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@romanhaa
romanhaa committed Apr 1, 2019
1 parent c1b1c4c commit fe87c2c
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Showing 4 changed files with 89 additions and 90 deletions.
2 changes: 1 addition & 1 deletion notes.md
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Expand Up @@ -11,7 +11,7 @@
* Remove `as.vector()` for gene expression, not necessary.
* Check/update export scripts.
* Move to z-score instead of log-counts?
* Not possible because occupy much more data.
* Not possible because occupy much more data.
* Use `formattable`.
* Make only RDS files selectable.
* Change text in some panels.
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6 changes: 3 additions & 3 deletions source/app.R
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@@ -1,17 +1,17 @@
##----------------------------------------------------------------------------##
## Cerebro
## version 1.0
## version 1.0.0
##
## Author: Roman Hillje
## Institute: IEO
## Lab: PGP
## Date: 2019-03-29
## Date: 2019-04-01
##----------------------------------------------------------------------------##

##----------------------------------------------------------------------------##
##
##----------------------------------------------------------------------------##
if (grepl(tolower(Sys.info()['sysname']), pattern='^win')) {
if (grepl(tolower(Sys.info()["sysname"]), pattern="^win")) {
.libPaths(paste0(getwd(), "/R-Portable-Win/library"))
plot_export_path <- paste0(Sys.getenv("USERPROFILE"), "\\Desktop\\")
} else {
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160 changes: 80 additions & 80 deletions source/main.js
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@@ -1,83 +1,83 @@
// Modules to control application life and create native browser window
const { app, BrowserWindow, Menu, MenuItem } = require('electron')
const { app, BrowserWindow, Menu, MenuItem } = require("electron")

const path = require('path')
const url = require('url')
const port = '8080'
const child = require('child_process')
const MACOS = 'darwin'
const WINDOWS = 'win32'
const path = require("path")
const url = require("url")
const port = "8080"
const child = require("child_process")
const MACOS = "darwin"
const WINDOWS = "win32"

var killStr = ''
var appPath = path.join(app.getAppPath(), 'app.R' )
var execPath = 'RScript'
var killStr = ""
var appPath = path.join(app.getAppPath(), "app.R" )
var execPath = "RScript"

// log file
var log = require('electron-log')
log.transports.console.level = true;
log.transports.file.level = true;
log.transports.file.level = 'info'
var log = require("electron-log")
log.transports.console.level = true
log.transports.file.level = true
log.transports.file.level = "info"

//
if ( process.platform == WINDOWS ) {
appPath = appPath.replace(/\\/g, '\\\\')
execPath = path.join(app.getAppPath(), 'R-Portable-Win', 'bin', 'RScript.exe' )
appPath = appPath.replace(/\\/g, "\\\\")
execPath = path.join(app.getAppPath(), "R-Portable-Win", "bin", "RScript.exe" )
} else if ( process.platform == MACOS ) {
var macAbsolutePath = path.join(app.getAppPath(), 'R-Portable-Mac')
var env_path = macAbsolutePath+((process.env.PATH)?':'+process.env.PATH:'');
var env_libs_site = macAbsolutePath+'/library'+((process.env.R_LIBS_SITE)?':'+process.env.R_LIBS_SITE:'');
var macAbsolutePath = path.join(app.getAppPath(), "R-Portable-Mac")
var env_path = macAbsolutePath+((process.env.PATH)?":"+process.env.PATH:"")
var env_libs_site = macAbsolutePath+"/library"+((process.env.R_LIBS_SITE)?":"+process.env.R_LIBS_SITE:"")
process.env.PATH = env_path
process.env.R_LIBS_SITE = env_libs_site
process.env.NODE_R_HOME = macAbsolutePath
execPath = path.join(app.getAppPath(), 'R-Portable-Mac', 'bin', 'R' )
execPath = path.join(app.getAppPath(), "R-Portable-Mac", "bin", "R" )
} else {
log.error('Not on Windows or macOS?')
throw new Error('Not on Windows or macOS?')
log.error("Not on Windows or macOS?")
throw new Error("Not on Windows or macOS?")
}

//
log.info('Environment:\n', process.env)
log.info("Environment:\n", process.env)

//
const childProcess = child.spawn(execPath, ['--vanilla', '-e', "shiny::runApp(file.path('" + appPath + "'), port=" + port + ")"])
childProcess.stdout.on('data', (data) => {
log.info('stdout:\n', `${data}`)
const childProcess = child.spawn(execPath, ["--vanilla", "-e", "shiny::runApp(file.path('" + appPath + "'), port=" + port + ")"])
childProcess.stdout.on("data", (data) => {
log.info("stdout:\n", `${data}`)
})
childProcess.stderr.on('data', (data) => {
log.info('stderr:\n', `${data}`)
childProcess.stderr.on("data", (data) => {
log.info("stderr:\n", `${data}`)
})

// Keep a global reference of the window object, if you don't, the window will
// Keep a global reference of the window object, if you don"t, the window will
// be closed automatically when the JavaScript object is garbage collected.
let mainWindow

// Create the browser window.
function createWindow () {
log.info('Working directory: ' + process.cwd())
log.info('create-window')
log.info("Working directory: " + process.cwd())
log.info("create-window")

let loading = new BrowserWindow({
show: false,
frame: false
})

log.info('showing loading');
loading.loadURL('data:text/html;charset=utf-8;base64,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');
log.info("showing loading")
loading.loadURL("data:text/html;charset=utf-8;base64,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")

loading.once('show', () => {
log.info('show loading')
loading.once("show", () => {
log.info("show loading")
mainWindow = new BrowserWindow({
webPreferences: {
nodeIntegration: false
},
show: false,
width: 1200,
height: 800,
title: 'Cerebro'
title: "Cerebro"
})

mainWindow.webContents.once('dom-ready', () => {
log.info('mainWindow loaded')
mainWindow.webContents.once("dom-ready", () => {
log.info("mainWindow loaded")
// 5 seconds delay so most machines will start with the application loaded
// instead of a white window + having to refresh the page
setTimeout( () => {
Expand All @@ -88,37 +88,37 @@ function createWindow () {
}, 5000)
})

log.info('Using port '+port)
log.info("Using port "+port)

// long loading html
mainWindow.loadURL('http://127.0.0.1:' + port)
mainWindow.loadURL("http://127.0.0.1:" + port)

// mainWindow.webContents.on('did-finish-load', function() {
// log.info('did-finish-load')
// mainWindow.webContents.on("did-finish-load", function() {
// log.info("did-finish-load")
// })

// mainWindow.webContents.on('did-start-load', function() {
// log.info('did-start-load')
// mainWindow.webContents.on("did-start-load", function() {
// log.info("did-start-load")
// })

// mainWindow.webContents.on('did-stop-load', function() {
// log.info('did-stop-load')
// mainWindow.webContents.on("did-stop-load", function() {
// log.info("did-stop-load")
// })

// mainWindow.webContents.on('dom-ready', function() {
// log.info('dom-ready')
// mainWindow.webContents.on("dom-ready", function() {
// log.info("dom-ready")
// })

// Emitted when the window is closed.
mainWindow.on('closed', function () {
log.info('mainWindow.closed()')
mainWindow.on("closed", function () {
log.info("mainWindow.closed()")
cleanUpApplication()
})

// prevent CSS code from appearing in application window title
mainWindow.on('page-title-updated', function(e) {
mainWindow.on("page-title-updated", function(e) {
e.preventDefault()
});
})

})

Expand All @@ -130,8 +130,8 @@ function createWindow () {
function cleanUpApplication(){
app.quit()
if ( childProcess ) {
childProcess.kill();
if ( killStr != '' ) {
childProcess.kill()
if ( killStr != "" ) {
child.execSync(killStr)
}
}
Expand All @@ -140,55 +140,55 @@ function cleanUpApplication(){
//
function setMainMenu() {
const template = [{
label: 'Cerebro',
label: "Cerebro",
submenu: [
{ label: 'About', role: 'about' },
{ type: 'separator' },
{ label: 'Quit', accelerator: 'Command+Q', click: function() { app.quit(); }}
{ label: "About", role: "about" },
{ type: "separator" },
{ label: "Quit", accelerator: "Command+Q", click: function() { app.quit() }}
]}, {
label: 'Edit',
label: "Edit",
submenu: [
{ label: 'Undo', accelerator: 'CmdOrCtrl+Z', role: 'undo' },
{ label: 'Redo', accelerator: 'Shift+CmdOrCtrl+Z', role: 'redo' },
{ type: 'separator' },
{ label: 'Cut', accelerator: 'CmdOrCtrl+X', role: 'cut' },
{ label: 'Copy', accelerator: 'CmdOrCtrl+C', role: 'copy' },
{ label: 'Paste', accelerator: 'CmdOrCtrl+V', role: 'paste' },
{ label: 'Select All', accelerator: 'CmdOrCtrl+A', role: 'selectAll' }
{ label: "Undo", accelerator: "CmdOrCtrl+Z", role: "undo" },
{ label: "Redo", accelerator: "Shift+CmdOrCtrl+Z", role: "redo" },
{ type: "separator" },
{ label: "Cut", accelerator: "CmdOrCtrl+X", role: "cut" },
{ label: "Copy", accelerator: "CmdOrCtrl+C", role: "copy" },
{ label: "Paste", accelerator: "CmdOrCtrl+V", role: "paste" },
{ label: "Select All", accelerator: "CmdOrCtrl+A", role: "selectAll" }
]}, {
label: 'View',
label: "View",
submenu: [
{ label: 'Refresh', accelerator: 'CmdOrCtrl+R', role: 'reload'}
{ label: "Refresh", accelerator: "CmdOrCtrl+R", role: "reload"}
]}, {
label: 'Window',
label: "Window",
submenu: [
{ label: 'Minimize', accelerator: 'CmdOrCtrl+M', role: 'minimize'},
{ label: 'Close', accelerator: 'CmdOrCtrl+W', role: 'close'}
{ label: "Minimize", accelerator: "CmdOrCtrl+M", role: "minimize"},
{ label: "Close", accelerator: "CmdOrCtrl+W", role: "close"}
]}
];
Menu.setApplicationMenu(Menu.buildFromTemplate(template));
]
Menu.setApplicationMenu(Menu.buildFromTemplate(template))
}


// This method will be called when Electron has finished
// initialization and is ready to create browser windows.
// Some APIs can only be used after this event occurs.
app.on('ready', function () {
createWindow();
setMainMenu();
app.on("ready", function () {
createWindow()
setMainMenu()
})

// Quit when all windows are closed.
app.on('window-all-closed', function () {
log.info('window-all-closed')
app.on("window-all-closed", function () {
log.info("window-all-closed")
// On OS X it is common for applications and their menu bar
// to stay active until the user quits explicitly with Cmd + Q
cleanUpApplication()
})

//
app.on('activate', function () {
// On OS X it's common to re-create a window in the app when the
app.on("activate", function () {
// On OS X it"s common to re-create a window in the app when the
// dock icon is clicked and there are no other windows open.
if ( mainWindow === null ) {
createWindow()
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11 changes: 5 additions & 6 deletions source/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,12 @@
"scripts": {
"start": "electron .",
"package-mac": "electron-packager . --overwrite --platform=darwin --arch=x64 --out=App --icon=icon/icon.icns",
"package-win": "electron-packager . --overwrite --platform=win32 --arch=ia32 --out=App --icon=icon/icon.ico",
"package-linux": "electron-packager . --overwrite --platform=linux --arch=x64 --out=App --icon=icon/icon.png --prune=true"
"package-win": "electron-packager . --overwrite --platform=win32 --arch=ia32 --out=App --icon=icon/icon.ico"
},
"repository": "https://github.com/romanhaa/cerebro",
"keywords": "",
"author": "GitHub",
"license": "CC0-1.0",
"repository": "https://github.com/romanhaa/Cerebro",
"keywords": "scRNAseq",
"author": "Roman Hillje",
"license": "MIT",
"devDependencies": {
"electron": "^2.0.17"
},
Expand Down

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