Merge branch 'main' into linux-dev

.storybook/main.ts

@@ -3,7 +3,7 @@ import type { StorybookConfig } from '@storybook/web-components-vite';
 import ViteYaml from "@modyfi/vite-plugin-yaml";
 
 const config: StorybookConfig = {
-    stories: ["../src/**/*.mdx", "../src/**/*.stories.@(js|jsx|ts|tsx)"],
+    stories: ["../stories/**/*.mdx", "../stories/**/*.stories.@(js|jsx|ts|tsx)"],
     addons: ["@storybook/addon-links", "@storybook/addon-essentials"],
     framework: {
         name: "@storybook/web-components-vite",

generateInterfaceSchema.py

@@ -4,7 +4,7 @@
 from neuroconv import NWBConverter, converters, datainterfaces
 
 filepath = Path("src") / "supported_interfaces.json"
-generatedJSONSchemaPath = Path("schemas", "json", "generated")
+generatedJSONSchemaPath = Path("stories") / "inputs" / "interface_schemas"
 generatedJSONSchemaPath.mkdir(exist_ok=True, parents=True)
 
 f = filepath.open()
@@ -29,9 +29,11 @@ class CustomNWBConverter(NWBConverter):
         outfile.write(json.dumps(schema, indent=4))
 
 
-sourceDataStoryPath = Path("src/electron/renderer/src/stories/pages/guided-mode/SourceData.stories.js")
+sourceDataStoryPath = Path("stories/pages/SourceData.stories.js")
 
-importCode = "\n".join(map(lambda arr: f"import {arr[0]}Schema from '../../../../../../{arr[1]}'", paths.items()))
+importCode = "\n".join(
+    map(lambda arr: f"import {arr[0]}Schema from '../inputs/interface_schemas/{arr[1]}'", paths.items())
+)
 storyCode = "\n".join(
     map(
         lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});

src/electron/renderer/src/pages.js

@@ -16,11 +16,11 @@ import { GuidedInspectorPage } from "./stories/pages/guided-mode/options/GuidedI
 
 import logo from "../assets/img/logo-guide-draft-transparent-tight.png";
 import { GuidedPathExpansionPage } from "./stories/pages/guided-mode/data/GuidedPathExpansion";
-import uploadIcon from "./stories/assets/dandi.svg?raw";
-import inspectIcon from "./stories/assets/inspect.svg?raw";
-import neurosiftIcon from "./stories/assets/neurosift-logo.svg?raw";
+import uploadIcon from "../assets/icons/dandi.svg?raw";
+import inspectIcon from "../assets/icons/inspect.svg?raw";
+import neurosiftIcon from "../assets/icons/neurosift-logo.svg?raw";
 
-import settingsIcon from "./stories/assets/settings.svg?raw";
+import settingsIcon from "../assets/icons/settings.svg?raw";
 
 import { UploadsPage } from "./stories/pages/uploads/UploadsPage";
 import { SettingsPage } from "./stories/pages/settings/SettingsPage";

src/electron/renderer/src/server/globals.ts

@@ -1,8 +1,8 @@
 import { isElectron, app, port } from '../electron/index.js'
 
-import serverSVG from "../stories/assets/server.svg?raw";
-import webAssetSVG from "../stories/assets/web_asset.svg?raw";
-import wifiSVG from "../stories/assets/wifi.svg?raw";
+import serverSVG from "../../assets/icons/server.svg?raw";
+import webAssetSVG from "../../assets/icons/web_asset.svg?raw";
+import wifiSVG from "../../assets/icons/wifi.svg?raw";
 
 // Base Request URL for Python Server
 export const baseUrl = `http://127.0.0.1:${port}`;
@@ -56,7 +56,7 @@ export const activateServer = () => {
 export const serverGlobals = {
     species: new Promise((res, rej) => {
       onServerOpen(() => {
-        fetch(new URL("get-recommended-species", baseUrl))
+        fetch(new URL("/dandi/get-recommended-species", baseUrl))
           .then((res) => res.json())
           .then((species) => {
             res(species)
@@ -67,7 +67,7 @@ export const serverGlobals = {
     }),
     cpus: new Promise((res, rej) => {
       onServerOpen(() => {
-        fetch(new URL("cpus", baseUrl))
+        fetch(new URL("/system/cpus", baseUrl))
           .then((res) => res.json())
           .then((cpus) => {
             res(cpus)

src/electron/renderer/src/stories/FileSystemSelector.js

@@ -4,7 +4,7 @@ import { fs, remote } from "../electron/index";
 import { List } from "./List";
 const { dialog } = remote;
 
-import restartSVG from "./assets/restart.svg?raw";
+import restartSVG from "../../assets/icons/restart.svg?raw";
 import { unsafeSVG } from "lit/directives/unsafe-svg.js";
 
 function getObjectTypeReferenceString(type, multiple, { nested, native } = {}) {

src/electron/renderer/src/stories/FullScreenToggle.ts

@@ -1,7 +1,7 @@
 import { LitElement, css, html } from "lit";
 
-import fullScreenIcon from './assets/fullscreen.svg?raw'
-import fullScreenExitIcon from './assets/fullscreen_exit.svg?raw'
+import fullScreenIcon from '../../assets/icons/fullscreen.svg?raw'
+import fullScreenExitIcon from '../../assets/icons/fullscreen_exit.svg?raw'
 
 import { unsafeHTML } from "lit/directives/unsafe-html.js";
 

src/electron/renderer/src/stories/Search.js

@@ -1,7 +1,7 @@
 import { LitElement, html, css } from "lit";
 import { styleMap } from "lit/directives/style-map.js";
 
-import searchSVG from "./assets/search.svg?raw";
+import searchSVG from "../../assets/icons/search.svg?raw";
 
 import tippy from "tippy.js";
 import { unsafeHTML } from "lit/directives/unsafe-html.js";

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

@@ -23,7 +23,7 @@ import { header, tempPropertyKey } from "../../../forms/utils";
 import { createGlobalFormModal } from "../../../forms/GlobalFormModal";
 import { Button } from "../../../Button.js";
 
-import globalIcon from "../../../assets/global.svg?raw";
+import globalIcon from "../../../../../assets/icons/global.svg?raw";
 
 const parentTableRenderConfig = {
     Electrodes: (metadata) => {

src/electron/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js

@@ -14,7 +14,7 @@ import { Button } from "../../../Button.js";
 import { Modal } from "../../../Modal";
 import { header } from "../../../forms/utils";
 
-import autocompleteIcon from "../../../assets/inspect.svg?raw";
+import autocompleteIcon from "../../../../../assets/icons/inspect.svg?raw";
 
 const propOrder = ["path", "subject_id", "session_id"];
 

src/electron/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js

@@ -11,7 +11,7 @@ import { createGlobalFormModal } from "../../../forms/GlobalFormModal";
 import { header } from "../../../forms/utils";
 import { Button } from "../../../Button.js";
 
-import globalIcon from "../../../assets/global.svg?raw";
+import globalIcon from "../../../../../assets/icons/global.svg?raw";
 
 import { baseUrl } from "../../../../server/globals";
 

src/electron/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js

@@ -2,7 +2,7 @@ import { html } from "lit";
 import { Page } from "../../Page.js";
 
 import { unsafeSVG } from "lit/directives/unsafe-svg.js";
-import folderOpenSVG from "../../../assets/folder_open.svg?raw";
+import folderOpenSVG from "../../../../../assets/icons/folder_open.svg?raw";
 
 import { electron } from "../../../../electron/index.js";
 import { getSharedPath, removeFilePaths, truncateFilePaths } from "../../../preview/NWBFilePreview.js";

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

@@ -2,7 +2,7 @@ import { html } from "lit";
 import { Page } from "../../Page.js";
 
 import { unsafeSVG } from "lit/directives/unsafe-svg.js";
-import folderOpenSVG from "../../../assets/folder_open.svg?raw";
+import folderOpenSVG from "../../../../../assets/icons/folder_open.svg?raw";
 
 import { electron } from "../../../../electron/index.js";
 import { NWBFilePreview, getSharedPath } from "../../../preview/NWBFilePreview.js";

src/electron/renderer/src/stories/pages/guided-mode/options/GuidedUpload.js

@@ -10,7 +10,7 @@ import { until } from "lit/directives/until.js";
 
 import { Button } from "../../../Button.js";
 
-import keyIcon from "../../../assets/key.svg?raw";
+import keyIcon from "../../../../../assets/icons/key.svg?raw";
 
 import { validate } from "../../uploads/utils";
 import { global } from "../../../../progress/index.js";

src/electron/renderer/src/stories/pages/guided-mode/results/GuidedResults.js

@@ -1,6 +1,6 @@
 import { html } from "lit";
 import { unsafeSVG } from "lit/directives/unsafe-svg.js";
-import folderOpenSVG from "../../../assets/folder_open.svg?raw";
+import folderOpenSVG from "../../../../../assets/icons/folder_open.svg?raw";
 
 import { Page } from "../../Page.js";
 import { getStubArray } from "../options/GuidedStubPreview.js";

src/electron/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js

@@ -10,7 +10,7 @@ import { Button } from "../../../Button.js";
 import { createGlobalFormModal } from "../../../forms/GlobalFormModal";
 import { header } from "../../../forms/utils";
 
-import globalIcon from "../../../assets/global.svg?raw";
+import globalIcon from "../../../../../assets/icons/global.svg?raw";
 
 export class GuidedSubjectsPage extends Page {
     constructor(...args) {

src/electron/renderer/src/stories/pages/preview/PreviewPage.js

@@ -18,7 +18,12 @@ export class PreviewPage extends Page {
 
     updatePath = async (path) => {
         if (path) {
-            const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
+            // Enable access to the explicit file path
+            const result = await fetch(`${baseUrl}/files/${path}`, {
+                method: "POST",
+            }).then((res) => res.text());
+
+            // Set Neurosift to access the returned URL
             if (result) this.neurosift.url = result;
         } else this.neurosift.url = undefined;
     };

src/electron/renderer/src/stories/pages/settings/SettingsPage.js

@@ -15,10 +15,10 @@ import { merge, setUndefinedIfNotDeclared } from "../utils";
 import { homeDirectory, notyf, testDataFolderPath } from "../../../dependencies/globals";
 import { SERVER_FILE_PATH, electron, path, port, fs } from "../../../electron/index.js";
 
-import saveSVG from "../../assets/save.svg?raw";
-import folderSVG from "../../assets/folder_open.svg?raw";
-import deleteSVG from "../../assets/delete.svg?raw";
-import generateSVG from "../../assets/restart.svg?raw";
+import saveSVG from "../../../../assets/icons/save.svg?raw";
+import folderSVG from "../../../../assets/icons/folder_open.svg?raw";
+import deleteSVG from "../../../../assets/icons/delete.svg?raw";
+import generateSVG from "../../../../assets/icons/restart.svg?raw";
 
 import { header } from "../../forms/utils";
 

src/electron/renderer/src/stories/pages/uploads/UploadsPage.js

@@ -32,7 +32,7 @@ import { validateDANDIApiKey } from "../../../validation/dandi";
 
 import * as dandi from "dandi";
 
-import keyIcon from "../../assets/key.svg?raw";
+import keyIcon from "../../../../assets/icons/key.svg?raw";
 
 import { AWARD_VALIDATION_FAIL_MESSAGE, awardNumberValidator, isStaging, validate } from "./utils";
 import { createFormModal } from "../../forms/GlobalFormModal";

src/electron/renderer/src/stories/preview/NWBFilePreview.js

@@ -56,7 +56,10 @@ class NWBPreviewInstance extends LitElement {
         const isOnline = navigator.onLine;
 
         return isOnline
-            ? new Neurosift({ url: getURLFromFilePath(this.file, this.project), fullscreen: false })
+            ? new Neurosift({
+                  url: getURLFromFilePath(this.file, this.project),
+                  fullscreen: false,
+              })
             : until(
                   (async () => {
                       const htmlRep = await run("html", { nwbfile_path: this.file }, { swal: false });

src/electron/renderer/src/stories/preview/Neurosift.js

@@ -80,7 +80,9 @@ export class Neurosift extends LitElement {
     render() {
         return this.url
             ? html` <div class="loader-container">
-                      ${new Loader({ message: `Loading Neurosift view...<br/><small>${this.url}</small>` })}
+                      ${new Loader({
+                          message: `Loading Neurosift view...<br/><small>${this.url}</small>`,
+                      })}
                   </div>
                   ${this.fullscreen ? new FullScreenToggle({ target: this }) : ""}
                   <iframe

src/pyflask/app.py

@@ -1,5 +1,6 @@
 """The primary Flask server for the Python backend."""
 
+import collections
 import json
 import multiprocessing
 import sys
@@ -10,13 +11,12 @@
 from os.path import isabs
 from pathlib import Path
 from signal import SIGINT
+from typing import Union
 from urllib.parse import unquote
 
 # https://stackoverflow.com/questions/32672596/pyinstaller-loads-script-multiple-times#comment103216434_32677108
 multiprocessing.freeze_support()
 
-
-from apis import data_api, neuroconv_api, startup_api
 from flask import Flask, request, send_file, send_from_directory
 from flask_cors import CORS
 from flask_restx import Api, Resource
@@ -27,12 +27,22 @@
     is_packaged,
     resource_path,
 )
+from namespaces import (
+    dandi_namespace,
+    data_namespace,
+    neuroconv_namespace,
+    neurosift_namespace,
+    startup_namespace,
+    system_namespace,
+)
 
-app = Flask(__name__)
+neurosift_file_registry = collections.defaultdict(bool)
+
+flask_app = Flask(__name__)
 
 # Always enable CORS to allow distinct processes to handle frontend vs. backend
-CORS(app)
-app.config["CORS_HEADERS"] = "Content-Type"
+CORS(flask_app)
+flask_app.config["CORS_HEADERS"] = "Content-Type"
 
 # Create logger configuration
 LOG_FOLDER = Path(GUIDE_ROOT_FOLDER, "logs")
@@ -50,63 +60,39 @@
     title="NWB GUIDE API",
     description="The REST API for the NWB GUIDE provided by the Python Flask Server.",
 )
-api.add_namespace(startup_api)
-api.add_namespace(neuroconv_api)
-api.add_namespace(data_api)
-api.init_app(app)
+api.add_namespace(startup_namespace)
+api.add_namespace(neuroconv_namespace)
+api.add_namespace(data_namespace)
+api.add_namespace(system_namespace)
+api.add_namespace(dandi_namespace)
+# api.add_namespace(neurosift_namespace)  # TODO: enable later
+api.init_app(flask_app)
 
-registered = {}
 
+@flask_app.route("/preview/<path:file_path>")
+def send_preview(file_path):
+    return send_from_directory(directory=STUB_SAVE_FOLDER_PATH, path=file_path)
 
-@app.route("/files")
-def get_all_files():
-    return list(registered.keys())
 
+@flask_app.route("/files/<path:file_path>", methods=["GET", "POST"])
+def handle_file_request(file_path) -> Union[str, None]:
+    if ".nwb" not in file_path:
+        raise ValueError("This endpoint must be called on an NWB file!")
 
-@app.route("/files/<path:path>", methods=["GET", "POST"])
-def handle_file_request(path):
     if request.method == "GET":
-        if registered[path]:
-            path = unquote(path)
-            if not isabs(path):
-                path = f"/{path}"
-            return send_file(path)
+        if neurosift_file_registry[file_path] is True:
+            file_path = unquote(file_path)
+            if not isabs(file_path):
+                file_path = f"/{file_path}"
+
+            return send_file(path_or_file=file_path)
         else:
             app.abort(404, "Resource is not accessible.")
 
     else:
-        if ".nwb" in path:
-            registered[path] = True
-            return request.base_url
-        else:
-            app.abort(400, str("Path does not point to an NWB file."))
-
-
-@app.route("/conversions/<path:path>")
-def send_conversions(path):
-    return send_from_directory(CONVERSION_SAVE_FOLDER_PATH, path)
-
-
-@app.route("/preview/<path:path>")
-def send_preview(path):
-    return send_from_directory(STUB_SAVE_FOLDER_PATH, path)
-
-
-@app.route("/cpus")
-def get_cpu_count():
-    from psutil import cpu_count
-
-    physical = cpu_count(logical=False)
-    logical = cpu_count()
-
-    return dict(physical=physical, logical=logical)
-
-
-@app.route("/get-recommended-species")
-def get_species():
-    from dandi.metadata.util import species_map
+        neurosift_file_registry[file_path] = True
 
-    return species_map
+        return request.base_url
 
 
 @api.route("/log")
@@ -154,13 +140,13 @@ def get(self):
         )
         log_handler.setFormatter(log_formatter)
 
-        app.logger.addHandler(log_handler)
-        app.logger.setLevel(DEBUG)
+        flask_app.logger.addHandler(log_handler)
+        flask_app.logger.setLevel(DEBUG)
 
-        app.logger.info(f"Logging to {LOG_FILE_PATH}")
+        flask_app.logger.info(f"Logging to {LOG_FILE_PATH}")
 
         # Run the server
         api.logger.info(f"Starting server on port {port}")
-        app.run(host="127.0.0.1", port=port)
+        flask_app.run(host="127.0.0.1", port=port)
     else:
         raise Exception("No port provided for the NWB GUIDE backend.")