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External plugin framework to my JAVA application

I built a large JAVA web application using SPRING & MongoDB,
In some scenarios, I want to allow my users to upload their own code, and the application will run it later on when necessary.
I called this operation "Plugin framework", the plugin is the user's code of course which I prefer to be in NodeJS for now.
There is any recommended / known architecture for that purpose?
I've read about pf4j and senecajs, but they quite different from my needs.
Thanks!

You loose complete control over code running on node. The uploaded code can access network, files, database, you name it. That is not a good plan.
I suggest to work with the embedded JS module in Java, called rhino. Here, you define which environment the code can access.
You find samples of using the scripting in Java here http://docs.oracle.com/javase/7/docs/technotes/guides/scripting/programmer_guide/index.html for jdk7, the Javadocs https://docs.oracle.com/javase/8/docs/api/javax/script/ScriptEngine.html and here some info on Java8 changes http://www.oracle.com/technetwork/articles/java/jf14-nashorn-2126515.html
UPDATE:
On the comment below, you state that you think you are safe, if the code runs on the other server. Actually, the problem is still the same. Just it won't hit your application's server but the JS code server.
My advice stands. Implement a JS execution service using the built-in Javascript engine (Rhino or Nashorn) and restrict the running JS to a sandbox, you control the script's reach out of the box through carefully implemented env-access methods. It is actually pretty easy to get started, no more complicated than implementing a remote javascript implementation engine on top of node...

Chrome Browser and Java Message Passing

I have developed a Chrome extension and it captures some data in a webpage.
My ultimate goal is to pass this final result to my Java Application.
I have following few options in my mind, but I was not able to find any resources for them yet.
Access the localStorage externally.
Run Chrome browser through the Java app, So I guess we have the control of its data.
If no API found, write the result to a file and access it from the
Java App.
Is there any API to achieve any of the first 2 options? Or any other interface other than the file system?
I checked with berkelium and The Chromium Embedded Framework. But they are just chrome wrappers, and we cannot run a chrome instance from it.
Edit
For the 2nd option I tried with Selenium Webdriver, but I think it hasn't any method to access the localStorage.

It sounds like you are looking for Native Messaging, which allows communication between a Chrome Extension and a native application (e.g. a Java Desktop Application).
There are plenty of question here on SO regarding the implementation of Native Messaging and there is, also, the "official" example.
I suggest the above solution, but if your application will heavily interact with the extension (and you feel like reverse engineering) there is the open-source **[NetBeans Connector Chrome Extension][3]**, which uses a different approach (Sockets or WebSockets - I am not sure).
Take a look at **[this answer][4]** for info on how to get at the sources.

Is there a limitation preventing you from exposing a REST API with your java application?

Which option is suitable to replace Java Applet?

I would like to replace Java Applet which currently needs to use client's resources, i.e. external readers, and to communicate with a server via socket.
Reason:
1. I have thousands of client machines using this Java Applet program, and most of them are running out-dated JRE. When the Java Applet program is updated / added new features, all client machines will need updating the latest JRE.
Expected Solution:
The Java Applet program would be expected to be replaced by a web-based application, which allows to compile and run source code at client's side such that the new web-based application could still use client's resources and communicate with server via socket.
Can I use JavaScript to achieve it?
I would very appreciate your help/suggestion for this problem. Thank you!

JavaScript is a scripting language that gets evaluated in the browser.
I would not describe it as compiling and running but yes, it does mean you can run code in the client and is commonly used to create applications that run in the browser.
There's a staggering amount of frameworks that you can use to write your application. Take a look at the TodoMVC site to see the same TODO app created using several different frameworks.
If you come from Java applets, GWT may be interesting to look at.
If you wish to let the JavaScript client listen for messages from the server, take a look at websockets.
The smart card reader is going to be a problem, though!
See Architectures to access Smart Card from a generic browser? Or: How to bridge the gap from browser to PC/SC stack?
By the way:
The real issue with outdated JREs is not that your code will not run on old JREs, you can create perfectly fine applets using java 1.4 or java 5. Any libraries you may need you can deploy alongside your applet. The pain is a security problem. Anything but the latest version Java plugin is getting actively exploited and puts the user at risk. Occasionally, even the latest version is not safe.

try socket.io
I think this is the latest technology you can use to communicate with client browsers. it support the latest browsers and mobile browsers too.
hope this will help you.

Javascript has become very powerful with HTML 5.0. Here is a list of new elements that you can use to access all kinds of resources, including local files, audio, video, GPU rendering (canvas + WebGL) and GPU compute (WebCL). Here are even more things you can do, including database connections and networking. You can even create offline Javascript applications.
jQuery and jQuery layout make robust GUI development a lot easier. Rich tool suites, such as Google Closure offer optimization and a compiler for improving performance and detecting obvious mistakes early in the development process.
W3 offers useful stats for making an informed decision on how many users on average have access to which features. Note that the most annoying guy in that list arguably is IE8 due to it's lack of proper HTML 5.0 support.

In case you want to stick with Java, then one alternative would be to use my http://bck2brwsr.apidesign.org project. It's goal is to create small Java that can run in 100% of modern browsers without any plugin installed.
There are Java bindings to HTML (via knockout - one of the four most popular frameworks for HTML5) and that is why one can code whole business logic in Java and just render it via HTML. Should be enough to replace most of the applet UI.
In addition to that there is an experimental API to render on HTML canvas. People use it to write Java games that run in a pure browser.
There is a simple way to communicate with server via JSON REST API or via WebSockets. A live example is here.

Native Java / Python / Objective C in Firefox?

Is it possible to integrate Java, Python, or Objective C directly with the Firefox browser? In particular to do "real", native tasks such as writing files or connecting to a local database, or better yet, directly calling systems level code ?
Notably, there is a post on native code execution, somewhat slanted towards windows, elsewhere on StackOverflow: Firefox extension: native code execution?

In particular to do "real", native tasks such as writing files or
connecting to a local database, or better yet, directly calling
systems level code ?
You don't need an extra language for that, Firefox extensions can do it already:
Writing files
Connecting to a local SQLite database
Calling system libraries directly
I would recommend against attempting to write the extension in anything other than JavaScript: while there are several possibilities they create a lot more trouble than they are worth. If anything, you could create a native library and call it from your JavaScript code via js-ctypes (see link above).

A "signed" Java applet, given the correct permissions and approved by the user, can run in the browser context and have access to files or databases. However, Java applets in the browser are almost never used today (I've had Java disabled in my browser for years).
Microsoft browsers offer ActiveX, which is a way of running native code in the browser, but I don't know whether anybody uses that today either.
Google's nativeclient is another method of running native code, but only works with Google browsers at this time. Not sure whether that allows direct access to files at all.

PythonExt brings Python support to Firefox:
http://code.google.com/p/pythonext/
I'm not sure how quickly they update it for Firefox's rapid releases, and you do need to install an extension, and then it will only work in a trusted context (i.e. an extension you right yourself)

Alternatively you could build Windows 8 Metro style apps that let you use web technologies and native code together:
http://channel9.msdn.com/posts/Raman-Sharma-Building-Metro-Style-Apps-with-C-and-JavaScript
http://code.msdn.microsoft.com/Hybrid-JavaScript-and-C-e6dc77fa

GWT interaction with external standalone application

I work on a standalone Java application that is a command-and-control system for an assortment of hardware. The C&C software basically runs from a command line, and controls the system hardware which is spread out all over the place. It does not require a GUI to meet the business requirements. I have written a small swing GUI just so I can see what the overall status is of the system, but again, that is not essential.
Going forward, we would like to have a Administrative web GUI with system status and something that would give a user some level of control over the hardware. We were thinking that GWT might be a viable solution. Our GWT app would have to have some sort of IPC with the C&C software. I don't know how viable that is, I don't know that we want the C&C software bundled as a web app that has to run under application server.
I just don't have much experience with this. I was thinking that the GWT client would interact through RPC with the GWT server, and the GWT server would have some sort of RPC (RMI???) with the C&C.

Another option you have is to run a Java Applet that can interact with both GWT (using JSNI) and with the OS. A simple example would be to open a common file in the user's home folder and read/write to that file (with the C&C app doing the same as well).

You can embed embedded tomcat or Jetty into your application and let it run a simple servlet/JSP - based or GWT-based web UI. In fact, when you debug/run your GWT application from Eclipse, it starts in an embedded Tomcat instance.

I found a solution by using Spring. We have modified much of our Command and Control app to use Spring IoC, and then we used other Spring libraries to extend its functionality. To interact with GWT, we exposed services and used httpInvokers to make calls from the GWT server code.
Of course, this meant we needed to use Spring with our GWT application too in order to make the http calls from the GWT server code. But all is working.

you dont have direct control on the client system with JavaScript (which GWT is based on). in your use-case that wouldn't even make sense, why using an external server for a website controlling a local program?
If you reverse this (the app server is running on the same system as the C&C software, and the web client is available from everywhere) than that would be possible, but that wouldn't have much to do with GWT. On the server you can write normal java code. GWT just would be used for the web GUI and the RPC-calls to the server.
The call to the C&C software from the app server could be realised with the following line (windows example):
Runtime.getRuntime().exec("C:\\PathTo\\Program.exe")
This function return a instance of class Process which provides an Input- and OutputStream to simulate user input and to read and process the programs output.
Please note that you lose platform independence with this method, because the parameter for exec() looks different for every OS.
EDIT
After re-reading your question, it would even make more sense to integrate the C&C software into the server code directly, as the comment on your question suggests. you need a application server to use GWT-RPC, not a webserver, but thats hairsplitting.
Informations on how GWT-RPC generally works can be found here: (tutorial), (detailed description)