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Can we make communication between Jnlp and Browser?

I am invoking applet through JNLP from my application (which is hosted on tomcat server) and it is working fine. Now from applet I need to send the response back to the application or browser.
In my search, I found that we can do this using web socket. But not sure from where to start.
Can you please let me know any idea on this.

I think you need some kind of push notifications. One way of doing this as you already mentioned is with websockets and there are bunch of tutorials on the web as well as a question here on stackoverflow How to implement push to client using Java EE 7 WebSockets?
The second way is with server polling (frequently sending requests and checking for new events/states/subscribers etc.)

View running application output in the browser, how?

I have a simple cloud IDE,I want to make it able to build and run applications remotely, the target application's source files will be in a remote server in isolated virtual machine (e.g Windows 8.1,or Ubuntu 14.04). It's not difficult to build that application but how to run it and view its output to users ?
What if it's a desktop application (suppose it's written in C# or Java or Python)?
Note: users access there applications only using browsers (e.g Firefox,Chrome,...)
Edit: desktop application may contains GUI stuff not only console ;)

You need a web application.Now this web application when loads send request to backend code that backend code will do SSH to remote machine and read the file from specific location.Now that read stream will be send back in response and displayed on web based UI. In these type of application few thinks matters.
1) Like if you whole file at once then it will take time to display that content to user.Better idea will be read around 100 lines at once and when user scroll down then again send request to web server to read next 100 lines in this way you can decrease response time and better user experience.

Each of the languages you mentioned offers a Web Services framework of some kind. Pick one, and implement something that a) starts your app, b) shows the output. Depending on the processing time (how long it takes to complete) you might even get away with just one.
You can go for a self-contained, standalone service:
C#: Is it possible to create a standalone, C# web service deployed as an EXE or Windows service?
Python:
Best way to create a simple python web service
Java:
https://technology.amis.nl/2009/06/05/publish-a-webservice-from-a-poja-plain-old-java-application-that-is-out-of-the-container-using-endpoint-class/
Alternatively, you might use a container (server) for your app, like Apache with mod_mono or IIS for C#, Tomcat, Jetty, Jboss for Java, Apache with mod_wsgi for Python (just examples).
The web service would probably sit on the remote machine, so it could use system calls ('command line') to run your core app, and then it would send the results over http. Since you mention GUI, there could be more layers to the solution:
The GUI - static HTML, desktop app, sending requests to the 2nd layer, say displaying dropdowns for parameter1 and -2
The Web Service - takes the params from the request, say http://remote.machine.land/start/app?parameter1=X&parameter2=Y, runs a local command like /home/users/myapp.sh -parameter1=X -parameter2=Y
The application itself - not necessarily aware of any internet out there.
This way you stay free to change/enhance any part at a time, call the 2. layer programmatically, introduce load-balancing, etc.
3.

call gui from JSP?

I am currently learning JSP and Java Servlets. I was wondering if there is any way to call a java GUI from a JSP, not necessarily to load into the page, but to load onto the screen for database input. I am struggling trying to find some reference on how to do this on the net, but no luck so far.

You could use Java Webstart to start up the application on the client side. Or, ask the user to install a local client differently (like a daemon service).
The "GUI application" must have some kind of RPC (=remote procedure call) service running in background.
Once the client has your gui application installed, the JSP can invoke urls on http://localhost:port (ajax would help sending messages to the GUI application). The GUI application must have some rpc system (rest, webservice) that receives the requests from your web application (your jsp app) and start the GUI requested by the URL.
The problem here is to make sure the client has the port of choice available.
Another possibility is to register some URL to your application in the client side, so that when the user clicks a url like myapp://form/123 the OS automatically invokes your application to handle that URL. This kind of thing must be done differently per operating system. It's the way it works when you click on a magnet link or a skype://link. The procedure to register urls in the operating system is different per OS, you need to do some research (I never did that, but I am sure it is possible). You can also register a file extension to your app, and make sure that the specified extension is registered to your app. When the browser downloads the file and opens it, your app is invoked with the file downloaded as parameter (which will contain the instruction for your GUI). But most browser will not start automatically the app associated to the file after the download: again, you need to do some tricks on the client's operating system to make the "download and open" the default behavior for the browser.

How to create voice chat in web browser with java

I want to create a voice chat which runs on the web browser.
The basic idea is that when I run the server.jar file, it will listen to a socket for connection, and when I type the ip and port on another computer on web browser(ex. 1.1.1.1:8082), the server will accept the connection and display an voice chat applet. Server.jar should contain all voice handlers. For example, if we have three computers, one with the server running while other two has web browser applet running and connected to the server, user1 talking will transmit over to the server, which then transmit over to user2.
So far, I have the applet and the server, but I am having trouble using the web browser to open the applet. It seems I need to use servlet and apache tomcat for the server side to make this work.
Can anyone confirm that I need to use servlet and apache tomcat to achieve this? Or can anyone suggest a better way to approach this project?

if it's peer-to-peer, everything can be written inside the applet.
Oh and as far as i know, there is no java voip libraries so you're going to have to port one from a C/C++ library or write it yourself.

Hardware support from a web application

I have a web application running with support for some specific pieces of hardware. This is achieved in the following steps:
User runs a small installer that places java files (and a couple
others) on the client machine. The main piece is a jar called "hardwareManager"
User visits web app. The web app runs a java applet which, due to
a .java.policy file placed during the install, has permission to
interact with the client machine outside the browser sandbox.
The applet checks to make sure the hardwareManager is running,
and if not runs a command to start it.
User interacts with the web app which sends commands to the applet via
javascript. The applet then writes commands to a text file
on the client machine. The text file is constantly monitored by the
hardwareManager which runs any commands it reads in.
This works, but seems clunky. I have a couple ideas on how to improve it, but I don't know which, if any, are even worth trying.
Would it be better to set up the hardwareManager as a socketServer and have the applet connect directly to it, rather than going through text files? Is that even possible?
Is there a way to eliminate the applet altogether and have the javascript talk directly to the hardwareManager? Maybe by writing the hardwareManager to be a local http server? What port should it run on? Do javascript xss limitations fit in here somewhere?

It would be less clunky to start the Java application using Java Web Start. This would remove the need to daemonize or install the Java hardware manager.
Another alternative is to use a built-in browser inside Java. I supose this is not an option, since you depend heavily on Javascript (I suppose to provide a rich client experience).
If you already have to install something on the client machine, why did you make the choice to go with a web application?
Talking from experience: We had a Java EE application which needed to print to PoS printers at the client site. We installed a small "synchronizer" application that connects through SSH and synchronizes all clients files. Afterwards, it loads the JAR and executes the program. This program connects through RMI with the server and subscribes to a JMS queue to receive the print assignments.
Applied to your case: Why not let your Java application connect to the server directly? You can use HTTP, SOAP or even JMS over RMI. You can then launch the hardware command from the server (instead of from the limited JavaScript webbrowser environment). This way, you get tons of features: authentication, buffering of commands, and you can even share hardware between multiple clients.
Schematic:
<----AJAX------> Web browser
ApplicationServer
<---HTTP/SOAP--> Java hardware manager application
You can launch the Java application using Java Web Start, which allows you to update the application automatically (instead of needing to pass every client a new installer).