NWB file dialog will not allow the user to select an existing file (unless they approve the overwrite)
+                    ...this.info.globalState.results[subject][session], // source_data and metadata are passed in here
+                    ...conversionOptions, // Any additional conversion options override the defaults
+
+                    interfaces: this.info.globalState.interfaces,
+                },
+                { swal: popup, ...options }
+            ).catch((e) => {
                 this.notify(e.message, "error");
+                popup.close();
                 throw e.message;
             });
 
+            completed++;
+            if (isMultiple) {
+                const progressInfo = { b: completed, bsize: 1, tsize: toRun.length };
+                elements.progress.value = progressInfo;
+            }
+
             results.push({ file, result });
         }
 
+        popup.close();
+
         return results;
     }
 

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

@@ -27,10 +27,16 @@ export class GuidedMetadataPage extends ManagedPage {
 
         const instanceId = `sub-${subject}/ses-${session}`;
 
+        const schema = this.info.globalState.schema.metadata[subject][session];
+
+        // NOTE: This was a correction for differences in the expected values to be passed back to neuroconv
+        // delete schema.properties.Ecephys.properties.Electrodes
+        // delete results['Ecephys']['Electrodes']
+
         const form = new JSONSchemaForm({
             identifier: instanceId,
             mode: "accordion",
-            schema: this.info.globalState.schema.metadata[subject][session],
+            schema,
             results,
             ignore: ["Ecephys", "source_script", "source_script_file_name"],
             conditionalRequirements: [
@@ -76,9 +82,11 @@ export class GuidedMetadataPage extends ManagedPage {
                         if (subject.startsWith("sub-")) subject = subject.slice(4);
                         if (session.startsWith("ses-")) session = session.slice(4);
 
-                        const [{ file, result }] = await this.runConversions({ stub_test: true }, [
-                            { subject, session },
-                        ]).catch((e) => this.notify(e.message, "error"));
+                        const [{ file, result }] = await this.runConversions(
+                            { stub_test: true },
+                            [{ subject, session }],
+                            { title: "Running conversion preview" }
+                        ).catch((e) => this.notify(e.message, "error"));
 
                         const modal = new Modal({
                             header: file,

src/renderer/src/stories/pages/guided-mode/options/GuidedConversionOptions.js

@@ -15,7 +15,9 @@ export class GuidedConversionOptionsPage extends Page {
 
             // Preview a random conversion
             delete this.info.globalState.preview; // Clear the preview results
-            const results = await this.runConversions({ stub_test: true }, 1);
+            const results = await this.runConversions({ stub_test: true }, 1, {
+                title: "Testing conversion on a random session",
+            });
             this.info.globalState.preview = results; // Save the preview results
 
             this.onTransition(1);

src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js

@@ -11,7 +11,9 @@ export class GuidedStubPreviewPage extends Page {
         onNext: async () => {
             this.save(); // Save in case the conversion fails
             delete this.info.globalState.conversion.results;
-            this.info.globalState.conversion.results = await this.runConversions();
+            this.info.globalState.conversion.results = await this.runConversions({}, true, {
+                title: "Running all conversions",
+            });
             this.onTransition(1);
         },
     };

src/renderer/src/stories/pages/guided-mode/options/utils.js

@@ -1,34 +1,43 @@
 import Swal from "sweetalert2";
 import { baseUrl } from "../../../../globals.js";
 
-export const run = async (url, payload, options = {}) => {
-    Swal.fire({
-        title: options.title ?? "Requesting data from server",
-        html: "Please wait...",
-        allowEscapeKey: false,
-        allowOutsideClick: false,
-        heightAuto: false,
-        backdrop: "rgba(0,0,0, 0.4)",
-        timerProgressBar: false,
-        didOpen: () => {
-            Swal.showLoading();
-        },
+export const openProgressSwal = (options) => {
+    return new Promise((resolve) => {
+        Swal.fire({
+            title: options.title ?? "Requesting data from server",
+            html: `Please wait...`,
+            allowEscapeKey: false,
+            allowOutsideClick: false,
+            showConfirmButton: false,
+            heightAuto: false,
+            backdrop: "rgba(0,0,0, 0.4)",
+            timerProgressBar: false,
+            didOpen: () => {
+                Swal.showLoading();
+                resolve(Swal);
+            },
+        });
     });
+};
+
+export const run = async (url, payload, options = {}) => {
+    const needsSwal = !options.swal;
+    if (needsSwal) openProgressSwal(options).then((swal) => (options.onOpen ? options.onOpen(swal) : undefined));
 
     const results = await fetch(`${baseUrl}/neuroconv/${url}`, {
         method: "POST",
         headers: { "Content-Type": "application/json" },
         body: JSON.stringify(payload),
     }).then((res) => res.json());
 
-    Swal.close();
+    if (needsSwal) Swal.close();
 
     if (results?.message) throw new Error(`Request to ${url} failed: ${results.message}`);
 
     return results || true;
 };
 
-export const runConversion = async (info) =>
+export const runConversion = async (info, options = {}) =>
     run(`convert`, info, {
         title: "Running the conversion",
         onError: (results) => {
@@ -38,4 +47,5 @@ export const runConversion = async (info) =>
                 return "Conversion failed with current metadata. Please try again.";
             }
         },
+        ...options,
     });

tests/metadata.test.ts

@@ -7,6 +7,8 @@ import baseMetadataSchema from '../schemas/base-metadata.schema'
 import { createMockGlobalState } from './utils'
 
 import { Validator } from 'jsonschema'
+import { textToArray } from '../src/renderer/src/stories/forms/utils'
+
 var v = new Validator();
 
 describe('metadata is specified correctly', () => {
@@ -18,3 +20,10 @@ describe('metadata is specified correctly', () => {
         expect(res.errors).toEqual([])
     })
 })
+
+test('empty rows are not kept for strings converted to arrays', () => {
+    expect(textToArray(' v1\n v2 ')).toEqual(['v1', 'v2'])
+    expect(textToArray(' v1\n\n   v2 ')).toEqual(['v1', 'v2'])
+    expect(textToArray(' v1\n \n   v2 ')).toEqual(['v1', 'v2'])
+    expect(textToArray(' v1\n v3\n   v2 ')).toEqual(['v1', 'v3', 'v2'])
+})