Merge branch 'main' into time-alignment-ui

NeurodataWithoutBorders · May 30, 2024 · ad094dc · ad094dc
2 parents 518c17a + fb4da85
commit ad094dc
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diff --git a/.github/workflows/example_data_cache.yml b/.github/workflows/example_data_cache.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.12"]
-        os: [ubuntu-latest, macos-latest, macos-13] #, windows-latest]
+        os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
 
     steps:
 

diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml
@@ -26,8 +26,8 @@ jobs:
           - os: macos-13  # Mac x64 runner
             label: environments/environment-MAC-intel.yml
 
-#          - os: windows-latest
-#            label: environments/environment-Windows.yml
+          - os: windows-latest
+            label: environments/environment-Windows.yml
 
 
     steps:
@@ -95,33 +95,18 @@ jobs:
           path: ./behavior_testing_data
           key: behavior-datasets-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_behavior_DATASET }}
 
-      - name: Save working directory to environment file
-        run: echo "GIN_DATA_DIR=$(pwd)" >> .env
-        if: runner.os != 'Windows'
-
-      - name: Save working directory to environment file (Windows)
-        run: echo GIN_DATA_DIR=%cd% >> .env
-        shell: bash
-        if: runner.os == 'Windows'
-
-      # Display environment file for debugging
-      - name: Print environment file
-        run: cat .env
-        if: runner.os != 'Windows'
-
-      - name: Print environment file
-        run: type .env
-        shell: bash
-        if: runner.os == 'Windows'
-
       # Run pipeline tests
       - if: matrix.os != 'ubuntu-latest'
         name: Run tests
         run: npm run test:pipelines
+        env:
+          GIN_DATA_DIRECTORY: ${{ github.workspace }}
 
       - if: matrix.os == 'ubuntu-latest'
         name: Run tests with xvfb
         run: xvfb-run --auto-servernum --server-args="-screen 0 1280x960x24" -- npm run test:pipelines
+        env:
+          GIN_DATA_DIRECTORY: ${{ github.workspace }}
 
       - name: Archive Pipeline Test Screenshots
         if: always()

diff --git a/package.json b/package.json
@@ -25,6 +25,8 @@
     "test:app": "vitest run --exclude \"**/pipelines.test.ts\"",
     "test:tutorial": "vitest tutorial",
     "test:pipelines": "vitest pipelines",
+    "test:progress": "vitest progress",
+    "test:metadata": "vitest metadata",
     "test:server": "pytest src/pyflask/tests/ -s -vv",
     "wait5s": "node -e \"setTimeout(() => process.exit(0),5000)\"",
     "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait5s && pytest src/pyflask/tests/ -s --target http://localhost:3434\"",

diff --git a/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js b/src/electron/frontend/core/components/pages/guided-mode/data/GuidedPathExpansion.js
@@ -381,76 +381,71 @@ export class GuidedPathExpansionPage extends Page {
 
                 const interfaceName = parentPath.slice(-1)[0];
 
-                if (fs) {
-                    const baseDir = form.getFormElement([...parentPath, "base_directory"]);
-                    if (name === "format_string_path") {
-                        if (value && baseDir && !baseDir.value) {
-                            return [
-                                {
-                                    message: html`A base directory must be provided to locate your files.`,
-                                    type: "error",
-                                },
-                            ];
-                        }
+                const baseDir = form.getFormElement([...parentPath, "base_directory"]);
+                if (name === "format_string_path") {
+                    if (value && baseDir && !baseDir.value) {
+                        return [
+                            {
+                                message: html`A base directory must be provided to locate your files.`,
+                                type: "error",
+                            },
+                        ];
+                    }
 
-                        const base_directory = [...parentPath, "base_directory"].reduce(
-                            (acc, key) => acc[key],
-                            this.form.resolved
-                        );
+                    const base_directory = [...parentPath, "base_directory"].reduce(
+                        (acc, key) => acc[key],
+                        this.form.resolved
+                    );
 
-                        if (!base_directory) return true; // Do not calculate if base is not found
+                    if (!base_directory) return true; // Do not calculate if base is not found
 
-                        const entry = { base_directory };
+                    const entry = { base_directory };
 
-                        if (value.split(".").length > 1) entry.file_path = value;
-                        else entry.folder_path = value;
+                    if (value.split(".").length > 1) entry.file_path = value;
+                    else entry.folder_path = value;
 
-                        const results = await run(
-                            `neuroconv/locate`,
-                            { [interfaceName]: entry },
-                            { swal: false }
-                        ).catch((error) => {
+                    const results = await run(`neuroconv/locate`, { [interfaceName]: entry }, { swal: false }).catch(
+                        (error) => {
                             this.notify(error.message, "error");
                             throw error;
-                        });
+                        }
+                    );
 
-                        const resolved = [];
+                    const resolved = [];
 
-                        for (let sub in results) {
-                            for (let ses in results[sub]) {
-                                const source_data = results[sub][ses].source_data[interfaceName];
-                                const path = source_data.file_path ?? source_data.folder_path;
-                                resolved.push(path.slice(base_directory.length + 1));
-                            }
+                    for (let sub in results) {
+                        for (let ses in results[sub]) {
+                            const source_data = results[sub][ses].source_data[interfaceName];
+                            const path = source_data.file_path ?? source_data.folder_path;
+                            resolved.push(path.slice(base_directory.length + 1));
                         }
+                    }
 
-                        if (resolved.length === 0)
-                            return [
-                                {
-                                    message: html`No source files found using the provided information.`,
-                                    type: "warning",
-                                },
-                            ];
-
+                    if (resolved.length === 0)
                         return [
                             {
-                                message: html` <h4 style="margin: 0;">
-                                        <span style="margin-right: 7px;">✅</span>Source Files Found for
-                                        ${interfaceName}
-                                    </h4>
-                                    <small>${base_directory}</small>
-                                    <small
-                                        >${new List({
-                                            items: resolved.map((path) => {
-                                                return { value: path };
-                                            }),
-                                            editable: false,
-                                        })}</small
-                                    >`,
-                                type: "info",
+                                message: html`No source files found using the provided information.`,
+                                type: "warning",
                             },
                         ];
-                    }
+
+                    return [
+                        {
+                            message: html` <h4 style="margin: 0;">
+                                    <span style="margin-right: 7px;">✅</span>Source Files Found for ${interfaceName}
+                                </h4>
+                                <small>${base_directory}</small>
+                                <small
+                                    >${new List({
+                                        items: resolved.map((path) => {
+                                            return { value: path };
+                                        }),
+                                        editable: false,
+                                    })}</small
+                                >`,
+                            type: "info",
+                        },
+                    ];
                 }
             },
         }));

diff --git a/src/electron/frontend/core/components/pages/settings/SettingsPage.js b/src/electron/frontend/core/components/pages/settings/SettingsPage.js
@@ -15,15 +15,9 @@ import { merge, setUndefinedIfNotDeclared } from "../utils";
 import { notyf } from "../../../dependencies.js";
 import { homeDirectory, testDataFolderPath } from "../../../globals.js";
 
-import {
-    SERVER_FILE_PATH,
-    electron,
-    path,
-    port,
-    fs,
-    onUpdateAvailable,
-    onUpdateProgress,
-} from "../../../../utils/electron.js";
+import { SERVER_FILE_PATH, electron, path, port, fs } from "../../../../utils/electron.js";
+
+import { onUpdateAvailable, onUpdateProgress } from "../../../../utils/auto-update.js";
 
 import saveSVG from "../../../../assets/icons/save.svg?raw";
 import folderSVG from "../../../../assets/icons/folder_open.svg?raw";

diff --git a/src/electron/frontend/core/globals.js b/src/electron/frontend/core/globals.js
@@ -1,9 +1,11 @@
-import { app, path, crypto, isElectron } from "../utils/electron.js";
+import { os, path, crypto, isElectron, isTestEnvironment } from "../utils/electron.js";
 
 import paths from "../../../paths.config.json" assert { type: "json" };
 
 import supportedInterfaces from "../../../supported_interfaces.json" assert { type: "json" };
 
+export { isTestEnvironment };
+
 export const joinPath = (...args) => (path ? path.join(...args) : args.filter((str) => str).join("/"));
 
 export let runOnLoad = (fn) => {
@@ -17,24 +19,27 @@ export const reloadPageToHome = () => {
 }; // Clear all query params
 
 // Filesystem Management
-const root = globalThis?.process?.env?.VITEST ? joinPath(paths.root, ".test") : paths.root;
-export const homeDirectory = app?.getPath("home") ?? "";
-export const appDirectory = homeDirectory ? joinPath(homeDirectory, root) : "";
-export const guidedProgressFilePath = appDirectory ? joinPath(appDirectory, ...paths.subfolders.progress) : "";
+const root = isTestEnvironment ? joinPath(paths.root, ".test") : paths.root;
+
+export const homeDirectory = os ? os.homedir() : "/";
+
+export const appDirectory = joinPath(homeDirectory, root);
+
+export const guidedProgressFilePath = joinPath(appDirectory, ...paths.subfolders.progress);
 
-export const previewSaveFolderPath = appDirectory ? joinPath(appDirectory, ...paths.subfolders.preview) : "";
-export const conversionSaveFolderPath = appDirectory ? joinPath(appDirectory, ...paths.subfolders.conversions) : "";
+export const previewSaveFolderPath = joinPath(appDirectory, ...paths.subfolders.preview);
+export const conversionSaveFolderPath = joinPath(appDirectory, ...paths.subfolders.conversions);
 
-export const testDataFolderPath = appDirectory ? joinPath(appDirectory, ...paths.subfolders.testdata) : "";
+export const testDataFolderPath = joinPath(appDirectory, ...paths.subfolders.testdata);
 
 // Encryption
 const IV_LENGTH = 16;
 const KEY_LENGTH = 32;
-export const ENCRYPTION_KEY = appDirectory
+export const ENCRYPTION_KEY = isElectron
     ? Buffer.concat([Buffer.from(appDirectory), Buffer.alloc(KEY_LENGTH)], KEY_LENGTH)
-    : null;
+    : "";
 
-export const ENCRYPTION_IV = crypto ? crypto.randomBytes(IV_LENGTH) : null;
+export const ENCRYPTION_IV = isElectron ? crypto.randomBytes(IV_LENGTH) : "";
 
 // Storybook
 export const isStorybook = window.location.href.includes("iframe.html");

diff --git a/src/electron/frontend/core/index.ts b/src/electron/frontend/core/index.ts
@@ -1,5 +1,7 @@
 import "./pages.js"
 import { isElectron, electron } from '../utils/electron.js'
+import { isTestEnvironment } from './globals.js'
+
 const { ipcRenderer } = electron;
 
 import { Dashboard } from './components/Dashboard.js'
@@ -55,8 +57,6 @@ async function isOnline() {
 
   statusBar.items[1].status = true
 
-  const isTestEnvironment = globalThis?.process?.env?.VITEST
-
   if (isTestEnvironment) return
 
   notyf.open({

diff --git a/src/electron/frontend/core/progress/index.js b/src/electron/frontend/core/progress/index.js
@@ -8,6 +8,7 @@ import {
     ENCRYPTION_KEY,
     ENCRYPTION_IV,
 } from "../globals.js";
+
 import { fs, crypto } from "../../utils/electron.js";
 
 import { joinPath, runOnLoad } from "../globals";
@@ -87,8 +88,7 @@ class GlobalAppConfig {
     save() {
         const encoded = encodeObject(this.data);
 
-        if (fs) fs.writeFileSync(this.path, JSON.stringify(encoded, null, 2));
-        else localStorage.setItem(this.path, JSON.stringify(encoded));
+        fs.writeFileSync(this.path, JSON.stringify(encoded, null, 2));
     }
 }
 
@@ -115,7 +115,7 @@ export const save = (page, overrides = {}) => {
 };
 
 export const getEntries = () => {
-    if (fs && !fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
+    if (!fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
     const progressFiles = fs ? fs.readdirSync(guidedProgressFilePath) : Object.keys(localStorage);
     return progressFiles.filter((path) => path.slice(-5) === ".json");
 };

diff --git a/src/electron/frontend/core/progress/operations.js b/src/electron/frontend/core/progress/operations.js
@@ -7,17 +7,13 @@ export const remove = (name) => {
     const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
 
     //delete the progress file
-    if (fs) {
-        if (fs.existsSync(progressFilePathToDelete)) fs.unlinkSync(progressFilePathToDelete);
-    } else localStorage.removeItem(progressFilePathToDelete);
+    if (fs.existsSync(progressFilePathToDelete)) fs.unlinkSync(progressFilePathToDelete);
 
-    if (fs) {
-        // delete default preview location
-        fs.rmSync(joinPath(previewSaveFolderPath, name), { recursive: true, force: true });
+    // delete default preview location
+    fs.rmSync(joinPath(previewSaveFolderPath, name), { recursive: true, force: true });
 
-        // delete default conversion location
-        fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
-    }
+    // delete default conversion location
+    fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
 
     return true;
 };
diff --git a/src/electron/frontend/core/progress/update.js b/src/electron/frontend/core/progress/update.js
@@ -15,11 +15,7 @@ export const rename = (newDatasetName, previousDatasetName) => {
         // update old progress file with new dataset name
         const oldProgressFilePath = `${guidedProgressFilePath}/${previousDatasetName}.json`;
         const newProgressFilePath = `${guidedProgressFilePath}/${newDatasetName}.json`;
-        if (fs) fs.renameSync(oldProgressFilePath, newProgressFilePath);
-        else {
-            localStorage.setItem(newProgressFilePath, localStorage.getItem(oldProgressFilePath));
-            localStorage.removeItem(oldProgressFilePath);
-        }
+        fs.renameSync(oldProgressFilePath, newProgressFilePath);
     } else throw new Error("No previous project name provided");
 };
 
@@ -56,9 +52,9 @@ export const updateFile = (projectName, callback) => {
 
     var guidedFilePath = joinPath(guidedProgressFilePath, projectName + ".json");
 
+    console.log(guidedProgressFilePath);
+
     // 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(data, null, 2));
-    } else localStorage.setItem(guidedFilePath, JSON.stringify(data));
+    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));
 };
diff --git a/src/electron/frontend/core/server/index.ts b/src/electron/frontend/core/server/index.ts
@@ -1,6 +1,8 @@
-import { isElectron, electron, app, port } from '../../utils/electron.js'
+import { isElectron, electron, app } from '../../utils/electron.js'
 const { ipcRenderer } = electron;
 
+import { isTestEnvironment } from '../globals.js'
+
 import {
   notyf,
 } from '../dependencies.js'
@@ -35,7 +37,6 @@ export async function pythonServerOpened() {
 
     if (openPythonStatusNotyf) notyf.dismiss(openPythonStatusNotyf)
 
-    const isTestEnvironment = globalThis?.process?.env?.VITEST
     if (isTestEnvironment) return
 
     openPythonStatusNotyf = notyf.open({