Merge branch 'development' of github.com:MannLabs/alphadia into devel…

…opment

gui/src/main/electron.js

@@ -1,4 +1,4 @@
-const { app, BrowserWindow, ipcMain, dialog, shell, nativeTheme } = require('electron')
+const { app, BrowserWindow, Menu, ipcMain, dialog, shell, nativeTheme } = require('electron')
 const osu = require('node-os-utils')
 const path = require("path");
 const writeYamlFile = require('write-yaml-file')
@@ -7,14 +7,17 @@ const os = require('os')
 
 const { handleGetSingleFolder,handleGetMultipleFolders, handleGetSingleFile, handleGetMultipleFiles} = require('./modules/dialogHandler')
 const { discoverWorkflows, workflowToConfig } = require('./modules/workflows')
-const { getEnvironmentStatus, lineBreakTransform, CondaEnvironment} = require('./modules/cmd');
+const { CondaEnvironment} = require('./modules/cmd');
+const { buildMenu } = require('./modules/menu')
+const { Profile } = require('./modules/profile')
 
 // Handle creating/removing shortcuts on Windows when installing/uninstalling.
 if (require('electron-squirrel-startup')) app.quit();
 
 let mainWindow;
 let workflows;
 let environment;
+let profile;
 
 function createWindow() {
   // Create the browser window.
@@ -32,14 +35,18 @@ function createWindow() {
     },
   });
     mainWindow.setTitle("alphaDIA");
-    mainWindow.removeMenu()
     mainWindow.loadFile(path.join(__dirname, "../dist/index.html"));
 
+    profile = new Profile()
+
+    Menu.setApplicationMenu(buildMenu(mainWindow, profile));
+
     // Open the DevTools if NODE_ENV=dev
     if (process.env.NODE_ENV === "dev"){
         mainWindow.webContents.openDevTools({ mode: "detach" });
     }
-    environment = new CondaEnvironment("alpha")
+
+    environment = new CondaEnvironment(profile)
     workflows = discoverWorkflows(mainWindow)
 }
 
@@ -82,7 +89,7 @@ function handleStartWorkflow(workflow) {
     // save config.yaml in workflow folder
     writeYamlFile.sync(configPath, config, {lineWidth: -1})
 
-    return environment.spawn(`conda run -n ${environment.envName} --no-capture-output alphadia extract --config ${configPath}`)
+    return environment.spawn(`conda run -n ${profile.config.conda.envName} --no-capture-output alphadia extract --config ${configPath}`)
 }
 
 // This method will be called when Electron has finished
@@ -122,15 +129,6 @@ app.whenReady().then(() => {
     powerMonitor.on("suspend", () => {
         powerSaveBlocker.start("prevent-app-suspension");
     });
-
-    mainWindow.webContents.on('render-process-gone', function (event, detailed) {
-        console.log("!crashed, reason: " + detailed.reason + ", exitCode = " + detailed.exitCode)
-        if (detailed.reason == "crashed"){
-            // relaunch app
-            app.relaunch({ args: process.argv.slice(1).concat(['--relaunch']) })
-            app.exit(0)
-        }
-    })
 });
 
 app.on('window-all-closed', () => {

gui/src/main/modules/cmd.js

@@ -46,7 +46,6 @@ function testCommand(command, pathUpdate){
 const CondaEnvironment = class {
 
     pathUpdate = ""
-    envName = "";
     exists = {
         conda: false,
         python: false,
@@ -65,8 +64,8 @@ const CondaEnvironment = class {
     std = [];
     pid = null;
 
-    constructor(envName){
-        this.envName = envName;
+    constructor(profile){
+        this.profile = profile;
 
         this.initPromise = this.discoverCondaPATH().then((pathUpdate) => {
             this.pathUpdate = pathUpdate;
@@ -81,7 +80,7 @@ const CondaEnvironment = class {
                 // check if info exist and active_prefix is not null
                 if (info != null){
                     if (info["active_prefix"] != null){
-                        if (path.basename(info["active_prefix"]) == this.envName){
+                        if (path.basename(info["active_prefix"]) == profile.config.conda.envName){
                             //dialog.showErrorBox("Conda environment already activated", "The conda environment " + this.envName + " is already activated. Please deactivate the environment and restart alphaDIA.")
                             return Promise.reject("Conda environment already activated")
                         }
@@ -103,8 +102,8 @@ const CondaEnvironment = class {
 
     discoverCondaPATH(){
         return new Promise((resolve, reject) => {
-
-            const paths = ["", ...condaPATH(os.userInfo().username, os.platform())]
+ 
+            const paths = [this.profile.config.conda.path, ...condaPATH(os.userInfo().username, os.platform())]
             Promise.all(paths.map((path) => {
                 return testCommand("conda", path)
                 })).then((codes) => {
@@ -124,7 +123,6 @@ const CondaEnvironment = class {
             this.exec('conda info --json', (err, stdout, stderr) => {
                 if (err) {console.log(err); reject(err); return;}
                 const info = JSON.parse(stdout);
-                console.log(info)
                 this.versions.conda = info["conda_version"];
                 this.exists.conda = true;
                 resolve(info);
@@ -134,7 +132,8 @@ const CondaEnvironment = class {
 
     checkPythonVersion(){
         return new Promise((resolve, reject) => {
-            this.exec(`conda run -n ${this.envName} python --version`, (err, stdout, stderr) => {
+
+            this.exec(`conda run -n ${this.profile.config.conda.envName} python --version`, (err, stdout, stderr) => {
                 if (err) {console.log(err); reject(err); return;}
                 const versionPattern = /\d+\.\d+\.\d+/;
                 const versionList = stdout.match(versionPattern);
@@ -150,7 +149,7 @@ const CondaEnvironment = class {
     }
     checkAlphadiaVersion(){
         return new Promise((resolve, reject) => {
-            this.exec(`conda list -n ${this.envName} --json`, (err, stdout, stderr) => {
+            this.exec(`conda list -n ${this.profile.config.conda.envName} --json`, (err, stdout, stderr) => {
                 if (err) {console.log(err); reject(err); return;}
                 const info = JSON.parse(stdout);
                 const packageInfo = info.filter((p) => p.name == "alphadia");
@@ -170,7 +169,7 @@ const CondaEnvironment = class {
 
     buildEnvironmentStatus(){
         return {
-            envName: this.envName,
+            envName: this.profile.config.conda.envName,
             versions: this.versions,
             exists: this.exists,
             ready: this.ready
@@ -189,6 +188,7 @@ const CondaEnvironment = class {
 
     spawn(cmd){
         console.log(cmd)
+        this.std = [];
         return new Promise((resolve, reject) => {
             if (!this.ready){
                 reject("Environment not ready");
@@ -240,94 +240,6 @@ const CondaEnvironment = class {
 
 }
 
-
-function getCondaInfo() {
-    return new Promise((resolve, reject) => {
-        exec('conda info --json', (err, stdout, stderr) => {
-            if (err) {
-                reject(err);
-            }
-            const info = JSON.parse(stdout);
-            resolve(info);
-        });
-    });
-}
-
-function getPythonVersion(envName){
-    return new Promise((resolve, reject) => {
-        exec(`conda run -n ${envName} python --version`, (err, stdout, stderr) => {
-            if (err) {
-                reject(err);
-                return;
-            }
-            const versionPattern = /\d+\.\d+\.\d+/;
-            const versionList = stdout.match(versionPattern);
-            // check if versionList is null
-            if (versionList == null){
-                reject("Python version not found");
-                return;
-            }
-            if (versionList.length == 0){
-                reject("Python version not found");
-                return;
-            }
-            resolve(versionList[0]);
-        });
-    });
-}
-
-function getPackageVersion(envName, packageName){
-    return new Promise((resolve, reject) => {
-        exec(`conda list -n ${envName} --json`, (err, stdout, stderr) => {
-            if (err) {
-                reject(err);
-            }
-            const info = JSON.parse(stdout);
-            const packageInfo = info.filter((package) => package.name == packageName);
-            if (packageInfo.length == 0){
-                reject(`Package ${packageName} not found in environment ${envName}`);
-            }
-            resolve(packageInfo[0].version);
-        });
-    });
-}
-
-function getEnvironmentStatus(envName){
-    environment = {
-        envName: envName,
-        hasConda: false,
-        condaVersion: "",
-        hasEnv: false,
-        hasPython: false,
-        pythonVersion: "",
-        hasAlphadia: false,
-        alphadiaVersion: "",
-        ready: false
-    }
-
-    return getCondaInfo().then((info) => {
-        environment.hasConda = true;
-        environment.condaVersion = info["conda_version"];
-        environment.hasEnv = info["envs"].map((env) => path.basename(env)).includes(envName);
-        return getPythonVersion(envName).then((version) => {
-            environment.hasPython = true;
-            environment.pythonVersion = version;
-            return getPackageVersion(envName, "alphadia").then((version) => {
-                environment.hasAlphadia = true;
-                environment.alphadiaVersion = version;
-                environment.ready = [environment.hasConda, environment.hasEnv, environment.hasPython, environment.hasAlphadia].every(Boolean);
-                return environment
-            }).catch((error) => {
-                return environment
-            })
-        }).catch((error) => {
-            return environment
-        })
-    }).catch((error) => {
-        return environment
-    })
-}
-
 function lineBreakTransform () {
 
     // https://stackoverflow.com/questions/40781713/getting-chunks-by-newline-in-node-js-data-stream
@@ -359,12 +271,6 @@ function lineBreakTransform () {
 
 
 module.exports = {
-    getCondaInfo,
-    getPythonVersion,
-    getPackageVersion,
-    getEnvironmentStatus,
-    lineBreakTransform,
-    testCommand,
     CondaEnvironment
 }
 

gui/src/main/modules/menu.js

@@ -0,0 +1,69 @@
+const {app, Menu} = require('electron')
+const path = require('path')
+const {shell} = require('electron')
+
+function buildMenu(mainWindow, profile) {
+
+    const isMac = process.platform === 'darwin'
+
+    const template = [
+    ...(isMac
+        ? [{
+            label: app.name,
+            submenu: [
+            { role: 'about' },
+            { type: 'separator' },
+            { id: 'preferences', label: 'Preferences', click: () => { profile.openProfile() } },
+            { type: 'separator' },
+            { role: 'hide' },
+            { role: 'hideOthers' },
+            { role: 'unhide' },
+            { type: 'separator' },
+            { role: 'quit' }
+            ]
+        }]
+        : []),
+    {
+        label: 'File',
+        submenu: [
+        isMac ? { role: 'close' } : { role: 'quit' },
+        ...(isMac ? []: [{ id: 'preferences', label: 'Preferences', click: () => { profile.openProfile() } }])
+        ]
+    },
+    {
+        label: 'Window',
+        submenu: [
+        { role: 'minimize' },
+        { role: 'zoom' },
+        ...(isMac
+            ? [
+                { type: 'separator' },
+                { role: 'front' },
+                { type: 'separator' },
+                { role: 'window' }
+            ]
+            : [
+                { role: 'close' }
+            ])
+        ]
+    },
+    {
+        role: 'help',
+        submenu: [
+        {
+            label: 'Learn More',
+            click: async () => {
+            const { shell } = require('electron')
+            await shell.openExternal('https://electronjs.org')
+            }
+        }
+        ]
+    }
+    ]
+
+    return Menu.buildFromTemplate(template)
+}
+
+module.exports = {
+    buildMenu
+}

gui/src/main/modules/profile.js

@@ -0,0 +1,48 @@
+
+const fs = require("fs")
+const path = require("path")
+const { app, shell} = require("electron")
+
+const Profile = class {
+
+    config = {
+        "version": "1.3.0",
+        "conda": {
+            "envName": "alpha",
+            "path": ""
+        },
+        "clippy": false,
+    }
+
+    constructor() {
+
+        // check if profile exists
+        if (!fs.existsSync(this.getProfilePath())) {
+            this.saveProfile()
+        } else {
+            this.loadProfile()
+        }
+
+        console.log(this.getProfilePath())
+    }
+
+    saveProfile() {
+        fs.writeFileSync(this.getProfilePath(), JSON.stringify(this.config, null, 4))
+    }
+
+    loadProfile() {
+        this.config = JSON.parse(fs.readFileSync(this.getProfilePath()))
+    }
+
+    getProfilePath() {
+        return path.join(app.getPath("userData"), "profile.json")
+    }
+
+    openProfile() {
+        shell.openPath(this.getProfilePath())
+    }
+}
+
+module.exports = {
+    Profile
+}